February 12, 2014

Ancient Clovis genome from Montana yields no surprises (Rasmussen et al. 2014)

Ancient DNA has consistently managed to surprise us, with pretty much no direct genetic continuity revealed between Pleistocene and modern populations anywhere in the world. So, it is refreshing to see that at least in the case of the Americas the people who lived there ~13 thousand years ago are clearly related to the people who lived there in pre-Columbian times, with no real evidence of subsequent gene flows from Eurasia (at least in the case of Central/South Americans).

Many people suspected this because of the difficulty to access the Americas from Eurasia: this must have limited gene flow between the two regions to a handful of migrants and a restricted set of time periods where geological and climatic conditions were advantageous. The much reduced genetic diversity of Native Americans also argues in favor of them being a relatively simple population, with low heterozygosity and a handful of unique "founder lineages" in both the Y-chromosome and mtDNA.

Nonetheless, there are also several theories in the realm of alernative history, involving Solutreans from Europe, trans-Pacific boat riders, bearded "White Gods", Minoans/Phoenicians/Atlanteans/Ancient Egyptians, "African" Olmecs, "Caucasoid" Paleo-Indians, lost Israelite tribes, to mention only a few of the most well-known ones.

The new study does not, of course, disprove any of the proposals in the preceding paragraph: one can still claim that diverse groups once inhabited the Americas and  Rasmussen et al. (2014) just happened to chance upon one that looked just like modern native Americans. But, this certainly improves the odds of early "Native American simplicity", offering no evidence for the complexity postulated by many of the alternative theories.

Moreover, while the existence of other human groups in the Americas cannot be disproved by the study of a single ancient individual, what can be proved is the antiquity of the ancestors of Native Americans. Rather than being late arrivals arriving from Asia after the initial colonization, perhaps with derived Mongoloid physical morphology, we now know that they were already there as early as ~13 thousand years ago. It is remarkable that a single ancient DNA sample can sweep away much of the nonsense that has been written on the topic in the past.

A piece in Nature News addresses some of the "ethics" debate that seems ever-present in studies involving Native American remains. I don't know how this study will be perceived by living Native Americans: a possibility is that they'll be more receptive to ancient DNA research now that a team of scientists have stretched the time depth of their ancestry in the Americas to the earliest studied sample, revealing themselves not to be the evil-doers that western scientists are generally assumed to be according to a certain kind of mentality. A different -and more alarming- possibility, is that radical anti-science elements will be emboldened by these findings to claim that continuity with the earliest Americans (which in itself seems true enough) adds support to claims of ownership to pretty much all archaeological samples whose relationship to living Amerindians was hitherto uncertain in light of the many alternative theories.

In any case, it is remarkable that this ~13 thousand year old genome now exists while the genomes of modern native Americans that can be had for a fraction of the cost and technical difficulty do not. Indeed, not even genotype data exist from most Amerindian groups from the USA, which creates the rather bizarre state of affairs that the Anzick-1 genome had to be compared with native groups from several countries in the Western hemisphere except the one in which it was found.


Nature 506, 225–229 (13 February 2014) doi:10.1038/nature13025

The genome of a Late Pleistocene human from a Clovis burial site in western Montana

Morten Rasmussen et al.

Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 14C years before present (BP) (13,000 to 12,600 calendar years BP)1, 2. Nearly 50 years of archaeological research point to the Clovis complex as having developed south of the North American ice sheets from an ancestral technology3. However, both the origins and the genetic legacy of the people who manufactured Clovis tools remain under debate. It is generally believed that these people ultimately derived from Asia and were directly related to contemporary Native Americans2. An alternative, Solutrean, hypothesis posits that the Clovis predecessors emigrated from southwestern Europe during the Last Glacial Maximum4. Here we report the genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana. The human bones date to 10,705 ± 35 14C years BP (approximately 12,707–12,556 calendar years BP) and were directly associated with Clovis tools. We sequenced the genome to an average depth of 14.4× and show that the gene flow from the Siberian Upper Palaeolithic Mal’ta population5 into Native American ancestors is also shared by the Anzick-1 individual and thus happened before 12,600 years BP. We also show that the Anzick-1 individual is more closely related to all indigenous American populations than to any other group. Our data are compatible with the hypothesis that Anzick-1 belonged to a population directly ancestral to many contemporary Native Americans. Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual.

Link

244 comments:

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andrew said...

The fact that the Clovis individual is more closely related to Central and South Americans than to high latitude North Americans is not surprising (given that there are known later Inuit and Na-Dene affliated migrations to Northern North America, but not to Central and South America), but is notable. It suggest that the North-South distinction in Native Americans was not present in Clovis times and that subsequent migration rather than population structure in the founding population explains these disparities in modern populations.

Grognard said...

Clovis sites cluster around the eastern half of USA. The only clovis sites in montanna are some transient caches that look like scouting parties. So it's very doubtful this is really a Clovis skeleton being sequenced. If it were from east coast it would be much more conclusive.

barakobama said...

A lot of the theories about the first Americans being African, European, near eastern, etc. were based on racism. I guarantee you that most of the people supporting the theory the first Americans were African are African, that the first Americans were European are European, etc.

I assumed a long time ago that the genetic history of native Americans is simple. All evidence points to them being close to full blooded descendants from the same ancestral population that had arrived in north America over 20,000 years ago. MA-1 boy made things more complicated and proved there is pre Colombian west Eurasian ancestry in native Americans. It seems pretty obvious native Americans are part west Eurasian but I don't see any evidence in their physical features and mtDNA(besides X2). I guess possibly Y DNA Q is from MA-1 related people.

Eastern View said...
This comment has been removed by the author.
Valikhan said...

"We determined the Y-chromosome haplogroup to be Q-L54*(xM3)
and, along with 15 previously analysed Y-chromosome sequences
20
,we
constructed a tree to illustrate the phylogenetic context within haplogroup Q (Supplementary Information section 13 and Extended Data
Fig. 2). Confining our analyses to transversion single nucleotide polymorphisms (SNPs), we leveraged the date of Anzick-1 to estimate a
divergence time between haplogroups Q-L54*(xM3) and Q-M3, two
of the major founding Y-chromosome lineages of the Americas, of approximately 16,900 years ago (95% confidence interval: 13,000–19,700; Supplementary Information section 13)."

Valikhan said...

"We determined the Y-chromosome haplogroup to be Q-L54*(xM3)
and, along with 15 previously analysed Y-chromosome sequences
20
,we
constructed a tree to illustrate the phylogenetic context within haplogroup Q (Supplementary Information section 13 and Extended Data
Fig. 2). Confining our analyses to transversion single nucleotide polymorphisms (SNPs), we leveraged the date of Anzick-1 to estimate a
divergence time between haplogroups Q-L54*(xM3) and Q-M3, two
of the major founding Y-chromosome lineages of the Americas, of approximately 16,900 years ago (95% confidence interval: 13,000–19,700; Supplementary Information section 13)."

Raimo Kangasniemi said...

It's not really "anti-science" from the part of Native groups when they oppose studies, mostly just bitterness resulting from the long years when their graves were dig up without permission.

Gary Moore said...

Eske Willerslev is to be praised for his efforts to show respect for the Native American peoples by seeking their guidance with regard to analyzing the DNA of the Anzick boy. If all genomics researchers and archeologists displayed the same attitude, they receive more cooperation from Native American communities.

I visit the Pyramid Lake Reservation in Nevada every year, and I have often thought about contacting the community leaders to persuade them to drop their objections to having the DNA of Spirit Cave Man analyzed. Perhaps if Dr. Willerslev approached the Paiute and Shoshone people of western Nevada in the same fashion, he might have some success.

Africa Gómez said...

I rarely comment, but I just wanted to thank you for your wonderful blog. This post is a great analysis of the paper and state of affairs. I always look forward to your analysis after a paper comes out.

terryt said...

"I just wanted to thank you for your wonderful blog. This post is a great analysis of the paper and state of affairs. I always look forward to your analysis after a paper comes out".

Very true.

"For those who don't bother to read the papers, the above is the only 'prove' these scientists have for assuming Native American admixture"

I'm surprised German hasn't chimed in.

"And then these 'generated data' are used by armchair scientists to support Native American admixture, creating a self-reinforcing loop".

So Native Americans didn't arrive from anywhere else? They have always been there?

"It seems pretty obvious native Americans are part west Eurasian but I don't see any evidence in their physical features"

Apart from populations in the far north very few of them look 'East Asian' though.

Tobus said...

@Eastern:It seems to have become customary to refer to Mal'ta gene flow into Native Americans, since Raghavan et al. Based on what I remember from Lazaridis et al., I think the argument for that is that Mal'ta is equidistant in f4 stats to Oceanians and some southern East Asians, so therefore Mal'ta can't be admixed with Native Americans because then it should be closer to East Asians then to Oceanians, so it has to be Mal'ta admixing into Native Americans.

It was Onge, not Oceanians and the logic holds. Close affinity and haplogroups show that modern East Asians and Amerindians share a common ancestor that post-dates the West/East Eurasian divergence, and this common ancestor can't have been much earlier (if at all) than MA-1. If MA-1 received admixture from this Eastern Eurasian branch as early as 24kya we'd expect him to show some degree of increased affinity to all of that branch's descendants, not just one them. Since MA-1 shows high affinity with Amerindians but none at all with East Asians this suggests that the gene flow could only have gone one way - from MA-1 into the ancestral Amerindian.

If you claim Amerindian admixture into MA-1 then you are essentially claiming a completely alternative history of modern humans, one in which East Asians and Amerindians already had significant divergence at 24k (essentially necessitating before the West/East Eurasian divergence), and yet somehow still show close affinity today (and according to this Anzick paper, for at least the last 13kya).

Annie Mouse said...

From the evidence I have seen I think there is a reasonable argument for pre-Columbian European admixture in NE American tribes. This is a separate issue.

I am not however convinced that there is global European admixture in the Americas, the data is open to interpretation, and one person (Mal'ta, 24 kya) does not make an entire culture. We could just be looking at Mal'ta 's unique family position (one granny from the east, another from the west for example). His plot position does look a lot like a recently admixed person.

If there is a Mal'ta-esque contribution in the Americas then I am inclined to think it might be 'European but not as we know it'. That is, that there were folk like Mal'ta following game along the snow line. Some could have contributed to the Amerindian gene pool (along with other East Asian types), some could have contributed to the European gene pool (along with more southern types). Does that really make the contribution in the Americas European admixture? Not in my opinion.

Interesting to me is here we have a trans Eurasian population (clearly connections between east and west in Mal'ta's family at least). Presumably with a characteristic and possibly unique culture. Carrying U as they travel in and out of Europe's far north. An excellent candidate for atypical European population with a more durable (eg burial/entombment) burial practice.

So if most ancient Europeans are cremating folk in houses and boats or allowing them to be eaten by birds (as literature suggests), and some are using burials. Then it would be the burials that we would find.

Eastern View said...
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About Time said...

I didn't see if paper showed when gene flow between Beringians and Clovis was cut off. Is there any LD evidence (ADLER etc) if Clovis ancestry in Asia or Europe? Amerind % shows up weird places with GEDmatch etc (like Irish).

German Dziebel said...

The data presented by the study confirms the new paradigm in Amerindian prehistory.

1. Amerindians are an unadmixed population predating the split between East Asians and West Eurasians.
2. Several Amerindian components are observed across Eurasia suggesting the colonization of Eurasia out of the Americas.
3. The Clovis population was not closer to East Asians than modern Amerindians suggesting that the Clovis population was not derived from Asia but from more ancient populations in the New World. mtDNA hg D4h3 therefore doesn't represent a separate migration from Asia to America. D4h3 used to be pan-American but its distribution has shrunk to more costal areas. Again, D4h3 has nothing to do with a costal migration into the Americas.
4. The Clovis population is closer to Mal'ta than are modern Amerindians but just like Mal'ta it's closer to South and Central Amerindians than to northern Amerindians.
5. Northern Amerindians is a post-25,000 YBP spinoff from Southern Amerindians that likely yielded modern East Asians through a back migration.

Gary Moore said...

Raimo Kangasniemi wrote:

"It's not really "anti-science" from the part of Native groups when they oppose studies, mostly just bitterness resulting from the long years when their graves were dig up without permission."

It's partly true, though. Many Native Americans believe that they are autochthonous to North America and reject alternative explanations for their origins. Others are fundamentalist Christians and reject scientific speculation that contradicts the Biblical accounts placing the age of the world at only 6,000 years. There is even a competing pseudo science that claims that groups such as the Cherokee originated with the immigration of peoples from the Levant during late Bronze Age or Classical times who were originally Greek-speaking, and its proponents (lead by Donald Panther-Yates) cherry-pick DNA and linguistic evidence to prove it - for instance, they claim that mtDNA type U5 is present among Cherokee women, which would not be insistent with the "out of Siberia" origin of Native Americans.

There is, though, a layer of distrust resulting from previous studies in which DNA was collected under false pretenses, or for which researchers were suspected of profiting from without sharing revenue from the Native populations from which there were collected (i.e., Karitiana).

http://www.newscientist.com/article/mg22129561.100-ancient-genome-wont-heal-rifts-with-native-americans.html#.Uvxh2fZ96Hk

German Dziebel said...

@Tobus

"Close affinity and haplogroups show that modern East Asians and Amerindians share a common ancestor that post-dates the West/East Eurasian divergence, and this common ancestor can't have been much earlier (if at all) than MA-1. If MA-1 received admixture from this Eastern Eurasian branch as early as 24kya we'd expect him to show some degree of increased affinity to all of that branch's descendants, not just one them. Since MA-1 shows high affinity with Amerindians but none at all with East Asians this suggests that the gene flow could only have gone one way - from MA-1 into the ancestral Amerindian."

Northern Amerindians are closer to modern East Asians than other Amerindians. Mal'ta shows that there were no East Asians at 25,000 ybp (at least not in Siberia) but there were West Eurasians. So there was Amerindian admixture in MA-1 (clearly seen in the ADMIXTURE runs) at a time when there were no East Asians around. The reason MA-1 doesn't have any affinity with East Asians is because East Asians didn't exist. They emerged later as an offshoot of a northern Amerindian population (mixed with a Tyanyaun-like population). Hence, East Asians have recent, hence strong Amerindian affinity but no West Eurasian affinity.

Regarding mtDNA haplogroups, all the clades linking Amerindians and East Asians show a very specific Amerindian version in East Asia. E.g., hg D4h3a is found all over America, while D4h3b has a unique occurrence in China. Hg A2 again shows up in Siberia. Hg C1 is found in Japan and the Amur River basin (plus all the way out west in Mesolithic Karelia and modern Iceland). So all Asian clades (D, C and A) have very specific Amerindian versions in Asia but not the other way around. On the other hand, hgs B and X, which have broad links with Tianyuan and West Eurasia are barely found in Siberia and/or East Asia.

@Eastern View

"I think this means Plains Indians (and indeed many if not most Amerind groups) are more Mongoloid than Chinese."

Good data point. Shovel shaped incisors are also more frequent in the New World than in Asia. On the molecular level the derived EDAR gene is likely too but we don't have conclusive data on this. Also skulls with a generalized Mongoloid morphology appear first in the New World than in Asia. So the gradient of Mongoloidness goes from northern Amerindians through Southern Siberians into East Asians, then drops off in SE Asia and disappears in PNG and Australia.

Dr. Clyde Winters said...

@barakobama
The view that the first Americans were Africans is not racist. In your post you claim that Africans supported the idea that the first Americans were Africans, as if this view was only shared by Black/African people. This is false it was the Jewish writer Leo Wiener, in Africa and the discovery of America (3 Vols.) and the Brazilian physical Anthropologist: Walter Neves and Hubbe who claimed that the cranial morphology of early Americans from Lagos Santa, Brazil were “more similar to present Australians, Melanesians, and Sub-Saharan Africans “ See: http://www.pnas.org/content/102/51/18309.full . Clearly it was Europeans who first fostered the idea the first Americans were Africans—not Africans.

Eastern View said...

@Kristina: At higher K Mal'ta breaks down to a Uralic component and a Kalash component, so the fact it's mostly similar to admixed populations says something about what it is itself.

@Tobus: There could be a host of reasons why that is, and I think it's too soon for you to be so sure when there are a lot of loose ends and ambiguities. I could go on and on but here are some:

1. There is no equidistant relationship. The southern East Asian populations they used are slightly closer to Mal'ta than Oceanians are (and yes they listed Papuans and Melanesians besides Onge).

2. Northern East Asian groups would be even closer to Mal'ta. Extreme cases would be Beringians like Eskimo. So, Mal'ta is not really equidistant between Oceanians and East Asians, but then you can argue Siberians aren't East Asian. But then if you google pics of pure Eskimos they way more extreme Mongoloid than Han or Taiwanese aborigines.
3. Which leads to the point that people in East Asia have changed more than people in the Americas, which could also put more distant between East Asians and Mal'ta than between Amerinds and Mal'ta. I bet there is even a lot of selection from glacial times through agriculture to now, selection for temperament, intelligence, light skin, neoteny.. the Asian anti- alcohol gene, etc.

3. Yes, Amerinds and East Asians could've separated prior to 24,000 years ago. East and West Eurasian separation would be 60-50 thousand years ago, and Siberian Upper Paleolithic spans back 40,000 years. Why would be a 24,000-year separation be a problem? You act like Mal'ta at 24,000 years is the beginning of everything when for adecades archaeologists have noted it's intrusive nature.

This is not to mention that if it's Mal'ta-->Native Americans, in ADMIXTURE at K3 should be all "west" and Native Americans should be partly "west", which even Oceanians are. No Native American cluster has formed at K3 yet to pull itself together or pull Mal'ta away. It Native Americans are admixed and then panmicticized, then they should behave like Kalash, breaking down at lower K and integral at higher K. The same phenomenon has to behave the same way mathematically.

Matt said...

Tobus - Close affinity and haplogroups show that modern East Asians and Amerindians share a common ancestor that post-dates the West/East Eurasian divergence, and this common ancestor can't have been much earlier (if at all) than MA-1. If MA-1 received admixture from this Eastern Eurasian branch as early as 24kya we'd expect him to show some degree of increased affinity to all of that branch's descendants, not just one them. Since MA-1 shows high affinity with Amerindians but none at all with East Asians this suggests that the gene flow could only have gone one way - from MA-1 into the ancestral Amerindian.

As you seem like a sane person to discuss this with, it is also possibly within the statistics that Mal'ta itself is mixed between

- a Western population

- a "Siberia X" Eastern population which split off from Oceanians and East Asians before they split from one another

and that only "Siberia X" contributed to Native Americans, along with East Asian ancestors.

But if this is true, "Siberia X" or sister clades must have mixed very widely and deeply with all present day West Eurasians, for all are closer to Native Americans than they would be to a purely East Asian derived population with the same drift as Native Americans.

For the moment, it's just currently more parsimonious that Mal'ta itself is a member of a broad population ancestral to Native Americans. Investigation of genetic patterns or ancient samples may eventually make this disfavorable.

In any case, the following look like they not going to change -

- Native Americans have dual structure between a East Asian population and a population X, which may be like Mal'ta and if not certainly contributed to all West Eurasians.

- Whether population X is like Mal'ta or not, it must have split off from Oceanian and East Asian ancestors before they split from one another, yet after they both split from West Eurasians.

- Thus, if population X did contribute to West Eurasians, this is not going to be morphological "Mongoloid" admixture in West Eurasians, and Native Americans are going to be partially East Asian in their ancestry.

Eastern View said...

@German: I can only agree with some of your points. Judging from mtDNA, East Asians are derived from a post-glacial Siberian population with an East Asian population that is not East Asian as we know it now, judging from the M7 and N9 that is shared with Jomon and judging from the pre-Neolithic fossils in East Asia that are very unlike the repesent. Once you get more south the mtDNA is even more aboriginal southern Asian. post-Siberians Siberians are themselves more derived then Amerinds, who should be pre-glacial.

From Mal'ta to East Asians are several levels of derivation and admixture and probably selection since agriculture (for neoteny, temperament, intelligence, skin color, alcohol susceptiblility, etc.)

These all have to be taken for considering why Amerinds are closer to Mal'ta than East Asians are. Nothing has been proven so far. I really don't think people should be jumping on one band wagon too soon. Theories are overturned constantly and the only people who are enthusiastic are always the ones with a disgusting political agenda.

Dienekes said...

If Mal'ta had "Siberian X" Eastern ancestry, then Eastern groups (Chinese, Papuans, Onge, etc.) would be closer to Mal'ta than to Loschbour or Motala, but they're not.

Matt said...

If Mal'ta had "Siberian X" Eastern ancestry, then Eastern groups (Chinese, Papuans, Onge, etc.) would be closer to Mal'ta than to Loschbour or Motala, but they're not.

If Mal'ta did and Loschbour or Motala didn't. My point is that "Siberian X" ancestry would have to be distributed throughout West Eurasia, if it exists, to give the signal of additional closeness of all West Eurasians to Native Americans, and would have to split off before Papuan and Han split from one another.

About Time said...

Why isn't Tianyuan part of this discussion? 40 kya, older than Mal'ta, and def related to East Asians.

We don't have to speculate about undifferentiated Asian/Native American ancestors. We have Tianyuan.

Also, to reiterate (sans typo): when did Clovis split from Tianyuan etc? Did Clovis keep feeding in (back migrating) to Asia/Europe after crossing to Alaska/Canada? If so, when did Clovis finally split off, and do any Eur/Asian pops have Clovis derived segments today?

Eastern View said...
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terryt said...

"If there is a Mal'ta-esque contribution in the Americas then I am inclined to think it might be 'European but not as we know it'. That is, that there were folk like Mal'ta following game along the snow line".

Yes. To call Mal'ta 'European' is completely wrong. 'Central Asian' is perhaps more correct.

"I think this means Plains Indians (and indeed many if not most Amerind groups) are more Mongoloid than Chinese".

I agree 100%. Both Amerindians and Mongoloids also contain some 'Mal'ta' element. Dienekes' recent post on admixture shows recent admixture through much of China. This presumably occurred when the Mongoloid people move south through the region with the Neolithic expansion mixing with the pre-existing non-Mongoloid population. This makes the Chinese less Mongoloid that the northern populations.

"1. Amerindians are an unadmixed population predating the split between East Asians and West Eurasians".

Hang on. The same admixture paper shows Amerindians are admixed.

"Northern Amerindians are closer to modern East Asians than other Amerindians".

That is impossible to explain under your 'out-of-America' idea. It is most easily explained as representing later flow from East Asia once that region had become more Mongoloid through genetic contribution from south of Mal'ta. This is shown by your own comment:

"Mal'ta shows that there were no East Asians at 25,000 ybp (at least not in Siberia) but there were West Eurasians".

Yes. Mongoloids were hardly present in the region at that time.

"The reason MA-1 doesn't have any affinity with East Asians is because East Asians didn't exist. They emerged later as an offshoot of a northern Amerindian population (mixed with a Tyanyaun-like population)".

How could they have emerged in America yet have admixed with a Tyanyaun-like population?

" all the clades linking Amerindians and East Asians show a very specific Amerindian version in East Asia".

That is exactly what we would expect under an into America scenario. The haplogroups have diverged from their Asian relations.

"So all Asian clades (D, C and A) have very specific Amerindian versions in Asia but not the other way around".

Contradictory statement. In fact all non-American D, C and A clades are Asian-specific. And they exhibit far more variety than do the American versions. Because they have been there longer and have not suffered the reduction in diversity the American groups suffered as they moved from Asia to America.

Dienekes said...

@Dienekes, not if Siberian X admixed all the way to Europe.

If Mal'ta did and Loschbour or Motala didn't. My point is that "Siberian X" ancestry would have to be distributed throughout West Eurasia, if it exists, to give the signal of additional closeness of all West Eurasians to Native Americans, and would have to split off before Papuan and Han split from one another.

That would require X to make an equal contribution to Mal'ta to Loschbour and to Motala. Given that these are samples from all over Eurasia and from 24-8 thousand years ago, it seems very unparsimonious that they'd all have exactly the same amount of "Siberian X" ancestry.

If they had different amounts (e.g., Mal'ta had more or less) then Eastern groups would be closer to Mal'ta or Loschbour or Motala depending on the relative amounts.

terryt said...

"Why isn't Tianyuan part of this discussion? 40 kya, older than Mal'ta, and def related to East Asians".

To me Amerindians appear to be a mix of Mal'ta and Tianyuan (using both individuals as proxies for their respective populations). The lack of 'Tianyuan' in 'Mal'ta' suggests the Mongoloid element had been confined to more southerly regions before the western steppe population had been able to expand north. Once the two met in the Far East the Mongoloid element became progressively greater over time as they adopted the technology necessary for survival in Siberia. Early Amerindians contained less of this element than did the later arrivals, more or less confined to the far north of North America.

"Whether population X is like Mal'ta or not, it must have split off from Oceanian and East Asian ancestors before they split from one another, yet after they both split from West Eurasians".

I think it is far more complicated than simply 'splitting'. Isolation followed by admixture has been constant.

Matt said...

That would require X to make an equal contribution to Mal'ta to Loschbour and to Motala. Given that these are samples from all over Eurasia and from 24-8 thousand years ago, it seems very unparsimonious that they'd all have exactly the same amount of "Siberian X" ancestry.

Yep, I did say it was pretty unparsimonious.

As you say, it isn't likely for a "Siberian X" to make that uniform a contribution to all West Eurasians. And also as you say, the greater closeness of Mal'ta to Native Americans than Loschbaur, while identical closeness to Han and Papuans, would require population substructure in the "Siberian X" that putatively contributed to West Eurasian. So it couldn't be through a single event into a group to which Loschbour and Mal'ta are descendents, instead there would need to be separate events of almost exactly the same size by a structured population.

It just seems like the only alternative, unparsimonious and much less likely as it is.

German Dziebel said...

@Eastern View

mtDNA hg C1 is mostly Amerindian . It's not East Asian or Siberian. It's found there at low frequency but this doesn't make it Siberian. This what we would expect if populations were going from America through Siberia to western Eurasia. The pattern is similar to that of hg X which is found in Norh America but not Siberia. So mtDNA hgs C1 and X2 seem to be the Amerindian haploid signature in western Eurasia.

Eastern View said...
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Eastern View said...
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Tobus said...

@German:
The reason MA-1 doesn't have any affinity with East Asians is because East Asians didn't exist. They emerged later as an offshoot of a northern Amerindian population (mixed with a Tyanyaun-like population).

If that were the case (as pointed out many times now), then MA-1 would be just as related to East Asians and Amerindians, since the "Amerindian" DNA he got was from a common ancestor to both East Asians and modern Amerindians. Such a model doesn't fit the data.

GailT said...

Behar's age estimate for D4h3a is 12,954 years +/- 2580 years, which is a very close match with the date for the Anzick sample, which is dated to about 12,600 ybp. According to the supplement, D4h3b and D4h3 and its sister clades are found in Asia.

Behar estimated D4h3 to be about 18,000 ybp, so this would constrain the migration of D4h3b from Asia to North America to sometime after 18,000 ybp.

GailT said...

From the Der Sarkissian paper published 10 days ago:
"The place of origin of ancestral hg C1 was approximated in the Amur River region just south of Beringia (eastern Asia) on the basis of the current frequency distribution of hg C1 in Asia"

http://www.plosone.org/article/authors/info%3Adoi%2F10.1371%2Fjournal.pone.0087612

C1a, C1e and C1f have only been found in Europe and Asia, while C1b, C1c and C1d are restricted to Native American populations.

Tobus said...

@EasternView:
1. and 2. are talking about East Asian/Oceania not being equidistant, the point I'm making is that Amerindians/East Asian should be equidistant (or very nearly) under an Amerindian->MA-1 model.

3. Most random genetic mutations have no phenotype or functional effect and it's implicit in genetic comparisons that all human populations experience random mutations at an equal rate. So East Asians and Amerindians will have the exact same amount of random drift over a given period of time even if one looks "more different". The only thing that could cause an genetic result like you are proposing is non-Eurasian (or archaic) admixture in East Asians since divergence.

4. I think you misunderstood what I'm saying - Mal'ta proves the East Asian/Amerindian divergence has to be at or before 24kya. My point is that if the admixture was into MA-1 then this divergence has to be much earlier than this, early enough that Amerindian DNA at 24kya doesn't carry any detectable trace of East Asian DNA relative to the Onge (ie significant divergence, as old or older than the West/East Eurasian divergence).... in which case we wouldn't see modern Amerindians being so much closer to modern East Asians than to Onge and Europeans as they are today.

The only scenario that fits East Asians and Amerindians having close affinity, MA-1 and Amerindians having affinity but MA-1 and East Asians having effectively zero affinity is one where MA-1 contributes DNA to a very recently diverged Amerindian population: Amerindians closest to East Asians, MA-1 and Amerindians share DNA, MA-1 and East Asians as separate as they were before.

in ADMIXTURE at K3 should be all "west" and Native Americans should be partly "west"

That is a reasonable expectation on the surface, but consider that Europe has been the subject of lots of post-MA-1 admixture with at least 3 populations merging to form the present population, and it gets even more complicated if you add Central and South Asian populations into the picture (all of whom represent MA-1's DNA today). In contrast Amerindians underwent a bottleneck at about 15-18kya, has been almost totally isolated ever since and today has the lowest genetic diversity of any population in the world. Given that ADMIXTURE looks for discrete genetic signatures, it's not completely surprising that it detects an "Amerindian" component early in the piece and attributes this as a part of MA-1 instead of the other way around. MA-1's DNA today is like a scrambled patchwork spread across a number of otherwise diverse populations throughout western Eurasia, while a portion of it remains relatively intact in Amerindians. ADMIXTURE is correct - the simplest way to present this based purely on the numbers is to say MA-1 has an Amerindian component, but this doesn't mean that MA-1 necessarily has Amerindian ancestors.

Alvah said...

EXCERPTS FROM MY PRESENTATION GIVEN AT THE PALEOAMERICAN ODYSSEY CONFERENCE: SANTA FE IN NEW MEXICO, OCTOBER 2013
INTERPRETING ARCHAEOLOGICAL SIGNATURES BEFORE CLOVIS:
AN AMERICAN WELLSPRING
AND THE PEOPLING OF THE EASTERN HEMISPHERE
AUTHOR ALVAH HICKS

Background
This Presentation will outline "warranting evidence" through a multidisciplinary approach hypothesizing that: Amerindian populations should be examined as a source for the Homo sapien sapien Peopling of the Eastern Hemisphere. An ancient pre-Clovis archeological signature, autochthonous in its nature, can be projected to precede the onset and evolution of the modern Paleolithic detected in the colonization and "Sudden Replacement" of Old World Hominids beginning less than 50,000 years ago. A conservative archaeological assessment of the initial arrival of Late Paleolithic Asians and Australians, European Upper Paleolithic Cultures, and African Later Stone Age People coincides in time with an evolving modern human behavior throughout the Eastern Hemisphere. A multidisciplinary alternative to the “Eve out of Africa” hypothesis will be presented that supports this archaeologically based chronology.

Introduction:
“If you want to establish the claim that modern humans came out of America, and not Africa, then you had better face head on the evidence for an African or Old World modern human origin. Because if you cannot show that there are problems with the African origin model, no one will be interested in your claims for an American origin (David Meltzer, personal correspondence May 6, 1992).”

“Success in understanding the problem to the initial peopling of any part of the globe depends on finding the archaeological, genetic, and skeletal signatures of individual migrations and in their singular contributions to adaptive radiation (Dillehay; PNAS 2008, pg. 971)…To do so requires both an interdisciplinary scientific and theoretical framework (ibid, pg. 976).”

Annie Mouse said...

I am wondering of some of the sources of disagreement here relate to different definitions of "East Asian". I know when I think of "East Asian" in the genetic sense I do NOT mean the modern Han Chinese, but an older population more northerly population.


"is also possibly within the statistics that Mal'ta itself is mixed between

- a Western population

- a "Siberia X" Eastern population which split off from Oceanians and East Asians before they split from one another

and that only "Siberia X" contributed to Native Americans, along with East Asian ancestors.

But if this is true, "Siberia X" or sister clades must have mixed very widely and deeply with all present day West Eurasians, for all are closer to Native Americans than they would be to a purely East Asian derived population with the same drift as Native Americans.
"
Substitute "Han Chinese" or "South East Asian" for "East Asian" and I might buy this. With a closer look at the data.

"So mtDNA hgs C1 and X2 seem to be the Amerindian haploid signature in western Eurasia."

I think this might actually be true, for both haplogroups.

"To me Amerindians appear to be a mix of Mal'ta and Tianyuan"


Yep. To me also, although probably not exclusively.

Annie Mouse said...

I am wondering of some of the sources of disagreement here relate to different definitions of "East Asian". I know when I think of "East Asian" in the genetic sense I do NOT mean the modern Han Chinese, but an older population more northerly population.


"is also possibly within the statistics that Mal'ta itself is mixed between

- a Western population

- a "Siberia X" Eastern population which split off from Oceanians and East Asians before they split from one another

and that only "Siberia X" contributed to Native Americans, along with East Asian ancestors.

But if this is true, "Siberia X" or sister clades must have mixed very widely and deeply with all present day West Eurasians, for all are closer to Native Americans than they would be to a purely East Asian derived population with the same drift as Native Americans.
"
Substitute "Han Chinese" or "South East Asian" for "East Asian" and I might buy this. With a closer look at the data.

"So mtDNA hgs C1 and X2 seem to be the Amerindian haploid signature in western Eurasia."

I think this might actually be true, for both haplogroups.

"To me Amerindians appear to be a mix of Mal'ta and Tianyuan"


Yep. To me also, although probably not exclusively.

terryt said...

"mtDNA hg C1 is mostly Amerindian . It's not East Asian or Siberian. It's found there at low frequency but this doesn't make it Siberian. This what we would expect if populations were going from America through Siberia to western Eurasia".

You are conveniently neglecting the fact that C1's 'sisters' include C4 (American and Altai) C5 (Siberia) and C7 (SE Asia and Tibet). That is exactly what we'd expect if Chad arisen in Central Asia and entered the various regions it is found today from there. Unless you're demanding that the phylogeny of C is completely wrong.

"The pattern is similar to that of hg X which is found in Norh America but not Siberia".

Once more you conveniently ignore the fact that American X2 is almost entirely X2a, (a sister to X2j) with a presence of X2g inone Objibwa (sister to X2l). The sisters of X2a'j and X2g'l include X2b'd and X2c (scattered through Eurasia) X2e in (Altai and Georgia) along with X2o, X2m'n, X2i and X2h, all 'Eurasian'. And we have more basal X branches in the Caucasus, the Druze and in Northeast Africa.

"So mtDNA hgs C1 and X2 seem to be the Amerindian haploid signature in western Eurasia".

No. They are the Amerindian haploid signature of western Eurasia. The other mt-DNA haplogroups in America are the Amerindian haploid signature of eastern Eurasia. That seems so obvious to me I find it difficult to understand how anyone can't see it. Unless you're claiming the whole phylogeny is totally wrong, in which case you need to propose an alternative (with evidence).

eurologist said...

"Does that really make the contribution in the Americas European admixture? Not in my opinion."

Annie,

Not European, but Caucasian and/ or proto-Caucasian. I think there can be little doubt that y-DNA haplotypes Q and R, having been brought there by P from the SE of the subcontinent, originate from the extreme NW subcontinent, up to quite north into that part of Central Siberia, and West of the Himalayas. In that sense, they are West Eurasian, and the same people also moved West into Europe proper during the Gravettian.

Alvah said...

Continuation of a thread from Paleoamerican Odyssey Conference
The Modern Human Odyssey as seen from the Americas
When I first started this investigation back in 1984 I was looking for the hard evidence for modern human origins in the Old World. I was also asking: ‘Why the Western Hemisphere was not included as a source for the 45ky “sudden replacement” of Home erectus populations who had settled the entire Eastern Hemisphere more than 1,500,0000 years before.’ There is an explanation for why an American Wellspring remains an uncharted hypothesis and it goes back to the discovery of “The New World.” After 367 years of Theological (1492-1859) meanderings scientific determinations became the norm (1859-1912). Two main opinions emerged, one that the Native Indian of the Americas originated in Asia and two, they or any other “living race” could not have preceded the Neandertal of Europe. However, there were many early evolutionists who challenged this opinion, (among them; Ameghino, Wallace, Keith, Whitney, Sidis, Loomis, Curtis, Kollman, and Native Americans intellectuals), arguing that the human anatomy had been relatively stable over time (e.g. LaPierie’s “Men before Adam”).

From: Frank Spencer, The Neandertals and Their Evolutionary Significance: A Brief Historical Survey in Smith /Spencer , 1984 pg. 7
“Another problem confronting late 19th century human evolutionists was the incipient argument for the relative stability of the human form. From accumulating skeletal evidence it appeared as if the modern human skeleton extended far back in time, an apparent fact which led many workers to either abandon or modify their views on human evolution. One such apostate was Alfred Russell Wallace (1823-1913). In 1887, Wallace examined the evidence for early man in the New World, and like the German anatomist Julian Kollman (1834-1918), who three years earlier had made a similar survey, found not only considerable evidence of antiquity for the available specimens, but also a continuity of type through time.” emphasis added

Differing opinions can be found to support "multiregional evolution" and "rapid replacement," the two main camps defining modern human evolutionary research. In the Western Hemisphere origins are defined against the backdrop of migrations from Asia cast from the nineteenth century British-school's contention that Homo s.s. could not pre-date the Neandertal. The fact that ancient American fossil man finds (the vast majority remain undated) were/are anatomically modern led Holmes and Hrdlicka to cast career threatening suspicions on researchers contending great antiquity of man in the Americas. In 1929, twenty one years from its initial Folsom discovery by New Mexico’s own George McJunkin in 1908, Clovis theory began to draw its own line in the sand and a terminal Pleistocene presence has reigned ever since. Damage control to the ideas and careers of professors and students studying American origins has not wavered while archaeologists and geneticists and their theories alike have been forced to adopt limitations drawn from these mistaken starting points. Dogma lies at the heart of the problem while I had no idea it would be so difficult to overcome. By example, the 20,000 years separating Monte Verde I and II will remain unaccounted for without a well rounded theory to guide researchers in accepting a contemporary presence in Europe the 33,000 ybp dates embrace.

“The Clovis theory, over time, acquired the force of dogma. “We all learned it as undergraduates,” [Michael] Waters recalled. “Any artifacts that scholars said came before Clovis, or competing theories that cast doubt on the Clovis-first idea, were ridiculed by the archaeological establishment, discredited as bad science or ignored (From: G. Gugliotta, Smithsonian Mag. February 2013).”

terryt said...

"Yep. To me also, although probably not exclusively [Amerindians appear to be a mix of Mal'ta and Tianyuan]"

Yes. Certainly not 'exclusively'. As far as I'm aware neither Mal'ta nor Tianyuan have the 'East Asian' EDAR mutation for a start.

German Dziebel said...

@Tobus

"If that were the case (as pointed out many times now), then MA-1 would be just as related to East Asians and Amerindians, since the "Amerindian" DNA he got was from a common ancestor to both East Asians and modern Amerindians. Such a model doesn't fit the data."

The data at hand is not perfect. Fu et al. showed that Tianyuan is closest to Karitiana. Rasmussen et al. showed that it's not. Who should we use as the data that fits the model? East Asians are as far from West Eurasians as Papuans (Raghavan's argument). But this is what we would expect if East Asians (moving out of the Americas at the end of the Ice Age) admixed with a "Negrito"/"Papuan"- like population in East Asia.

"My point is that if the admixture was into MA-1 then this divergence has to be much earlier than this, early enough that Amerindian DNA at 24kya doesn't carry any detectable trace of East Asian DNA."

Mal'ta's (without the West Eurasian BLUE and South Asian GREEN) is a good proxy for Amerindians at 24,000 years. And it doesn't have any East Asian DNA. Same for Anzick at 12,000 years, now in Montana. We don't have any special proximity to East Asians but we do see a pull toward Mal'ta (or, better to say, Mal'ta's Amerindian component because BLUE is not really in Anzick either).

"in which case we wouldn't see modern Amerindians being so much closer to modern East Asians than to Onge and Europeans as they are today."

This "speed bump" is very easy to explain: the northern Amerindian population that gave rise to modern East Asians expanded within America as well around 12,000 years ago. That's how we can reconcile the paleoanthropological evidence for two migrations in the New World with the genetic evidence for the unity of the Amerindian gene pool from Alaska to Tierra del Fuego. Clovis seems to have originated in Texas, with the dates going younger as one progresses north into Alaska and NE Asia, but it's next-of-kin, the fish-tail point technology, is found all the way down the Andes.

@TerryT

"You are conveniently neglecting the fact that C1's 'sisters' include C4 (American and Altai) C5 (Siberia) and C7 (SE Asia and Tibet). That is exactly what we'd expect if Chad arisen in Central Asia and entered the various regions it is found today from there. Unless you're demanding that the phylogeny of C is completely wrong."

Yes, it's likely wrong. You should get used to it by now. Lippold et al. just showed you that mtDNA phylogeny is a moving target. mtDNA C1 is likely the oldest (it has several sites miscoded by PhyloTree as "derived") since it's found over such vast geographic expanses from Iceland to Patagonia, while C5 and C7 are geographically localized, hence younger.

GailT said...

"Yes, it's likely wrong. You should get used to it by now. Lippold et al. just showed you that mtDNA phylogeny is a moving target."

Here is what Lippold et al. said:

"The resulting phylogenies are quite consistent with the existing mtDNA and NRY phylogenies with some small discrepancies involving lineages that are not well-resolved. The age of the mtDNA ancestor is estimated to be about 160 thousand years (ky), and the ages of the non-African mtDNA lineages M and N are about 65-70 ky, in good agreement with previous estimates."

So, essentially identical results with every other recent mtDNA study, and remarkably similar results to the original Cann et al. 1987 study.

terryt said...

"mtDNA C1 is likely the oldest (it has several sites miscoded by PhyloTree as 'derived') since it's found over such vast geographic expanses from Iceland to Patagonia, while C5 and C7 are geographically localized, hence younger".

How does a geographically localized haplogroup automatically mean it is younger? Surely it simple means the haplogroup hasn't expanded since it first formed. If anything geographically localized haplogroups give us a better idea of where haplogroups branches originated than do those found over vast geographic expanses.

"Yes, it's likely wrong".

Are you now claiming Z is in no way related to C? Or that M8 is not related to either C or Z in any way?

Tobus said...

@German:This "speed bump" is very easy to explain: the northern Amerindian population that gave rise to modern East Asians expanded within America as well around 12,000 years ago.

I don't think you quite understand, for a 24kya sample to show significant affinity to population A over population B, then populations A and B *must* have been different at 24kya. If they hadn't yet diverged then the affinity would be to BOTH of them since they were the exact same population at the time.

Whichever way you propose the gene flow went, in a scenario where East Asians share a common ancestor with modern Amerindians *after* MA-1, then any DNA interchange between MA-1 and this common ancestor would affect them both in roughly equal amounts. The fact that MA-1 shows up as being close to Amerindians but not very close at all to East Asians is very solid evidence that East Asians and Amerindians had already diverged at the time of MA-1.

Alvah said...

Excluding the Western Hemisphere and an entire once unknown world of People from the search for human ancestors has left researchers with an ongoing “Paradigm Crisis” that continues to leave unresolved our common human beginnings. Doe’s the Americas offer us a solution? Is Pre-Clovis really pre Paleolithic? Do links to the earliest genetic data found in Tyanyuan, Mal’ta, and Anzick 1, offer researchers alternatively, ancestral ties to the New World? Although most everyone continues to look the other way the scope of the ongoing debate should obligate researchers to openly examine, as the late Professor Bruce E. Raemsch suggests, Native American Antecedents (an Encyclical) Our Obligation to Test a Theory on Native American Antiquity-A Research Letter 1990, unpublished. Consensus opinion and alternating Old World theories of Human Origins remain constrained with “with no resolution in sight” as the following quotes articulate…

From: Howell, F.C., 1984, "Preface" to The Origins of Modern Humans: A World Survey of the Fossil Evidence, Eds. Smith FH, F. Spencer

"There is now a near consensus among students of human evolutionary biology that the origins of our own species, Homo sapiens, is somehow intimately linked with the first intercontinental ancient hominid, Homo erectus. However, neither the transformation of erectus to sapiens nor the transformation of ancient (archaic) populations of Homo sapiens to their anatomically modern successors (H s sapiens) are matters of agreement in this scientific fraternity. Undoubtedly, there are many factors that make this the case, and any reader of this volume will discern some of those that are most obvious. In fact, there is no consensus among the authors represented in this volume, although the major issues are generally well delineated, and the limitations of the diverse and often disparate lines of evidence are usually apparent (p. xiii.)."

Another example of the scope of the “crisis”:
From: Willamette, C. M., and G. A. Clark. Paradigm crisis in modern human origins research Journal of Human Evolution (1995) 29, 487-490.
“Despite the considerable efforts of many well-informed investigators, however, no resolution of the controversy is in sight.
How selectively biased are researchers? An extensive literature review of published multivariate data invoked in support of "continuity" and "replacement" positions produced some dramatic results (Willamette, 1993, 1994). A total of 680 data points were collected, representing 61 variables on 55 fossils. Of these, only 72 variables on 11 fossils, or 11% of the reported database, were common to both paradigms. This means that in the sample, 89% of the data collected were used by members of only one paradigm (p. 488).
Given the construal of the paradigm just outlined, theories (more accurately the hypotheses deduced from them), can only be confirmed or disconfirmed according to the tenets of the metaphysic (the construal of "reality" defined by the biases and preconceptions of the paradigm). Outside a particular paradigm, its constituent theories ("hypotheses") might appear nonsensical.
Despite assertions to the contrary (e.g. Klein, 1989), the venerable history of the debate suggests that simply acquiring more data will not help us choose between opposing paradigms. The reason is that data have no meaning or existence independent of a paradigm that defines and contextualizes them. In light of the plethora of articles and books that have appeared in the last 10 years, it is worth asking ourselves whether we are any closer to solving the question of our origins than we were a century ago. If there is a lesson to be learned from the debate, it is that students of human evolution must begin to confront the inferential basis for their knowledge claims. So far, they have not been much concerned to do so. The result is an interminable debate, now well into its second century, with no resolution in sight (p. 489-489 emphasis added).”

German Dziebel said...

@Tobus

"Whichever way you propose the gene flow went, in a scenario where East Asians share a common ancestor with modern Amerindians *after* MA-1, then any DNA interchange between MA-1 and this common ancestor would affect them both in roughly equal amounts. The fact that MA-1 shows up as being close to Amerindians but not very close at all to East Asians is very solid evidence that East Asians and Amerindians had already diverged at the time of MA-1."

OK, now you are bringing value. Will it work if we hypothesize that "northern Amerindians" and "southern Amerindians" diverged prior to 25,000 YBP, with MA-1 receiving gene flow from "southern Amerindians" and East Asians receiving gene flow from "northern Amerindians"? (I put it all in quotation marks to indicate that 25,000 YBP those ancient Amerindian populations may have been not so much northern and southern as coastal vs. inland, western vs. eastern or something else. It's just their descendants ended up being distributed across the north-to-south axis.) I still think that "Mongoloids" resulted from a recent (12,000-10,000 YBP) backflow from the New World but their ancestral Amerindian population may have been isolated from the "southern Amerindian" population for much longer.

German Dziebel said...

@GailT

"Here is what Lippold et al. said:

"The resulting phylogenies are quite consistent with the existing mtDNA and NRY phylogenies with some small discrepancies involving lineages that are not well-resolved. The age of the mtDNA ancestor is estimated to be about 160 thousand years (ky), and the ages of the non-African mtDNA lineages M and N are about 65-70 ky, in good agreement with previous estimates."

So, essentially identical results with every other recent mtDNA study, and remarkably similar results to the original Cann et al. 1987 study. "

I don't care what they say. And, Gail, don't turn to your favorite tactic which is to heckle. I'm not talking about opinions, I'm talking about the data. Of course, they are going to say that. Most people are afraid to create a splash and cause peer ire and prefer to believe that science is somehow exempt from evolution. But their data speaks otherwise and we discussed it in a different string. The L3'M'N nexus is now treated as L3'M vs. N, which is a huge change from L3 > M vs. N. It's now more consistent with the Y-DNA tree topology, where the Afro-Eurasian clade DE is opposed to the Eurasian-only clade CF. Effectively, the most frequent and/or most widely spread African lineages are a subset of a Eurasian clade.

@TerryT

"How does a geographically localized haplogroup automatically mean it is younger? Surely it simple means the haplogroup hasn't expanded since it first formed. If anything geographically localized haplogroups give us a better idea of where haplogroups branches originated than do those found over vast geographic expanses."

Nothing is automatic of course but here are a few rules of thumb:

It takes time for a haplogroup to spread. Larger distances are colonized over longer periods of times. If a haplogroup didn't expand further, the neighboring niches had likely already been taken. A colonizing group is smaller than the source population and bigger populations need more space.

If a haplogroup introgressed from an "archaic" population then of course it can be localized and old but the date of its absorption by the "modern" population is still young.

I don't think the typical logic that basal diversity means greater age or that a daughter population takes a subset of genes from the parent population holds any water as a general principle. People put the cart before the horse when they fortune-tell population movement in geographic space from an abstract phylogeny. Instead, the geographic distribution of sequences should be one of the inputs into a phylogeny.

Rokus said...

'[...] The age of the mtDNA ancestor is estimated to be about 160 thousand years (ky), and the ages of the non-African mtDNA lineages M and N are about 65-70 ky, in good agreement with previous estimates."

So, essentially identical results with every other recent mtDNA study, and remarkably similar results to the original Cann et al. 1987 study.

Except that even Out of Africa now has to deal more explicitly with this enormous gap of at least 100 ky wherein modernity developed further in Eurasia and came back to Africa.

Eastern View said...
This comment has been removed by the author.
Eastern View said...
This comment has been removed by the author.
Alvah said...

Examining an American Wellspring

“In contrast, multiregional evolution can easily be disproved if it can be shown that all of the ancestors of living humans at some discrete time in the Middle or Late Pleistocene lived in only one area of the world. If this were the case, then we should be able to trace the ancestry of every human genetic locus to a single population existing at some time in the past million years.” (Milford Wolpoff et al. pg.131, Multiregional, Not Multiple Origins, in AJPA 112:129-136 (2000) (emphasis added)

Geographic isolation as long been identified as a problem for advocates of “Replacement” by “Multiregional” proponents from Weisenrich and Hrlichka to Wolproff and Thorne and others today. However, the geographic constraints in exiting the Americas are perhaps the most compelling insight as to why Homo sapiens sapiens are so recent to the Eastern Hemisphere.
The barriers in exiting an old New World into a new Old World would have been extremely encumbering. Getting to the backdoor, out of the Americas, and into northeastern Asia, would be feasible only after de-glaciations and this timing would coincide with the existence of a Bering Sea not a Bering Land Bridge. This issue has been heralded by a number of discussants I have held conversations and correspondences with, including Lewis Binford…

“‘Should modern humans have evolved in the Americas in the first place, as you suggest, they would have never found the Old World, this isolation would have been impossible to overcome (Lewis Binford, personal conversation, 1994).’” Lew had summoned the ever so Binfordinan ‘got you’. My reply, it seemed, had been forthcoming, “‘Lew, you may have answered one of this theory’s most challenging problems, why was it just 45 thousand years ago and not much earlier, that our species crossed into the Eastern hemisphere(?).’” I can still recall the silence before we continued on from there. We remained friends in dialog through 2011.

GailT said...

@German:

"I don't care what they say."

That's obvious, as Lippold et al. say exactly the opposite of what you claimed that they say.

"And, Gail, don't turn to your favorite tactic which is to heckle."

Quoting from the paper that you cited is not heckling. You repeatedly make claims that are very easily shown to be false. As Terry previously requested, if you believe the current tree is wrong, or that Lippold et al. misinterpreted their data, please provide your evidence for an alternate tree.

German Dziebel said...

@Eastern View

"Proto-Native American admixture is the most parsimonious model because it explains the data with no hypothetical populations of Ancestral North Eurasians or Basal Eurasians."

Bingo!

"German maybe eccentric on most points.."

Eccentric? I never argued that Indo-Europeans came from Anatolia ;)

"Any admixture of "Siberian X"/Native American into Europeans will pull them towards Native Americans and do very little to pull Europeans towards East Asians."

That's a good way to think about it.

"From a multi-dimensional plot you will see East Asians and Native Americans occupy very different space."

Yes, but then how do we explain the multiple over genetic, phenotypic and cultural similarities between East Asians and Amerindians? And then we have a clear "attraction" between "northern Amerindians" and East Asians. Maybe East Asians would have been even further apart from Amerindians had recent gene flow from America not brought them closer? West Eurasians are very non-Amerindian on the surface but the Amerindian component can unmistakably be unearthed from MA-1, La Brana, Loschbour, Motala, Yuzhnyi Olenii Ostrov. East Asians are overtly Amerindian-looking but apparently only remotely related to them once recent admixture is removed.

terryt said...

"Here is what Lippold et al. said"

Thanks for pointing that out Gail.

"I don't care what they say".

Of course not. German is desperate to avoid having to face the fact that the phylogenies fail completely to support his belief.

"I'm not talking about opinions, I'm talking about the data".

You're consistently either ignoring or twisting the data. You are certainly not taking it at face value.

"The L3'M'N nexus is now treated as L3'M vs. N"

No, the L3'M'N nexus forms, or becomes, L3'M and N. The term 'vs.' is not at all involved.

"which is a huge change from L3 > M vs. N".

I disagree that it is 'a huge change'. We merely have N forming earlier than what the data previously available showed although it has long been apparent that N was older than M.

"I don't think the typical logic that ... a daughter population takes a subset of genes from the parent population holds any water as a general principle".

What? Do you really believe that every time a population breaks off from another it takes an entirely representative sample of genes from the source population?

"the geographic distribution of sequences should be one of the inputs into a phylogeny".

Exactly. And that geographic distribution is what you are ignoring on the matter of mt-DNA C.

"The fact that MA-1 shows up as being close to Amerindians but not very close at all to East Asians is very solid evidence that East Asians and Amerindians had already diverged at the time of MA-1".

Or Amerindians were yet to form through a hybridisation event between an MA-1 population and an East Asian one.

"Is Pre-Clovis really pre Paleolithic?"

Obviously not. It is completely within the Upper Paleolithic.

"Apparently there only assumption was that there were East Asians in Siberia 24K ago and for Mal'ta to be admixed"

The evidence is reasonably strong there were no 'East Asians' in Siberia 24k ago. The arrival of East Asian haplogroups appears to be later than that of a more western population, although some mt-DNAs were picked up by that western population and carried to America.

"Except that even Out of Africa now has to deal more explicitly with this enormous gap of at least 100 ky wherein modernity developed further in Eurasia and came back to Africa".

But that 'modernity' may be only partly genetic. The development of the Upper Paleolithic is certainly primarily cultural although it did involve some level of migration, especially into previously unoccupied Northern Eurasia.

Alvah said...

@GailT So, essentially identical results with every other recent mtDNA study, and remarkably similar results to the original Cann et al. 1987 study.
Excuse US,
Templeton demonstrated that the Berkley Groups original contentions were not only flawed but biased (1993). The Stanford Group Johnson et al. (1983) had it right (out of Asia into Africa) based on phylogenetic data that did not rely then (nor now) on still unproven molecular clocks.

From: “Alan R. Templeton Washington University The "Eve" Hypotheses: A Genetic Critique and Reanalysis American Anthropologists 1993

“Using an even larger data set than Excoffier (1990), Merriwether et al. (1991:552) concluded that "the evidence that human mtDNA variation is not in mutation-drift equilibrium is incontrovertible" and offered several possible explanations, including expanding population size and selection. (pg. 59)
“This rejection of neutral equilibrium also invalidates the argument given in Cann, Stoneking, and Wilson (1987) and Vigilant et al. (1991) that African populations are the oldest because they have the most genetic diversity (a proposition that has not yet been proven, as discussed in the previous section). The diversity in a region does not necessarily reflect the age of the regional population but rather could reflect the age since the last favorable mutation arose in the population, the demographic history of population size expansion, the extent of gene flow with other populations, and so on. As argued by Merriwether et al. (1991:553), "Because it is clear that mtDNA diversity is not in equilibrium among human populations, estimates of population age based on coalescence time need to be interpreted. (pp. 59-60)”

Merriwether et al. (1991) recently presented an expanded version of this data set, but, unfortunately, much of the new data consists of New World populations, which are not relevant, or old World populations that were not scored for all the same restriction enzymes as the earlier samples used to construct the cladogram given in Excoffier (1990). ”
Hmmm… “the new data consists of New World populations, which are not relevant”, NOT RELEVANT, because of Clovis First dogma which has now been proven a flawed theory or stating point. Hypotheses are fundamentally based on when the New World was Peopled. Not open for discussion is the autochthonous genetic signature accompanying Amerindian Tribal data (except here at Dienekes' Blog harborage of German Dziebel’s insights).

Excoffier and Langaney Origin and Differentiation of Human Mitochondrial DNA 1989
“This also indicates that these types may have been present in early populations of modern humans. Very differentiated types might have appeared later in isolated populations. This partial phylogeny does not indicate which population could have been ancestral to others, but it becomes clear that the hypothesis of the African Eve is based on a "genealogical tree" biased by topological errors–and that it thus cannot be supported by these data. (pg. 81)
Johnson et al. (1983) as well as Whittam et al. (1986) have carried out homozgosity tests (Watterson 1978) on mtDNA which tend to show that the hypothesis of equilibrium under neutrality is not always supported. The exact nature of this selection, and why it does not occur in some populations, remains to be understood. (pg. 81)”

“in some populations”, like Individual Amerindian Tribes!

In an after dinner conversation German and I shared with Theodore G. Schurr in Santa Fe New Mexico 10-18-2013, U of Penn Geneticist reaffirmed a major contention of ours after I straightforwardly asked Tad “why would all the supposedly older mtDNA L lineages not be included in a recent out of Africa phylogeny? His response: ‘That is a good point and know-one has adequately explained it.’
Perhaps, M is basal to L3 and the acceleration of novel haplotypes in African L2, L1, L0, etc. lineages are a byproduct of adaptations to a new African environment.

Tobus said...

@German: Will it work if we hypothesize that "northern Amerindians" and "southern Amerindians" diverged prior to 25,000 YBP, with MA-1 receiving gene flow from "southern Amerindians" and East Asians receiving gene flow from "northern Amerindians"?

If by "receiving gene flow" you mean "diverged from" then, no it won't work: East Asians should still be as close to MA-1 as North Amerindians are... plus in such a scenario South Amerindians would be closer to Europeans than to East Asians.

If instead you mean adxmiture into existing African-derived populations in Eurasia by a completely separate human lineage in America, then we'd expect to see this reflected the Tianyuan data - Amerindians would be further away than anyone else, then East Asians then European. Tianyuan being roughly equally related to all Euruasian/American populations (and Fu's data only shows a small variance of about 5% here too) strongly suggests a common African-derived Asian ancestor for all of these populations.

Tobus said...

@EasternView:Any admixture of "Siberian X"/Native American into Europeans will pull them towards Native Americans and do very little to pull Europeans towards East Asians.

That's only true if East Asians and Native Americans were unrelated 24kya, something that is at odds with all available evidence.

German Dziebel said...

@Tobus

"plus in such a scenario South Amerindians would be closer to Europeans than to East Asians."

Well, they South Amerindians (Karitiana as a poster child) are closer to West Eurasians, with northern Amerindians (Eskimo-Aluets, Na-Dene and a few other North American populations in Rasmussen) being closer to East Asians. That's why I suggested this interpretation from the beginning.

terryt said...

"except here at Dienekes' Blog harborage of German Dziebel’s insights"

I must congratulate Dienekes on being prpepared to accept discussion on a wide variety of theories on human origins, unlike some blog sites.

"why was it just 45 thousand years ago and not much earlier, that our species crossed into the Eastern hemisphere(?)".

How do you then explain how the Upper Paleolithic is apparently older in western Eurasia (45,000 years) than it is in eastern Eurasia (30,000 years)?

"I can still recall the silence before we continued on from there".

Stunned silence in disbelief you had ignored that problem? You even hinted you were very well aware of the contradiction when you said, 'Homo sapiens sapiens are so recent to the Eastern Hemisphere'.

"The Stanford Group Johnson et al. (1983) had it right (out of Asia into Africa) based on phylogenetic data that did not rely then (nor now) on still unproven molecular clocks".

I'm prepared to serioulsy consider an 'Out of Asia' aspect, even the Cann, Stoneking, and Wilson group considered that as being a possible but less likely option, but that is not 'out of America'.

"why would all the supposedly older mtDNA L lineages not be included in a recent out of Africa phylogeny?"

Isn't that exactly what we would expect in an out of Africa scenario? Unless you're claiming that every time a population breaks off from another it takes an absolutely representative sample of genetic variation in the source population. That is surely very unlikely to be the case.

"Perhaps, M is basal to L3"

Possible under the proposed M'L3/N split but it seems we are yet to see the resolution of that problem.

"the acceleration of novel haplotypes in African L2, L1, L0, etc. lineages are a byproduct of adaptations to a new African environment".

Even the newly proposed phylogeny shows that is extremely unlikely to be the case.

German Dziebel said...

@GailT

"That's obvious, as Lippold et al. say exactly the opposite of what you claimed that they say."

I never claimed anything about what they say. They presented evidence which stands on its own without their commentary. You can't master a simple skill of making a coherent argument, how can you be trusted with interpreting a phylogenetic tree for the human species?

"You repeatedly make claims that are very easily shown to be false. As Terry previously requested, if you believe the current tree is wrong, or that Lippold et al. misinterpreted their data, please provide your evidence for an alternate tree. "

I never make false claims. I'm too well educated for this. If you prefer to align with cryptocreationist and out-of-Antarctica believer, TerryT, you are placing yourself outside of science. Judging from your statements on Anthrogenica, this is the place where you likely belong. And I'm not planning to change this. It's unethical to answer informed criticism with a plea to provide an alternative tree. Imagine a scholar who, in response to a critique from a peer reviewer, would refuse to correct his submission but instead demand the reviewer to write his own paper on the given topic.

The mtDNA tree is flawed in its method (ancestral states are not properly determined and many branches are rooted in recurrent mutations) and the African branches are untested against ancient DNA. But even in its current rendition, African L0 ,L1, L2, L4, L5 are likely products of archaic admixture in Africa and not the "basal branches of the human tree." Otherwise, we would have seen them all over Eurasia as they would've been taken out of African by the putative immigrants to Eurasia.

terryt said...

Returning to one of German's earlier comments that he has failed to elaborate on:

"mtDNA C1 is likely the oldest (it has several sites miscoded by PhyloTree as 'derived') since it's found over such vast geographic expanses from Iceland to Patagonia, while C5 and C7 are geographically localized, hence younger".

The following is what the currently accepted mt-DNA C phylogeny tells us. I will be the first to concede the phylogeny may change, I suspect mainly through the resolution of basal connections within M. C is such a widespread haplogroup it is impossible to discern its origin without considering its deeper origins.

As it stands we have a basal branch within M, M8, forming two surviving branches: M8a and CZ. M8a is almost entirely confined to the mountainous region of Laos and neighbouring southern China. I doubt it has become isolated there after some Israelite-type prolonged wandering in the wilderness. To me it is far more likely that M8a has remained very close to where it first formed from M8. That, in turn, would place CZ's origin as being not too far away. C7, a basal branch within C, is also present in Laos although it is usually associated with Tibeto-Burman-speaking groups. Perhaps CZ originated through the Tibetan/Chinese border region through the northward extension of the same mountain zone. Members of Z are present in India and so it need not have been very far north.

The C haplogroups are spread through Siberia from America to Europe. Even in between the extremities, in Iceland. To me that looks like a rapid expansion through the whole region from somewehre else. From the mountainous region between Tibet and China? Exactly where the EDAR370A mutation is said to have originated. Haplogroup C cannot have originated in America.

Alvah said...

Hearths, defined by imported matrixes and transported stones make up a key evidentiary component offering significant proof for a modern human presence in Ancient America. Many pre-Clovis sites are defined by these modern features but lack enhance Paleolithic comparisons. The lack of elaborate Paleolithic elements points to the pre-Clovis as a basal condition, an ancestral sate rather than a descendant state. This situation, the lack of a contemporary Paleolithic, remained(s) a pretentious point of contention fanning the Clovis First scenario with the first uncontested “Paleolithic” link to the Old World. An autochthonous presence counters that a basal archaeological signature predates the onset of an emerging modern Old World Paleolithic that only becomes more sophisticated as the Peopling of the Eastern Hemisphere progressed. The differences distinguishing the Middle Paleolithic and the Upper Paleolithic are out lined below. The pre Clovis and Clovis are distinguished by the lack of a definable Paleolithic signatures in the former.

Pre-Clovis is in reality Pre Paleolithic, sorry I confused you with a ? mark.

@alvah said "Is Pre-Clovis really pre Paleolithic?"
@Terrtt Obviously not. It is completely within the Upper Paleolithic.

Please google “Clovis First Theory ” or just get the lowdown. Wow, now I know why German has so much trouble making the crooked road strait.

@Rokus Except that even Out of Africa now has to deal more explicitly with this enormous gap of at least 100 ky wherein modernity developed further in Eurasia and came back to Africa.

That said, thank you, some quotes to back that up.


From: In Search of the Neanderthals: Solving the Puzzle of Human Origins. Cambridge Archaeological Journal, 4, pp 95-119.
“A Levantine Perspective
Anthony E. Marks
“Having postulated that there was a movement out of Africa at about 100,000 BP, the obvious first step to confirm this archaeologically would be to document a spread of African materials into the Levant at that time. Yet the authors are amazingly silent about what material culture the early 'Moderns' had when they moved into the Levant. They do note that Qafzeh and Kebara both 'have Middle Palaeolithic tools' (p. 153). They fail to mention, however, that the Levantine Mousterian cannot be traced back into Africa; that the strong African tendency for bifacilally retouched points and foliates is not seen in the Levant until the Neolithic (pg. 105)!”
“The 'Aurignacian' aspect of this level is limited to some carinated tools. There are no personal ornaments, no figurines, no engravings, and no evidence of any 'well-organized' campsite. Pierced bone and shell, as well as numbers of bone and antler tools, do appear in the Levant at c. 30,000 BP, some 10,000 years later than their appearance in Europe (pg. 105)!”
“The reality of Near Eastern prehistory raises some serious questions about the authors' scenario. How can the 'modern' Aurignacian, as they define it, be associated with the spread of anatomically modern people into Europe from the Levant before 40,000 BP, when the 'early' Levantine Aurignacian does not include those elements which they consider evidence for 'modern' behavior (pg. 105)?”
“Where, how, and why did this 'modern' behaviour develop? It is merely stated to be part of the Aurignacian in Europe by 40,000 BP. Why, if anatomically modern people were around from 100,000 BP, did their potential 'modernity' not manifest itself for 60,000 years (pg. 105)?”

Again I ask where does this place pre-Clovis behaviors (?); ancestral not descendant.

Alvah said...

Continuing a thread from my last post…

“The European Evidence
Paul Mellars
“What none of us has yet managed to do, of course, is to provide a clear and coherent explanation of how this dramatic transformation in behavioural patterns came about – evidently long after the initial emergence of distinctively anatomically modern humans in either Africa or Asia. Clive Gamble talks happily about 'big surprises' or 'flicking a switch' in human cultural development. These may be catchy and convenient labels, but they hardly help us to unravel the actual mechanisms by which these dramatic behavioral changes originated. This remains, in my view, by far the greatest challenge facing students of the 'human evolution' over the next decade (Cambridge Archaeological Journal, 1994 pg. 104).”

“In their… Reply: Christopher Stringer & Clive Gamble
Instead we agree with Bar-Yosef who reiterates a point he has made before (1987, 34) that 'it is not in the lithics, but in features such as hearths, the spatial distribution of debris, etc., that the emergence of modern humans is reflected' (Cambridge Archaeological Journal pg. 114).”


What preceded this sudden behavioral and anatomical life-way? We know it evolved itself, but from where did this seed find its way to Europe?

Tobus said...

Well, they South Amerindians (Karitiana as a poster child) are closer to West Eurasians, with northern Amerindians (Eskimo-Aluets, Na-Dene and a few other North American populations in Rasmussen) being closer to East Asians. That's why I suggested this interpretation from the beginning.

Try not to get confused by the wording - South Americans might be closer to Europeans than North Americans are, but they are not closer to Europeans than they are to North Americans.

South Americans closest relatives are North Americans, followed by East Asians and then only distantly West Eurasians. But in the scenario you describe the North/South American split is before any East/West Eurasian split, so South Americans should be closest to West Europeans with only a distant affinity to the North American/East Asian lineage... this scenario doesn't work.

Given the pattern and timing of modern and ancient genetic affinities, the only plausible order for the divergence of modern humans is East/West Eurasian, then East Asian/Amerindian, then North/South Amerindian. Any other order causes an inconsistency with some aspect of the data at hand.

terryt said...

"It's unethical to answer informed criticism with a plea to provide an alternative tree".

It is unethical to claim some scientific consensus is totally wrong without providing some sort of alternative explanation.

"African L0 ,L1, L2, L4, L5 are likely products of archaic admixture in Africa and not the "basal branches of the human tree." Otherwise, we would have seen them all over Eurasia as they would've been taken out of African by the putative immigrants to Eurasia".

As usual you are assuming that any population moving out odf some huge region takes a completely representative sample of the genetic variation across that huge region. Ever heard of 'bottleneck'?

"Please google 'Clovis First Theory' or just get the lowdown".

I have no problem accepting Clovis was not the first American technology. What I believe there is no evidence for is that humans had been in America tens of thousands of years before Clovis. What we have at present is reasonable claims for a culture contemporary with, or a little older than, Clovis. I see no difficulty.

"Pre-Clovis is in reality Pre Paleolithic, sorry I confused you with a ? mark".

It is extremely doubtful that Pre-Clovis is other than Upper Paleolithic. There is so little evidence for the sites that absence of UP markers is hardly surprising.

"the authors are amazingly silent about what material culture the early 'Moderns' had when they moved into the Levant. They do note that Qafzeh and Kebara both 'have Middle Palaeolithic tools'"

There is no reason to suppose that the first modern humans to emerge from Africa had an UP technology. In fact the evidence argues against it.

"This remains, in my view, by far the greatest challenge facing students of the 'human evolution' over the next decade"

That was published in 1995. We are now reasonably sure that the UP developed within the Homo sapians sapiens population somewhere outside Africa.

"South Amerindians (Karitiana as a poster child) are closer to West Eurasians, with northern Amerindians (Eskimo-Aluets, Na-Dene and a few other North American populations in Rasmussen) being closer to East Asians. That's why I suggested this interpretation from the beginning".

Surely that is most easily explained as being through a later arrival from East Asia for those northern populations rather than the convoluted and unlikely explanation you are forced to propose.

"If you prefer to align with cryptocreationist and out-of-Antarctica believer, TerryT, you are placing yourself outside of science".

German is obviously worried that by using his logic I have provided as much evidence for modern humans having originated in Antarctica or (perhaps even likely) in Australia as he has that they originated in America. Come on German. Prove that modern humans cannot have originated in Australia!

German Dziebel said...

@TerryT

"The following is what the currently accepted mt-DNA C phylogeny tells us. I will be the first to concede the phylogeny may change, I suspect mainly through the resolution of basal connections within M. C is such a widespread haplogroup it is impossible to discern its origin without considering its deeper origins."

So you decided to add M8 and Z to make the lineages under consideration even more widespread. Then you somehow managed to find a source for the more widespread group of lineages but not for the less widespread one? You just killed your own argument, Terry.

In any case, instead of relying on "accepted phylogenies" (Note: phylogenies shouldn't be accepted before they are tested) to construct conjectural historical scenarios, take a look at PhyloTree and compare all the stem mutations on M8, Z and C against Sima, Denisovan and Neandertals. You'll see that, among M8, Z and C stems, only hg C's stem has an underived mutation (site 11914). Phylotree posits a reverse mutation here (G11914A! ), which is completely unfounded. Hg C shares ancestral G11914 with L0. So what we have here is an split between hg C and hgs M8'Z. PhyloTree posits A249d as defining hg CZ. Instead, this should be interpreted as homoplasy on C and Z lineages considering that A249d occurs multiple times on different lineages (at least 3 times in mhg M).

So here goes with the wind your out-of-Laos theory for the origin of mtDNA hg C. If you want to be helpful, Terry, you should comb through every lineage of human mtDNA "tree" and compare its mutations to the know ancient hominin sequences. Without this, you are wasting your own, and, what is vastly more valuable, my time.

GailT said...

@German:

"I never claimed anything about what they say. They presented evidence which stands on its own without their commentary. You can't master a simple skill of making a coherent argument, how can you be trusted with interpreting a phylogenetic tree for the human species?"

As a matter of fact, you claimed that the mtDNA tree is incorrect and you supported this by claiming that: "Lippold et al. just showed you that mtDNA phylogeny is a moving target", a statement that is in direct contradiction to both their data and their description of the data.

Every time I point out your factual errors, you respond by attacking me personally. I have never attacked you personally, I simply point our your very obvious mistaken or false statements. Please provide a tree that is supported by the data, and then I'll take you seriously.

Alvah said...

@TerryT “Haplogroup C cannot have originated in America.”
This Holocene Migration out of the Americas into Asia will be explained for you, shortly, and has been highlighted already, … See Boas 1905, 1910; S. D. Ousley Human Biology 1995; and Hicks Human Biology 1998; and others.
@Terryt I must congratulate Dienekes on being prepared to accept discussion on a wide variety of theories on human origins, unlike some blog sites.
This open discussion could or should lead to something BIG. Why the skepticism? Nothing else is offering more than just casual antidotes when we have the cure at hand.
And Dienekes’ seems to agree that there are weaknesses with the out of Africa” hypothesis. Into Africa with a basal older sister M is what will emerge as a true alternative explanation as it does explain why, it was not any Ls out of Africa.
@Teeryt “but that is not 'out of America'”
It most certainly is…just wait, pay attention, and invite Cinderella to the Ball, or uncover an “Invisible Truth” as the Micmac put it.
@Terryt “Isn't that exactly what we would expect in an out of Africa scenario?”
NO! We should expect it wholly unlikely that none of the proposed ancestral L lineages would not be part of the exodus. The only logical exercise is that the accumulation of novel African L mtDNA lineages is a better fit, and supported by the “Out of America” into Asia and then into Africa hypothesis.
@Terryt ‘Stunned silence’ in disbelief you had ignored that problem?
To have the answer at hand is not to say I was not thinking about the difficulties exiting the Western hemisphere would have been for an autochthonous Amerindian ancestor to us Old World inhabitants, only that he was stopped in his step with the adequacy of my immediate response. He would have had you for lunch on your recent statement about pre Clovis behaviors…
@Terryt Obviously not. It [pre-Clovis] is completely within the Upper Paleolithic.
Pre Clovis is not Pre-Middle Paleolithic either, it stands alone as the most primal state before during and until the sudden arrival of technologies honed during colonization of the Old World.
I don’t think you get the full scope of the picture, let’s put it this way. It would take a rocket ship to colonize another world unless the other world was on the same space ship, EARTH. We are not recent to the New World or the Earth only the Old World. Please do not continue judge the Theory wrong in the first place and you might see the unison of the evidence.
This might help
From: Knecht, Heidi: Anne Pike-Tay; and Randall White; editors. Before Lascaux: The complex Record of the Early Upper Paleolithic, 1993 pg. 1.
"One of the most hotly debated topics of research in the past decade has been that surrounding the first appearance in Western Eurasia of hominids that can be considered anatomically and culturally modern. Between 50,000 and 30,000 years ago, the Neanderthals and Mousterian [Middle Paleolithic] industries were replaced, from the Near East to the Atlantic seaboard, by physically modern humans whose culture showed significant innovations, many of them never seen before on earth. These included graphic representations, true blade technology, personal ornaments, complex weapon and propulsion systems, long distance procurement of a variety of durable raw materials, subsistence systems based on strategically organized use of the landscape over the course of the year, rapid and continual technological change through time, and cultural systems that very greatly from region to region.

It came from the East Kara Bon 43,000 ybp.
In Siberia, new AMS 14C dates from Kara-Bom demonstrate that initial Upper Paleolithic industries appeared as early as 43,000 years B.P. or earlier Goebel et al. 1999."

German Dziebel said...

@GailT

"Every time I point out your factual errors, you respond by attacking me personally. I have never attacked you personally, I simply point our your very obvious mistaken or false statements."

This is what you need to understand. I've never made any factual errors. What you believe are factual errors are in fact valid criticisms of the current version(s) of the mtDNA tree by a highly trained professional. Your irresponsible and persistent denial of this simple fact amounts to heckling and a personal attack. I, on the contrary, don't attack you personally but I do debunk your "presentation of self" as a legitimate expert in human origins.

""Lippold et al. just showed you that mtDNA phylogeny is a moving target""

How is it in contradiction with the data that they presented? They redefined the L3 node, and I had told you a while ago that L3 was a problem. You responded by saying that 25 years of research makes the mtDNA phylogeny bulletproof. Via Lippold et al. I've proved you wrong and now you are denying it. This is a fact, and not a personal attack.

"Please provide a tree that is supported by the data."

Once again, this is not how scholarly ethics works. You need to respond back to me with a proof that all the ancestral states in the current mtDNA phylogeny are correctly identified, that there's enough ancient mtDNA testing to prove the reality of the present topology and that the recurrent mutations are not used to define a branch.

German Dziebel said...

@Tobus

I thought we were making progress, but you are still mired in absurdities.

"Try not to get confused by the wording - South Americans might be closer to Europeans than North Americans are, but they are not closer to Europeans than they are to North Americans."

Of course Southern Amerindians are not closer to Europeans than to northern Amerindians. If they were, this would've been a good argument for a Western Eurasian origin for southern Amerindians and East Asian origin for northern Amerindians. Compare: all Sub-Saharan Africans are closer to each other than they are to non-Africans. I've never heard anybody using this as an argument that Africans emerged from non-Africans.

"South Americans closest relatives are North Americans, followed by East Asians and then only distantly West Eurasians."

This is where your bias takes you. Here's an unbiased picture. West Eurasians are closer to Amerindians than to East Asians, East Asians are closer to Amerindians than to West Eurasians, East Asians are closer to Northern Amerindians than to Southern Amerindians, South Amerindians are closer to West Eurasians than Northern Amerindians. The only conclusion is that West Eurasians and East Eurasians split from a subdivided Amerindian population. Like I said, subsequent gene flow may have obliterated the divergence between northern and southern Amerindians that you are seeking to make it all fit together.

"Given the pattern and timing of modern and ancient genetic affinities, the only plausible order for the divergence of modern humans is East/West Eurasian, then East Asian/Amerindian, then North/South Amerindian. Any other order causes an inconsistency with some aspect of the data at hand."

This goes against all the mounting evidence from genetics to archaeology to linguistics to kinship studies. You just got it from an old textbook and just can't go past it. I call it "the power of myth." Here's the reality that you refuse to accept: the Amerindian genetic component is present all over Eurasia from at least 25,000 YBP on. It was detected in South Siberia, Karelia, Sweden, Luxemburg and Spain. This is ancient DNA. This is a fact. I'm sorry if facts tend to cause "inconsistencies" in your thinking.

terryt said...

"So you decided to add M8 and Z to make the lineages under consideration even more widespread".

Stop talking rubbish, German. I did not 'add M8 and Z' to C. That is what the phylogeny tells us about C's deeper relationships. Just because you don't want to believe it doesn't make it untrue.

"Then you somehow managed to find a source for the more widespread group of lineages but not for the less widespread one?"

I didn't rely on 'a' source for the distributions. It come from a huge number of sources that you could easily find if you were not so frightened of what it shows. And if you insist here is the distribution for the C haplogroups: C7 especially in Laos and nearby regions, C5 in South Siberia with C5a in northern Asia and C5c in Europe as well as Siberia, C4 from through Siberia from Altai to C4c in America, C1 mostly in America with C1a in Beringia. If you have any alternative distributions please let us all know what they are. I look forward to seeing your commnets on the various C haplogroups' distributions.

"You'll see that, among M8, Z and C stems, only hg C's stem has an underived mutation (site 11914). Phylotree posits a reverse mutation here (G11914A! )"

I'm presuming the constructors of phylotree know at least as much about the subject as you do.

"Hg C shares ancestral G11914 with L0. So what we have here is an split between hg C and hgs M8'Z. PhyloTree posits A249d as defining hg CZ. Instead, this should be interpreted as homoplasy on C and Z lineages considering that A249d occurs multiple times on different lineages"

So why have you not yet offered an alternative tree?

"NO! We should expect it wholly unlikely that none of the proposed ancestral L lineages would not be part of the exodus".

You appear not to understand the phylogeny nomenclature. Both M and N are actually L haplogroups. They have just historically been assigned a special name because they are so widespread outside Africa.

"This might help"

I notice every one of your references pre-dates the discovery of the genetic evidence.

"uncover an 'Invisible Truth' as the Micmac put it".

Now we have the real source of the idea: myth.

Alvah said...

German Dziebel and I liken the American mid-Pleistocene to a basal archaeological state, just as Amerindians contain only basal genetic lineages and few, if any, derived lineages generated by their progeny after exiting the Americas. Most significantly, the primary dilemma(s) archaeologists have with early early Man sites dating before Clovis is that they require:
1: an alternative to the “Clovis First” model
2: a validation of lesser Paleolithic signatures?
3. new implications encompassing the Old World odyssey of Modern Humans

There are two holy grails; one encompassing the Origins of Modern Humans, the other; the Peopling of the Americas. Perhaps the two are related! It is in migrating outside of the Americas that we find compelling archeological compliance, specifically, a carry-over of bone, ivory, and antler tools and an assimilation of stone tools, the later drawn, we propose, from encounters with Hominids during the initial modern Peopling of the Eastern Hemisphere. It is in bringing the two worlds into the same equation that we might find solutions. Empirical archaeological evidence transcends the field of anthropology. A continued archaeologically based denial of a human occupation of the Americas before the onset of the last Pleistocene epoch because we cannot define a theory to guide undeniable attestation is not good science. Archaeology is anthropology not a battle field where generals call in the reserves when they know it - the Clovis First paradigm - is a lost cause.

“I prefer archeological dates, when available, but archeology of the Americas seems more like a battlefield than a research topic. Given the circumstances, I suppose it is reasonable to be cautious. Only if I were forced to bet I would probably prefer older dates (Luca Cavalli-Sforza, M.D. Professor of Genetics, Stanford University, Personal Correspondence 11/25/1991).”

Scientists looking for real answers CAN NOT SIMPLY DISMISS Monte Verde I with its 26 stone tools -10% modified- , one or more with mastodon blood on the cutting surface and three identically modified heaths with a matrix that is identical to the accepted more recent occupation, because they are unwilling to tackle the significance of dating it to 33,000 ybp. It and other like/earlier dated archaeological sites have similar diagnostic signatures, even though they are not laid in a layer of peat or compose a Paleo-LITHIC link to the Old World. Contemporary Amerindian Pleistocene sites offer evidence of human behavior similar to MV I and II, while it is in the preserved peat layer that we should be defining common ground. This is symptomatic of a basal state where “learned economies” suggest an ancient perhaps autochthonous condition ancestral to later Bone Industries that in the Old World incorporated a more advanced lithic repertoire.
The significance of Pleistocene New World sites will remain insignificant unless we contemplate their significance. For the Record, I have no idea why the SAA and AJPA meet during the same week every year. Archaeology and Anthropology offer more than just casual links.
"Although it is true that we frequently acknowledge that we would like to know what life was like in the past, it should have been clear that we sought to understand processes, particularly the processes that brought into being the facts of the archaeological record. In our view these processes were much more complicated than previously thought (or imagined)" (Binford 1983b, Working at Archaeology p. 6).

Alvah said...

Theoretical Applications
@Terryt It is unethical to claim some scientific consensus is totally wrong without providing some sort of alternative explanation.

The Anthropology of Human Origins works like rocket science, we know in principle it should work but known-one would bet their life on riding consensus opinion on a science that can’t reliably get off the ground with a fully engineered rendering of the past.
Without examining the Western Hemisphere as a source for primal human origins scientists are left to put the pieces of our puzzling human past together in a way that must fit the picture on the cover of their box. Numerous reasons suggest we know a great deal about hominid evolution from an Eastern hemispherical point of view but Native American Cultures have been unwilling to be included in such a limited view and hold strong to their Tribal history that portends that they have always been here. In a sense they have their own consensus and for them their picture of the past is what should be on the cover of the box. The Opening Blessing at the Paleoindian Conference was given by Tewa Tribal Elder Mr. Jose Lucero, he spoke at length in his native language and then in English sharing with the audience the Story of Four Worlds that brought them to where they are today. It was great! After the Blessing thought it was business as usual has the conference Chairs outlined how they were going to spend the rest of our time on making their ‘crooked road strait’ limiting the discussion to how the Americas became Peopled. This ‘treatment’ is one of many reasons Native Americans are reluctant to participate in scientific queries when, in this case, science looks skeptically at their own Teachings and Beliefs Systems.

From: Lightman and Gingerich Smithsonian Magazine 1992
“Science is a conservative activity, and scientists are reluctant to change their explanatory frameworks. Scientists may also be reluctant to change paradigms for the purely psychological reasons that the familiar is often more comfortable than the unfamiliar and that inconsistencies in belief are uncomfortable. When dissonance is present, in addition to reducing it, the person will actively avoid situations and information which would likely increase the dissonance. If unexplained facts can be glossed over or reduced in importance or simply accepted as givens, the possible inadequacy of the current theory does not have to be confronted. Then, when a new theory gives a compelling explanation of the previously unexplained facts, it is "safe" to recognize them for what they are (Lightman and Gingerich 1992 pp. 694).”

From: Ousley, Stephen 1995. Relationships between Eskimos, Amerindians, and Aleuts: Old Data, New Perspectives. Human Biology, v. 67, no. 3, pp. 428, 431, 433, 434, 447, 451.
“Based on data from the JNPE, Boas concluded that "comparisons of type, language and culture make it at once evident that the Northeast Siberian people are much more closely akin to the Americans than to other Asiatics (Boas 1905, p. 99)." Based on the greater biological diversity in the New World, Boas reasoned that Amerindians were in the New World earlier. Because the northeast Siberians represented a small part of the variation present in the New World, they could not have been there as long (Boas 1910). This pattern was confirmed recently by Torroni, Schurr et al. (1993), who found greater diversity in the mtDNA of Amerindian tribes than in native Siberian groups.”

GailT said...

@German

"They redefined the L3 node, and I had told you a while ago that L3 was a problem."

Another false claim. They specifically said that their phylogenies are "quite consistent with the existing mtDNA and NRY phylogenies with some small discrepancies involving lineages that are not well-resolved." Nowhere did they say that they redefined L3.

And you repeatedly mischaracterize my statements - you write:
"You responded by saying that 25 years of research makes the mtDNA phylogeny bulletproof."

I have repeatedly said that I would be thrilled to find new mtDNA samples that lead to a revised tree. Minor revisions continue to be made at the younger branches of the tree. You have never provided a single bit of data that would challenge the basic structure of the tree, and yet you constantly claim that the entire scientific community has misinterpreted the tree. If you actually tried to construct a mtDNA tree, you would realize that your Out of America theory is pure nonsense.


terryt said...

This 'out of America' theory being proposed by several here is absolutely full of problems.

Alvah claimed the pre-Clovis was Middle paleolithic. That means the UP in America can be no older than some 12,000 years. In northern China the UP dates from about 30,000 years and further west dates from some 45,000 years ago. That doesn't sound like 'Oo America'.

No dates proposed for human presence in America approach the dates accepted for Australia. That doesn't sound like 'Oo America'.

No matter what age we accept for pre-Clovis presence one thing is clear: there weren't many of them. The human environmental footprint in America is minute until Clovis. Yet the Oo America supporters are asking us to believe that population and/or environmental pressure pushed humans north into difficult environments and so out into Eurasia. That doesn't sound like 'Oo America'.

With German's proposed adjusted phylogeny we have C (an M haplogroup), U (an N haplogroup) and L0 (a basal haplogroup) combined in a single haplogroup. Yet at the same time he accepts the M/N division of mitochodrial DNA haplogroups. How can those two positions be reconciled? And we have L0 in Africa, U in Eurasia and C in Eurasia/America. That doesn't sound like 'Oo America'.

terryt said...

Sorry. Second comment:

"they are unwilling to tackle the significance of dating it to 33,000 ybp."

That is still just half as long ago as humans have been in Australia.

"Native American Cultures have been unwilling to be included in such a limited view and hold strong to their Tribal history that portends that they have always been here".

So do Australian Aborigines. You believe tham too?

"Here's an unbiased picture. West Eurasians are closer to Amerindians than to East Asians, East Asians are closer to Amerindians than to West Eurasians, East Asians are closer to Northern Amerindians than to Southern Amerindians, South Amerindians are closer to West Eurasians than Northern Amerindians. The only conclusion is that West Eurasians and East Eurasians split from a subdivided Amerindian population".

It is certainly not 'The only conclusion', especially when we consider your earlier comment:

"Of course Southern Amerindians are not closer to Europeans than to northern Amerindians. If they were, this would've been a good argument for a Western Eurasian origin for southern Amerindians and East Asian origin for northern Amerindians".

So one minute you're claiming North and South Americans are not different, next minute you're claiming they are. Surely the explanation for the fact that 'East Asians are closer to Northern Amerindians than to Southern Amerindians, South Amerindians are closer to West Eurasians than Northern Amerindians' is that Northern Amerindians have received more East Asian admixture than have Southern Amerindians. In other words it is true to a large extent that we have 'a good argument for a Western Eurasian origin for southern Amerindians and East Asian origin for northern Amerindians'. But both American populations are actually a mix of west (more correctly 'central') and east Eurasians. It is just the proportions that are different.

"the Amerindian genetic component is present all over Eurasia from at least 25,000 YBP on. It was detected in South Siberia, Karelia, Sweden, Luxemburg and Spain. This is ancient DNA. This is a fact".

Yes. All those populations share a proportion of their ancestry, but it is drawing an incomprehensibly large bow to jump to an American ancestry.

German Dziebel said...

@TerryT

"I'm presuming the constructors of phylotree know at least as much about the subject as you do."

I don't think you should bring up mtDNA anymore in support of your beliefs. You don't have an in-depth understanding of it. Your appeal to authority is ludicrous.

"So why have you not yet offered an alternative tree? "

You should direct it to those people who've put together the current one(s). It's their job. I may do it in some point or I may not, but they need to learn how to build good trees.

Alvah said...

@terryt “Now we have the real source of the idea: myth.”
@Terryt “I notice every one of your references pre-dates the discovery of the genetic evidence.”

Excuse you, some of the data from the 1980 and 1990s come from cutting edge research Labs like Stanford and Emory Universities’ who’s genetic departments date back to before you were ‘wet behind the ears’. Please be considerate and not make outright misleading statements that wastes the time of readers of this wonderful blog.

The CavaliSfoza Lab at Stanford, e.g. Ballenger et al. 1991, Johnson et al. 1993; the Wallace Lab at Emory U, e.g. Schurr, Tarroni et al.; first articulated the basal condition for M and N Haplogroups while the bootstrap method articulated by the @ Wilson Lab UoCal Berkley, e.g. Cann, Stoneking, Vigilant, et al. 1980 and 90’s do not portend in the literature that L (L3) and M and/or N are one in the same but sub clades. The Bootstrap Model is the only way to explain all of the novel Mutations and comprising L0, 1, and 2, as they are, as a matter FACT, missing in the recent Out of Africa scenario.

The Wallace Lab talk's about “Dramatic Founding Effect…” ‘for the Americas’ where only rare Asian Lineages satisfy an Asian Origin when Holocene migration into Asia from the Americas has now risen as a better more parsimonious explanation. What geneticists now call back-migration represents, rather, a second Holocene exodus.

@Terryt Both M and N are actually L haplogroups. They have just historically been assigned a special name because they are so widespread outside Africa."

As mentioned before in this blog, M is now classified as a Sister group. One, it fits, two, they had it wrong in the First Place. Next it will predate all the Ls and turn the baobab tree used to back-light the Wilson Labs African origins into what it 'Baobab' translates too, “roots standing up.”
@Terryt Now we have the real source of the idea: myth.

First I use the standard @Terryt or @German.. to give credit to quotes used in this specific blog. I may be a newcomer but I would appreciate the same acknowledgement. May I offer an additional reference to the value of Myth in interpreting stories as told by those we are attempting to like… study…

Dixon, R.B. Mythology.
“In its relations to the mythologies of other areas, the most important associations are to be found with northeastern Asia. Here the degree of similarity is most striking, the myths of northeastern Asia and of northwestern America forming practically one great group, the members of which are allied not by form alone, but by actual content of the myths themselves. Except for this area, no clear evidence of relationship has been shown.
This Asiatic relationship must not, however, be regarded as furnishing evidence relating to the origin of the American Indian. It indicates a cultural relationship only, and far from pointing to an Asiatic source for the culture even, the bulk of the evidence would favor the theory that the similarity shown in the mythologies is the result of influences passing from America to Asia, and not in the reverse direction. Such cultural influence, moreover, belongs to a stage in culture far above that which must have been possessed by the ancestors of the present Indian at the time when they first came to America and belongs to a period far more recent than that at which the peopling of the American continent must have taken place. (date unknown p. 59).”

Alvah’s comment: The preceding concepts helped to one; illuminate the Americas in the search for human origins while the concordance of evidence would seem to re-qualify the theory of a “back-migration” or better put, second separate migration from the Americas into Siberia at the end of the last Ice Age. Funny how we continue to dismiss, without testing further, the idea of human ancestors in the Americas or, even, the fundamental "Boasian" contention – the results of the Jesup Expedition – of “back-migration” by Natives Americans into Siberia more recently, [after the termination]then Last Glacial.

Alvah said...

@ Terryt said, “Alvah claimed the pre-Clovis was Middle paleolithic. That means the UP in America can be no older than some 12,000 years. In northern China the UP dates from about 30,000 years and further west dates from some 45,000 years ago. That doesn't sound like 'Oo America'.”

Where did I say that? Please do not misinterpret what I say. This might help you.

2124 2014 Let’s get back to what we call “the Old World”

From: Klein, Richard G. 1995. Anatomy, Behavior, and Modern Human Origins. Journal of World Prehistory, Vol 9, No. 2 pp. 167-198.
“Were Neanderthals fundamentally incapable of fully modern behavior? As I have outlined it, Out-of-Africa 2 postulates that the Neanderthals were replaced because they could not compete culturally with their modern human successors. The argument is bolstered over most of Europe by the relatively abrupt nature of the replacement. At many sites, Cro-Magnon/Upper Paleolithic occupations overlie Neanderthal/Middle Paleolithic layers with no evidence for a major break in time or for any transition between the two, suggesting the replacement took only decades, or at most, centuries (p. 183).”
Klein continues: “For proponents of Out-of-Africa 2 the problem, then, is not that 60,000-year-old Australian dates imply an especially early, non-African emergence of art, but that they raise two other fundamental questions: (a) Is it possible that modern humans left Africa as much as 60,000 years ago? and (b) Assuming that they did, how is it that they reached the Far East (Australasia) 20,000 years before they reached the Far West (France and Spain)? In this context, it is important to note that the Middle Paleolithic/Upper Paleolithic interface in France and Spain cannot be much older than 40,000 years. This estimate is based not on radiocarbon dates, which provide only minimal ages in the 40,000 year range, but on thermoluminescence dates from Le Moustier (France) (Valladas et al., 1986) and uranium-series dates from Abric Romani (Spain) (Bischoff et al., 1988, 1994) which show that the Middle Paleolithic survived in western Europe until roughly 40,000 years ago (pg. 198).”

The perspective’s outlined here-in offer a conservative assessment for dating the replacement of H. erectus populations. The idea that the replacement emanates from Asia is suggested by the early Australian dates and those from central Siberia. At any rate our sudden appearance throughout the Old World has a relative hypothetical New World comparison in the rapid colonization scenarios that have been put forth by Clovis First proponents. The Clovis’ second alternative foretells a diffusion of hunting technologies into pre-existing Amerindian populations. Why are earlier mid-Pleistocene American archaeological signature(s) so difficult to digest? We have long assumed we should be finding an Old World relationship entailing sophisticated lithic Industries. What we happen to be finding is a rudimentary Paleolithic stage that challenges us to draw conclusions concerning its evolutionary implication. Since the earliest archaeological, or proposed genetic lineages, were not carried out of Africa doubt about Africa being the homeland for modern human lies in defining an alternative. Archaeological and genetic links conform with an Asian source for the spread of modern humans into the rest of the Old World.

The significance of Pleistocene New World sites will remain insignificant unless we contemplate their significance. Be part of the process and not a ‘’’’burr under the blanket’.’

Gary Moore said...

Alvah wrote -

"Dixon, R.B. Mythology.
“In its relations to the mythologies of other areas, the most important associations are to be found with northeastern Asia. Here the degree of similarity is most striking, the myths of northeastern Asia and of northwestern America forming practically one great group, the members of which are allied not by form alone, but by actual content of the myths themselves. Except for this area, no clear evidence of relationship has been shown.
This Asiatic relationship must not, however, be regarded as furnishing evidence relating to the origin of the American Indian. It indicates a cultural relationship only, and far from pointing to an Asiatic source for the culture even, the bulk of the evidence would favor the theory that the similarity shown in the mythologies is the result of influences passing from America to Asia, and not in the reverse direction. Such cultural influence, moreover, belongs to a stage in culture far above that which must have been possessed by the ancestors of the present Indian at the time when they first came to America and belongs to a period far more recent than that at which the peopling of the American continent must have taken place. (date unknown p. 59).”

In one key area, Native American religions of northern North America resemble the religions of the steppe peoples of Asia and the early Indo-Europeans. For instance, on the eve of the Battle of the Wabash in which the tribes of the NA Northwest Confederacy inflicted a crushing defeat on the infant United States, the Shawnee leader Blue Jack urged his men to pray to the "Great Father in the Sky" to stop the snow and provide a clear sky for their army to fight under as a way to show his favor. The "Great Father in the Sky" meets the description of none other than Dyas Pitr. When early French explorers reported that the native Americans there worshiped "Jupiter", the were literally correct. (Their wish, BTW, was granted and the outnumbered Native American force destroyed the US army.)

Tobus said...

@German:
Here's an unbiased picture.

I find your picture extremely biased - you're presenting minor facts as if they were important while totally ignoring the major facts. Here's an picture I think we can both agree on without getting confused by wording or undue emphasis (distances not to scale, but in correct order of relative affinity):

WEu-------SAm-NAm---EAs

This fits:
- SAm/NAm closer to each other than to EAs or WEu
- EAs closer to Am than to WEu, closer to NAm than to SAm
- WEu further from both Am/EAs than they are to each other, closer to Am than to EAs, and closer to SAm than Nam

The only conclusion is that West Eurasians and East Eurasians split from a subdivided Amerindian population.

This is rejected by the extremely close affinity of North and South Americans - we'd expect the exact opposite if they had the deepest divergence. Based on the genetic distances, the only conclusion is that earliest divergence was between West Eurasian and the Amerindians/East Asian ancestor, next was the East Asian/Amerindians divergence and South Amerindians diverged from North Amerindians relatively recently. Known admixture events (MA-1 and recent Siberian/Alaskan) explains the asymmetrical position of Amerindians and East Asians relative to Europeans, and of North/South Amerindians relative to East Asians.

Like I said, subsequent gene flow may have obliterated the divergence between northern and southern Amerindians that you are seeking to make it all fit together.

This is at odds with the genetic data - Amerindians have the highest "intragroup" diversity in the world, meaning that each individual Amerindian population is genetically distinct and thus *cannot* have had significant admixture with other Amerindian populations since their divergence. A theory of deep Amerindian divergence obliterated by subsequent admixture is not consistent with the facts, and you cannot use an impossible scenario to justify another impossible scenario.

German Dziebel said...

@Tobus

"I find your picture extremely biased - you're presenting minor facts as if they were important while totally ignoring the major facts. Here's an picture I think we can both agree on without getting confused by wording or undue emphasis (distances not to scale, but in correct order of relative affinity):

WEu-------SAm-NAm---EAs>"

Yes, unless I misunderstand your graph, this is correct. This is a typical picture of divergence between two populations - WEu and EAs from their source in the New World.

"This is rejected by the extremely close affinity of North and South Americans - we'd expect the exact opposite if they had the deepest divergence."

This is where one of your many fundamental flaws lies. You can't reject facts with a model. You test the model against facts. The facts at hand reject the model whereby genetic divergence is only and always a function of time. All the high-profile genetic studies from 2010 on have documented admixture from Neandertals, Denisovans and Amerindians into Old World (including Africa) modern human populations suggesting that a simple serial bottleneck model doesn't work. Consequently, divergence is not a function of time and lack divergence is not an indication of population recency.

"Known admixture events (MA-1 and recent Siberian/Alaskan) explains the asymmetrical position of Amerindians and East Asians relative to Europeans, and of North/South Amerindians relative to East Asians."

This is just preaching. MA-1 is not a "known admixture event." MA-1 is a clear admixed population with West Eurasians and Amerindians being the contributing populations. There were no East Asians in the regions adjacent to Beringia 25,000 years ago. MA-1 has proven that. So there's no origin of Amerindians from East Asians. This medieval in nature idea got falsified my modern scientific evidence. Can we just go with science for a change?

"This is at odds with the genetic data - Amerindians have the highest "intragroup" diversity in the world, meaning that each individual Amerindian population is genetically distinct and thus *cannot* have had significant admixture with other Amerindian populations since their divergence. A theory of deep Amerindian divergence obliterated by subsequent admixture is not consistent with the facts, and you cannot use an impossible scenario to justify another impossible scenario."

First of all, Amerindians have the highest INTER-group diversities and lowest INTRA-group diversities. This makes them similar to Papuans, Denisovans and Altai Neandertals suggesting a shared Mid-Pleistocene population structure. (African Hadza show the same pattern and they are a relic in Africa.) This means that every Amerindian deme is more divergent from another Amerindian deme than any Old World population from another Old World population. This is precisely what we would expect from an ancient population. Linguistics is fully consistent with this genetic picture: Amerindians and Papuans are the most diverse linguistically in terms of the number of genetic (in the linguistic sense) stocks.

You are confusing and misinterpreting two kinds of divergence. When we say that South Amerindians are close to Northern Amerindians but both of them are highly subdivided, this means that these two populations are similar to each other because they are the least divergent from a common proto-human population. In the Old World, the cleavage between Northern and Southern Amerindians is amplified as the split between East Asians and Western Eurasians. Their Fst values progressively go down: Western Eurasians are lower and East Asians are higher. This is what we would expect if populations grow in size, colonize a vast geographic terrain and likely absorb an archaic substrate. The initial split gets progressively wider.

terryt said...

In deference to Alvah:

@German:

"I don't think you should bring up mtDNA anymore in support of your beliefs. You don't have an in-depth understanding of it".

German, you appear to have no understanding of mt-DNA whatsoever. I agree with Gail when she says, 'If you actually tried to construct a mtDNA tree, you would realize that your Out of America theory is pure nonsense'.

The remainder is in reply to Alvah's commnets:

"the myths of northeastern Asia and of northwestern America forming practically one great group"

Which is no surprisa at all. That is the area where the haplogroups match closely, as opposed to the greater region of America.

"Such cultural influence, moreover, belongs to a stage in culture far above that which must have been possessed by the ancestors of the present Indian at the time when they first came to America and belongs to a period far more recent than that at which the peopling of the American continent must have taken place".

Exactly. That is what I have been saying all along. The northern American population represents a more recent, and more 'Mongoloid', entry into America. I agree it is possible some of this population has since moved back into Asia, but it has moved just a very short distance.

"M is now classified as a Sister group. One, it fits, two, they had it wrong in the First Place".

They never 'had it wrong' at all. M always was a sister group to L3. What the 'new' (as yet not universally accepted) phylogeny does is to remove N from being another sister group to L3 and M.

"Where did I say that? [pre-Clovis was Middle paleolithic] Please do not misinterpret what I say".

You wrote, 'Pre Clovis is not Pre-Middle Paleolithic either, it stands alone as the most primal state before during and until the sudden arrival of technologies honed during colonization of the Old World' and also 'Pre-Clovis is in reality Pre Paleolithic, sorry I confused you with a ? mark'. From those comments you certainly gave the impression you regarded pre-Clovis as in no way Upper Paleolithic.

"Since the earliest archaeological, or proposed genetic lineages, were not carried out of Africa doubt about Africa being the homeland for modern human lies in defining an alternative".

You are conflating two separate events: the spread of Homo sapiens sapiens and the spread of the Upper Paleolithic. The two events are separated in time although obviously the UP developed somewhere within the H. sapiens sapiens geographic range.

"Archaeological and genetic links conform with an Asian source for the spread of modern humans into the rest of the Old World".

I have no problem with that. But that idea is far from any out of America scenario.

German Dziebel said...

@GailT

"Another false claim. They specifically said that their phylogenies are "quite consistent with the existing mtDNA and NRY phylogenies with some small discrepancies involving lineages that are not well-resolved." Nowhere did they say that they redefined L3."

Open Suppl Mat and study the phylogeny between pp. 24 and 25.

"If you actually tried to construct a mtDNA tree, you would realize that your Out of America theory is pure nonsense. "

How do you know? Did you construct this kind of tree and then dismiss it? Can I see it then?

"You have never provided a single bit of data that would challenge the basic structure of the tree."

I've provided tons of evidence (most recently in my exchange with the out-of-Antarctica guy, TerryT, who you admire) - you're just not competent enough to respond. You prefer to hide behind the "consensus."

GailT said...

@Alvah

As mentioned before in this blog, M is now classified as a Sister group. One, it fits, two, they had it wrong in the First Place. Next it will predate all the Ls

No one has published a mtDNA Phylotree in which M and N are sister clades to L3. If you are referring to Lipold et al, they present results only from the samples in their study in an appendix, but they did not specify the defining mutations for the nodes, they did not used any of the more than 20,000 samples available in GenBank, and they specifically said that their results were consistent with the consensus tree.

M and N share the 3 mutations that define L3 and all of its daughter clades: A769G, A1018G and C16311T. We should call them L3m and L3n, and this would be a great help forpeople who have a poor understanding of cladistic analysis.

http://phylotree.org/tree/subtree_L3.htm

If you ignore the last 20 years of DNA research, you are literally still living in the 20th century academically.

Alvah said...

From: Ted Goebel et al. DATING THE MIDDLE-TO-UPPER-PALEOLITHIC TRANSITION AT KARA-BOM pg. 452 - CURRENT ANTHROPOLOGY.
"In Africa transitional Middle-Late Stone Age industries are now thought to lie beyond the range of conventional 14C dating and likely date to between 50,000 and 40,000 years before the present (B.P) (Brooks et al. 1990 Grun and Stringer 1991). Likewise, transitional early Upper Paleolithic materials in Israel have been recently AMS 14C-dated to as early as 42,000 years B.P. (Bar-Yosef et al. 1992:517; Hedges et al. 1990:103), and in Europe AMS Willendorf II, Austria, and L'Arbreda and El Castillo Caves, Spain, now suggest that the Upper Paleolithic was well under way by 40,000 years B.P. (Allsworth-Jones 1990:231,;Bischoff et al. 1989,; Kozlowski 1988: 219,; Valdes and Bischoff 1989)… In Siberia, new AMS 14C dates from Kara-Bom demonstrate that initial Upper Paleolithic industries appeared as early as 43,000 years B.P. or earlier." (emphasis added)

As for a settlement of the Americas the only linkage to Amerindians are in the more recently formed populations of northeast Asia. It is here that the two worlds coalesce after the Holocene, as Boas’ conclusions from the Jessup Expedition confirmed. But what is the framework for a basal ancestral condition for Native Americans, as we are presenting?

Emoke J.E. Szathmary 1993. Invited Editorial: mtDNA and the Peopling of the Americas Am. J. Hum. Genet. 53:793-799
“It is clear that uncritical use of hypotheses under dispute can be unwise (pg. 795).”
“Another way to demonstrate that ancient founder effects remain detectable in modern populations is to document that the pattern of mtDNA variation deviates from the steady-state balance characteristic of mutation-drift equilibrium. The only published information that exists on the Americas was provided by Chakraborty and Weiss (1991), who demonstrated precisely the reverse situation: they found that mtDNAs were in mutation-drift equilibrium in three Amerindian populations (pg. 796).” “If Chakraborty and Weiss's (1991) findings apply in general to the Americas, it means that not only is there no evidence for the presence of major bottlenecks in the evolutionary history of mtDNA in the New World but also that is not possible to establish the evolutionary source of mtDNA varieties. They are as likely to be the product of new mutations as of ancient founder effects (ibid pg. 796).”

Ranajit Chakraborty and Kenneth M. Weiss Genetic Variation of the Mitochondrial DNA Genome in American Indians is at Mutation-Drift Equilibrium. in American Journal of Physical Anthropology 86:497-506 (1991)

“The present work suggests that in three Amerindian populations (Pima, Maya, and Ticuna) a steady state has apparently been reached, and hence the initial found effect has probably dissipated during the evolution of Amerindians in the New World (pg. 497).”
“We should also note that a consequence of founder-effect (or equivalently, population bottleneck) is reduced gene diversity. . . . These strengthen our conclusion that probably the past bottleneck effect in Amerindians has dissipated and the contemporary populations of Amerindians are now at a mutation-drift equilibrium state (pg. 504).”

Mutation-drift equilibrium is not detected in Old World people and is a primary determination in suggesting a recent bottleneck for Asians, Africans, and Europeans. Clearly, mutation-drift equilibrium was not expected in Amerindian Population that are/were proposed to have been recently derived. Nor are they the product of just four or five, now in 2014 ten or more eves for each “proposed” Amerindian haplogroup. Thirty three (33) basally distinct mtDNA lineages was once proposed By Rebecca Cann.

German Dziebel said...

@GailT

"M and N share the 3 mutations that define L3 and all of its daughter clades: A769G, A1018G and C16311T. We should call them L3m and L3n, and this would be a great help forpeople who have a poor understanding of cladistic analysis."

As I explained in a discussion of which you were a part - and not the most lucid part, as always - (http://www.anthrogenica.com/showthread.php?1474-paleoamericanodyssey-tweets-on-24-000-year-old-Mal-ta-Siberian/page34) the L3 node on the mtDNA tree is not a valid node.

This is why (and I quote): "L3 agrees with Denisova at 769 (all African-specific mtDNA lineages agree with Neandertals [hence derived and not ancestral]), is uniquely derived at 1018 (all African specific mtDNA lineages agree with Denisova and Neandertals) and 16311 is hypervariable in modern humans with many actual L3 sequences classified as downstream from the L3 node (e.g., M1, M2a2, M4''67, etc.) carrying the ancestral site (C) and some actual African-specific sequences (L2, L5c2) carrying a derived site (T)." This kind of issues permeate the current mtDNA phylogenies and invalidate them.

Sometimes I'm thinking I should teach you a class on how to do cladistics but then I arrive at a stubborn thought that this would be a waste of my time.

"No one has published a mtDNA Phylotree in which M and N are sister clades to L3. If you are referring to Lipold et al, they present results only from the samples in their study in an appendix, but they did not specify the defining mutations for the nodes, they did not used any of the more than 20,000 samples available in GenBank, and they specifically said that their results were consistent with the consensus tree. "

So you're claiming that their published tree is fundamentally flawed because they didn't utilize the 20,000 samples. But then you draw on their own conclusion that the results are consistent with all the previous studies. You are just a troll!

"If you ignore the last 20 years of DNA research, you are literally still living in the 20th century academically."

20 years is nothing. Automotive manufacturers ignored thousands of years of horse-back riding in order to make a better product. mTDNA phylogenies are a relic from pre-genomewide and pre-ancient DNA analyses. They've never been revised to reflect better data and better methodologies. If you don't believe in the evolution of science, you don't believe in evolution.

German Dziebel said...

@TerryT

"German, you appear to have no understanding of mt-DNA whatsoever. I agree with Gail when she says, 'If you actually tried to construct a mtDNA tree, you would realize that your Out of America theory is pure nonsense'."

Facts are a stubborn thing, Terry, and no agreement with GailT will help you here. I just showed you that the current approach to resolve the CZM8 area of the phylogeny is flawed. You had no response. This is because you don't understand the sequence data behind the haplogroups and your compulsive fantasies (out-of-Antarctica, out-of-Australia or out-of-Laos) depend on the assumption that the accepted phylogenies are God's word. But they are not: they were built by humans and humans, alas, err.

terryt said...

"I just showed you that the current approach to resolve the CZM8 area of the phylogeny is flawed. You had no response".

Just two people unqualified in the subject claiming something on an anthroplogy site is not enough to convince nme you are correct. I'll believe you whan qualified people accept your claim.

"I've provided tons of evidence"

You have not provided a shred of evidence in favour of your theory. All you have provided is arguments against the currently accepted phylogeny without offering anything approaching an alternative phylogeny.

"This is a typical picture of divergence between two populations - WEu and EAs from their source in the New World. [WEu-------SAm-NAm---EAs]"

Well, no. It is typical of ahybrid population formed from WEu and EAs. Otherwise how can you explain why SAm and NAm are closer to each other than either is to either of the other two populations? You have to invoke an incredible amount of drift as well as an incredible amount of genetic mutation in the non-American populations as compared to the two American populations.

"MA-1 is a clear admixed population with West Eurasians and Amerindians being the contributing populations".

Only in your imagination.

"There were no East Asians in the regions adjacent to Beringia 25,000 years ago".

No-one disagrees with that. East asians had obviously become confined to regions south of Siberia until some time after populations from further west had entered Siberia. They were then able to move north and then mix and to some extent replace the western populations. To me that is so simple to see I'm amazed anyone can disagree.

"they were built by humans and humans, alas, err".

And the one who errs most is German Dziebel.

GailT said...

@German

"Sometimes I'm thinking I should teach you a class on how to do cladistics but then I arrive at a stubborn thought that this would be a waste of my time."

We established in another forum that you don't understand even the most basic principles of cladistic analysis. You argued that a single mutation shared between widely divergent branches of the phylotree meant that the entire tree was incorrectly constructed. You fail to understand that individual mutations occur independently in many different individuals and that cladistic analysis require the analysis of hundreds of mutations, not one or two.

And every single post you have insulted me, which is perhaps the best indicator that you don't understand how science works and that you never intended to discuss the science. I've never seen anyone so determined to remain ignorant, but of course, your entire theory of Out of America depends on the most astonishing degree of willful ignorance. I won't bother to engage you again, as it's obvious you have no desire to learn.

Alvah said...

R. H. Ryk Ward, University of Utah geneticist, in a letter to Alvah Hicks (personal correspondence, September 16, 1991, stated; “As you can see, some of our conclusions (such as the antiquity of Amerindian mitochondrial lineages) resonate with your ideas. However, I do not believe that our data can be used to determine the dates of entry of humans into the Americas. We have tried to make this distinction clear. emphasis not added).”

German and I and a few others at this blog are attempting to widen the discussion of “peopling events” be it, as for most, the Americas, against the backdrop of the sapient Peopling of the Eastern Hemisphere. I have my own way of assessing the data; measuring the diversity of an entire glass of liquid with one that has recently been derived from the pouring of only a subset of the substance and then tracing its disperse into a new sphere. Over time adaptation to a new area will be detected in the accumulation of novel traits that are distinguished from the original basal condition. The sure number of Native American Tribal groups, the greater genetic diversity on the Tribal level outlined above), the concordance of a well defined Holocene migration out of the Americas to make clear recent genetic links with Northeast Asians, the fact the Homo sapiens are relatively new to the Old World, the lack of derived Old World Lineages in our the ancestral greater Amerindian Populations, and the basal archaeological signature of pre-Clovis humans all point to an alternative that itself, does not defy the nature of scientific revolutions.

That Clovis First reigned for so many years, and has now been accepted as wide of the mark does not underscore the difficulties of defining the nature of pre-Clovis signatures. That they were and continue to be difficult to characterize based on settlement patterns and behaviors, be they Middle or Upper Paleolithic, is at the heart of finding a resolution. Anthropology, archaeology, and genetics mirror the past if we can find common ground and start anew in reflection of the greater picture an American Wellspring offers human origins.

@ GailT “If you ignore the last 20 years of DNA research, you are literally still living in the 20th century academically.”

As for my 20th Century approach, you are invited to view my unpublished 20th Century blog. Might I suggest http://anthropogenesis.kinshipstudies.org/out-of-america-family-of-hypotheses/bibliography-human-origins-and-amerindian-origins-wip/ From Germans Dziebel’s Website http://anthropogenesis.kinshipstudies.org/.
Look for Alvah “Hicks Bibliography” and scan past, all that stuff, to my Dienekes like 1995-1999 Yearly Treatises of the hundred plus years past sealed in the last Five Years of the Century and Millennium. Here you will find hundreds of pages of references I had accumulated in an attempt to overcome Academic Apartheid. If you want to investigate more than just the genetic history, not in the least but also in regards to Mitochondrial DNA, (and/or another Cowboys’ guided thoughts on the matter: i.e. see stories of George McJunkin who first discovered Clovis), then I invite you.

If you would critique the ideas as presented rather than the methods or sources cited we might be able to get to the heart of the mater.
As for more recent twenty first century contact with academia do presentations or encounters with authors offering academic documents at the Paleoamerican Odyssey Conference in October 2013 count? Everything evolves but it all begins from a basal state. Initial or Basal studies do impact later opinions and/or discussion points even if they are held captive by consensus opinion. It is not enough to ignore evidence from the recent past concerning Archeological Apartheid on pre-Clovis advocates, but to ignore the implications that have been fortuitously overshadowed goes further and can be liked to academic genocide. But this is just a blog, or is to be more!?

Tobus said...

This is where one of your many fundamental flaws lies. You can't reject facts with a model. You test the model against facts.

The fact is that North and South Americans aren't very divergent genetically. The model you provided is that they are - the model is rejected by the facts.

MA-1 is a clear admixed population with West Eurasians and Amerindians being the contributing populations. There were no East Asians in the regions adjacent to Beringia 25,000 years ago.

No, there's no model with MA-1 recieving Amerindian admixture that works with the facts. The only workable model is one where MA-1 gives DNA to an Amerindian ancestor. (You are supposed to be providing an alternate model that works but so far you've come up short). This ancestor was closely related to the ancestor of modern East Asians, and was physically situated in East Asia, so saying there were no "East Asians" is an oxymoron - unless you are for some reason expecting modern East Asians 24kya?

First of all, Amerindians have the highest INTER-group diversities and lowest INTRA-group diversities.

Are you sure? "Inter" means between and "Intra" means within - whatever terminology you use, we both agree Amerindians have the lowest genetic diversity compared to other groups worldwide, yet have the highest diversity (ie are least homogenous) within each group.

This means that every Amerindian deme is more divergent from another Amerindian deme than any Old World population from another Old World population.

No it doesn't - the "intragroups" compared weren't "Amerindians" and "Rest of the World"! What is means is that in constrast the Old World where the genetic diversity is relatively homogenous - spread widely though each population, in America each deme represents a small and distinct part of the overall diversity. This is completely at odds with your model of a deep North/South Amerindian divergence that has since been obliterated by admixture.

This is what we would expect if populations grow in size, colonize a vast geographic terrain and likely absorb an archaic substrate. The initial split gets progressively wider.

That explains the wider European/East Asian gap, but fails to explain why Amerindians are closer to each other than to their respective supposedly post-divergence sublineages.

German Dziebel said...

@GailT

"We established in another forum that you don't understand even the most basic principles of cladistic analysis. You argued that a single mutation shared between widely divergent branches of the phylotree meant that the entire tree was incorrectly constructed."

There was no "we" to establish anything. Neither you nor Jean (is that the name?) are qualified to talk about these matters. What I said was that a single mutation can define a clade at least from the point of view of what's currently admitted in the mtDNA phylogeny. L3 is defined by one single unique derived mutation. CZ is defined by one single recurrent mutation. You have a double standard for your self vs. other people.

"And every single post you have insulted me, which is perhaps the best indicator that you don't understand how science works and that you never intended to discuss the science."

In every single post, I provide you with factual evidence that we could discuss. L3, CZM8 or others - you back out of a conversation, while insulting me for challenging your self-proclaimed authority on things mitochondrial.

"I've never seen anyone so determined to remain ignorant, but of course, your entire theory of Out of America depends on the most astonishing degree of willful ignorance."

Just try and back your ad hominem attack up with a single fact!

"I won't bother to engage you again..."

That was my goal. The best way to fight trolls is to throw science at them. They will claim you are ignorant, but the good thing is that they will leave you alone.

German Dziebel said...

@Tobus

"Are you sure? "Inter" means between and "Intra" means within - whatever terminology you use, we both agree Amerindians have the lowest genetic diversity compared to other groups worldwide, yet have the highest diversity (ie are least homogenous) within each group."

No, it's the opposite. Fst measures INTER-group diversity and Fst values tend to be the highest among Amerindians. African have the highest INTRA-group diversities. This means that every Amerindian population is more distinct from another Amerindian population than an Old World population from another Old World population. Old World populations are indeed more homogeneous than New World populations. The latter are subdivided, the former are panmictic.

"why Amerindians are closer to each other than to their respective supposedly post-divergence sublineages."

Could you rephrase this. I don't understand it. The similarity to Amerindians increases as one comes closer to the New World geographically and to the initial migration event temporally, along both East Asian and West Eurasian lines.

"(You are supposed to be providing an alternate model that works but so far you've come up short). This ancestor was closely related to the ancestor of modern East Asians, and was physically situated in East Asia, so saying there were no "East Asians" is an oxymoron - unless you are for some reason expecting modern East Asians 24kya?"

I did provide it. It's hard for you to accept it, but it's a different matter. MA-1 shows that there were no East Asian component in South Siberia at that time, but there was an Amerindian component. So, Amerindians were ancient East Asians. Just like they were ancient West Eurasians as Mesolithic DNA from Europe attests. Where's the oxymoron?

" The only workable model is one where MA-1 gives DNA to an Amerindian ancestor. This ancestor was closely related to the ancestor of modern East Asians."

No, MA-1 shows that this ancient population in South Siberia was closely related to modern Amerindians and their ancestors but not to modern East Asians and their ancestors.

German Dziebel said...

@Tobus

"The fact is that North and South Americans aren't very divergent genetically. The model you provided is that they are - the model is rejected by the facts."

I left this one out. Considering that INTER-group diversities within these two divisions are world highest, what the overall similarity between the two New World megapopulations means is that they are the closest to each other because they are closest to the root, not because they emerged recently. What happened is that, say, 40,000 years ago, Northern and southern Amerindians diverged and then one population took a northern route across the Old World, the other one went down the coast in a southern direction. Since then, Amerindians who stayed behind have been accruing diversity between their subpopulations because their overall population size stayed small, while the migrants to the Old World were growing in size as they were colonizing the new lands and absorbing "archaic" genes along the way. So, they spawned more secondary megapopulations. So, Amerindians are much more "conservative" as two megapopulations but much more "evolved" on the level of subpopulations.

Niineta said...

http://www.biomedcentral.com/1471-2148/13/127/figure/F5

Look at the diagram in the link.

#1 there is NO evidence Amerindians descended/split from East Asians. Zero Nada Zilch.

#2 Claiming Europeans split from East Asians before Amerindians, is just plain ridiculous, Europeans are a Eurasian “derived” population. Europeans didn’t split from the rest of humanity.

#3 there is NO evidence of ancient Europeans/West Eurasian gene flow into Amerindians, from MA-1 or any other source. Europeans didn’t spawn the populations of Eurasia nor the Americas.

#4 North Amerindians are closer to West Eurasian than South Amerindians.

#5 South Amerindians are closer to their East Eurasian origins than North Amerindians.

I don't see what is so difficult to understand.

Niineta said...
This comment has been removed by the author.
terryt said...

@ Tobus:

"This ancestor was closely related to the ancestor of modern East Asians, and was physically situated in East Asia, so saying there were no 'East Asians' is an oxymoron - unless you are for some reason expecting modern East Asians 24kya?"

I'm presuming that what German means by 'East Asians' is 'Mongoloid'. In saying that there were no 'Mongoloid' people in Siberia before the 'Mal'ta' people he is correct. The Mongoloid phenotype didn't become dominant in Siberia until after America had become populated, although an increased Mongoloid presence eventually made it into northwestern America.

@ Gail-T
@ German

"You fail to understand that individual mutations occur independently in many different individuals and that cladistic analysis require the analysis of hundreds of mutations, not one or two".

Yes. German fails to realise that mitochondrial DNA has only some 16,000 base pairs and so recurrent mutations are quite common.

"I've never seen anyone so determined to remain ignorant, but of course, your entire theory of Out of America depends on the most astonishing degree of willful ignorance".

It is becomeing increasingly difficult to understand exactly what German and Alvah are trying to claim. It cannot be that the Upper Paleolithic began in America and spread from there because that dates don't fit. It cannot be that modern humans began in America and spread from there because even the earliest dates proposed for a presence in America doesn't reach as far back as dates accepted for a presence in Australia. What exactly are Alvah and German proposing?

@ Alvah "I have my own way of assessing the data"

Obviously.

Alvah said...

@TerryT “Exactly. That is what I have been saying all along. The northern American population represents a more recent, and more 'Mongoloid', entry into America. I agree it is possible some of this population has since moved back into Asia, … but it has moved just a very short distance.
You are missing entirely the main point, not a second Holocene migration into the Americas but a Holocene “out of the Americas” (mtDNA A2a A2b, D2b and D4h1, and C4b see Figure 1) as all branches containing the “Asian” lineages twig from the end of the Amerindian Tree; see the graft at Achilli et al. 2008). This migration did not move “just a short distance” but everywhere these lineages are found in the Old World. The Native American Circum-arctic Sea Mammal Hunting Cultures encircle the arctic north and are/were a “wedge” between the Boreal adapted Reindeer Cultures that were also Amerindian descendants living in northeast Asia. That’s the way the Father of American Anthropology, Franz Boas, saw it, as did RG Dixon the first American to graduate with a Doctorate in Anthropology. So have numerous specialists in this area of study including Emoke Szathmary who was Editor of the AJPA during most of the first decade of the new Millennium. Your opinions are just that, not based on expertise in this or other Amerindian scenarios. German and I and others perceptions, including many that do not choose to participate in this forum, could be considered at face value, not as a target for a spit wad or other childish exercises.
As for the Middle Paleolithic prank, we are not targets only messengers of a greater cause, TRUTH.
As For Australia and the Americas, the Americas have Higher Order Primates, Australia Marsupials. The outside limits should be adjusted accordingly as autochthonous applies to only one of these locals.
Excerpts of.. “An interview with Drs. Niède Guidon†, Anne-Marie Pessis†*, Fabio Parenti†,Claude Guérin**, Evelyne Peyre~, and Guaciara M. dos Santos‡
“The theories on the peopling of America are only theories, and in prehistory it is not possible to say that something does not exist only because we do not find them. A theory is not a law, but may and must be changed each time new facts are discovered. And I am sure of our discoveries because our team is very good with specialists in different sciences. I have degrees in both Natural History and Prehistory, and decades of fieldwork. I know when I am digging a place where people placed stones in order to make a fire inside the structure, and when I am facing a natural fire. And forest fires were not common events in the rain forest before the arrival of white men. http://www.athenapub.com/10pfurad.htm
“A total of seven charcoal samples from hearths at site BPF 1 were subjected to the full ABOX-SC procedure and their radiocarbon contents were determined by accelerator mass spectrometry at the Australian National University. Five of the samples proved to be even beyond the limit of this new technique, returning ages of greater than 56,000 BP. Finite ages of 53,000 and 55,000 BP were obtained for the remaining two (Santos et al., in manuscript)”
As for Monte Verde, I offer this tidbit with more to come.
“The lithic material found in association with the features have little meaning for their discrete distribution and for the presence of use-wear on a few specimens (see Chapter 15). … The multiple and intense use seen three lithics of the deeper level, especially one hammerstones and a percussion flake, may suggest either possibility or both.” (Dillehay 1997:94)

When combined the two features together offer more evidence to support an archaeological context. The expectation that the first Americans would bring with them to the Americas lithic projectile point technologies is what made the Clovis-First model so attractive. It makes little sense that Pleistocene explorers would have left these refinements behind, as the pre-Clovis suggests.

terryt said...

@ German:

"40,000 years ago, Northern and southern Amerindians diverged and then one population took a northern route across the Old World, the other one went down the coast in a southern direction".

Would you mind explaining to us exactly how, and when, the ancestors of these 40,000 year old Americans arrived on the double continent?

@ Alvah:

"As For Australia and the Americas, the Americas have Higher Order Primates, Australia Marsupials. The outside limits should be adjusted accordingly as autochthonous applies to only one of these locals".

So you're claiming Homo erectus first appeared in America? And H. sapiens evolved from it within the Americas? I'm sure you're on your own there as I doubt German accepts that hypothesis.

"a Holocene 'out of the Americas' (mtDNA A2a A2b, D2b and D4h1, and C4b see Figure 1) as all branches containing the 'Asian' lineages twig from the end of the Amerindian Tree"

That is not how phylotree has it:

http://www.phylotree.org/tree/main.htm

I agree that any of the above branches in Eurasia are possibly a back migration from America, but all of those haplogroups are confined to just the very far northeast of Eurasia. Anyway, according to phylotree, A2a and A2b are subsets of A2, which is in turn a subset of a whole raft of A haplogroups (1, 2, 6, 12, 15-22, all previoulsy lumped into A4). Therefore A2 is not a basal haplogroup but is a twig from the end of the Eurasian Tree. C4b is a subset of C4a'b'c (C4e has been found in Altai), which is a subset of C4, which is a subset of C. Again we have C4b as a twig from the end of the Eurasian Tree. D is more complicated because it seems not yet fully resolved. But D2 is a subset of D4e and D4h1 is a subset of D4h. Once more we have the D haplogroups you mention comprising twigs from the end of the Eurasian Tree.

"This migration did not move 'just a short distance' but everywhere these lineages are found in the Old World".

Where in Eurasia are any of those haplogroups you mentioned found apart from in the very far northeast?

Tobus said...

@German:
No, it's the opposite. Fst measures INTER-group diversity and Fst values tend to be the highest among Amerindians. African have the highest INTRA-group diversities.

"Inter-" and "Intra-" are context-based terms, I suspect we are talking cross-contexts here. Can you please show me the source saying Amerindians have the "highest intergroup diversity" and hopefully I'll be able to put it into context. For the record, my source is Tishkoff 2009, and they don't use the terms "inter-/intra-group" at all.

This means that every Amerindian population is more distinct from another Amerindian population than an Old World population from another Old World population.

No it doesn't, as I pointed out in my last post "Amerindian" and "Old World" aren't the groups being compared. Yoruba and Sardinian are more distinct than Karitiana and Mayan.

Old World populations are indeed more homogeneous than New World populations. The latter are subdivided, the former are panmictic.

Panmictic or not, the lack of homogeneity in New World populations suggests that very little admixture has occurred between New World populations. This is directly contrary to your posit that North and South Amerindians are deeply diverged but with so much subsequent admixture that this divergence is hardly detectable today.

Could you rephrase this. I don't understand it.

Your model posits diverged North/South Amerindian populations with each lineage giving rise to a sublineage (South to Europeans, North to East Asians). Why are North and South Amerindians closer to each other than they are to their own later sublineages (ie South Americans to Europeans, and North Americans to East Asians). Don't say admixture again, the high within-population genetic diversity rules this out.

I did provide it. It's hard for you to accept it, but it's a different matter

The original model you provided doesn't fit the facts. Your explanation for why it doesn't fit the facts doesn't fit the facts. You have not provided a model that works.

No, MA-1 shows that this ancient population in South Siberia was closely related to modern Amerindians and their ancestors but not to modern East Asians and their ancestors.

Yes, so the ancestors of East Asians and (all!) Amerindians must have already been diverged by this point. This fits perfectly with the model of MA-1 admixture into an East Asian population that then migrated to America without admixing with it's more southern East Asian counterparts.

Where's the oxymoron?

Here: "There were no East Asians in the regions adjacent to Beringia 25,000 years ago."
and: "So, Amerindians were ancient East Asians."

Furthermore, since there is no evidence for modern humans in America 25,000 years ago, so your use of "Amerindians" in this temporal context is inconsistent. MA-1's encounter was with an ancient East Asian population, not an Amerindian one.

Tobus said...

@German (cont. too big):

Amerindians who stayed behind have been accruing diversity between their subpopulations because their overall population size stayed small, while the migrants to the Old World were growing in size as they were colonizing the new lands and absorbing "archaic" genes along the way. So, they spawned more secondary megapopulations

These "megapopulations" are only very recent - since the Neolithic, and population sizes before this were similar to other hunter-gather groups worldwide. If the vast bulk of modern genetic diversity only happened during the recent population expansions, then pre-Neolithic archaic samples like LB, MA-1, Tianyuan should reflect this with an incredibly strong affinity to Amerindians and very little to the modern, post-megapopulation, samples. But on the contrary, all of these archaic populations show an affinity to modern "megapopulation" samples, suggesting that the high genetic diversity in the modern Old World is similar to extant pre-Neolithic diversity, and not primarily a result of the massive population increase in the last few thousand years.

Amerindians show the same small degree of archaic admixture as East Asians, which is very similar to that of Europeans. This rules out archaic admixture being responsible for the increased genetic diversity of Old World populations. It seems that earlier divergence is the most likely explanation.

So, Amerindians are much more "conservative" as two megapopulations but much more "evolved" on the level of subpopulations.

Given that this explanation fails to apply to other pre/non-megapopulation examples, a much more workable interpretation is that Amerindians are a branch of East Eurasians who who underwent a bottleneck and subsequently expanded into a vast and uninhabited territory, breaking into small groups that have remained relatively isolated. This is consistent with low genetic diversity, low homogeneity, recent MCRA and their close affinity to each other.

terryt said...

@ Alvah:

"all branches containing the 'Asian' lineages twig from the end of the Amerindian Tree; see the graft at Achilli et al. 2008)".

I just had another look at that paper and the authors certainly do not support your viewpoint:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001764

Quote:

"The average of about 19,000 years somewhat contrasts with the corresponding lower age of about 13,500 years that was recently proposed by employing a different calibration and estimation approach. Our estimate indicates a human entry and spread of the pan-American haplogroups into the Americas right after the peak of the Last Glacial Maximum and comfortably agrees with the undisputed ages of the earliest Paleoindians in South America".

The authors do not claim the haplogroups originated in America. In fact they write:

"America was the last continent to be colonized by humans, and molecular data provided by different genetic systems [1], [2] have been extensively employed to shed light on the routes and times of human arrival and dispersion into the New World".

In some degree of agreement with your position they do write:

"all the abovementioned scenarios do not support the ‘Clovis-first’ hypothesis, but are well in agreement with the undisputed ages of the earliest Paleoindians in South America".

But, as for all branches containing the Asian' lineages being twigs from the end of the Amerindian Tree, the authors explain it thus:

"for a better discrimination from closely related Native American counterparts, some Asian (or Beringian) branches (B4b1a2, A2a, A2b, C1a, C4a, C4b, D2b, and D4h1) are illustrated".

Note: 'some Asian (or Beringian) branches'. By no means a complete set of branches. The authors also write:

"it is quite plausible that some intra-haplogroup variation – hardly noticeable at the level of HVS-I motifs – already existed in Beringia and was carried directly further south into the American double-continent. If one assumes that at least the root haplotypes of A2, B2, D1, as well as of C1b, C1c, and C1d were of Beringian origin, then the entry time would come slightly down (19.0 kya), that is, falling exactly at the end of the LGM."

Fairly unequivocal.

Alvah said...

Terryt said @Alvah "I have my own way of assessing the data"

I/we, and others of like mind past and present, do, and it has no flaws except minor interpretations that the authors miss. We are messengers and the TRUTH has no disguise. If you guess right by willingly leaving no stone unturned, you might find everything falls into place. German and I have often discussed what field of evidence has the most warranting evidence. In discussions with Professor Lew Binford I was warned by others not to claim you have the answer or any or all the answers. Well, German holds that the genetic data offers the most compelling circumstantial evidence. It is substantial and I had been articulating its merits with researchers until I took a sabbatical through part of first decade of this millennium. For me the most compelling evidence, in coordination with genetics, is archaeological perceptions outlined in Clovis Theory and the facts as they relate to pre-Clovis archaeological signatures. Moreover the archaeological data from the Old World, the Binfordian issue of the “Mousterian Problem” and with it, the anatomical replacment of one species by another, are directly relevant when interpreting the American pre-Clovis as a ‘basal archaeological signature.’

@ Terryt “It is becoming increasingly difficult to understand exactly what German and Alvah are trying to claim. It cannot be that the Upper Paleolithic began in America and spread from there because that dates don't fit…. What exactly are Alvah and German proposing?”

Again, please stop referring to the pre-Clovis as Middle Paleolithic (thank you for the retraction), or Upper Paleolithic either. Again, and again, researchers are failing to deal with the uniqueness of the numerous definitions entailing ubiquitous pre-Clovis Cultures.

There are over 500 hundred pre-Clovis sites (Adovasio 2014; reference @ Paleoamerican Odyssey Conference), but only Monte Verde II (14,500 ybp), buried beneath a layer of peat has been able to shake the Clovis-First paradigm loose from the grips of forty too eighty years of career threatening assaults. By example, its main author, Thomas Dillehay, has had to deal with intimidation and outright unprofessional academic apartheid as the next quote articulates…

“Of the researchers working sites that seemed to precede Clovis people, Dillehay was singled out for special criticism. He was all but ostracized by Clovis advocates for years. When he was invited to meetings, speakers stood up to denounce Monte Verde. “It’s not fun when people write to your dean and try to get you fired,” he recalled. “And then your grad students try to get jobs and they can’t get jobs.”(G. Gugliotta, Smithsonian Magazine, January 2013)”

Not only is the pre-Clovis unique, but the disposition confronts scientific axioms. As for Monte Verde I dated at 33,000 (with more investigation currently underway, (Dillehay personal conversation 2014)), I can offer that Eric Trinkas 1996 stated that “if Monte Verde at 33 kyp was confirmed it would be a game changer.” No doubt, to have modern humans (‘Ancestors’) in Chile 33,000 ybp has to entail the Worldly significance of such a phenomenon!

The basis for reevaluating Monte Verde II (14,500 ybp) as more than just some part of an initial New World “settlement pattern” can be reconditioned when we accept, even theoretically, the significance of the 20,000 years separating it with its older relative, Monte Verde I (dated at 33,000 ybp). Clearly, the time-span separating Monte Verde I and II would eliminate the more recent site’s classification as related to an initial “Peopling of the Americas”. Rather, it could represent an ongoing pattern of habitation distinctly conforming to a prolonged occupation of the area, and the Americas in general (e.g. Krieger 1964: Wormington 1957; and others).

The significance encompassing human habitation before Clovis has much to offer if our human behavioral evolution can be linked to a pre-projectile lifestyle.

Niineta said...

One more comment:

The Greenland/Inuit arrived in North America some 5,000 years ago.

The Eskimo/Aleut arrive in North America about 1,000 years ago.

Neither population contributed genetically to the Amerindians. But both populations inherit 50+% of their DNA from Amerindians; likely through absorbing Amerindians populations as they colonized the area.

Although they show the closest relationship to Amerindians they are not the Amerindian ancestors as is propose by the; Altai/Siberian > Chukchi/Kamchatka >> Eskimo/Aleut > Amerindian, scenario.

As I said before the Amerindians and the Eskimo/Aleut are NOT the same people. Depicting them as a single population simply skews the results.

Take out the Amerindians and the Eskimo/Aleut would show a range across the Arctic regions. Take out the Eskimo/Aleut and the North Amerindians would be more align with the South Amerindians.

Ignoring these admixture events simply skews the results.

Tobus said...

@Niineta:
Look at the diagram in the link.

That diagram is a PCA plot with 2 axes, the primary one being the X-axis and the secondary one being the Y-axis. The magnitude and order of the discovered components indicates the European-East Asian/Amerindian component came first, followed by the East Asian-Amerindian one.

#1 there is NO evidence Amerindians descended/split from East Asians. Zero Nada Zilch.

Yes there is. The fact that both East Asians and Amerindians plot on the far right of the primary axis indicates that they were both one branch of the primary East/West split in Eurasia. The fact that they are at the opposite extremes on the secondary axis indicates that they subsequently split from each other.

#2 Claiming Europeans split from East Asians before Amerindians, is just plain ridiculous, Europeans are a Eurasian “derived” population. Europeans didn’t split from the rest of humanity.

All distinct populations split (or "diverged" if you prefer) from the rest of humanity at some point, otherwise there'd be no distinction. This PCA confirms that the order of divergence is the one you label "ridiculous" - East/West Eurasians first, then East Asians/Amerindians.

#3 there is NO evidence of ancient Europeans/West Eurasian gene flow into Amerindians, from MA-1 or any other source. Europeans didn’t spawn the populations of Eurasia nor the Americas.

Don't get confused by the nomenclature - nobody is saying that Europeans "spawned the populations of Eurasia and the Americas". It can get very confusing as "European" in an ancient context doesn't usually mean "in Europe" or "white people" - it means the branch that eventually lead to modern Europeans. At the time of Mal'ta was this was geographically in North East Asia and probably looked more like modern South Asians than any other modern population. As I think AnnieMouse pointed out on another thread, calling MA-1 "European" is misleading in lots of aspects - he does represent the "European" side of modern European/Amerindian affinity though, so the label in perhaps justified in this context (but in my head I imagine Slumdog Millionaire, not Home Alone 2).

#4 North Amerindians are closer to West Eurasian than South Amerindians.

I assume you mean the Aleutian Islands (and Greenland?) as "North Amerindians" as the plot doesn't distinguish Na Dene or other Northern US/Canadian populations. These populations have known Siberian admixture/origins in the last few thousands years which is probably the reason for them appearing pulled towards both Europeans and East Asians on the plot.

#5 South Amerindians are closer to their East Eurasian origins than North Amerindians.

Where do you see this in the graph - I see the opposite with the "Eskimo-Aleut" populations being closer to both Europeans and East Asians than the Amerindian populations are. There is a cline in the Amerindian group however, but it's not labelled so we can't discern if it's a North-South cline. A similar PCA plot in Raghavan et. al.'s original Mal'ta paper does have labels, and it puts Karitiana as the most extreme Amerindian population and Na Dene groups towards the centre. From this I'd assume the cline is probably South at the extreme top and North closer to both Europeans and East Asians.

I don’t know what is so difficult to understand.

Me either, but people like you and German keep making inconsistent interpretations of what is pretty obvious to me from the data.

German Dziebel said...

@Tobus

""Inter-" and "Intra-" are context-based terms..For the record, my source is Tishkoff 2009, and they don't use the terms "inter-/intra-group" at all."

Tishkoff et al is a good source. So we got that going for you at least. Now, just open the dictionary and learn what "inter" and "intra" mean.

"No it doesn't, as I pointed out in my last post "Amerindian" and "Old World" aren't the groups being compared. Yoruba and Sardinian are more distinct than Karitiana and Mayan."

You are missing the point. Subpopulations within Maya and Karitiana are more divergent from each other than subpopulations within Sardinian and Yoruba.

"Panmictic or not, the lack of homogeneity in New World populations suggests that very little admixture has occurred between New World populations. This is directly contrary to your posit that North and South Amerindians are deeply diverged but with so much subsequent admixture that this divergence is hardly detectable today."

If you look at Y-DNA you'll see that Amerindians show two highly divergent lineages, namely Q and C. Same for mtDNA: mhg N and mhg M are both represented in the Americas. There's greater gravitation of Y-DNA C and mhg N to North America, but all lineages are found in both South and North America. This can be interpreted as the mixture of two divergent ancient populations. So there's no contradiction between facts and my idea that Northern Amerindians expanded into the Old World and also into South America.

"Your model posits diverged North/South Amerindian populations with each lineage giving rise to a sublineage (South to Europeans, North to East Asians). Why are North and South Amerindians closer to each other than they are to their own later sublineages (ie South Americans to Europeans, and North Americans to East Asians). Don't say admixture again, the high within-population genetic diversity rules this out."

The only thing that's ruled out if your ability to think using facts. Haploid evidence cited above can be interpreted as favoring admixture between two divergent ancient Amerindian populations. Highest worldwide INTER-population differentiation values within the Americas suggest that Amerindians populations are more divergent than Old World populations. You acknowledged that colonization pressures on demography, incorporation of archaic "substrates" would result in the divergence of East Asians and West Eurasians after they left America. So what is your issue exactly?

"The original model you provided doesn't fit the facts. Your explanation for why it doesn't fit the facts doesn't fit the facts. You have not provided a model that works."

You can't get facts straight in the first place. How can we talk about models? I'm open to a number of models of how Amerindians colonized Eurasia but you keep taking the conversation into the pseudoscientific denial of facts. "Amerindian admixture" is Eurasia has been detected in ancient and modern DNA from Siberia to Spain. We won't make any progress while you continue to deny it.

German Dziebel said...

@Tobus (contd.)

"Yes, so the ancestors of East Asians and (all!) Amerindians must have already been diverged by this point. This fits perfectly with the model of MA-1 admixture into an East Asian population that then migrated to America without admixing with it's more southern East Asian counterparts."

In your dreams only. If you were not dreaming, instead of the "Amerindian" component, we would have seen an "East Asian" component in MA-1 at 25,000 YBP. Once those two populations mixed, they woudl've given rise to Amerindians at 15,000 YBP who in this case would've been a mix of West Eurasians and East Asians. What we would've seen in Raghavan ADMIXTURE charts is a) West Eurasian BLUE and East Asian ORANGE in MA-1; b) West Eurasian BLUE and East Asian ORANGE in Karitiana at K=3 followed by a new Amerindian color at higher Ks. In reality, Karitiana stays unadmixed from K=2 up on most charts and MA-1 is a mix of West Eurasians and Amerindians.

These are facts. And the most basic interpretation of those facts is an expansion out-of-America. We can speculate about how exactly this happened but at least we need to get the facts straight and lay down the ground rules of interpretation.

"Here: "There were no East Asians in the regions adjacent to Beringia 25,000 years ago." and: "So, Amerindians were ancient East Asians."

This is not an oxymoron. That's another way of saying that Amerindian-derived populations were occupying the areas adjacent to Beringia, not East Asian-derived populations. So Amerindians were de facto ancient (geographic) East Asians.

"Furthermore, since there is no evidence for modern humans in America 25,000 years ago, so your use of "Amerindians" in this temporal context is inconsistent. MA-1's encounter was with an ancient East Asian population, not an Amerindian one."

We have evidence for people in the New World at 25,000 YBP and older. We went over this already. And, in your typical style, you distort the facts by saying that MA-1 was East Asian. Raghavan made it loud and clear that MA-1 was unrelated to "East Asians."

German Dziebel said...

@Tobus (contd.)

"These "megapopulations" are only very recent - since the Neolithic.."

This is an unproven assumption. Old World could've been demographically different from the New World for much older, just like hominin population in Africa and Europe were much more populous than the populations east of the Movius line at least from the Lower Pleistocene on. Plus Old World was inhabited by several hominin species that once absorbed would make modern human demes megapopulations.

"pre-Neolithic archaic samples like LB, MA-1, Tianyuan should reflect this with an incredibly strong affinity to Amerindians."

There was a time when you denied that Tianyuan's proximity to Amerindians makes sense from an out-of-America perspective. Now you are positing this as a requirement for it. The data on Tianyuan is ambiguous. LB is only 7,000 years old and is geographically most remote from the New World out of all ancient samples. MA-1 is 25,000 years old and it's closest to Amerindians. Altai Neandertals show greater proximity to Karitiana than to other human populations. We clearly need more data but at the moment you're just filibustering the debate.

"Amerindians show the same small degree of archaic admixture as East Asians..."

From the out-of-America II, some of that "admixture" is common descent from an ancient Eurasian hominin that best survived in America. Then there are additional layers of later admixture, which are limited to Old World populations, once modern humans re-expanded from the New World. Africans, on the other hand, have a large amount of archaic African admixture on top of what modern humans brought with them from Eurasia. Since labs don't test these models, it's hard to say if facts support them or reject them.

"Given that this explanation fails to apply to other pre/non-megapopulation examples,"

What pre-non-megapopulation examples?

"a much more workable interpretation is that Amerindians are a branch of East Eurasians who who underwent a bottleneck and subsequently expanded into a vast and uninhabited territory, breaking into small groups that have remained relatively isolated. This is consistent with low genetic diversity, low homogeneity, recent MCRA and their close affinity to each other. "

An interpretation that contradicts facts. The problem with you, Tobus, is that you ignore facts in favor of a favorite model. Granted that it's easier to think with models because you can always arrive at what you want rather quickly, but thinking with facts is a necessary skill if you want to "talk science."

German Dziebel said...

@Tobus (contd.)

" The fact that both East Asians and Amerindians plot on the far right of the primary axis indicates that they were both one branch of the primary East/West split in Eurasia. "

On any global plot, Africans would be closer to West Eurasians than to East Eurasians and Amerindians would be closer to East Eurasians. This is consistent with geography. A STRUCTURE run in Rosenberg 2002 clearly shows that at K=2 the world is divided between Africans and Amerindians. All subsequent continental clusters are a "mixture" of those two primary ones. Ancient DNA documents the wide distribution of the Amerindian component in Eurasia, but the African component is nowhere to be found.

"That diagram is a PCA plot with 2 axes, the primary one being the X-axis and the secondary one being the Y-axis. The magnitude and order of the discovered components indicates the European-East Asian/Amerindian component came first, followed by the East Asian-Amerindian one."

Nonsense. It shows that West Eurasians and East Asians diverged from Amerindians proportionately to the geographic distance between New World and East Asia and New World and West Eurasia and that East Asia and West EUrasia were colonized via different routes of migration (one down the Pacific Coast into Asia, the other over the Circumpolar route to Europe) or, alternatively, that modern East Asians are derived from a subsequent wave of migration from America.

"people like you and German keep making inconsistent interpretations of what is pretty obvious to me from the data."

You've ignored all the facts and now you want me to treat your pseudoscientific "models" as "data" ?

terryt said...

@ Alvah:

"its main author, Thomas Dillehay, has had to deal with intimidation and outright unprofessional academic apartheid"

Americans of all sorts seem prone to fundamentalism. I can sympathise with Thomas Dillehay, and I assume he is correct. But that still leaves 'Monte Verde I' long after humans had reached Australia. Neither you nor German have yet even attempted to explain that anomaly.

"We are messengers and the TRUTH has no disguise".

American fundamentalism again? Are you able to enlighten us as to what the truth is? Tobus has provided the most succint explanation for the Amerindian origin:

1) "so the ancestors of East Asians and (all!) Amerindians must have already been diverged by this point [MA-1's time]. This fits perfectly with the model of MA-1 admixture into an East Asian population that then migrated to America without admixing with it's more southern East Asian counterparts".

And 2) "Amerindians are a branch of East Eurasians who who underwent a bottleneck and subsequently expanded into a vast and uninhabited territory, breaking into small groups that have remained relatively isolated. This is consistent with low genetic diversity, low homogeneity, recent MCRA and their close affinity to each other".

What alternative 'truth' can you or German offer? All I can do is repeat my question of a few days ago, 'Would you mind explaining to us exactly how, and when, the ancestors of these 40,000 year old Americans arrived on the double continent?'

"German holds that the genetic data offers the most compelling circumstantial evidence".

Yes, the genetic data offers the most compelling evidence but both you and German ignore any inconveniences in the data and misinterpret much of the remainder.

"please stop referring to the pre-Clovis as Middle Paleolithic (thank you for the retraction), or Upper Paleolithic either".

Instead of just sniping all the time why not offer us an alternative for what we should call it. Neither of you has yet offered any real indication of what you believe to be the history of the Amerindians. Just continual sniping at already widely accepted conclusions.

German Dziebel said...

@terryT

"Yes. German fails to realise that mitochondrial DNA has only some 16,000 base pairs and so recurrent mutations are quite common."

Your knowledge of mtDNA is abominable. If recurrent mutations are quite common, why are you believing that CZ is a valid clade if the only mutation C and Z share is a recurrent one?

"What is German proposing?"

Just study my book The Genius of Kinship as well as www.anthropogenesis.kinshipstudies.org. You can leave your comments there. If they bring value, I'll clear them.

"I'm presuming that what German means by 'East Asians' is 'Mongoloid'. In saying that there were no 'Mongoloid' people in Siberia before the 'Mal'ta' people he is correct."

Yes, Tobus just refuses to accept what is obvious to people even so backward in their beliefs as you, Terry.

Tobus said...

@Alvah:
We are messengers and the TRUTH has no disguise

"Messengers of the TRUTH"?? Seriously? This is science, not religion.

Well, German holds that the genetic data offers the most compelling circumstantial evidence.

German has a poor understanding of the fundamentals of the genetic studies, he cherry-picks superceded data (like insisting that a 10yr old ADMIXTURE analysis of 300 SNPs is better than one from last year using 300,000 SNPs), he makes invalid interpretations (like insisting parallel f3 plots show affinity between populations when direct measurements show no such affinity) and makes widespread generalizations that simply aren't correct (like saying Amerindians are genetically closer to West Eurasians than to East Asians). If you are geniune about wanting to know the truth, I suggest you take the pronouncements of your fellow believers with a grain of salt, and instead make an independent assessment of the data for yourself.

As for Monte Verde I dated at 33,000

Modern Amerindians have an MCRA of ~15-20kya. If Monte Verde I is ever confirmed as proof of human habitation 33kya (and Dillehay has apparently reopened excavations late last year, so there may be some clarification later this year), this would more likely be proof of America being inhabited BEFORE modern Amerindians arrived than proof of continuous habitation by the ancestors of today's Amerindians.

Alvah said...

NO ANIMAL WENT EXTICTY BY THE MEANS OF pre-CLOVIS TECHNOLOGIES! Hmmmm.

@Terryt said @Alvah said "This migration did not move 'just a short distance' but everywhere these lineages are found in the Old World".

@Terryt “Where in Eurasia are any of those haplogroups you mentioned found apart from in the very far northeast?”

See Summerer et al. BMC 2014 14-17 http://www.biomedcentral.com/1471-2148/14/17 Large-scale mitochondrial DNA analysis in Southeast Asia reveals evolutionary effects of cultural isolation in the multi-ethnic population of Myanmar Summerer et al. 2014 (Additional file 1: Table S1). F1a1a with 15.9% of all sequences was by far the most frequent haplogroup in this study, followed by C4b1 (7.0%), B6 (6.4%) and A4 (5.2%). R9b1a1a, D4 and G2b1a reached 4.6% each.

@Terryt “So you're claiming Homo erectus first appeared in America? And H. sapiens evolved from it within the Americas? I'm sure you're on your own there as I doubt German accepts that hypothesis.”

Please do not put words in my mouth. I am stating that to be truly to the autochthonous to the Americas you have to be derived from the Primates of the Americas. See Germans website for Out of America I and the several authors of this theory. We have been walking (1.3m) and talking as Homo sapiens just as long or longer then their have been Homo erectus populations in the Old World. The fallowing quote identifies the evolutionary nature of this in comparison with other species histories. Looking for answers from the Old World limits the possibilities.

An evolutionary afterthought:

EVOLUTIONARY ANTHROPOLOGY: ISSUES, NEWS, AND REVIEWS
Volume 17, Issue 1, January/February 2008, Pages: 49–54, Ian Tattersall and Jeffrey H. Schwartz
Article first published online: 22 FEB 2008, DOI: 10.1002/evan.20153


“For a variety of historical reasons explored above, our species has contrived to elude satisfactory morphological definition. Through a sort of self-reinforcing process, whereby each reasonable large-brained extinct form that was shoehorned into the taxon has appeared to enlarge its permissible morphological limits, a huge variety of morphologies has been admitted into H. sapiens, albeit sometimes into archaic varieties of the species. Acceptance of this muddled variety has been facilitated by a view of evolution that emphasizes gradual transformation in lineages, in which species are basically units of convenience rather than of biology, and that are expected in principle to be undefinable in morphological terms. To systematists studying other groups of mammals, this situation would be untenable; it would indeed, effectively prevent them from plying their trade using currently fashionable approaches, but paleoanthropologists have remained fairly unperturbed because, after all, as human being we “know who we are,” and do not really need to be told, which absolves us, of course, from having to find out (Tattersall and Schwartz 2008, pg. 52).”

Epilog:
In an email from University of Pennsylvania geneticist Theodore G. Schurr, April 24, 2000 Dr. Schurr assured me;
“You have your work cut out for you. I don’t consider this a hopeless effort, but you have to understand that these are the circumstances under which you are working. Remember, that if it has taken over fifty years to finally force many Clovis-first archaeologists to admit that there really is a pre-Clovis substratum in the Americas (except Fidel of course), then think how long it will take to sway their opinion towards an “Out of the Americas” interpretation of modern human origins (Personal Correspondence, 2000).

‘Yes we have our work cut out for us..’ But nature works in natural ways and we stand on solid ground when you incorporate the Big Picture. Old World theories of human origins still offer equivocal solutions, why the long discussions here. Let’s cut to the chase.

terryt said...

"German has a poor understanding of the fundamentals of the genetic studies, he cherry-picks superceded data ..., he makes invalid interpretations ... and makes widespread generalizations that simply aren't correct"

Most of us are agreed on that. Some examples:

"We have evidence for people in the New World at 25,000 YBP and older".

And we have evidence of humans in Australia at 60,000 YBP and older. Why are you so fixated on America? Haploid evidence actually supports an origin for many haplogroups very near Australia, unlike the complete lack of haplogroup evidence for an American origin. Claiming that haploid phylogenies are a mess is no 'proof' of American origin for the haplogroups.

"This can be interpreted as the mixture of two divergent ancient populations".

Exactly, one from Central Eurasia and one from East Eurasia. Y-DNA Q and mt-DNA X from central Eurasia and Y-DNA C and the other mt-DNAs from East Asia. The two populations mixed as they moved towards America.

"If you look at Y-DNA you'll see that Amerindians show two highly divergent lineages, namely Q and C. Same for mtDNA: mhg N and mhg M are both represented in the Americas. There's greater gravitation of Y-DNA C and mhg N to North America, but all lineages are found in both South and North America".

Yes, all are actually widespread and mixed, just as Tobus said.

"I'm open to a number of models of how Amerindians colonized Eurasia but you keep taking the conversation into the pseudoscientific denial of facts".

Hang on German. It is you who have failed to provide any facts to support your out of America belief apart from your rather suspect claim that 'Highest worldwide INTER-population differentiation values within the Americas suggest that Amerindians populations are more divergent than Old World populations'. For a start inter-population differentiation can arise for reasons other than age of the populations. And you are yet to propose any date for an American arrival of any type of human that can provide a source population for your belief.

terryt said...

@ Alvah:

"Large-scale mitochondrial DNA analysis in Southeast Asia reveals evolutionary effects of cultural isolation in the multi-ethnic population of Myanmar"

Thanks for linking to the complete paper but how exactly does that prove any haplogroups originated in America? I see no such claim in the paper.

"F1a1a with 15.9% of all sequences was by far the most frequent haplogroup in this study, followed by C4b1 (7.0%), B6 (6.4%) and A4 (5.2%). R9b1a1a, D4 and G2b1a reached 4.6% each".

None of the above haplogroups are present in America, and so cannot have originated there.

"Please do not put words in my mouth. I am stating that to be truly to the autochthonous to the Americas you have to be derived from the Primates of the Americas".

With nostrils pointing sideways instead of straight ahead?

http://en.wikipedia.org/wiki/New_World_monkey

Quote:

"The noses of New World monkeys are flatter than the narrow noses of the Old World monkeys, and have side-facing nostrils".

How many Amerindians fit that description?

"We have been walking (1.3m) and talking as Homo sapiens just as long or longer then their have been Homo erectus populations in the Old World".

And you can provide evidence for that?

"our species has contrived to elude satisfactory morphological definition".

And how does that fact prove our species evolved in America?

"Acceptance of this muddled variety has been facilitated by a view of evolution that emphasizes gradual transformation in lineages, in which species are basically units of convenience rather than of biology, and that are expected in principle to be undefinable in morphological terms".

As I wrote elsewhere:

'The problem we have is: where do we draw the line between 'archaic' and 'modern'? It is actually impossible to draw such a line. Darwin's idea of 'gradual change' has been unjustifiably overthrown by the idea of 'punctuated equilibrium', rapid change over a short period. But 'punctuated equilibrium' is just 'gradual change' sped up for a time. The change is never 'sudden'. In fact it is doubtful if it has ever been 'sudden' since before humans and chimps parted ways".

"Let’s cut to the chase".

Yes, let's. How about some evidence instead of unsubstantiated claims.

German Dziebel said...

@Tobus

"German has a poor understanding of the fundamentals of the genetic studies, he cherry-picks superceded data (like insisting that a 10yr old ADMIXTURE analysis of 300 SNPs is better than one from last year using 300,000 SNPs), he makes invalid interpretations (like insisting parallel f3 plots show affinity between populations when direct measurements show no such affinity) and makes widespread generalizations that simply aren't correct (like saying Amerindians are genetically closer to West Eurasians than to East Asians)."

Complete baloney, Tobus! Your pseudoscientific antics are now well known: filibustering, twisting facts, ignoring facts, whistleblowing, heckling, contradicting yourself, sporting a bias, etc. And all of this coming from a person without any academic credentials or a even real name! All STRUCTURE and ADMIXTURE analyses published in academic papers to date document that Amerindians are an unadmixed population and that the Amerindian component is present across Eurasia from East to West. Rosenberg et al. 2002 was just the first one to do this and I was lucky enough to hear Marcus Feldman present these results live. I remember the room was silent when the Amerindian color showed up among Finns. This was at a time when everyone was still building insane phylogenetic trees of "human prehistory" built from a single locus. Raghavan's ADMIXTURE run again shows Amerindians unadmixed but, unlike Rosenberg et al., Raghavan didn't present K=2 results. Same for Rasmussen et al. 2014. So, contrary to your claim that I'm reviving an outdated study, that study was a step above all the previous single-locus studies and all the subsequent studies down to the one from a month ago confirm the fundamental findings of Rosenberg et al. 2002. Instead, you are indeed stuck in the ideas about human origins developed on the basis of single-locus studies untested by ancient DNA.

Your interpretation of f3 results are plain ludicrous. Every f3 run measures exactly the same thing between 3 populations. Once you do many of them against the same outgroup and the same anchor you get clusters of populations based in shared genetic history. It's only your anti-Amerindian bias that allows you to easily accept the West Eurasian provenance of La Brana in one plot but prevents you from accepting the Amerindian provenance of La Brana in another plot. Direct measurement against Karitiana confirms the presence of an Amerindian shift in most if not all populations of Eurasia. The resulting continuum of increasing Amerindianness from modern West Eurasians through La Brana to MA-1 is the most accurate inference from EDF 5 in Olalde.

On plots anchored in the 24,000 year old geographically East Asian sample (MA-1) West Eurasians are closer to Amerindians than they are to modern East Asians and Amerindians are closer to West Eurasians than to East Asians. A Mesolithic sample from westernmost Europe (LB) falls into the Amerindian cluster (none of the modern East Asian samples are that close to Amerindians!). On all other plots modern Amerindians are shifted toward modern West Eurasians compared to modern East Asians. How is this "generalization" not correct? How old are you, Tobus? Do you need a new pair of prescription glasses? Amerindians do share genetic history with East Asians (as represented by their mutual positions on the Y axis). This pattern is most consistent with the split of an ancestral New World population into two population with their subsequent progressive divergence into what would become modern West Eurasians and modern East Asians.

Alvah said...

All fields of study lead to a common soundness for this idea, for me the archaeological data offers corporeal behavioral evidence.

What is clear is that the Upper Paleolithic is in it’s infancy at 43,000 and that it continued to develop following its derivation, becoming full blown Upper Paleolithic as sapiens migrated into Europe. If the dates are correct the first encounters between Homo sapiens and Homo erectus may have occurred in Western Siberia. Following this encounter the use of lithic tools by H sapiens expanded along with their range. If this trail is traced back into the Americas then the use of “bone before stone” could help in linking pre-Clovis bone tool technologies to Alaska and then into western Siberia. Only in the Americas does an ancestor to Homo sapiens exist that would not require a metamorphous from the separate species that was H erectus.

What Monte Verde provides is: a verified site to now compare other less well preserved potential habitations to. Certainly, everyone should have an archaeological site set in peat! The acceptance of Monte Verde as a late Pleistocene site must be attributed to not only the painstaking energy of the discoverer but to the viability of the archaeological signature left behind (preserved in the peat) by the inhabitants 14,000 years ago. Fagan suggests that discriminating archaeologists would believe that other - early New World - sites exist if researchers were as thorough as Dillehay's team. That it has taken over 20 years - from the initial discovery in 1976 - for archaeologists to finally accept Monte Verde as a late Pleistocene human settlement does not surprise other archaeologists with "pre-Clovis" discoveries - not preserved in peat.
As for the activities associated with Monte Verde, could they represent a specialized form of subsistence economy born from generations of occupation of the Americas? The evidence shows little, if any, of the signatures suggesting contact with Old World hunter/gathers, in direct conflict with the now disproved theory being; "Clovis First." A new theory must emerge from the "rancor" of the past century by developing a paradigm to test the relationships that now do not link the first Americans as descendants of Old World Paleolithic hunters. The subsistence behavior defining Monte Verde's "learning economy" may represent the ancestral condition the human primate was born into. The untested hypothesis - offering an autochthonous isolation for the human species within the confines of the Americas - is compatible with Monte Verde's Pleistocene definition as a definition supporting an ancient lifeway. The "replacement" of Old World hominids by modern humans from the Americas requires that we interpret the significance of a Pleistocene Amerindian presence. As Fagan asserts, the archaeological signatures from Monte Verde requires we deliberate their "international significance." They also should allow Americanists a comparison for validating what are "simple technologies" being employed by "highly diverse human groups capable of adapting to almost any environment (p. 62)."

Monte Verde promises to offer to New World archaeologists what Jackie Robinson did for African American athletes and baseball. It will grow beyond these first steps - allow new (and the reevaluation of earlier) sites onto the playing field - and provide a new measure for the verification of what we should and should not expect in accepting New World Pleistocene sites. The significance of Monte Verde may never be repeated in either, the magnitude its acceptance holds in dismantling barriers "consensus opinion" has brought mid-Pleistocene human occupation of the Americas, or, the treasure of scientific information the authors have uncovered in substantiating the early ecological balance man once held with-in this, as this author believes, our primordial niche.

Tobus said...

@German:
Tishkoff et al is a good source. So we got that going for you at least. Now, just open the dictionary and learn what "inter" and "intra" mean.

I take it you don't have a source that stating Amerindians have the "highest intergroup diversity"?

According to Collins:
"Inter-" means "between or among"
"Intra-" means "within; inside"
and
"Intergroup" means "occurring between two or more groups"
"Intragroup" means "being or occurring within a single group" (from Miriam-Webster, Collins doesn't have it)

So, in a global diversity context "intergroup" means Amerindians compared to Africans, Europeans etc. while "intragroup" means Amerindians compared to Amerindians.

"Amerindian admixture" is Eurasia has been detected in ancient and modern DNA from Siberia to Spain. We won't make any progress while you continue to deny it.

We're actually trying to come up with a model where such an interpretation is possible... it would be a circular argument to use that interpretation to "prove" the model.

You first presented a model that meant North and South Americans are the most divergent groups on the planet - but the fact is that they are the least divergent groups on the planet.

You then said that this lack of divergence between North and South Americans was due to extensive admixture between these populations - but the fact is that there has been relatively very little admixture between them as evidenced by their high within population diversity.

You followed this up with suggesting that population size, not time, and ancient hominin admixture is largely responsible for the relatively huge distance between West and East Eurasians compred to the distance between North and South Americans - but the fact is that ancient populations from times where these populations were still small show little divergence from modern populations, and that Amerindians show the same degree of ancient admixture as Eurasians.

If you are going to posit that MA-1 and Europans descended from Amerindians, you need to provide a scenario where this is possible within the known facts. What you have presented so far falls well short.

Tobus said...

@Alvah:
Here is a decent overview including some things you might have missed in your sabbatical: http://csfa.tamu.edu/who.php

@German:
And all of this coming from a person without any academic credentials or a even real name!

That's right! I've never been to school and I have no name! You truly are an intellectual giant.

All your other comments just confirm what I'm saying to Alvah - you don't have a very good understanding of the underlying workings of the data you are trying to interpret and are making fundamental mistakes. He'd be well advised to assess the data himself and come to his own conclusions.

Niineta said...
This comment has been removed by the author.
Alvah said...

@Terryt “None of the above haplogroups are present in America, and so cannot have originated there.”

No they (A2, C1a C4a C4b, and D2b and D4h1), are at the twig of the tree and post-date ancestral Haplotypes A2, C1 and C4, D1 and D4, out of the Americas in Holocene times, as they are not basal to the Amerindian Tree and thus (as most all the authors agree), the location of these markers on the Amerindian Tree precludes them as being “founding haplotypes).” Thus, as they point out, “Beringian ancestors” must have gone extinct after the proposed ancestors to the Amerindian departed for a new world. Hmmm!

BTW, this second Holocene exodus Out of the Americas” is distinctly not related to the earlier initial exodus accompanying the initial Peopling of the Eastern Hemisphere 45 ybp) and that is the power of genetics in that it can distinguish basal similarities and subsequent alignment(s). In the initial Peopling the basal M N and R hoplotypes (all three groups founded in the Americas), were the principle root components. The fact that few, if any, of the post nodal derived Old World haplotypes are not part of some “hypothesized migration” into the Americas is just as significant as the fact that none of the “proposed” more ancient African derived L haplotypes does not accommodate the out of Africa scenario. These are similar points German has made for a decade and again have been highlighted in this Anzick-1 archival blog.

@Terryt "The noses of New World monkeys are flatter than the narrow noses of the Old World monkeys, and have side-facing nostrils". How many Amerindians fit that description?
Hershkovitz, Philip 1977 Living New World Monkeys (Platyrrhini)
.... (4) "Aotus and Alouatta are definitely platyrrhines according to the presence of an internarium. There is no similarity whatsoever with the catarrhine condition. (5) The division of the higher primates into platyrrhina and catarrhina is justified. This may indicate a very early evolutionary separation of the Old World and New World primates. (6) The internarium of the New World monkeys shows sinus hairs and is accordingly a sensorial area, at least on the sense of touch" (Hershkovitz 1977 p.1002).

Not speculative, however, is that the resemblance's between living South American and African simians are to numerous and close to be products of parallel evolution alone (Hershkovitz 1977 p. 70).

Yes, humans have nasal hair also, a diminished brow-ridge, a flat face or diminutive proboscis, a Forman magnum that enters the braincase from the central base of the skull, all features we share in common with the Platyrrhini condition, along with a shared number of chromosomes. Perhaps longer faces have tightened our nose.

Jalles-Filho, Euphly 1995. Manipulative Propensity and Toll Use in Capuchin Monkeys. Current Anthropology p. 664.

“Their work suggests that capuchins use bone tools in a way functionally and formally similar to the way the early hominids are hypothesized to have used them, a finding with important implications for the genesis of tool use-and the development of the earliest technologies-in human evolution (p. 664).”

For more see Germans website… http://anthropogenesis.kinshipstudies.org/out-of-america-family-of-hypotheses/

The current disposition countering New World hominid evolution is illustrated by Bruce MacFadden's appraisal that
"paleontologists studying the fossil history of primates have good reason to lament the fragmentary record that must be used to decipher the evolution of this important group. With the great strides that have been made in recent years in the Old World, it can truly be said that the paleontological record of the New World platyrrhines is indeed the weakest of the lot. There are many reasons for this, but these mostly stem from the fact that, with the push to find human ancestors, emphasis has been outside of South America (Bruce MacFadden, source misplaced 1990 pg. 7)." I will continue to cut to the chase after work today.

Niineta said...

#5 South Amerindians are closer to their East Eurasian origins than North Amerindians.

Tobus said... Where do you see this in the graph

The South Amerindians (at the top (America)) occupy the most far Right (Eastern) position of the populations in the Americas, which shows the South Amerindians have a closer genetic relationship to their East Eurasian origins than do the North Amerindians.

- This indicates the South Amerindians represent the oldest unadmixed population in the Americas and are likely genetically representative of the colonizing population from East Eurasia.

- The PCA plot shows the West Eurasians are pulled upward off the X axis while the East Asians are not. That does not show Amerindians have a closer relationship with modern East Asians than with modern West Eurasians.

Secondly it’s known (from other studies) the North Amerindians are divergent from the South Amerindians because the North Amerindians are admixed populations.

- The Athabaskan/Na-Dene have a genetic connection to South Amerindians and another undefined population.

- The Algonquin show a genetic connection to the South Amerindians, the Athabaskan/Na-Dene and another undefined population.

This admixture is why the North Amerindians are divergent from the South Amerindians.

German Dziebel said...

@Tobus

"That's right! I've never been to school and I have no name! You truly are an intellectual giant."

I may be an intellectual giant when it comes to the origins of modern humans but in case of your personal intellectual origins, it doesn't take to be an intellectual giant to notice that when I click on the name "Tobus" nothing comes up under "About Me" in the Blogger profile. I know scientific data is not your forte but apparently you can't furnish any personal data either to beef up your verbal vitriol.

"I take it you don't have a source that stating Amerindians have the "highest intergroup diversity"?"

Tishkoff et al. about African Americans that you yourself brought up has it. Still need glasses?

"So, in a global diversity context "intergroup" means Amerindians compared to Africans, Europeans etc. while "intragroup" means Amerindians compared to Amerindians."

Amerindians and Papuans tend to be the most divergent from Africans. They also tend to have the largest intergroup diversity values globally. But these values are exceeded by such populations as Denisovans and Altai Neandertals suggesting that Amerindians followed by Papuans have a demographic structure closest to Mid-Pleistocene hominins. Although technically speaking gene flow reduces genetic drift, the hypothesis of admixture between Northern and Southern Amerindians doesn't contradict the data that shows that Amerindians have the highest Fst values globally. This only means that those values were much higher prior to the admixture and probably matched Denisovans and Altai Neandertals much more closely.

"You then said that this lack of divergence between North and South Americans was due to extensive admixture between these populations - but the fact is that there has been relatively very little admixture between them as evidenced by their high within population diversity."

It's not WITHIN. It's BETWEEN. And see above for an explanation regarding how admixture in the New World and high Fst are compatible in view of the even higher between-group variation and genetic drift among Denisovans and Altai Neandertals.

"You first presented a model that meant North and South Americans are the most divergent groups on the planet - but the fact is that they are the least divergent groups on the planet."

I don't know what "meant" is supposed to mean here. Populations diverge, some of them come back together, others diverge and don't come back together. Some populations maintain low eff population size, others grow exponentially. It all depends on the population scenario. The mistake labs commit is that they assume only one population scenario (splitting and losing INTRA-group diversity) working in a clockwork fashion throughout human evolution. This is the nonsense that I'm fighting with and what I'm putting in place is a more nuanced modeling of the evolutionary. process.

"If you are going to posit that MA-1 and Europans descended from Amerindians, you need to provide a scenario where this is possible within the known facts. What you have presented so far falls well short."

No, it didn't. You just don't have the education and the tools to properly test it, hence you fall back onto old models that clearly fall short to explain new facts. I wish you subjected Ragahavan et al.'s "Amerindians are a mix of West and East Eurasians" argument to the same degree of biased scrutiny. Instead, you just mindlessly bought into their argument.

terryt said...

@ German:

"If recurrent mutations are quite common, why are you believing that CZ is a valid clade if the only mutation C and Z share is a recurrent one?"

Until someone constructs a credible alternative phylogeny we have to make do with the one we've got. In fact the paper Alvah linked to above provides some incredibly revealing information:

http://www.biomedcentral.com/1471-2148/14/17

@ Alvah:

"In the initial Peopling the basal M N and R hoplotypes (all three groups founded in the Americas), were the principle root components."

That completely contradicts what your link says. The paper in fact supports exactly what I suggested some time back: that the Burma/Northeast India/Southwest China/Laos hill region has been the centre of dispersal for a high proportion on M haplogroups. A centre of dispersal in that region argues against any sort of 'coastal migration'. Some quotes:

"The remaining new haplogroup M90 with its subgroup M90a as well as the three new lineages with only one representative support the assumption of a native emergence of basal M-lineages in this region".

And:

"Migration analyses of Myanmar and four Southeast Asian regions displayed a vivid exchange of genetic material between the countries and demonstrated a strong outwards migration of Myanmar to all analyzed neighboring regions"

And:

"Myanmar turned out to be a hotspot for mitochondrial DNA diversity in Southeast Asia (SEA): The analyzed 327 mitochondrial control region sequences could be assigned to 113 different haplogroups (Additional file 1: Table S1) and from 44 complete mitochondrial genome sequences 11 new lineages emerged (Figure 1). This diversity can partly be explained by SEA’s long population history of over 60,000 years"

That is much earlier than any date anyone has proposed for any out of America population expansion.

Continued:

terryt said...

Continued:

"Such great variety of M-lineages as we found in Myanmar has only been described before in India [33]. Therefore, the prior hypothesis that the diversification of macrohaplogroup M originated in India [33] and that basal M-lineages spread to Myanmar could be extended by the theory that the radiation of M-lineages took place in a geographically wider area including Southeast Asia".

The authors actually ignore the fact that many 'Indian' lineages almost certainly first arose in Northeast India, not in wider India (M13'46'61, M37, M48, M52'58, M60, M71 and M76 for example).

"The new haplogroup M49e and its subgroup M49e1, in contrast, derive from a lineage (M49) only described from tribal populations in Northeast India"

Northeast India is part of the same ecological region as Southwest China, northern Burma and Laos. Other more widespread haplogroups could easily have originated in the same region, notably M1, a subset of M1'20'51. Quote:

"A closer look on the newly described lineages (Figure 1) further supports an astonishing intermediate biogeographic position of Myanmar: M20a descends from a recently described haplogroup M20, found in Mainland SEA [32] and southern China".

All the East Asian mt-DNA M haplogroups probably first entered that region through the same hill country (M7, M8, M9, M10, M11,M12'G, M21, M22, M72, M77 and M80'D for example). Before the Australia/New Guinea M haplogroups arrived they had presumably earlier been resident at the southern end of Sundaland, and earlier still emerged from the same hill country region.

The paper does consider the presence of 'northern' M haplogroups in Burma. Quote:

"the five other frequent mitochondrial haplogroups from our Burma sample (C4b1, B6, A4, D4 and G2b1a, together 27.8%) mainly represented Northeast and East Asian lineages"

They explain the presence of these derived haplogroups:

"Much later, probably driven by a Neolithic agricultural revolution, the Tibeto-Burman (Burmese-Lolo and Karen) branches of Sino-Tibetans moved back southwards through Yunnan to Myanmar and the SEA peninsula"

Another notable feature is:

"The distribution of N-lineages (without A, B and R9’F) was eye-catching with very low percentages in Southeast and East Asia, about 50% in Central Asia, more than 75% in Afghanistan and 100% in the sample of Russian origin".

In contrast basal N haplogroups are well-represented in Australia (N13, N14, S and O). This indicates N's itinerary on its route to Australia did not include Burma.

It is extremely difficult to reconcile this Burma data with any out of America belief. Certainly for mt-DNA M.

Tobus said...

@German:
Tishkoff et al. about African Americans that you yourself brought up has it

No it doesnt - it makes no mention of "inter-" or "intra-" group diversity at all.

But these values are exceeded by such populations as Denisovans and Altai Neandertals suggesting that Amerindians followed by Papuans have a demographic structure closest to Mid-Pleistocene hominins.

No, Denisovan and Altai diversity is *extremely* low - Amerindian diversity is some 300% higher, and much much closer to that of other modern humans. This suggests that Amerindian demographic structure is much more similar to modern Eurasians than to any of the ancients.

Populations diverge, some of them come back together, others diverge and don't come back together.

We have ancient samples that we can use as snapshots for population divergence at various points it time. If you put the divergence shown by these samples up against the divergences implied by your theory you can see that it's unworkable (even with a hypothetical diverging and recombining North/South Amerindian lineage). Tianyuan says all Eurasian/Amerindian lineages were very close at 40kya, MA-1 means the East Asian lineage has been divergent from Europeans for at least 24kya and Anzick requires the North/South Amerindian lineages to be very similar at 11kya and closer to East Asians than Europeans.

I wish you subjected Ragahavan et al.'s "Amerindians are a mix of West and East Eurasians" argument to the same degree of biased scrutiny.

Rest assured I gave it a great deal of scrutiny. Get a piece of paper and a pen and try to draw a tree that matches the patterns of ancient and modern DNA affinity - you'll find it's not possible to do with Amerindians as the ancestors of MA-1, yet very easy with gene flow going the other way. Raghavan's argument is the only scenario that holds up when all the factors are taken into account.

Alvah said...


Footprints can be found dated to 1.3 Million years from Mexico as well as numerous other footprints from the New World that remain undated, like some held by the Smithsonian from Guatemala and another set from Montana. .The lack of interests in dating the former is in question as to the (lack of scholarly) research into Native American antiquity.

@Tobus said,
@Alvah:
Here is a decent overview including some things you might have missed in your sabbatical:http://csfa.tamu.edu/who.php

I was a presenter or the Odyssey Conference sponcered by CSFM this past October and well aware of this organization. I referenced the opening presentation in this Blog Mr. Jose Lucero (Santa Clara Pueblo, NM).

Alvah said...

@terryt "the five other frequent mitochondrial haplogroups from our Burma sample (C4b1, B6, A4, D4 and G2b1a, together 27.8%) mainly represented Northeast and East Asian lineages"

And they post date the Holocene and their origin stories reveal;

“The ethnic origin of the Karen and the migration routes before their arrival in Myanmar around the sixth century AD is largely unknown [42]. Their own legends tell about an ancestry from a “sandy region in the North”, sometimes interpreted as the Gobi Desert,” from Marshall HI: The karen people of Burma: a study in anthropology and ethnology. Ohio State University Bulletin 1922, 26:1-329.

This reference source is from 1922 almost as old as the people he was studying while I still like old citations and MYTHS from the People studied.

@Terryt “It is extremely difficult to reconcile this Burma data with any out of America belief. Certainly for mt-DNA M.”

M was first so that has nothing to do with the Holocene migration and the origins of the Karen.

For the Karen the data fits very well if you entertain the Holocene Peopling of northeast Asia from the Americas as the initial source, which you cannot so whats the point(?). This includes boreal adapted people south into Tibet and yes further south in Myanmar.

Circum-arctic People may have arisen near the Bering Strait and migrated across into northern Europe Boas 1905 1910 and others Ackerman, R. E. 1992. Earliest stone industries on the north Pacific coast of North America. Arctic Anthropol. 29:18-27.

Frequencies for the Amerindian mtDNA haplotypes outlined follow these paths out of North America (as mentioned before).

terryt said...

Neither German nor Alvah have attempted to answer some simple and straightforward questions:

1) What, or who, exactly are the two of you proposing migrated out of America and into Eurasia?
2) When did they do it?
3) When did their ancestors arrive in America?

Alvah has made a feeble attempt, full of irrelevant quotes, to answer the third question but he avoided the main point: If ancient Americans descend from a New World ape of some kind (for which there is no evidence) how come they do not have nostrils that point sideways? That is a defining characteristic of New World primates. Therefore we can safely say Native Americans, just like all other humans, descend from an Old World ape. Almost certainly from an African ape.

German has made a feeble attempt to answer the second question but provided no evidence at all, just guesswork. As near as I can tell he postulates two separate migrations, each containing a completely different gene collection. Far more different from each other than their East Asian/West Eurasian descendant populations.

I await a credible answer to all three questions.

Tobus said...

@Niineta:
The South Amerindians (at the top (America)) occupy the most far Right (Eastern) position of the populations in the Americas, which shows the South Amerindians have a closer genetic relationship to their East Eurasian origins than do the North Amerindians.

Thanks for the explanation, I can see what you are getting at and agree with you in terms of Amerindian-only "East Asian origins" (ie a post-MA-1 ancestor). South Amerindians have a closer genetic representatives to the original Amerindians.

I was thinking in terms of the origins of the entire East Eurasian branch. Modern East Asians are further to the right than Amerindians suggesting that they are closer to a common ancestor, and North Americans are closer genetically to modern East Asians, so an argument could be made that modern East Asian admixture has brought North Americans closer to the common East Eurasian ancestor.

The PCA plot shows the West Eurasians are pulled upward off the X axis while the East Asians are not. That does not show Amerindians have a closer relationship with modern East Asians than with modern West Eurasians.

No, but the axes themselves do. PC1 is the primary difference and PC2 is the secondary - note that the X-axis is really 2.5x smaller than the Y-axis (see the %ages listed), it's just drawn way out of scale. This means that the distance between West and East Eurasia is much larger than the distance between Asia and America... and thus Amerindians are closer to modern East Asians than to modern West Eurasians. This fact is confirmed in every piece of genetic data on the subject.

This admixture is why the North Amerindians are divergent from the South Amerindians.

I think recent admixture is only part of the issue - the Anzick specimen shows a divergence going back 11kya, so it's possible a North/South split happened shortly after (or during) the Beringian migration.

German Dziebel said...

@Tobus

"No it doesnt - it makes no mention of "inter-" or "intra-" group diversity at all."

OK, they call it "between" and "within." Don't filibuster.

"No, Denisovan and Altai diversity is *extremely* low - Amerindian diversity is some 300% higher, and much much closer to that of other modern humans. This suggests that Amerindian demographic structure is much more similar to modern Eurasians than to any of the ancients."

Amerindians occupy the lowest bound of modern human intragroup diversity spectrum. Compared to other modern humans, they are the closest to Denisovans and Altai Neandertals. Looks like you are the one who doesn't get relative proximity. Like I said, there's "room to grow" for Amerindian intergroup diversity reduction before they reach the Denisovan and Altai Neandertal values. You estimated the distance between D and AN and Amerindians compared to the distance between Amerindians and the rest to be 300%. Well, this is the 300% that may have got eaten up by the merger between northern and southern Amerindians.

"Get a piece of paper and a pen and try to draw a tree that matches the patterns of ancient and modern DNA affinity>"

You make me laugh. Instead of drawing imaginary trees of divergence, study the data and make logical inferences. The panmictic models with clockwork divergence models have already compromised themselves by posing the isolation between haploid Khoisan lineages and the rest of humanity for some 150,000 years.

"Tianyuan says all Eurasian/Amerindian lineages were very close at 40kya, MA-1 means the East Asian lineage has been divergent from Europeans for at least 24kya."

East Asians weren't in East Asia at 24,000 YBP, as MA-1 suggests. But Amerindians were already there. Yes, just like craniology suggests that all Pleistocene skulls from Lagoa Santa in America to Hofmeyr in South Africa form a single cluster opposed to Holocene samples and to Neandertals, all Eurasians and Amerindians were closer to each other than they ended up being in Holocene. That's called divergence. How does it make out-of-America unworkable? By your logic, into-America is unworkable, too.

"Anzick requires the North/South Amerindian lineages to be very similar at 11kya and closer to East Asians than Europeans."

Bullshit! Anzick is closer to MA-1 than other Amerindians. And MA-1 is very divergent from East Asians. hence, Anzick is not closer to East Asians.

"Rest assured I gave it a great deal of scrutiny."

Well, in this case you must be unable to understand how science works. You can join TerryT for a Bible-reading hour.

@TerryT

"I await a credible answer to all three questions."

I'm waiting for you to make a sensible contribution to the conversation. I'm not going to explain my theories to you, Terry, any more than I already did. Buy my book, read my site. These are the first steps. You should be working hard and making an effort to bring good logic and good data to help me grow the theory. I'm not here to satisfy your curiosity. Like I said, I don't care what you believe in. You're useless as a resource, hence it's a waste of my time to talk to you.

German Dziebel said...

@Niineta

"Secondly it’s known (from other studies) the North Amerindians are divergent from the South Amerindians because the North Amerindians are admixed populations.

- The Athabaskan/Na-Dene have a genetic connection to South Amerindians and another undefined population.

- The Algonquin show a genetic connection to the South Amerindians, the Athabaskan/Na-Dene and another undefined population.

This admixture is why the North Amerindians are divergent from the South Amerindians."

There are no studies that show that Northern Amerindians is an admixed population. Northern Amerindians split from Southern Amerindians but they didn't admix with anybody. This is consistent with you referring to those putative contributing populations as "undefined."

"This indicates the South Amerindians represent the oldest unadmixed population in the Americas and are likely genetically representative of the colonizing population from East Eurasia."

Earlier you wrote, "#1 there is NO evidence Amerindians descended/split from East Asians. Zero Nada Zilch."

I agree with the latter and, from the out-of-America II perspective (which is my favorite), Amerindians did descend from an East Eurasian hominin, but how do YOU reconcile your two statements?

"The PCA plot shows the West Eurasians are pulled upward off the X axis while the East Asians are not. That does not show Amerindians have a closer relationship with modern East Asians than with modern West Eurasians."

This Y axis on this PCA clearly shows that West Eurasians and East Asians diverged from Amerindians. The pattern of divergence of West Eurasians and East Asians from Amerindians in both directions on the X axis shows that it likely represent first geography, then genetic history. West Eurasians are more divergent from Amerindians than East Asians because they are geographically more remote from the New World.

@Tobus

"Modern East Asians are further to the right than Amerindians suggesting that they are closer to a common ancestor."

No, it's just genetic geography. East Asians are closer to Amerindians without getting closer to West Eurasians because they are geographically closer to Amerindians, while West Eurasians are geographically more remote.

Alvah said...

Any relationship between South Americans and Eurasians must precede a closer affinity between Siberians and North American Tribal Entities who have more recent Biological affinities (Holocene migration out of the Americas, period!!!). Distinctly more recent Amerindian Lineages found in “Northern Hemispheres” have multi-factual renderings that would point to even more ancient connections to the Americas:

1. Myth, see, Boas, Dixon, and others
2. Linguistic, 2/3 of the Worlds languages, also see Sapir and others
3. Archaeological over and over again…
4. Genetic, out, again and again…
5. Behavioral, Pre-Clovis becoming the Old World … Upper Paleolithic, Late Paleolithic, Later Stone Age
6. Kinship, greater diversity in relationship sorting
7. Traditions/Culture and autochthonous primate behavioral and anatomical symmetry.

So what we are left with is closer affinities in time with the Holocene than the more remote ties between all human populations since all are preceding populations are more ancient. If Europe and southeast Asian genetic markers, (like, respectively, U and the multitude of regionally specific M Lineages, and/or African L Lineages), would have been carried to the Americas we would not have a problem with an Asian Origin for the multi-hood of Amerindian Cultures/ethnic identities. But this is not the case. Only Rare “Asian mtDNAs and an incredible bottleneck that accompanies the Asian Origin hypothesis is accommodated by such a scenario. Alternatively, only a subsequent Holocene migration out of the Americas answers all the data and it’s implied who’s closer to who data in this discussion. Think about it before you shout it down as con-strictest’ discussants. We are following this seemingly unwarranted exercise in futility with the hope that we might help (you and others) “make the cooked road strait” and in respect to the Anzick I Childs genetic codes contribution to this debate.

@Tobus said “Get a piece of paper and a pen and try to draw a tree that matches the patterns of ancient and modern DNA affinity - you'll find it's not possible to do with Amerindians as the ancestors of MA-1, yet very easy with gene flow going the other way.”

It is not, nor is it a factual statement to state such an incompletely analyzed BLOGETT. So you and Terryt have no reckonings when you offer ‘just a minute man’ responses. There is truly something bigger than who is right or wrong going on here but you both seem to have no idea. The alternatives being offered do not ascend any higher because you both don’t follow the logic; if you understood the significance of resolving our human origins as doable you might see the Truth of Day. In some ways I think you are trying but that would be a reach. I hold out hope.

As for some of the earlier evidence of prolonged habitation of the Americas I will offer these, some, insufficiently, analyzed locations.

Mirambell, L. 1978. Tlapacoya: A Late Pleistocene Site in Central Mexico. In A.L. Bryan ed.: "Early Man in America: From a Circum-Pacific Perspective." Occas Papers 1, Dept of Anthro, Univ of Alberta, pp 221-230.
Abbott, Charles C. 1889. Evidences of the antiquity of man in Eastern North America. Proceedings of the American Association of Science 37:293-315
Ameghino, Florentino 1893. New Discoveries of Fossil Mammalia of southern Patagonia. American Naturalist
--------. 1911. "Une Noubelle Industrie Lithique." Anales del Museo Nacional de Buenos Aires, vol. 13, ser. 3, 189-204. Buenos Aires.;
--------. 1915. La Antiguedad de los Hombres en El Plata, Obras Completas Correspondencia de Florentino Amighino, vol. 3. La Plata.
Berger Rainer and Phi C. Orr 1966. The Fire Areas of Santa Rosa Island, 11. in Anthropology Vol. 56, pp. 1678-1682
Carter, George F. 1980. Earlier Than You Think: A Personal View of Man in America. Texas A and M Univ Press.

To be continued:

Alvah said...

Continued;

Cook H. J. 1927. New geological and paleontological evidence bearing on the antiquity of man in America. Natural History 27:240-247
Krieger, Alex D. 1958. Review of: Pleistocene Man at San Diego by G.F. Carter. Am Anthropol 60:974-978.
--------. 1964. "Early Man in the New World." In Prehistoric Man in the New World, J.D. Jennings and E. Norbeck, eds., 23-84. Chicago: University of Chicago Press. California, Science 160, 1022-3.
MacNeish, Richard S. 1979. The Early Man Remains from Pikimachay Cave, Ayacucho Basin, Highland, Peru. In Humphrey RL, Stanford D (eds): "Pre-Llano Cultures of the Americas: Paradoxes and Possibilities." Washington D.C.: Anthropol Soc. Washington, pp 1-47.
MacNeish, R.S., A. Garcia-Cook, L. G. Lumbreras, R. K. Vierra and A. Nelken-Terner 1981. Prehistory of the Ayacucho Basin, Peru.. University of Michigan Press, Ann Arbor. Vol. 2: Excavations and Chronology.
MacNeish, R.S. 1992. The 1992 Excavations of Pendejo Caves near OroGrande, New Mexico. Andover Foundation for Archaeological Research, Annual Report
Morlan, Richard E. 1970. "Wedge-shaped Core Technology in Northern North America," Arctic Anthropology, vol. 7, 17-37.
--------. 1980. Taphonomy and Archaeology in the Upper Pleistocene of the Northern Yukon Territory: A Glimpse of the Peopling of the New World. National Mus. of Canada, Mercury Series, Arch. Survey of Canada Paper 94.
--------. 1983. "Pre-Clovis Occupation North of the Ice Sheets" in Early Man in the New World, edited by R. Shutler, Jr., pp. 47-63. Sage Publications, Beverly Hills.
--------. 1987. The Pleistocene Archaeology of Beringia. In The Evolution of Human Hunting, Edited by M.H. Nitecki And D.V. Nitecki, pp.267-307. Plenum Press, New York.
O'Connell, J.F. 1977. Aspects of Variation in Central Australian Lithic Assemblages. In Stone Tools as Cultural Markers; Change, Evolution, and Complexity, edited by R.V.S. Wright. Canberra: Australian Institute of Aboriginal Studies. Pp. 269-281.
Raemsch, B.E., Vernon, W.W. 1977. Some Paleolithic Tools from Northeast North America. Curr Anthropol. 18:1:97-99.
Raemsch, Bruce E. 1990. Native American Antecedents (an Encyclical) Our Obligation to Test a Theory on Native American Antiquity-A Research Letter. unpublished material
Wormington, H. Marie 1957. Ancient Man in North America, 4th ed., Denver Museum of Natural History Popular Series, no. 4. Denver.
Leakey, L.S.B., R.D. Simpson, and T. Clements 1968. Archaeological Excavations in the Calico Mountains, California, Science 160, 1022-3.
Krieger, Alex D. 1958. Review of: Pleistocene Man at San Diego by G.F. Carter. Am Anthropol 60:974-978.
Ameghino, Florentino 1893. New Discoveries of Fossil Mammalia of southern Patagonia. American Naturalist
MacNeish, R.S. 1992. The 1992 Excavations of Pendejo Caves near Oro Grande, New Mexico. Andover Foundation for Archaeological Research, Annual Report
Whitney, Josiah D. 1879. The Auriferous Gravels Of the Sierra Nevada of California, Memoirs of the Museum of Comparative Zoology. Harvard College Vol. VI, No. 1 (1st. Part)
@Terryt said “Neither German nor Alvah have attempted to answer some simple and straightforward questions:

1) What, or who, exactly are the two of you proposing migrated out of America and into Eurasia?
2) When did they do it?
3) When did their ancestors arrive in America?”

All of your questions have been answered if you would pay better attention to what has already been stated and the dates given < 47,538.365 ybp +- 5,000 >. Do you understand the word autochthonous?

terryt said...

@ Tobus:

"an argument could be made that modern East Asian admixture has brought North Americans closer to the common East Eurasian ancestor".

That is almost certainly the case, and exactly what I have been suggesting all along.

@ Alavah:

"Frequencies for the Amerindian mtDNA haplotypes outlined follow these paths out of North America (as mentioned before)".

What 'Amerindian mtDNA haplotypes'? Unless you are prepared to make up completely new imaginary phylogenies that statenment is totally wrong.

"And they post date the Holocene and their origin stories reveal"

Yes, but nowhere does the paper even hint at the possibility any originated in America.

"This reference source is from 1922 almost as old as the people he was studying while I still like old citations and MYTHS from the People studied".

The authors are deliberately quoting old ideas and myths to show they are unreliable. On the other hand you have often used myths to support your belief in an American origin for some as yet undefined group of modern humans. In fact the paper actually says that because the Karen speak Tibeto-Burman languages they probably originated in the mountain region between China and Tibet. As I quoted above:

"Much later, probably driven by a Neolithic agricultural revolution, the Tibeto-Burman (Burmese-Lolo and Karen) branches of Sino-Tibetans moved back southwards through Yunnan to Myanmar and the SEA peninsula"

You are deliberately ignoring inconvenient data. Nothing unusual in that for either you or German.

"M was first so that has nothing to do with the Holocene migration and the origins of the Karen".

You seem not to have understood the paper at all. The authors do not claim for a moment that basal M has anything to do with the Karen. In fact I repeat, 'moved back southwards through Yunnan to Myanmar'. The authors also make it obvious that basal M cannot possibly have anything to do with America, but everything to do with the region around Burma.

"Circum-arctic People may have arisen near the Bering Strait and migrated across into northern Europe Boas 1905 1910"

'May have', but almost certainly not actually in America. And what were you saying about ancient references?

terryt said...

"I'm waiting for you to make a sensible contribution to the conversation".

Neither you nor Alvah have provided anything sensible to any debate. You consistently avoid explaining what you actually think because you know it will not stand up to any sort of scrutiny. Simply saying scientists have it all wrong is in no way 'proof' of any alternative belief.

"All of your questions have been answered"

Perhaps you'd like to remind me. I have not been able to gain any idea 'What, or who, exactly are the two of you proposing migrated out of America and into Eurasia'. One minute it seems to be members of the Upper Paleolithic, at others it seems to be an earlier population, at others the whole of modern humanity's ancestors. It cannot be the first because the Upper Paleolithic is much earlier outside America than within it. And it cannot be the last because:

"the dates given < 47,538.365 ybp +- 5,000"

That answers, 'When did they do it?' but humans were in Australia before that time. Besides which German appears to accept Australian Aborigines are a separate group from Amerindians anyway. And you said: 'Any relationship between South Americans and Eurasians must precede a closer affinity between Siberians and North American Tribal Entities who have more recent Biological affinities (Holocene migration out of the Americas, period!!!)'. So you are immediately proposing two separate migrations out of America for your system. Like German you are completely inconsistent in what you actually say.

"Do you understand the word autochthonous?"

Yes, but that doesn't answer my question, 'When did their ancestors arrive in America?' unless you are you claiming the Amerindians arose within America from American apes (for the existence of which there is no evidence at all). Do you really believe that to be so? If that is your belief I must say you have no idea at all of human evolution. As a result I am unable to take anything you say seriously. German takes a somewaht different view in that he suggests, 'Amerindians did descend from an East Eurasian hominin'. Of course there is no evidence for any ancient hominin in America, but that has never stopped either of you from making outrageous claims. Amerindians are not autochthonous either way.

"The alternatives being offered do not ascend any higher because you both don’t follow the logic"

My comments above expose your own complete lack of logic and consistency.

"if you understood the significance of resolving our human origins as doable you might see the Truth of Day".

Understanding human origins has become entirely 'doable', in fact obvious to all except the two of you. And it doesn't include refusing to accept inconvenient data, and doesn't include any substantial out of America.

"You can join TerryT for a Bible-reading hour".

All the evidence from the correspondence concerning the origin of Amerindians demonstrates clearly it is German and Alvah whose views are most opposed to the acceptance of a simple evolution of humans. Those two are the Bible Bashers.

"Buy my book"

Suddenly it all makes sense. You are engaged in a money-making venture. But the inconsistency and nonsense you have demonstrated recently shows I would be wasting my money.

Alvah said...

@ Terryt said @Alavah said:

"Frequencies for the Amerindian mtDNA haplotypes outlined follow these paths out of North America (as mentioned before)".

@Terryt “What 'Amerindian mtDNA haplotypes'? Unless you are prepared to make up completely new imaginary phylogenies that statenment is totally wrong.”

The same C4b1, B6, A4, D4 derived Lineages carried by Holocene Migrations out of the Americas that are found throughout Asia.

@Terryt said “The authors are deliberately quoting old ideas and myths to show they are unreliable. On the other hand you have often used myths to support your belief in an American origin for some as yet undefined [I have defined them as Native Americans] group of modern humans. In fact the paper actually says that because the Karen speak Tibeto-Burman languages they probably originated in the mountain region between China and Tibet. As I quoted above:”

Where, or better yet, why, did you assume the authors … “are deliberately quoting old ideas and myths to show they are unreliable.”

You have proven in numerous citations in this blog that your revelations are more often than not, plain blasphemous.

From Marshall HI: The karen people of burma: a study in anthropology and ethnology. Ohio State University Bulletin 1922, 26:1-329.

"Much later, probably driven by a Neolithic agricultural revolution, the Tibeto-Burman (Burmese-Lolo and Karen) branches of Sino-Tibetans moved back southwards through Yunnan to Myanmar and the SEA peninsula"

Yes, and the same Sino/Dene-Tibetans are linguistically linked to the Greater Dene-Speakers including Native American Athapaskan found throughout the Northern Hemisphere having origins near the Northwest Pacific coast where this language and genetic correlate started. Again see Sapir’s work from 1917 and the continuing consensus supporting the Dene-Caucasian hypothesis (John Bengston, Editor, Mother Tongue, ASLIP 2000s).

@Terryt “And what were you saying about ancient references?”

Again anthropology did not begin during the 1980’s and 1990’s while geneticists often cite beliefs held by ancient societies as valid interpretations and accurate clues to test the past. Without these clues empirical data can run amuck, just what is happening with Peopling scenarios for Amerindians that ignore Siberian and Native American Traditional Cultural contributions to reality (Holocene back migration out of the Americas) gleaned by the Jesup Expedition…

From Boas; Boas, F. The Jesup North Pacific Expedition. Proceedings of the Thirteenth International Congress of Americanists. (1905) Easton, PA: Eschenback Printing pp. 91-100.

“The diversity of types, languages, customs and beliefs is so great that even a brief sketch of the fundamental features would occupy too much space and time.” p. 95

“While it is impossible to trace linguistic relationship between the numerous stocks inhabiting the area in question, it has become clear that morphologically the languages of northeastern Asia are not related to the Ural-Altaic group of languages. The Chukchee, Koryak and Kamchadal, which are closely related to each other, are polysynthetic, like many of the American languages. They incorporate the noun in the verb, and resemble in all their fundamental traits typical American languages. To a less extent the same may be said of the Yukaghir. In a broad classification of languages, the languages of northeastern Siberia should be classed with the languages of America.” p. 95
“The results of the expedition in regard to probable migrations in the Arctic are even more remarkable, and have an important bearing upon the question of the relationship between the tribes of Siberia and those of America.” p. 97

To be continued.

Tobus said...

@German:
OK, they call it "between" and "within."

Tishkoff et al make two direct measurements of genetic diversity, one from microsatellite allele variance size and one from heterozygosity, and Amerindian score the lowest in both. They also calculate a "diversity ratio" by dividing the variance size diversity by the heterozygosity, for which Amerindians have the highest value, in their words "suggesting a strong bottleneck followed by a recent and rapid
expansion in Native Americans"

I suspect you are getting your "between" and "within" from the AMOVA results (Table 3) headings "Among Populations
within Regions" and "Within Populations". These are *NOT* direct measurements of genetic diversity, they are proportions of components within the diversity. The Amerindian score of 8.3% means that more of the Amerindian diversity is explained by differences in sub-populations than in any of the other regions. This confirms there has not been significant within-America admixture.

You can quibble about the terms I've used, but the fact remains: the Amerindian genetic signature contradicts a deep North/South divergence followed by extensive North/South admixture. We can safely cross that hypothesis off the list.

Amerindians occupy the lowest bound of modern human intragroup diversity spectrum. Compared to other modern humans, they are the closest to Denisovans and Altai Neandertals.

According to the Prufer et. a. Altai Neanderthal paper, non-Africans have a heterozygosity range of 0.65 to 0.8, not including Amerindians. Amerindians score 0.58-0.6 while the Altai specimen has 0.18 and the Denisovan 0.2. Amerindians may be technically the "closest" but they are nowhere near the archaics. So what's going on here? Did you see the phrase "low diversity" used about both Amerindians and Neandertals and jump to a conclusion without looking at the data? Or did you look at the data, see there was no correlation but decide to present your argument anyway and hope no-one would notice?

On top of this, the population estimates for the Neanderthal and Denisovan specimens is lucky to reach 5,000 individuals, while estimations for Amerindians are in the millions if not tens of millions - there is simply no comparison in the demographic structure of the two groups. We can safely cross this hypothesis off the list too.

Instead of drawing imaginary trees of divergence, study the data and make logical inferences.

That's exactly what I have done, and found it impossible to reconcile an Amerindian-into-MA-1 scenario with the data. I'm giving you an opportunity to provide a scenario I may have missed, but if you're unable to do it then say so and we can safely cross that hypothesis of the list too.

Tobus said...

@German (cont):

East Asians weren't in East Asia at 24,000 YBP, as MA-1 suggests.

On the contrary, MA-1 proves that East Asians *were* in existence at 24,000 YBP (and the most obvious location would be central/southern East Asia). If they came into existence after that time then MA-1 would have the same affinity to them as other populations derived from their common post-24kya ancestor. The lack of any East Asian affinity in MA-1 proves that the East Asian ancestor at that time had already diverged from the the ancestors of both modern West Eurasian and modern American populations.

Anzick is closer to MA-1 than other Amerindians. And MA-1 is very divergent from East Asians. hence, Anzick is not closer to East Asians.

Indirect interpretation of the data again? Take another look at EDF 5defg and EDF 6 - East Asians score higher than Europeans on the Anzick axis in every single case.

all Pleistocene skulls from Lagoa Santa in America to Hofmeyr in South Africa

Hofmeyr is 37ky old, Lagoa Santa is 11ky - you do the maths.

Well, in this case you must be unable to understand how science works. You can join TerryT for a Bible-reading hour.

Is there supposed to be an actual argument in there? I understand you have a passion for the ad hominen attack but please try to say something rational as well.

German Dziebel said...

@Tobus

"The Amerindian score of 8.3% means that more of the Amerindian diversity is explained by differences in sub-populations than in any of the other regions."

Yes, that's what I explained to you earlier. And note in the same paper that Papuans follow Amerindians. This is exactly what we see in the recent Altai Neandertal paper. Denisovans > Altai Neandertals > Karitiana > Papuans > the rest.

"This confirms there has not been significant within-America admixture."

Why? I just explained to you how this is possible. For Denisovans and Altai Neandertals, this score will be even higher than for Amerindians suggesting that Amerindians are more heterozygous than Denisovans and Altai Neandertals. Consequently, the hypothesis of an internal admixture between divergent Amerindian populations fits the data.

"According to the Prufer et. a. Altai Neanderthal paper, non-Africans have a heterozygosity range of 0.65 to 0.8, not including Amerindians. Amerindians score 0.58-0.6 while the Altai specimen has 0.18 and the Denisovan 0.2."

So, you are looking at the right data.

"Amerindians may be technically the "closest."

So, you accept that Amerindians are the closest (followed, importantly, by Papuans) to Altai Neandertals.

"but they are nowhere near the archaics. So what's going on here? "

That's called "evolution," my creationist friend.

"On top of this, the population estimates for the Neanderthal and Denisovan specimens is lucky to reach 5,000 individuals, while estimations for Amerindians are in the millions if not tens of millions - there is simply no comparison in the demographic structure of the two groups. "

So, there was an original bottleneck followed by population growth. This is common sense.

"We can safely cross this hypothesis off the list too."

Not not until we cross you off the list of scientifically-minded people.

"That's exactly what I have done, and found it impossible to reconcile an Amerindian-into-MA-1 scenario with the data."

All the data screams that this is what happened. You have two widely divergent populations called West Eurasians and East Asians. But both of them are most closely related to Amerindians. A 24,000 year old sample from East Asia shows that Amerindian genes were in East Asia at that time. A 7,000 year old West European sample shows that it's related to that Amerindian-derived population. Subject closed.

"Indirect interpretation of the data again? Take another look at EDF 5defg and EDF 6 - East Asians score higher than Europeans on the Anzick axis in every single case."

Good try. EDF 6 in two instances shows Anzick as being more shifted to the right on the MA-1 axis than Amerindians. This makes it EVEN MORE removed from East Asians than modern Amerindians. In a third graph, modern Amerindians and Saqqaq are MA-1-shifted and pulled away from East Asians. In other graphs, Anzick and Amerindians are more like French than East Asians are. On Han-anchored axes Amerindians are shifted toward West Eurasians. Saqqaq is everywhere closer to East Asians supporting the notion that East Asians derive from northern Amerindians. Everything is consistent with what the data in Raghavan and Olalde is telling us. East Asians and West Eurasians are variably related to Amerindians, but not to each other. Nowhere do we see Anzick being closer to East Asians than other Amerindians refuting the notion that Paleoindians are East Asian-derived. (This is very consistent with archaeology, BTW.)

German Dziebel said...

@Tobus (contd.)

"MA-1 proves that East Asians *were* in existence at 24,000 YBP (and the most obvious location would be central/southern East Asia)."

Tobus, you are a mess. How can an ancient East Asian sample that's free from modern East Asian affinities PROVE that East Asians were in existence but lived somewhere else? MA-1 has West Eurasian, South Asian, Papuan, Amerindian affinities, which pretty much exhausts all of Eurasia plus Oceania. Were East Asians hiding in a secret place? West Eurasians are as divergent as East Asians and they are abundantly represented in MA-1, which is geographically in East Asia. But East Asians are divergent, too, at least according to you, but somehow not represented in East Asia at 24,000 YBP? Maybe they were residing in North America? What do you think?

"I understand you have a passion for the ad hominen attack but please try to say something rational as well."

The rational thought here is that you walk around holding a Bible in your hand (the consensus of how America was recently peopled from East Asia supposedly written in the archaeological record) and refuse to look at the data. It's not ad hominem. It's a statement of fact. I'm just trying to have fun, too, while ploughing my way through your medieval biases.

terryt said...

@ Alavah:

"You have proven in numerous citations in this blog that your revelations are more often than not, plain blasphemous".

Well, this is an outright lie:

"The same C4b1, B6, A4, D4 derived Lineages carried by Holocene Migrations out of the Americas that are found throughout Asia".

Stop making things up. For a start American C is C1b, C1c1 and C4c, all confined to America in fact. C4b1 is not found in America at all as far as I'm aware but has been found in 'South Siberia'. B6 has never been found anywhere near America either. American B is B2, probably more correctly called 'B4b2', also found only in America. Just a specific branch of A4 has been found in America: A2. Again confined to America although with a minor presence in the Aleutian Islands and the neighbouring Northeast Asian mainland. And the main American branch of D4 is called D1 although a subgroup of D4e (named 'D2a') is present in Aleuts and Eskimos, and another subroup D4h3 with close relations in Japan has also been found in America. To claim the four haplogroups are 'found throughout Asia' is a gross misrepresentation of the data.

"the same Sino/Dene-Tibetans are linguistically linked to the Greater Dene-Speakers including Native American Athapaskan"

Probably true, but on what grounds do you next claim:

"having origins near the Northwest Pacific coast where this language and genetic correlate started".

That is just 'belief' on your part, supported by an ancient idea from 1917.

"anthropology did not begin during the 1980’s and 1990’s while geneticists often cite beliefs held by ancient societies as valid interpretations and accurate clues to test the past".

Very valuable when supported by more modern studies, especially genetic studies, but worhtless on their own.

"In a broad classification of languages, the languages of northeastern Siberia should be classed with the languages of America".

And that proves the languages originated in America ... how? It is surely exactly what we would expect if Americans had entered America from northeastern Siberia.

terryt said...

"the fact remains: the Amerindian genetic signature contradicts a deep North/South divergence followed by extensive North/South admixture. We can safely cross that hypothesis off the list".

Exactly. German's hypothesis requires a double migration out of America comprising totally different populations. That in itself is unlikely, although possible I suppose. But then he claims these two population threads became completely different from each other yet at the same time remained similar to the popualtions of orgin. That necessitates an extreme level of drift for the two out of America populations, yet none at all for the two stay-at-home American populations, after the departure of the second group. That is impossible to accept, especially when we consider the two Eurasian populations were apparently moving into previously uninhabited regions and so multiplied tremendously whereas the original population was presumably more constrained in its ability to multiply extensively. As well as this unlikely scenario we have both German and Alvah proposing a migration out of America long before the population grew to anything like a level likely to push any population out of that continent. The population of the Americas was obviously very sparse until the time of Clovis regardless of how long any humans had been living there.

The fact that West Eurasians diversified from Amerindians suggests they mixed with a population already in Eurasia. The case with East Eurasians is similar. It is therefore impossible to tell from the raw data which direction the movement was. In fact the data supports the idea that Amerindians are a hybrid between West and East Eurasians rather than being the product of a split within any 'original' American population. The haplogroup data also supports such a conclusion but Grman has tied himself in knots trying to dismiss the haplogroup data because it so absolutely contradicts what he wants to believe.

"I'm giving you an opportunity to provide a scenario I may have missed, but if you're unable to do it then say so and we can safely cross that hypothesis of the list too".

Yes. We are yet to hear exactly what German actually believes. He concentrates on dismissing data that apparently contradicts his religious beliefs.

Alvah said...

Continued from my last contribution 2-9-2014

“This feature is so striking that Mr. Bogoras and Mr. Jochelson have independently reached the conclusion that a close affiliation exists between eastern Siberian folk-lore and that of southern Alaska and British Columbia. Mr. Jochelson finds that the Koryak have many incidents in their tales in common with the Old World and with the North American Indians, and quite a number which are common to the Koryak, the Eskimo and the Indians, but none that belong to the Koryak and to the Eskimo alone. ” p. 98

“This clew once given, we investigated the cultural similarities in this whole area, and found ample evidence that there must have been, at an early period, an intimate relationship between the Indian tribes of the Pacific coast and the peoples of eastern Siberia. p. 98”

Another more recent appraisal;
Ousley, Stephen 1995. Relationships between Eskimos, Amerindians, and Aleuts: Old Data, New Perspectives. Human Biology, v. 67, no. 3, pp. 428, 431, 433, 434, 447, 451.

Based on data from the JNPE, Boas concluded that "comparisons of type, language and culture make it at once evident that the Northeast Siberian people are much more closely akin to the Americans than to other Asiatics" (Boas 1905, p. 99). Based on the greater biological diversity in the New World, Boas reasoned that Amerindians were in the New World earlier. Because the northeast Siberians represented a small part of the variation present in the New World, they could not have been there as long (Boas 1910). This pattern was confirmed recently by Torroni, Schurr et al. (1993), who found greater diversity in the mtDNA of Amerindian tribes than in native Siberian groups. To explain these observations, Boas proposed that Asians first migrated across a land bridge to America and were cut off from Siberia by glaciers, allowing differentiation of the distinctive American types. When the glaciers retreated, the land bridge was open once more and Americans flowed back into Asia until they encountered Mongoloids migrating from the south and west (Boas 1905, 1912). The peoples on either side of the Pacific were then separated at the Bering Strait by an Eskimo wedge, that is, by a people culturally and morphologically distinct. For Boas, and others the Eskimo originated east of Alaska: "The much-discussed theory of the Asiatic origin of the Eskimos must be entirely abandoned" (Boas 1910, p. 534). The central Canadian Eskimo, who were land and rivertine hunters, were thought by many to represent the ancestral condition of the maritime-oriented Eskimo (Hrdlicka 1930)(p. 428).

Boas' theory took all his observations and assumptions into account, explaining why northeast Siberians were bordered by different peoples yet similar to Northwest Coast Amerindians (Ousley 1993). Boas based most of his conclusions on the ethnographic data, with which he was familiar. He never analyzed the Siberian anthropometric data that he made sure were collected, deferring to secondhand typologies and observations instead. This was no doubt partly due to the immense time required for statistical analyses in the precomputer era (p. 428).

With larger samples the picture becomes more complicated, as demonstrated by a tremendous time depth (78,000 years) for some Nuu-Chah-Nulth mtDNA lineages and relationships that contradict linguistically based waves (Ward et al. 1991, 1993). In addition, studies have shown that Amerindians have a relatively high amount of mtDNA variation compared with the rest of the world (Horai et al. 1993), especially Siberia (Torroni, Schurr et al. 1993)(p. 431).



@Terryt “So you are immediately proposing two separate migrations out of America for your system. Like German you are completely inconsistent in what you actually say.”

Far from it, we both hold true to two separate migrations one corresponding in time with the arrival of Modern humans into the Eastern Hemisphere ~50 kyp and another after the melting of glacial ice after the Holocene.

terryt said...

@ Alvah:

"and found ample evidence that there must have been, at an early period, an intimate relationship between the Indian tribes of the Pacific coast and the peoples of eastern Siberia".

Is that really such a surprise? Surely that would be the case if the Pacific coast Amerindians had come from Eastern Siberia.

@ German:

"How can an ancient East Asian sample that's free from modern East Asian affinities PROVE that East Asians were in existence but lived somewhere else?"

You are using confusing terminology. I presume by 'East Asians' you mean 'Mongoloid' rather than meaning just a geographically East Asian population. MA-1 is 'East Asian' geographically but not 'Mongoloid' genetically. Therefore it is quite possible that East Asians (Mongoloids) were hiding in a secret place. Not so 'secret' in fact. Most likely somewhere near the China/Mongolia/Tibet border.

"Maybe they were residing in North America? What do you think?"

Absolute rubbish.

"All the data screams that this is what happened".

Not so. It is your pre-determined belief that allows you to interpret the data that way. And certainly 'most of the data' shows you are wrong.

"You have two widely divergent populations called West Eurasians and East Asians. But both of them are most closely related to Amerindians".

Yes, 'widely divergent populations'. Therefore it is almost impossible they both spring from the same immediate ancestry. The fact both are 'closely related to Amerindians' supports other data which indicates Amerindians are a hybrid between the other two rather than demonstrating the other two descend from Amerindians.

"East Asians and West Eurasians are variably related to Amerindians, but not to each other".

If they are not related to each other how on earth can they have both descended from the same population?

"On Han-anchored axes Amerindians are shifted toward West Eurasians".

Yes, because Amerindians are mixed with Eurasians rather than being 'pure' East Eurasians.

"A 24,000 year old sample from East Asia shows that Amerindian genes were in East Asia at that time".

Yes, the genes of an Amerindian ancestor.

"A 7,000 year old West European sample shows that it's related to that Amerindian-derived population".

'Related to' in the sense that it too descends from this Amerindian ancestor.

"Subject closed".

I certainly hope so.

Tobus said...

@German:
Denisovans > Altai Neandertals > Karitiana > Papuans > the rest

You forgot to mention the massive gap between the ancient hominins and modern humans. You are obviously aware of this, so I can only conclude that you are deliberately trying to present a correlation where you know there isn't one. Amerindian demographic history is very similar to other modern humans and nothing at all like ancient hominins. The close affinity between North and South Amerindians under your suggested scenario still needs to be explained.

(and Altai comes before Denisovans).

All the data screams that this is what happened.

No, you're not paying attention - the data is that North and South Americans are the least divergent of all modern populations, but your theory is the exact opposite of this. The only theory that fits the data is that Amerindians separated from a common East Asian ancestor and recieved DNA from the West Eurasian-like MA-1 on route to America.

Good try. EDF 6 in two instances shows Anzick as being more shifted to the right on the MA-1 axis than Amerindians.

*Sigh* - affinity to MA-1 is not affinity to Amerindians nor affinity to Europeans. To find out if Anzick is closer to East Asians or to Europeans, look at the Anzick axis... he's clearly closer to East Asians.

How can an ancient East Asian sample that's free from modern East Asian affinities PROVE that East Asians were in existence

I just explained it - if East Asians diverged after MA-1 then they would share the same affinity to MA-1 as their Amerindian cousins (since they would have been a single population at that time). This is *NOT* the case, so East Asians must have already been diverged at the time of MA-1.

A single site in Siberia is not the entirety of East Asia. East Asians are closer to MA-1 than Papuans, and are in the range of the least-MA-1-like South Asians, so a location south and east of Siberia is the obvious (and not at all secret!) possibility. Thereare a number of archaeological sites attesting continous human habitation in the region from around that time and before. It's strange you are so critical about the lack of an East Asian sample in East Asia, yet have no problem with the similar lack of Amerindian samples in America.

It's not ad hominem. It's a statement of fact.

The two are not mutually exclusive - an ad hominen attack may well be true, it's fallacy is that it's irrelevant to the argument. Whether I carry a bible around all day or whether I don't doesn't change the fact that modern and ancient genetic affinities mean that MA-1 could not have received DNA from Amerindians.

Alvah said...

Two migrations does not imply that we are “completely inconsistent” but rather very specific. One Migration included Basal lineages M, N and R, the second additional later mutations post dating the initial ancestral basal Old World mutations (C4b1, A4, D4). We have developed the basis for these assertions for decades and are well aliened in our wide-ranging theory.

Merit Ruhlen (1989)

“Soon after Sapir proposed the Na-Dene family he became aware of many striking similarities between the Na-Dene family and the Asian language family known as Sino-Tibetan. In his correspondence with Alfred Kroeber, Sapir left no doubt that he was absolutely convinced that Na-Dene and Sino-Tibetan belonged to an even more ancient linguistic family: "If the morphological and lexical accord which I find on every hand between Na-Dene and Indo-Chinese [Sino-Tibetan] is "accidental" then every analogy on God's earth is an accident. It is so powerfully cumulative and integrated that when you tumble to one point a lot of others fall into line" (Golla 1984;374). ...Owing to the recent discovery of this family (or re-discovery, in light of Sapir's earlier proposal), there is not yet a consensus on precisely which language families constitute Dene-Caucasian. I believe that the following should be included: Basque, (North) Caucasian, Sumerian, Burushaski, Nahali, Sino-Tibetan, Yeniseian, and Na-Dene (Ruhlen 1989 pp.12-13).”


Your inconsistent and dubious slighting that we are “wrong” about either of these specific migrations just because YOU say so is an affront to good science. Not only do you state underwhelming criticisms but you are unable to fill in the blanks. You misinterpret and state inaccurate portrayals of the data we present in a vain attempt to underscore the sensible discourse we articulate. You act like some sort of Blogger Cop. Pre-Clovis advocates would liken you to “the Clovis First Police.”

This last section was about the second Holocene migration.

So you don’t get confused… the next is on an autochthonous origin for American Natives which we propose were/are our ancestors.


@Terryt said @Alvah said "Do you understand the word autochthonous?"

@Terryt said “Yes, but that doesn't answer my question, 'When did their ancestors arrive in America?' unless you are you claiming the Amerindians arose within America from American apes (for the existence of which there is no evidence at all).”
Please do not put words in my mouth, “American apes”. All Apes descended from primates, the idea that most hominids were once knuckle walking apes does not discount a direct advancement to a terrestrial niche from primates that were not knuckle walkers. The anatomy including the central brain case location of the Forman Magnum of New World members of the “Higher Primate Family” does not necessitate this transitional phase, even if this stage led to most Old World hominids.
Heymann, Eckhard W. Giant fossil New World primates: arboreal or terresrial? Jounral of Human Evolution (1998) 34, 99-101.

“This argument includes some circularity, and a different conclusion should be taken into consideration; if the habitat was in fact very similar to current conditions, it is possible that Protopithecus and Caipora led a way of life that included a high degree of terrestriality. Although terrestriality has evolved in all paleotropical primate radiations, the question regarding why this way of life is lacking in New World primates has remained enigmatic. Protopithecus and Caipora might fill this gap.” p. 100

“Finally, the alternative hypothesis of a high degree of terrestriality could also account for the very large body size observed in Protopithecus and Caipora in comparison with other atelines. p. 100.”

German Dziebel said...

@Tobus

"You forgot to mention the massive gap between the ancient hominins and modern humans. You are obviously aware of this, so I can only conclude that you are deliberately trying to present a correlation where you know there isn't one. Amerindian demographic history is very similar to other modern humans and nothing at all like ancient hominins."

So what's wrong with having the gap? Amerindians have always been considered the best modern human example of a Mid-Pleistocene demographic situation. Ancient DNA data fully confirms it.

"The only theory that fits the data is that Amerindians separated from a common East Asian ancestor and recieved DNA from the West Eurasian-like MA-1 on route to America."

There's no data whatsoever to support this interpretation.

1. West Eurasian BLUE and East Asian ORANGE components are not found in America. The Amerindian component is all over Eurasia, in ancient remains and in modern populations.

2. MA-1 haploid lineages are West Eurasian and they are not found in the Americas.

3. All of West Eurasians are shifted toward Amerindians. If a peripheral West Eurasian group admixed into Amerindians, we would have seen a shift toward Amerindians from only MA-1 but not from the rest of Eurasians.

4. The oldest Amerindian DNA sample, Anzick, doesn't show any greater proximity to East Asians, while it continues the tendency to be aligned with MA-1, which has no East Asian affinity.

5. West Eurasians and East Asians show variable affinity to Amerindians but not to each other.

Apart from the total misfit with the data, your/Raghavan's interpretation itself is highly unlikely as it requires a West Eurasian population to be in East Asia ready to inject its genes into a small group of proto-Amerindians, already separated from East Asians 10,000 years earlier than it's currently thought and apparently waiting at the doorstep to get to America, but not into supposedly a much more diversified and populous East Asian population.

All the data and logic supports the out-of-America scenario. From their New World homeland, West Eurasians went into one direction, East Asians into another direction. Hence, they share common genetic history with Amerindians, which progressively weakens with distance from the New World, but not with each other.

"The close affinity between North and South Amerindians under your suggested scenario still needs to be explained."

I don't see this as a problem. Populations diversify more when they grow in size and migrate over larger distances, so naturally East Asians and West Eurasians will be more dissimilar from Amerindians than two Amerindian populations from each other. All Africans always form one cluster. This doesn't prevent them from being conceived of as a source for populations outside of Africa. But internal fissioning between Amerindian subpopulations is greater than in the Old World indicating antiquity. Plus, again, there are indications that two divergent populations in America merged together. Whichever way you go, out of America is fully supported by the data.

"A single site in Siberia is not the entirety of East Asia."

Agree.

"affinity to MA-1 is not affinity to Amerindians nor affinity to Europeans."

Would you say MA-1 and Anzick are aliens then?

"To find out if Anzick is closer to East Asians or to Europeans, look at the Anzick axis... he's clearly closer to East Asians."

No. On the Anzick axis, East Asians and West Eurasians are closer to each other than either of them to Anzick or other Amerindians. 0.14-0.18 from Eurasians to East Asians but 0.18 to 0.26 from East Asians to Amerindians. East Asians are closer to Amerindians than West Eurasians because they are closer to them geographically. Once a very ancient sample is used, MA-1, the situation flips and West Eurasians become closer to Amerindians,. But again West Eurasians and east Asians are still closer to each other than to Amerindians.

German Dziebel said...

@Tobus (contd.)

"There're a number of archaeological sites attesting continous human habitation in the region from around that time and before."

Paleobiologically there's a clear break between older non-Mongoloid skulls in East Asia and younger, post-10,000 year old Mongoloid skulls. MA-1 is consistent with this lack of ancestors of modern East Asians in East Asia at 24,000 years ago. The slower rate of recovery of archaeological sites in America is fully consistent with low population size and low intragroup allele diversity found in the New World.

"Whether I carry a bible around all day or whether I don't doesn't change the fact that modern and ancient genetic affinities mean that MA-1 could not have received DNA from Amerindians."

They obviously could and have. Unless you are feeble-minded, I can only blame the Bible (its 6-10,000 years for the origin of the Earth being eerily similar to 12,000 years ago postulated by you for the origin of the American man) for your blindness.

Tobus said...

@Alvah:
we both hold true to two separate migrations one corresponding in time with the arrival of Modern humans into the Eastern Hemisphere ~50 kyp and another after the melting of glacial ice after the Holocene.

This is contradicted by the high affinity of modern East Asians and Amerindians, yet the very low affinity of modern East Asians and the 24kya Mal'ta sample.

If modern East Asians derive from the 50kya migration then they would show a higher affinity to West Eurasians than to modern Amerindians. If they derive from the 10kya migration they would have the same affinity to MA-1 as modern Amerindians do. Neither scenario works.

I have found it impossible to reconcile an Out Of America scenario with the pattern of genetic affinity we see in modern and ancient samples. Perhaps it was a workable theory at one time, but recent genetic data has shown it cannot be true.

terryt said...

@ Alvah:

"We have developed the basis for these assertions for decades and are well aliened in our wide-ranging theory".

'Aliened' is definitely the correct word here.

"Not only do you state underwhelming criticisms but you are unable to fill in the blanks".

What blanks would you like us to fill in? The only blanks I can see are in your trying to fit your own beliefs to existing data. Otherwise I am not aware of any major blanks at all.

"One Migration included Basal lineages M, N and R"

That is absolute rubbish. America has no basal lineages from any of those three branches and so it is impossible that any of them originated in America.

"the second additional later mutations post dating the initial ancestral basal Old World mutations (C4b1, A4, D4)".

None of those three support any notion of an origin in America either.

"the next is on an autochthonous origin for American Natives which we propose were/are our ancestors".

Once again totally unfounded beliefs. For example:

"All Apes descended from primates"

True, but not just any primates. You do not understand basic evolution. All apes descend from a particular branch of primates. Primates broke early into two branches, a New World population and an Old World population. The two are very easily distinguished. All apes, including humans (even Amerindians), descend from Old World apes.

"The anatomy including the central brain case location of the Forman Magnum of New World members of the 'Higher Primate Family' does not necessitate this transitional phase"

Perhap so. But multiple other factors preclude the possibility that any human branch descends from anything like New World monkeys.

"Finally, the alternative hypothesis of a high degree of terrestriality could also account for the very large body size observed in Protopithecus and Caipora in comparison with other atelines".

Yes, but they're still New World monkeys, not apes. Well Protopithecus is and seems to be a sort of howler monkey while Caipora is just mythical. The ancestors of any Amerindians must have entered America from Eurasia at some time, whether at H. erectus stage or later may be open to some debate but appears very unliklely to have been as early as that species.

"he became aware of many striking similarities between the Na-Dene family and the Asian language family known as Sino-Tibetan. In his correspondence with Alfred Kroeber, Sapir left no doubt that he was absolutely convinced that Na-Dene and Sino-Tibetan belonged to an even more ancient linguistic family"

That connection is quite possibly correct but if so it in no way follows that its origin was in America. As usual you leap instantly onto data with a possible ambiguous interpretation yet ignore data with completely unambiguous interpretations.

@ Tobus (in support):

"a location south and east of Siberia is the obvious (and not at all secret!) possibility".

Yes. As I wrote yesterday, 'Most likely somewhere near the China/Mongolia/Tibet border'. In fact exactly where the paper on the EDAR370A mutation placed the mutation's origin.

"The only theory that fits the data is that Amerindians separated from a common East Asian ancestor and recieved DNA from the West Eurasian-like MA-1 on route to America".

The only way it is possible to avoid that conclusion is to use only data capable of ambiguous interpretation and to dismiss all data that point unambiguously in that direction. That is the perspective Alvah and German have consitently adopted. Example:

"It's strange you are so critical about the lack of an East Asian sample in East Asia, yet have no problem with the similar lack of Amerindian samples in America".

Yes, inconsistency is the name of the game for those two.

Alvah said...

@Tobus said ”The lack of any East Asian affinity in MA-1 proves that the East Asian ancestor at that time had already diverged from the the ancestors of both modern West Eurasian and modern American populations.”

No, only that Amerindians fill an ancestral position for both West N/U and Eastern Eurasian mtDNA haplogroups M’s and R/B and more recent Holocene Northeast Asians harboring C4b1, A4, D4h1 haplotypes.

@Terryt "Subject closed".

WHY?

@ Alvah: Ousley/Boas concluded;

"and found ample evidence that there must have been, at an early period, an intimate relationship between the Indian tribes of the Pacific coast and the peoples of eastern Siberia".

@Terryt said “Is that really such a surprise? Surely that would be the case if the Pacific coast Amerindians had come from Eastern Siberia.”

The principle conclusion from the Jessup Expedition and all the data points pint to out of the Americas specifically the northwest Pacific coast. You are the one stuck in the mud so please do not muddle the conclusion!

"In a broad classification of languages, the languages of northeastern Siberia should be classed with the languages of America".

@Terryt “And that proves the languages originated in America ... how? It is surely exactly what we would expect if Americans had entered America from northeastern Siberia.”

The Siberian populations have a more recent origin; that is the point. Even Tamm et al. 2007 are unable define living populations in Siberia that would satisfy their Beringian Standstill scenario. See the new paper by John F. Hoffecker et al “Out of Beringia?” 2014, I did not add the “?” mark.

Another blast from the past, before your genetic studies existed;

Graciela Bailliet, et al. 1994 FOUNDER MITOCHONDRIAL HAPLOTYPES IN AMERINDIAN POPULATIONS; Am. J. Hum Genet.

“Confirmation of a relatively high number of founder haplotypes would indicate that early migration into America was not accompanied by a severe genetic bottleneck (Page 27).”

“The number of founder Amerindian haplotypes is a problem at the center of an unresolved dispute. According to Torroni et al. (1993b), the colonization from Asia into the American continent was accompanied by a severe bottleneck that markedly restricted the number of maternal lineages entering the New World. Ward et al. (1991) and Horai et al. (1993) propose an opposite view. The genetic diversity detected in Amerindians is, according to these investigators, too extensive and, consequently, does not support the hypothesis of the genetic bottleneck. Confirmation of the presence of more than four founder haplotypes in Amerindians would lend additional support to the positions of Horai et al. and Ward et al.
Haplotypes A and D are found not only in Asiatics, but also in a low number of Caucasians (Cann et al. 1987). .. This finding seems to confirm the Asiatic origin of Amerindians; yet, the ancestral Asiatic population(s) from which the Amerindians derived is matter of speculation and debate. (page 31 and 32)”

“The possibility of identifying the ancestral founder haplotypes of Amerindians has been questioned by some investigators. Chakraborty and Weiss (1991) re analyzed Schurr et al.'s (1990) data on three Amerindian populations and proposed that mtDNA is in mutation-drift equilibrium and that it is not possible to identify ancestral lineages. Additional arguments casting doubts on the models derived from the existence of founder Amerindian haplotypes have been put forward recently by Szathmary (1993).”

“At this time it seems too optimistic to think that the mtDNA of extant Amerindian populations will serve either to resolve all doubts about the origin of Amerindians or to reconstruct the evolution of primitive populations, some of which may have become extinct because of epidemics, wars, and the forced resettlements that occurred during the conquest of America. (page 32)”

Numerous lineages have been added through 2014.

terryt said...

"I have found it impossible to reconcile an Out Of America scenario with the pattern of genetic affinity we see in modern and ancient samples. Perhaps it was a workable theory at one time, but recent genetic data has shown it cannot be true".

That seems to be the problem alright.

@ Alvah:

"Even Tamm et al. 2007 are unable define living populations in Siberia that would satisfy their Beringian Standstill scenario. See the new paper by John F. Hoffecker et al 'Out of Beringia?' 2014, I did not add the '?' mark".

The paper actually seems to say, 'Evolutionary analysis applied to the relationship between North American and Central Siberian languages may indicate that people moved out from the Bering Land Bridge, with some migrating back to central Asia and others into North America'. In other words the migration was from Beringia 'back to central Asia', not from America back into Central Asia. The genes back up a language dispersal wider than the genetic expansion that started it off.

"The Siberian populations have a more recent origin; that is the point".

Only because you assume an ancient origin for American populations. However it appears extremely likely that Y-DNAs spread through Siberia is certainly post Amerindian departure from Eurasia.

"Amerindians fill an ancestral position for both West N/U and Eastern Eurasian mtDNA haplogroups M’s and R/B"

Not according to any phylogeny I'm aware of. Perhaps you have invented one that supports your scenario?

"more recent Holocene Northeast Asians harboring C4b1, A4, D4h1 haplotypes".

Yes, and just a small region of Northeast Asia, not the whole continent.

"Haplotypes A and D are found not only in Asiatics, but also in a low number of Caucasians (Cann et al. 1987). .. This finding seems to confirm the Asiatic origin of Amerindians; yet, the ancestral Asiatic population(s) from which the Amerindians derived is matter of speculation and debate".

And MA-1 significantly adds to our understanding of the several separate populations involved.

"Numerous lineages have been added through 2014".

All but a very few within the already discovered haplogroups.

@ German:

"MA-1 haploid lineages are West Eurasian and they are not found in the Americas".

Which show that cannot have come from America. On the othe hand a population similar autosomally to MA-1 must have contributed to American aDNA.

"MA-1 is consistent with this lack of ancestors of modern East Asians in East Asia at 24,000 years ago".

Tobus and I have both tried to explain why that is so but the blindness required for your fundamentalist belief system demands that you deny that explanation.

"The slower rate of recovery of archaeological sites in America is fully consistent with low population size and low intragroup allele diversity found in the New World".

Thus making it impossible that any of that 'low population' would have been inspired to move into the inhospitable northern regions required for them to be able to reach Eurasia. You've just destroyed your claim.

Tobus said...

@German:
So what's wrong with having the gap

The gap means that being "closest" is not the same as being "close". Failing to consider the gap means you might be fooled into thinking Amerindian demographic structure is somehow similar to Neanderthal/Denisovan demographic structure, when in fact was nothing like it.

There's no data whatsoever to support this interpretation.

Let's see:;
1. Amerindian isolation and lack of admixture makes it a standout target for ADMIXTURE logic, so it's expected that shared DNA will be seen as "Amerindian" before "European" or "East Asian".
2. Amerindians have much more "East Asian" ancestry than MA-1 ancestory, and it's well know that haploid lineages are poor representatives of genome-wide ancestry.
3. All modern Europeans have a degree of ANE ancestry.
4. Why would you expect East Asians to be closer to Anzick than to Amerindians on the f3 stats? They had already diverged from the lineage before Anzick so the should have roughly the same amount of shared drift with both Anzick and Amerindians.
5. I don't know you mean by "variable affinity to Amerindians", they are in pretty much the same relative positions on all the Amerindian axes... are you making the old "affinity to MA-1 is affinity to Amerindians" mistake again?

So that's 0 out of 5. The scenario of MA-1 contributing DNA to Amerindians is most certainly consistent with the known facts. The same cannot be said for your "Amerindian into MA-1" theory which requires a deep divergence then complete admixture in a population with a genetic profile precluding significant admixture, and a demographic history similar to ancient populations that show a completely different genetic and population profile.

From their New World homeland, West Eurasians went into one direction, East Asians into another direction. Hence, they share common genetic history with Amerindians

It's quite clear from the data that the Amerindian affinity in Europeans and East Asians is not common at all, but distinct. We've seem to have gone full circle back to the first problem in your theory - why does MA-1 have high Amerindian affinity yet no East Asian affinity?

On the Anzick axis, East Asians and West Eurasians are closer to each other than either of them to Anzick or other Amerindians

*sigh* The Anzick axis only measures distance to Anzick, not distance between the X populations. Anzick is definitely closer to East Asians than he is to Europeans.

East Asians are closer to Amerindians than West Eurasians because they are closer to them geographically.

Yeesss... because genes have a built-in GPS that tells them to mutate for each kilometre they travel. It's time, not distance that caused this genetic divergence.

They obviously could and have

Yet you've been unable to provide a scenario of such that is based on facts. Have you consideed that maybe it's you who is holding onto a work of faith here?

Tobus said...

Alvah:
No, only that Amerindians fill an ancestral position for both West N/U and Eastern Eurasian mtDNA haplogroups M’s and R/B

What's your logic for concluding that Amerindians are ancestral to MA-1? That proposition is explicitly rejected in the paper.

All Apes descended from primates

Are you aware that of the 20 primates genetically closest to modern humans not one is from America? I think this idea is pretty much dead in the water.

Alvah said...

New Paper suggests Out of the Americas is closer to reality. First how much diversity is really in the Western Hemisphere, another clue from the past and another clue from Yesterday follow;

Even Greenberg, Turner and Zegura (1986; 487) regard their 'genetic' data as "still without confirmation" and so as "supplementary." Therefore, since their dental/genetic claims are not supported, correlation's between such claims and Greenberg's linguistic classification (also not substantiated) can be of little value, and postulated migrations to the New World based on such correlations are unwarranted. Finally, as persuasively argued by Rebecca Cann (this volume), the mitochondrial DNA evidence indicates that there were at least eleven lineages from which American Indians descended, perhaps thirty-three; this indicates either several migrating groups or large migrating groups with many unrelated females (cf. Morell 1990; 440 in Campbell 1990).

Another paper just out suggests an eastern flow from Beringia (and Alaska, if you will), into Asia.

“Linguistic Phylogenies Support Back Migration from Beringia to Asia”, Sicoli and Holton march 12, 2014 available at Gisele Horvat’s “Human Migration” Blog.

Have a Great Day Everyone!

terryt said...

@ German:

"There's no data whatsoever to support this interpretation. 1. West Eurasian BLUE and East Asian ORANGE components are not found in America. The Amerindian component is all over Eurasia, in ancient remains and in modern populations".

So, 'West Eurasian BLUE and East Asian ORANGE' yet even though 'Amerindian component is all over Eurasia' it forms a minotrity in both West Eurasia and East Asia. How do you accomodate that fact? Surely if both West Eurasians and East Asians sprang from the Amerindians we should find both with a very substantial proportion of Amerindian component. Yoy attempts at explaining that anomaly are completely inadquate.

@ Alvah:

"Another paper just out suggests an eastern flow from Beringia (and Alaska, if you will), into Asia".

'Alaska', I won't. The paper specifically sattes 'Beringia' before sea level rose and separated America and Eurasia.

"Finally, as persuasively argued by Rebecca Cann (this volume), the mitochondrial DNA evidence indicates that there were at least eleven lineages from which American Indians descended, perhaps thirty-three; this indicates either several migrating groups or large migrating groups with many unrelated females (cf. Morell 1990; 440 in Campbell 1990)".

But we're still talking 'into America' not 'out of America'. Even if the original Amerindians comprised thirty-three haplogroups those thirty-three are all part of just 4 main clades and one minor one (X):

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000829

Quote:

"The mitochondrial DNA haplogroup nomenclature that is widely used today in population and medical genetics, forensic science, and in other interdisciplinary studies, traces back to the analysis of Native American populations by Torroni et al. [1],[2]. The first four letters of the phylogenetic alphabet for mtDNA haplogroups - A-D - were coined to refer to just four founding haplogroups that exhibit virtually all North and South American mtDNA diversity".

Som the modern phylogeny is actually based on Amerindian haplogroups. That is obvious, of course, because they have always been labelled 'A', 'B', 'C' and 'D'. Perhaps that has led to your confusion concerning the basal position of various haplogroups. Further quote:

"No more than four major pan American and three minor North American founding mtDNA haplotypes (A2, B2, C1, D1 and X2a, D2, D3, respectively) have been convincingly established in previous studies of control region sequence, RFLP markers and 30 complete mtDNA genomes (Table 1) [1]–[14]. The paucity of established founding mtDNAs suggests that the number of migrants that initially peopled the Americas was relatively low".

terryt said...

Sorry:

"'Linguistic Phylogenies Support Back Migration from Beringia to Asia', Sicoli and Holton march 12, 2014 available at Gisele Horvat’s 'Human Migration' Blog".

The full paper is here in case you haven't read it:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0091722

Alvah said...

What we have here are baby steps by the authors of both recent papers concerning Beringia. The fact remains that the Americas south of the Ice sheets harbored Humans during the last Pliestocene epoc, at the least. The authors are limiting the discussion by not looking further south for the source of the settlers that made the "back migration" into Asia. The Papers do not cite the Boas data and in personal conversations with some geneticists over the years, including recently in Santa Fe, are apparently oblivious to the conclusions of the Jesup Expedition. They are not cherry picking in this case, they simply don’t know or are ignoring the data as published. Dr. Steven Ousley cited from his article in Human Biology in this Blog, and German Dziebel’s Book, (and my own publication Human Biology 1998) seem to be missing in their archives. How can this be(?), if you Blog Franz Boas and recognize his stature you have to just wonder. Here is a clue as to why this is just so. The Expedition was funded by Jesup and the results were not to his liking. As a consequence, no definitive paper was published, period. Part of the Boas revival that took place in the late 1990’s had to do with the Centennial marking of the five plus year Expedition. Funny or sad how science works sometimes.

German Dziebel said...

@Tobus

"The gap means that being "closest" is not the same as being "close". Failing to consider the gap means you might be fooled into thinking Amerindian demographic structure is somehow similar to Neanderthal/Denisovan demographic structure, when in fact was nothing like it."

I have to disappoint you: my opinion that Amerindians have a mid-Pleistocene-like population structure is pretty standard among population geneticists. See Zhivotovsky's (with a further link to Cavalli-Sforza's opinion) quote at
http://anthropogenesis.kinshipstudies.org/2013/10/out-of-america-at-the-paleoamerican-odyssey-conference-october-17-19-2013/. Denisova and Altai Neandertal data just confirmed what people originally gathered from classical markers.

"1. Amerindian isolation and lack of admixture makes it a standout target for ADMIXTURE logic, so it's expected that shared DNA will be seen as "Amerindian" before "European" or "East Asian".

Hilarious! You are imputing software with a flaw of finding the truth. How is that Bible-reading class with TerryT working out for you?

"2. Amerindians have much more "East Asian" ancestry than MA-1 ancestory."

Wrong! Modern East Asians have more Amerindian ancestry than modern West Eurasians. At 24,000 YBP it was the opposite.

"3. All modern Europeans have a degree of ANE ancestry."

Yes, and ANE ancestry reaches it's peak in Karitiana, which makes it Amerindian ancestry.

"4. Why would you expect East Asians to be closer to Anzick than to Amerindians on the f3 stats? They had already diverged from the lineage before Anzick so the should have roughly the same amount of shared drift with both Anzick and Amerindians."

But this lineage before Anzick must have been East Asian, under your scenario. So we would expect Anzick to be 10,000 years closer to East Asians than modern Amerindians. But the fact is it's not. It's more MA-1-like and MA-1 is not East Asian.

5. I don't know you mean by "variable affinity to Amerindians". they are in pretty much the same relative positions on all the Amerindian axes.

The relationship of East Asians and West Eurasians is flipped depending on whether Karitiana or MA-1 are used as an anchor. Also, on some ADMIXTURE charts Amerindian are pure BLUE (West Eurasia) and pure YELLOW (East Asian) at lower Ks.

"... are you making the old "affinity to MA-1 is affinity to Amerindians" mistake again?"

Mistake? It's the most logical interpretation of the data because MA-1 is the closest to modern Amerindians. The ball is in your court to prove that it is not. And don't use Olalde EDF 5 because EDF 5d shows that LB is Amerindian on the MA-1 axis.

"The scenario of MA-1 contributing DNA to Amerindians is most certainly consistent with the known facts."

Too bad, you can't name a single such "fact." Your 1-5 list above is not facts. It's a bucket list for the old, stale, pseudoscientific paradigm of the "peopling of the Americas."

"Anzick is definitely closer to East Asians than he is to Europeans."

Considering that Anzick from Montana is more different from East Asians than East Asians are from West Eurasians, it's East Asians who are closer to a 10,000 year old Amerindian sample. This is consistent with a model whereby modern East Asians are a late offshoot of Northern Amerindians.

"Yeesss... because genes have a built-in GPS that tells them to mutate for each kilometre they travel. It's time, not distance that caused this genetic divergence."

Your ignorant comments just keep coming. Worldwide genetic variation is known to be proportionate to the geographic distance between Africa and America. This is one thing that's completely uncontroversial.

Alvah said...

I was in the Wallace Lab in 1990 when TG Schurr’s genetic data collection from Eskimo/Aleut’ Populations arrived via FedEx. I suggested to him then that they would mimic Amerindian Populations. He asserted ‘that it would be highly unlikely as this would require (2) two “Dramatic Founding Effects” with few if any of the more common Asian haplotypes being lost from both Asian migrations.’ Well, I called him a couple of weeks later and asked him what the results were. He told me, of course, that the results were confidential but that “I was not wrong.”

More from Steven Ousley Human Biology 1995

"With larger samples the picture becomes more complicated, as demonstrated by a tremendous time depth (78,000 years) for some Nuu-Chah-Nulth mtDNA lineages and relationships that contradict linguistically based waves (Ward et al. 1991, 1993). In addition, studies have shown that Amerindians have a relatively high amount of mtDNA variation compared with the rest of the world (Horai et al. 1993), especially Siberia (Torroni, Schurr et al. 1993)(p. 431)."

"Drucker (1955) saw a combination of Eskimo and Aleut cultural traits in Wakashan speakers, who also lacked significant cultural influences from the interior of North America. In contrast, the Haida, Tlingit, and Tsimshian showed greater interior influences and were the result of later population movements to the coast. Ritual autopsies were conducted by Aleuts, some south Alaskan Eskimo, Nootka, and many Koryak and Chukchi groups (Drucker 1955; Jochelson 1908)(p. 433)."

"Ethnographic studies also emphasize the minor role of language (and thus tribe) in population relationships on the Northwest Coast. Instead, socioeconomic organization was more important for what were essentially interactions on the village level. Clans included speakers of different languages and dialects (p. 433)."

"The diversity of American languages is remarkable. Austerlitz (1980) calculated that there are 71 genetic units (families and isolates) represented in North America and only 37 in continental Eurasia, South America could have as many as 70 more. Clearly, linguistic diversity alone cannot be used to date settlement times (p. 434)."

"As Boas noted, there is greater morphological diversity on the Northwest Coast than in northeast Siberia (p. 447)."

To place all this diversity in Beringia instead of the Americas is a reach but the authors don’t want to bend the branch as if they go much further we are going to touch new ground or brake the Ice.

The Na-Dene in eastern Siberia sets the stage for the Eskimo wedge theory. Once we get past the fact that Amerindian markers are in Asia because of recent genetic/linguistic correlations emanating from the Americas the big picture as to why this is the only link to a founding effect from Asia will come to light.

Alvah said...

Another blast from the past 1993
same interpretation as current analysis...

Gerald F. Shields, Andrea M. Schmiechen, Barbara L. Frazier, Alan Redd, Mikhail I. Voevoda, Judy K. Reed, and R.H. Ward mtDNA Sequences Suggest a Recent Evolutionary Divergence for Beringian and Northern North American Populations Am. J. Hum. Genet. 53:549-562, 1993

Low values for pairwise sequence differences within and between the far-flung Circumarctic populations contrast with higher difference values for the three Amerind-speaking tribes localized to the Pacific Northwest. . . . Hence, the most plausible explanation for these observations is that the evolutionary radiation of these Circumarctic groups, in concert with the evolution of their mitochondrial lineages, occurred within a shallow time depth. Low sequence diversity, coupled with the broad geographic distances over which some Circumarctic populations (e.g., Alaskan Inupiaqs and West Greenland Eskimos) have become established, suggests that the establishment of these far-flung populations occurred during a relatively short period of time. By contrast, the mtDNAs of Bella Coola, Nuu-Chah-Nulth, and Yakima are broadly divergent, even though the present geographic distribution of these people is confined to a relatively small region. This suggests that these Amerind tribes are much older than the Circumarctic tribes and have undergone considerable localized genetic differentiation. . . . By contrast, most mtDNAs of Circumarctic individuals either are identical or differ from one another by only a few (0-3) substitutions. . . . Moreover, lineages observed in distinct populations are intermingled among the branches of the tree, with no obvious clustering of lineages by the geographic location, or linguistic affiliation, of the tribe from which they were ascertained. For example, individual lineages of Chukchi, West Greenland Eskimos, Athapaskans, and Haida are scattered throughout the tree. This pattern is exactly what would be expected for populations which have recently undergone a demographic expansion and which are in the early stages of evolutionary divergence. (pg. 558)
All three instances of lineage sharing (lineage 11 found in Haida and Alaskan Athapaskans; lineages 60 and 61 found in Alaskan Athapaskans and West Greenland Eskimos) involve lineages which are situated on nodes of the molecular phylogeny and thus appear to be ancestral. Hence, we interpret the occurrence of these lineages in multiple populations as indicative of common ancestry rather than of recent admixture. . . . Buch (1979) suggested an early association between Alaskan Inupiaqs and Athapaskans on the basis of archaeological finds, and Dumond (1987) suggests that the archaeological distribution of blades and microblades is a reflection of extensive cultural ties between Eskimos and groups to the south. . . . Alternatively, as suggested by the mitochondrial data, all Circumarctic populations had their genetic origins about the same time, and the cultural differences that subsequently occurred were accompanied by relatively little biological differentiation. (pg 559-560)


Tobus said...

@German:
my opinion that Amerindians have a mid-Pleistocene-like population structure is pretty standard among population geneticists. See Zhivotovsky's (with a further link to Cavalli-Sforza's opinion) quote at
http://anthropogenesis.kinshipstudies.org/2013/10/out-of-america-at-the-paleoamerican-odyssey-conference-october-17-19-2013/.


Yes German, citing your own work misinterpreting what one other person said makes something "standard among population geneticists".

You are imputing software with a flaw of finding the truth.

The flaw is not in the software, it's in your literal interpretation of it, read http://dalexander.bol.ucla.edu/preprints/admixture-preprint.pdf for an understanding of exactly what the results indicate and how they are formulated. Note that the experts in the field don't take the results literally, as stated in the Anzick paper: "It is important to note that the five components do not imply five ancestral populations... Instead this analysis reveals that the genetic structure ... is best described in terms of five components". Admixture gives us the "best description" in terms of the selected number of components - this doesn't mean what it presents is a 100% accurate or definitive ancestry.

Wrong! Modern East Asians have more Amerindian ancestry than modern West Eurasians.

Yes German, using your theory as a fact to prove your theory is a valid logical argument.

Yes, and ANE ancestry reaches it's peak in Karitiana,

No, it reaches it's peak in Central/South Asians and Europeans. The Karitiana "peak" is only in the f3 stats which measure shared drift, not genome-wide affinity.

But this lineage before Anzick must have been East Asian, under your scenario. So we would expect Anzick to be 10,000 years closer to East Asians than modern Amerindians.

If the time of East Asian/Amerindian divergence was 24kya+ and Anzick is at 11kya, then Anzick's distance to modern East Asians in terms of branch length is 35kya, 3 times higher than his 11kya distance to Amerindians.

The relationship of East Asians and West Eurasians is flipped depending on whether Karitiana or MA-1 are used as an anchor.

The relationship between East Asians and West Eurarians is not measured on either of the MA-1 or Karitiana axes. As I thought, this is just more nonsense from not understanding how the f3 plots work.

Mistake? It's the most logical interpretation of the data because MA-1 is the closest to modern Amerindians.

East Asians are closer to modern Amerindians than MA-1 is. MA-1 has more modern Central/South Asian and European DNA than he has Amerindian. Affinity to MA-1 does not imply affinity to Amerindians.

It's East Asians who are closer to a 10,000 year old Amerindian sample

Yes as I first said, Anzick requires the North/South Amerindian lineages to be very similar at 11kya and closer to East Asians than Europeans. This makes Amerindian gene flow into the not-at-all-East-Asian MA-1 very hard to reconcile, yet makes perfect sense if the gene flow went the other way.

Worldwide genetic variation is known to be proportionate to the geographic distance between Africa and America

Yes, but as you'd know if you ever actually studied science, correlation is not causation.


terryt said...

@ German:

"How is that Bible-reading class with TerryT working out for you?"

Just fine, thank you. Much more closely aligned to reality than anything you've proposed.

"on some ADMIXTURE charts Amerindian are pure BLUE (West Eurasia) and pure YELLOW (East Asian) at lower Ks".

Exactly what we would expect to see if Amerindians are a hybrid between the other two populations.

"Worldwide genetic variation is known to be proportionate to the geographic distance between Africa and America".

According to Cavalli-Sforza's first PC of the world the greatest difference is between Africa and Australia. America pops out at the second PC. Then joins Africa at the third.

@ Alvah:

"What we have here are baby steps by the authors of both recent papers concerning Beringia".

So you're taking huge strides into the abyss.

"The fact remains that the Americas south of the Ice sheets harbored Humans during the last Pliestocene epoc, at the least".

The 'fact' is that the Pleistocene lasted until some 11,000 yeasr ago:

http://en.wikipedia.org/wiki/Pleistocene

Quote:

"The Pleistocene /ˈplaɪstəsiːn/ (symbol PS[1]) is the geological epoch which lasted from about 2,588,000 to 11,700 years ago, spanning the world's recent period of repeated glaciations".

As far as I'm aware no-one denies humans were in America by the end of the Pleistocene, and so you've introduced a red herring here.

"Dr. Steven Ousley cited from his article in Human Biology in this Blog, and German Dziebel’s Book, (and my own publication Human Biology 1998) seem to be missing in their archives".

Have you consisdered the possibility they may be missing for a reason?

"the most plausible explanation for these observations is that the evolutionary radiation of these Circumarctic groups, in concert with the evolution of their mitochondrial lineages, occurred within a shallow time depth".

How does that demonstrate an American origin? The 'Circumarctic groups' presumably have very little to do with the settlement of America apart from the very far north. We can be sure humans reached the very far north of Eurasia/America no more than some 6000 years ago because mammoths survived on Wrangel Island until that time:

http://en.wikipedia.org/wiki/Mammoth

Quote:

"Until recently, the last woolly mammoths were generally assumed to have vanished from Europe and southern Siberia about 12,000 years ago, but new findings show some were still present there about 10,000 years ago. Slightly later, the woolly mammoths also disappeared from continental northern Siberia.[18] A small population survived on St. Paul Island, Alaska, up until 3750 BC,[2][19][20] and the small[21] mammoths of Wrangel Island survived until 1650 BC.[22][23] Recent research of sediments in Alaska indicates mammoths survived on the American mainland until 10,000 years ago".

Now I know someone is going to complain that there is no evidence humans were involved in mammoth extinction but that stance involves ignoring a considerable amount of evidence.

"Low sequence diversity, coupled with the broad geographic distances over which some Circumarctic populations (e.g., Alaskan Inupiaqs and West Greenland Eskimos) have become established, suggests that the establishment of these far-flung populations occurred during a relatively short period of time".

Yes. Starting some 6000 years ago.

"This suggests that these Amerind tribes are much older than the Circumarctic tribes and have undergone considerable localized genetic differentiation"

Of course they are 'much older than the Circumarctic tribes'. They live in a much more amenable environment.

"This pattern is exactly what would be expected for populations which have recently undergone a demographic expansion and which are in the early stages of evolutionary divergence".

Exactly.

German Dziebel said...

@Tobus

"Yes German, citing your own work misinterpreting what one other person said makes something "standard among population geneticists".

You've lost your mind. I didn't misinterpret anything. I was hanging out in Zhivotovsky's office as he was wring that paper. And we talked a lot about this specific point. Cavalli recommended to him South Amerindians as a reference population because of their "archaic" genetic structure. This is something that's pretty well established among geneticists who grew up studying classical markers.

" read http://dalexander.bol.ucla.edu/preprints/admixture-preprint.pdf for an understanding of exactly what the results indicate and how they are formulated. Note that the experts in the field don't take the results literally, as stated in the Anzick paper: "It is important to note that the five components do not imply five ancestral populations... Instead this analysis reveals that the genetic structure ... is best described in terms of five components". Admixture gives us the "best description" in terms of the selected number of components - this doesn't mean what it presents is a 100% accurate or definitive ancestry."

The article you linked, which I know very well, is entitled "Fast Model-Based Estimation of Ancestry in Unrelated Individuals." But you are telling me that ADMIXTURE doesn't measure ancestry. I understand reading the Bible has made you spoiled and lazy but at least make an effort to finish reading the title of the paper you're linking to.

"Yes German, using your theory as a fact to prove your theory is a valid logical argument."

You are mumbling now...

"The relationship between East Asians and West Eurarians is not measured on either of the MA-1 or Karitiana axes. As I thought, this is just more nonsense from not understanding how the f3 plots work."

Just because you invented your own way of reading f3 plots doesn't mean you started making any sense.

"No, it reaches it's peak in Central/South Asians and Europeans. The Karitiana "peak" is only in the f3 stats which measure shared drift, not genome-wide affinity. "

Do you even understand what you're talking about? You've been spamming this thread for awhile but now it's becoming really annoying.

"Yes as I first said, Anzick requires the North/South Amerindian lineages to be very similar at 11kya and closer to East Asians than Europeans."

You said it wrong. Anzick is closer to MA-1 (who doesn't have East Asian ancestry) than other Amerindians, and both Anzick and modern Amerindians are more divergent from East Asians and West Eurasians than East Asians and West Eurasians are from each other.

"This makes Amerindian gene flow into the not-at-all-East-Asian MA-1 very hard to reconcile, yet makes perfect sense if the gene flow went the other way."

Another mumbo-jumbo from Tobus, the Bible Reader.

"but as you'd know if you ever actually studied science, correlation is not causation."

I know you're trying to sound "scientific" but what does the correlation vs. causation distinction have have to do with anything we're talking about?

Alvah said...

The initial Peopling of the eastern Hemisphere must have a progenitor population and an archaeological signature that was basal to the evolving behavior specializations accompanying the onset of the Asian Late Paleolithic, The African Later Stone Age and the European Upper Paleolithic. These new definitions for a modern Paleolithic suggest a new species not descendant of earlier multi-continental dispersals associated with Homo erectus groups. Interbreeding or environmental factors led to similatities derived from the colonization of new territories. The fact remains that these 0-1-5% new mutations were not ancestral to the original pure Homo sapiens state. Behaviorally the issue is much the same.

Pilbeam, David; In Major topics in Primate and Human Evolution, editors Wood, Martin, and Andrews, published by Cambridge (Cambridgeshire) New York 1986. pg. 335.

"Whatever the exact nature of the behavioral differences between modern humans and their ancestors, and of the transition between them there is a plausible case to be made for the argument that the biobehavioral gap was wide, that 'archaic' human behavior was different from the behavior of anatomically modern groups, and that we see in the 'archaic' the final representatives of a very long phase of human evolution, during which only limited changes took place... A case can be made that the nomen H. sapiens should apply only to hominids for which modern behavior patterns can reasonably be inferred: another name would then be needed for 'archaic' H. sapiens [Homo erectus] (pg 335).”

More from genetic studies from the last millennium;

Satoshi Horai, Rumi Kondo, Yuko Nakagawa-Hattori, Seiji Hayashi, Shunro Sonoda, and Kazuo Tajima Peopling of the Americas Founded by Four Major Lineages of Mitochondrial DNA in Mol. Giol. Evol. 10(1):23-47, 1993
Furthermore, the overall nucleotide diversity among the Native Americans is estimated to be 1.29%, which is slightly smaller than the value 1.44% from the total human population including Africans, Europeans, and Asians. (pg. 27)

O. Rickards, M. Tartaglia, C. Martinez-Labarga, and G.F. DeStefano Genetic Characterization of the Cayapa Indians of Ecuador and Their Genetic Relationships to Other Native American Populations, in Human Biology, April 1994, v. 66, no. 2 pp. 299-322

"The last common maternal ancestor of all Amerinds examined may have lived as long ago as 154,000 years B.P., and divergences within the four "clusters" may be as old as 53,000 years. This potentially lengthy period of time coupled with the retention of ancient genetic polymorphisms in geographically distant human groups (Takahata 1993) suggests that further investigations are warranted to achieve a deeper understanding of the peopling of the Americas. (pg. 315)"

Only the Americas offer’s enough geographic isolation compliment greater Amerindian diversity. A Beringian Refume hypothesis complicates the big picture but points us in the right direction, out of the Americas.

*Mother Tongue Issue 22, May 1994, Harold Fleming

“. . . is his [Merriwether] conclusion that Eskimos, Athapaskans and Amerind all go back to a single founding lineage before they join the rest of the world. (pg. 58)
At the moment, he seems to be saying that the three native American stocks are more like each other than they are like Asians but that the whole lot relates to eastern Asians more than to the rest of humanity. (pg. 58)”

terryt said...

"Yes German, using your theory as a fact to prove your theory is a valid logical argument".

That has been the only consistent element in the logic both German and Alvah use.

Alvah said...

@TerryT “As far as I'm aware no-one denies humans were in America by the end of the Pleistocene, and so you've introduced a red herring here.”

I did not say ”the end of the Pleistocene” you have again misplaced reality and implied something I did not say, you have no quality control and I now know why you have to be so often corrected by German Dziebel.

I said “"The fact remains that the Americas south of the Ice sheets harbored Humans during the last Pliestocene epoc, at the least".

This implies that the Holocene migration at the terminal edge of the last Glacial epoch was “out of the Americas” and the formation of Circum-Arctic Sea Mammal Hunting Cultures, was spawned by Amerindian/ later Eskimo populations. No “Red herring here” only you ‘eating Crow.’

"This suggests that these Amerind tribes are much older than the Circumarctic tribes and have undergone considerable localized genetic differentiation" Say Shields et al. said, please…

@Terryt said “Of course they are 'much older than the Circumarctic tribes'. They live in a much more amenable environment.”

Well, yes, they/we emanate from this much more “amenable environment.”

You quote my Quote from Shield et al. again with no reference to them…

"This pattern is exactly what would be expected for populations which have recently undergone a demographic expansion and which are in the early stages of evolutionary divergence". You missed the population they were referring too, see here…

“For example, individual lineages of Chukchi, West Greenland Eskimos, Athapaskans, and Haida are scattered throughout the tree. This pattern is exactly what would be expected for populations which have recently undergone a demographic expansion and which are in the early stages of evolutionary divergence. (Shields et al. pg. 558)”

Unless, as you said, “Exactly”, was to imply that Native Americans are their ancestors, which would imply a change in your thinking that would now acquiesce to what German and I have been saying all along. But this is not the case as…

You @Terryt said… “How does that demonstrate an American origin? The 'Circumarctic groups' presumably have very little to do with the settlement of America apart from the very far north. We can be sure humans reached the very far north of Eurasia/America no more than some 6000 years ago because mammoths survived on Wrangel Island until that time:”

Let the readers of this blog know when referencing quotes from 1. a reference, 2. my own statement, 3. or one of German’s, please. BTW, Shields et al. were not talking about Amerindians but Circumarctic and Siberian populations, so please don’t be so scheming.

You are wasting my time in responding to your diatribe. You and Tobus are not judge, jury, and executioners, as you assert, “case closed.”

Now for some facts:
Andrew Merriwether, et al. 1995. "Distribution of the Four Founding Lineage Haplotypes in Native Americans Suggests a Single Wave of Migration for the New World"

“it is unlikely that multiple migrations from the same area would continuously choose the same four lineages from a subset of the lineages available in the parent population. Clearly, examination of contemporary Asian and Siberian populations indicate that these four lineages are not the only lineages present."

"The current Native residents of Alaska and Siberia may be descendants of more recent migrations from the Siberian side of the Bering Strait, or from migrations back into the area from within the New World (Merriwether et al. 1995 pg. 424 )."

Merriwether et al. suggest that it is implausible for the more common Asian specific haplotypes to all have been lost, time and time again, in the founding Amerindian population(s) and as-well, the later populations comprising the Inuit and Athapascans. Merriwether et al. suggest that separate migrations into the Americas for Eskimo and Athapaskans carrying the same "rare" Asian mutations as the Amerinds, themselves, is not tenable.

terryt said...

"Whatever the exact nature of the behavioral differences between modern humans and their ancestors, and of the transition between them there is a plausible case to be made for the argument that the biobehavioral gap was wide, that 'archaic' human behavior was different from the behavior of anatomically modern groups"

The more scientists study those archaic humans the more obvious it become that that statement from 1986 is very wrong. The difference is nowhere near as great as what people liked to imagine.

"I did not say 'the end of the Pleistocene' you have again misplaced reality and implied something I did not say"

OK. What you actually wrote was:

"The fact remains that the Americas south of the Ice sheets harbored Humans during the last Pliestocene epoc, at the least".

Last Pleistocene, late Pleistocene, end of the Pleistocene, what's the difference?

"Well, yes, they/we emanate from this much more 'amenable environment'".

And that 'amenable environment' is circum-Polar? Come on.

" Shields et al. were not talking about Amerindians but Circumarctic and Siberian populations, so please don’t be so scheming".

So they were saying nothing to support 'out of America'.

"Merriwether et al. suggest that it is implausible for the more common Asian specific haplotypes to all have been lost, time and time again, in the founding Amerindian population(s) and as-well"

You are conveniently forgetting that since 1995 is has become obvious that many of those 'more common Asian specific haplotypes' did not reach the northern parts of East Asian until after the Americans had passed through.

Alvah said...

This post will get back to the special circumstance that led to a Childs, Anzick I’s, contribution to this forum.

From;Clark, G.A. NAGPRA, the Conflict between Science and Religion, and the Political Consequences. Society for American Archaeology (1998), Vol. 16, No. 5., pp. 22-25.

“Science can be defined as a collection of methods for evaluating the credibility of knowledge claims about the experimental world. Science does not pretend to certainty; it only seeks better and better approximations of it. Scientific conclusions are continuously subjected to critical scrutiny. Science is, therefore, self-correcting. No topic or question is "off-limits" to science. The only thing that is antithetical to the scientific worldview is dogma. Dogma is the stuff of religious belief. From the standpoint of science, the illusion of absolute, unchanging truth is the most pernicious of vanities (p. 22).”

"Science is not "about" religion, however. It is not about moral truth, although it can sometimes help us in our struggle to reach appropriate moral decisions. Clearly, humans did not evolve in this hemisphere. Indians haven't always been here, regardless of what their origin myths might say (p. 24).”

Another perspective is offered from a Ph’D Native American, Joe Watkins who has tried to calm the storm of controversy.
From; Watkins, J. Native Americans, Western Science, and NAGPRA. Society for American Archaeology (1998), Vol. 16, No. 5., pp. 22-25.

Like the philosophical tree in the forest, if "a precontact aboriginal culture of the New World vanishes without a trace," and there is no "Western observer there to record information about them," do they make a sound (p. 25)?

“We, as anthropologists, are standing on the edge of a forest with an almost impenetrable growth in front of us. We can try to bulldoze our way through it, but we will destroy all that might be ahead of us; we can try to circumvent the forest, and run the risk of losing our collective lives in the resultant uncharted wilderness; or we can look for the path between the trees, moving carefully, taking the journey one step (and roadblock) at a time. An army does not pass through a forest as a single body, but rather as an allied group of individuals. We must be an army on a common campaign–an army of individuals working to reach a common goal ( p. 25).”

Lets look at this scientifically, holding that we were descendants of Neadertals is no different than Europeans wanting the same thing Native Americans want, to be included in the search for human origins. The Clovis First hypothesis is now considered Dogma and the requiem of this dead horse should be applied to why the null hypothesis is relevant. Science is bound by our own predetermined consensus that very often turns into reality shifts when once unexplained or unheralded evidence makes its way into the forum.
Let’s examine Evidentialism.

From; Vieland, V.J., and Hodge, S.E. Book Review of Statistical Evidence: A Likelihood Paradigm, by Richard Royall. Am. J. Hum. Genet. (1998), 63:283-289.

Most of current statistical practice is based on frequentist principles–notably, on the Neyman-Pearson paradigm for hypothesis testing or on Fisher's conception of significance testing. Evidentialism is undoubtedly the least familiar school of statistical thought, both within the field of statistics itself and, certainly, among consumers of the statistical literature. This remains true, at least in part, because journal editors and peer reviewers almost invariably ask that statistical results be reported in familiar frequentist terms. But our predilection for the familiar notwithstanding, evidentialism is, arguably, the only body of statistical theory that is fully consistent with the practice of science (pg283).

to be continued...

Alvah said...

Continuation of my last thread,

From; Vieland, V.J., and Hodge, S.E. Book Review of Statistical Evidence: A Likelihood Paradigm, by Richard Royall. Am. J. Hum. Genet. (1998), 63:283-289.

“To justify this extravagant claim, we need to consider the purpose of statistical analysis in scientific contexts. Evidentialism views the purpose of statistical inference as the measurement of the strength of evidence conferred by a given set of data in favor of one hypothesis over another. This may seem a wholly natural objective for scientific data analysis, and we will take it as a given that this is the objective that we are pursuing. But, in fact, much of standard statistical practice is based on a quite different conception of statistical inference–namely, as a set tools for decision making in the face of uncertainty. This latter objective need not in any way involve the concept of evidence (p. 284).”

*We then select the "best" testing procedure, one that minimizes the probability that we will fail to reject the null hypothesis when it is in fact false (the type II error rate) for the selected significance level (p. 284).”

"Some statisticians might prefer to talk about testing a "null" hypothesis without reference to an alternative hypothesis. As we have already seen, however, the law of likelihood expressly applies to comparisons between two hypotheses: evidence counts against one hypothesis only insofar as it favors the other. This insistence that any proper measure of evidence must involve two hypotheses rather than one is a cornerstone of evidentialist theory p. (284-285).”

Alvah’s comment: These examples of genetic factors could be applied to an American Wellspring or Out of America, when the shoe finds the right foot or Cinderella (the fairest hypothesis in the land) is invited to the ball or an invisible truth keeps popping up. If back migrationinto Asia from the Americas occurred than there is virtually zero genetic links to ancestors from the Old World for ancient Native Americans. Moreover, the existence of Mutational-Drift equilibrium and greater genetic diversity on the Tribal Level in Native Americans is “Relevant”.

Tobus said...

@German:
This is something that's pretty well established among geneticists who grew up studying classical markers

It's "pretty well established among geneticists" (including Cavalli and Zhivotovsky) that all modern humans came from Africa and that Native Americans migrated into America from an ancient East Asian population. Your misunderstanding is thinking that these experts' words support your Out of America theory... perhaps you understand this very well, and "intentionally misrepresent" would have been a better description.

The article you linked, which I know very well, is entitled "Fast Model-Based Estimation of Ancestry in Unrelated Individuals.". But you are telling me that ADMIXTURE doesn't measure ancestry...at least make an effort to finish reading the title of the paper you're linking to

As the title says, it doesn't "measure" ancestry, it "estimates" it (using a "maximum likelihood model" which you'd know if you'd got past the title). Try reading the actual content of the paper - you may learn something, although perhaps the maths is a bit beyond you?

-Skip a whole lot of ad hominen nonsense-

and both Anzick and modern Amerindians are more divergent from East Asians and West Eurasians than East Asians and West Eurasians are from each other.

That is simply not correct - East Asians are (much!) closer to Anzick/Amerindians than they are to West Eurasians, which is why PC1 comes out as West/East, not Eurasia/America. This is evident in EDF6 of the Anzick paper where Amerindians score significanly higher than any West Eurasians on the Han axis, and higher than any East Asians on the French axis.

This leaves us at the core of the problem - Anzick and modern Amerindians show a close affinity to each other and to modern East Asians, yet MA-1 shows affinity to Anzick/Amerindians but no affinity to East Asians. This pattern of modern and ancient genetic affinities is incompatible with a scenario of Amerindian admixture in to MA-1... the only scenario that fits is one where the MA-1 lineage contributed DNA to the modern Amerindian lineage.

what does the correlation vs. causation distinction have have to do with anything we're talking about?

You stated that geographical distance and genetic distance correlate and implied that there was some causal link between the two (your exact words were "East Asians are closer to Amerindians than West Eurasians because they are closer to them geographically." and then "Worldwide genetic variation is known to be proportionate to the geographic distance between Africa and America"). My point is that there is no direct causal connection between geographic and genetic distance, even though they may correlate to some degree - one is a function of movement, the other is a function of time. It's perfectly possible for populations to increase in genetic distance while staying in close proximity to each other (African genetic diversity is a good example of this).

It should also be taken a broader reference to your similar misassignment of causation to other correlations, like those you see on isolated axes in the f3 plots.

Tobus said...

@Alvah:
More from genetic studies from the last millennium

Do you think you can stop pasting these huge chunks of outdated information? We have much more reliable modern studies and it's these that you should be referring to. Genetics has come leaps and bounds in the last 10 years (and continues to do so), so you're not going to sway anyone with these largely obsolete references - all you are proving is that you are out of touch with the field.

terryt said...

"The only thing that is antithetical to the scientific worldview is dogma. Dogma is the stuff of religious belief"

'Dogma' is all we have heard from yoy and German.

"Clearly, humans did not evolve in this hemisphere. Indians haven't always been here, regardless of what their origin myths might say"

Exactly. You should read your own extracts. Yet both you and German insist humans did evolve in America.

"The Clovis First hypothesis is now considered Dogma"

Why do you keep banging on about 'Clovis first'? I have been prepared for some years to accept they were not the first Americans. However I am not prepared to accept the evidence indicates a particularly ancient human presence in America. Any 'evidence' for such is so infrequent as to indicate temporary human existence at most. In other words the populations were too small to become self-sustaining long term. The same phenomenon apparently occurred in New Zealand with some evidence of human presence nearly 2000 years ago yet it is obvious that the earlier populations failed to contribute genes to the population that arrived some 800 years ago.

Alvah said...

@Terryt said “The more scientists study those archaic humans the more obvious it become that that statement from 1986 is very wrong. The difference is nowhere near as great as what people liked to imagine.”

That is your opinion and that of a ‘few’ others who actually publish(ed) the stuff articulated, but here are others who see it as “replacement”, period, ( I could cite many as I have read the Journals and Books) but Binford personal conversations 1992-2011 have sufficed for me.

@Terryt said "The more scientists study archaic humans the more obvious it becomes that that statement from 1986 is very wrong. The difference is nowhere near as great as what people liked to imagine."

(google (look up in pre-computer terms),,, LR “Binford the New archaeology” for directions.

Then you @Terryt sight me as saying; "The fact remains that the Americas south of the Ice sheets harbored Humans during the last Pliestocene epoc, at the least".

@Terryt…. Last Pleistocene, late Pleistocene, end of the Pleistocene, what's the difference?”

I ask you Terry … “what’s the difference(?)”,

The Pleistocene implies the Entire Pleistocene (and you could add more), so we might say 2.5 million or more in the least. Your definition is not mine but again you misinterpret reality, and I ask you, respectfully, to hold yourself accountable for misquoting me again and again in the future as I now know that I can predict the future.

Please, Dr. Dienekes, I need you to address inconsistencies of your ‘ancient’ blogger @Terryt who is less than articulate when it comes to factual accounts of what is actually said by German or Myself (and “who” or what we cite, in this blog.

I like to use quotes from the past; as I am sure you would like those from your present contribution to use (in the Future). Discretion in discussions central to resolving our actual human origins as we progress towards that destination/goal requires discretion. While you have included German’s and my desperate appeal for scientific address, I ask for discipline.

Again, thank you for not emitting the simple concepts advocates German Dziebel and I (more recently and others) have introduced into your Forum. The Bering Land Bridge and the Bering Strait overlap. That there were human inhabitants in the Americas south of the Ice Age Sheets of ice during the Last Ice Age precludes a recent Holocene contribution from the Americas into Siberian et al. populations. No need for Beringian holdovers as the out of Americas alternative has greater linguistic and genetic support. It is not unidirectional, it is “out of the Americas”, over and over again (45ky and 12,000ky).
That language is written in blood has now been proven; let’s accept the evidence at face value and run with it not away from it……..

To be continued…

Alvah said...

Continued,

@Terryt “And that 'amenable environment' is circum-Polar? Come on.”

No the autochthonous environment is Equatorial (not an “'amenable environment' that is circum-Polar?.’”

Terryt, would you please just cease and desist in your misquotations/misinterpretations? You make non-science not sense! If you continue to miss-quote my statements I will appeal to a higher source for moderation to this Great Blog, Zeus.

Again, you, Terryt, and others including Tobus, over and over again, can-not help but look at singular directionality into the Americas when there is NO evidence for into the Americas. Please for the fifth or sixth or .. time, do not misinterpret what the heck we/I are/am implying. Am I getting too far from religious ideals or are Higher Primates from the Americas too animalistic for human progenitors? Might I offer that the Neandertal’s offer only a missing link and have for a hundred and fifty plus years since the publication of Darwins/Wallace’s natural selection argument from 1859. This is not a creationist’s argument, and I want to cut you ( @Terryt ) off at the pass on this. We and other advocates of an “Amerindian Wellspring” are not afraid of evolutionary theory; we are the only advocates of a status quo when it comes to the natural occurring emphasis on stasis over time. Although you may want to be the descendant of a Neandertal, (even though you act like one); it don’t make it so. You and the rest of humanity were once all living in the Americas. That your and Tobus’ nose/nostrils don’t point to the side does not exempt you from being sideways in respecting your elders.

with no quotations from the last millennium that are over 14 years ago and thus, irrelevant,
@Tobus said
@Alvah: More from genetic studies from the last millennium
Tobus said “Do you think you can stop pasting these huge chunks of outdated information? We have much more reliable modern studies and it's these that you should be referring to. Genetics has come leaps and bounds in the last 10 years (and continues to do so), so you're not going to sway anyone with these largely obsolete references - all you are proving is that you are out of touch with the field.”

No, that I have been in touch with the field from the ‘beginning of genetic studies’ (what a laugh, I got that ‘ ‘ from your pal Terryt), “’quote ‘unquote’” and that my quotes are compatible and in fact integral to current assessments of weaknesses and strengths and of accommodating the accumulating data. For instance, there are now many more mtDNAs lineages 15+ (see Tamm et al. 2007 and others) in the Americas that have no Old World ancestors to derive them from. Look at the papers that just came out from Hoffecker et al. 2014 and Sicoli and Holton 2014 this March on Dienekes and other’s sources see the G. Horvat’s “Human Migrations” Blog line. There is no inconsistency, only the concordance showing that “there is no resolution in sight” and the exclusion of Native Americans from the search for Modern human origins continues, unabated.

German Dziebel said...

@Tobus

"It's "pretty well established among geneticists" (including Cavalli and Zhivotovsky) that all modern humans came from Africa and that Native Americans migrated into America from an ancient East Asian population. Your misunderstanding is thinking that these experts' words support your Out of America theory... perhaps you understand this very well, and "intentionally misrepresent" would have been a better description."

Yes, it's a general belief. A mistaken belief, I would add. Here's an actual misrepresentation: Cavalli made Zhivotovsky use Amerindians as a living example of a putative African ancestor. That's how facts get shoehorned into an ideology. I'm just correcting the error and making it all fit nicely - Amerindians are a living example of an Amerindian ancestor of modern humans. If it looks like a duck and walks like a duck, it's a duck.

"As the title says, it doesn't "measure" ancestry, it "estimates" it (using a "maximum likelihood model" which you'd know if you'd got past the title). Try reading the actual content of the paper - you may learn something, although perhaps the maths is a bit beyond you?"

First you denied that the paper is about ancestry in the first place. Now, you've corrected yourself. You should thank me for bringing your own nonsense to your attention. What is it that you want to discuss in the main body of the paper that suggests that f3 statistics works only for one population at a time?

"-Skip a whole lot of ad hominen nonsense-"

I've noticed that you like to skip facts because they seem like nonsense to you. Both facts about human origins and facts about your intellectual "merits."

"That is simply not correct - East Asians are (much!) closer to Anzick/Amerindians than they are to West Eurasians>"

Go to Rasmussen et al. EDF 6. PINK is East Asia, BLUE is Europe, BLACK America. Take any chart whatsoever. Put on your prescription glasses, take a magnifying glass in your right hand and now... on the Y axis count the distance between PINK squares and BLUE squares and then between PINK squares and BLACK squares. Report back to me about what you found.

"My point is that there is no direct causal connection between geographic and genetic distance, even though they may correlate to some degree - one is a function of movement, the other is a function of time. It's perfectly possible for populations to increase in genetic distance while staying in close proximity to each other (African genetic diversity is a good example of this)."

I honestly don't know how what you're saying here is relevant. The fact that East Asians are now closer to Amerindians than West Eurasians fits well with their respective geographic distance to the New World. As MA-1 shows, 24,000 years ago Amerindians and West Eurasians were closer to each other than either of them to modern East Asians but again MA-1 is a geographically East Asian sample. So, Amerindians are closer to an Amerindian-derived ancient East Asian sample than they are to modern West Eurasians and they continue to be closer to Amerindian-derived modern East Asians than to modern West Eurasians. Africans is an odd example here because they likely absorbed "archaic" African substrates that pulled the resulting megapopulations away from each other.

terryt said...

"there is NO evidence for into the Americas"

There is far more evidence for into America that either of you have mounted so far for out of America.

"a ‘few’ others who actually publish(ed) the stuff articulated"

Almost all the latest studies emphasise the similarities.

"Binford personal conversations 1992-2011 have sufficed for me".

Twenty year old 'personal conversations'? I'm talkoing about tresearch released in the last year or two. As Tobus said, 'Do you think you can stop pasting these huge chunks of outdated information? We have much more reliable modern studies and it's these that you should be referring to'.

"my quotes are compatible and in fact integral to current assessments of weaknesses and strengths and of accommodating the accumulating data".

Not a single quote you have provided supports your theory in any way. They merely question assumptions held at the time the quoted comments were made. If you can provide some quote that supports your position please provide it so we can examine its validity.

"The Pleistocene implies the Entire Pleistocene (and you could add more), so we might say 2.5 million or more in the least. Your definition is not mine"

Our definition of the Pleistocene is much the same although I would say 2 miilion rather than the slightly longer period you suggest.

"I ask you, respectfully, to hold yourself accountable for misquoting me again and again"

You originally said 'last Pliestocene epoc' which can only mean late in the Pleistocene because there has been only one Pleistocene. And if you maen humans have been in America for the whole of the Pleistocene you are surely on your own with that one.

"No the autochthonous environment is Equatorial"

Are you now claiming that the environment around the Poles was tropical in the past? Come on. Let's have some semblance of reality around here.

"Higher Primates from the Americas too animalistic for human progenitors?"

No. They are simply, and obviously, more distantly related to humans than are the Eurasian apes, especially those from Africa. As far as I'm aware you are the only person to ever have suggested humans descend from American primates.

"That your and Tobus’ nose/nostrils don’t point to the side does not exempt you from being sideways in respecting your elders".

But it does exempt us and all other humans from having descended from New World monkeys.

"there are now many more mtDNAs lineages 15+ (see Tamm et al. 2007 and others) in the Americas that have no Old World ancestors to derive them from".

That is complete rubbish. No American haplogroup exists that cannot be placed in a wider Old World grouping.

"We and other advocates of an 'Amerindian Wellspring' are not afraid of evolutionary theory"

You simply ignore it.

Tobus said...

@German:
Yes, it's a general belief. A mistaken belief, I would add.

Yes, you would, but as we've ssen you wouldn't be able to provide an alternative model that works with the known genetic data.

What is it that you want to discuss in the main body of the paper that suggests that f3 statistics works only for one population at a time?

I don't know - the fact that each f3 stat only measures one population at a time against the axis maybe? "We computed an ‘outgroup f3-statistic’, where the deviation from 0 will be a function of the shared genetic history of two populations A and B in their unrooted history with the outgroup O".. where do you think it says anything about measuring distance to a population not even included in the formula?

I've noticed that you like to skip facts because they seem like nonsense to you.

Unfortunately you obscure relevant facts in your post with liberal amounts of personal attacks, spurious logic, subjective opinions and the occasional conspiracy theory. If there a genuine fact with actual relevance to the discussion that I've skipped over, please feel free to restate it - minus the superfluous posturing.

Go to Rasmussen et al. EDF 6. Take any chart whatsoever...Report back to me about what you found.

I found that none of Y-axes actually measure distance between Europans and East Asians, they only measure the distance of various populations to Anzick and modern Amerindian samples. In each case East Asians are closer to the Amerindians than Europeans are.

The first two set of X-axes however were much more informative, directly measuring distances to East Asians and Europeans respectively. In every case Amerindians were closer to the subject population than the East Asian or European sample, confirming the relationship diagram you agreed to above (WEu-------SAm-NAm---EAs). As we both know, East Asians are indeed closer to Amerindians than they are to Europeans.

I honestly don't know how what you're saying here is relevant.

It's not, you just said something stupid so I corrected you... it appears however that you really do believe there is some kind of GPS-sensor in DNA that allows it to mutate directly relative to distance... it's not relevant though, so let's drop it.

Alvah said...

@ATerryt
[(Quoting Clovis First advocate and NAGPRA cynic G. A. Clark 1998) from my blog of 3-19-2014:)] "The only thing that is antithetical to the scientific worldview is dogma. Dogma is the stuff of religious belief [(pg 22)]."

No Dogma exists in science also, it depends what side of the fence/hemisphere you consider was “Peopled”.

@Alvah already quoted Water et al. in this blog…;

““The Clovis theory, over time, acquired the force of dogma. “We all learned it as undergraduates,” [Michael] Waters recalled. “Any artifacts that scholars said came before Clovis, or competing theories that cast doubt on the Clovis-first idea, were ridiculed by the archaeological establishment, discredited as bad science or ignored (From: G. Gugliotta, Smithsonian Mag. February 2013).”
Monday, February 17, 2014 3:45:00 am


@Terryt 3-20 2014 “ 'Dogma' is all we have heard from you and German [’] . ”

You (and Tobus) are of corse entitled to your opinions, but like most of them they are presented without merit and do not encompass factual refutation of the simple facts we continue to present. You (guys) are not qualified to just say it isn’t so in the first place and not back up what you are attempting to refute, (consensus does not make it so, and the lack of consensus is at the heart of the Old World evidence, being a lack thereof).

Another ‘ancient’ quote is called for here;

From; Carbonell, E. and Vaquero, M. Behaviroal Complexity and Biocultural Change in Europe Around Forty Thousand Years Ago. Journal of Anthropological Research (1998),

“Two types of factors have had an impact on the scientific community in recent years. On the one hand, empirical and methodological factors have affected the whole range of data published. On the other hand, theoretical and conceptual perspectives underlie the most polemic aspects of the discussion and reflect the multiplicity of paradigms current in the discipline.
The theoretical struggle between the multiregional model (e.g., Wolpoff 1989) and the "Out of Africa" theory (e.g. Stringer and Andrews 1988) has highlighted the explanatory weakness of scenarios concerning the transformations which affected hominids and their activities during isotopic stage 3 (p. 374).”

“Were the association of the cultural innovations of the UP and [anatomically modern humans] AMH valid, the "Out of Africa" hypothesis would imply an African origin for the UP. However, with the data available at the moment, it seems that the UP did not appear in Africa before it did in other places (Ambrose and Lorenz 1990; Van Peer and Vermeersch 1990 (p. 378).”

Another example of your inability to refute what we are articulating; post Holocene back migration from the American side of the Earth is gaining momentum; you and the mistaken consensus, on the other hand, are slip sliding away as are the few preconceived ‘facts’ to refute what we, and now others in papers, now several weeks old, are very specifically articulating.

@Terrtt said
Clark in my earlier citation said;
"Clearly, humans did not evolve in this hemisphere. Indians haven't always been here, regardless of what their origin myths might say"

@Terryt said;
“Exactly. You should read your own extracts. Yet both you and German insist humans did evolve in America.”

This was a presentation of the Dogmatic consensus and represents a fair just so is’t so opinion I am prepared to tackle.

@Terryt said posted yesterday,

“Why do you keep banging on about 'Clovis first'? I have been prepared for some years to accept they were not the first Americans. However I am not prepared to accept the evidence indicates a particularly ancient human presence in America. Any 'evidence' for such is so infrequent as to indicate temporary human existence at most. In other words the populations were too small to become self-sustaining long term.”

Is that is why two thirds of the Worlds languages are found in the America?

terryt said...

"post Holocene back migration from the American side of the Earth is gaining momentum"

Is it? So you've managed to gather three of you together and are awaiting a fourth.

"You (and Tobus) are of corse entitled to your opinions, but like most of them they are presented without merit and do not encompass factual refutation of the simple facts we continue to present".

Neither of you have presented a single 'fact' to support your 'out of America' belief. Please do so or forget the whole thing. For example:

"Is that is why two thirds of the Worlds languages are found in the America?"

That is not a 'fact'. It is a matter of classification. I am yet to see a realistic account of the relationships between the various Indigenous American languages. It is beyond belief that they are all totally unrelated. Perhaps you or German can provide us with some account of their inter-relatedness.

"Carbonell, E. and Vaquero, M. Behaviroal Complexity and Biocultural Change in Europe Around Forty Thousand Years Ago. Journal of Anthropological Research (1998)"

There are no 'facts' in that extract that support your belief. The claim:

"The theoretical struggle between the multiregional model (e.g., Wolpoff 1989) and the 'Out of Africa' theory (e.g. Stringer and Andrews 1988) has highlighted the explanatory weakness of scenarios concerning the transformations which affected hominids and their activities during isotopic stage 3"

simply indicates uncertainty over some details of our evolution. It certainly does not support any out of America scenario. The currently available facts indicate the truth lies somewhere between a simple, single out of Africa and the old multiregional idea.

"Were the association of the cultural innovations of the UP and [anatomically modern humans] AMH valid, the 'Out of Africa' hypothesis would imply an African origin for the UP".

The author obvioulsy originally made the mistake of assuming an 'out of Africa' necessitated the involvement of a fully developed Upper Plaeolithic. It has now become obvious the Upper Paleolithic was a later development and happened outside Africa. In reality most 'facts' available to us indicate your belief is totally wrong, irrespective of whether the Clovis theory is dogma or not.

Tobus said...

@Alvah:
You (and Tobus) are of corse entitled to your opinions, but like most of them they are presented without merit and do not encompass factual refutation of the simple facts we continue to present.

Modern genetics has revealed a pattern of ancient and modern genetic affinity that is impossible to reconcile with an Amerindian ancestry of modern humans. It's you (and German) who have failed to present a workable model in this respect.

Is that is why two thirds of the Worlds languages are found in the America?

Where did you get this "fact" from? There are an estimated 7000 languages currenlty spoken in the world, and even the highest estimate of pre-Columbian American languages is around 2,000 (the lowest estimates are less than 1000). This is not "two thirds" by anybody's reckoning.

German Dziebel said...

@Tobus

"Yes, you would, but as we've ssen you wouldn't be able to provide an alternative model that works with the known genetic data."

My alternative model works demonstrably better with the actual data from genetics, linguistics and all other sciences than out-of-Africa. Out-of-Africa provides a mechanistic population model (serial bottleneck plus molecular clock) rooted in cultural myths (Africans are primitive, Amerindians are a dead end) - no engagement with the actual data. Hence, out-of-Africa is so hard to overcome.

"I don't know - the fact that each f3 stat only measures one population at a time against the axis maybe? "We computed an ‘outgroup f3-statistic’, where the deviation from 0 will be a function of the shared genetic history of two populations A and B in their unrooted history with the outgroup O".. where do you think it says anything about measuring distance to a population not even included in the formula? "

All formulas measure the same thing, namely "shared genetic history" (ancestry, admixture) between 3 populations. Every time just one population out of 3 changes and another run is done. You only believe mathematical formulas that measure distances between all populations at once? Just one humongous mathematical formula that sprang from the mind of God? What are your thoughts on classic pairwise comparisons that out-of-Africa was launched with? I don't really want to know. You are a waste of my time.

"Unfortunately you obscure relevant facts in your post with liberal amounts of personal attacks, spurious logic, subjective opinions and the occasional conspiracy theory."

I think I've done a good job balancing the two. My description of your intellectual merits was just as objective as my reading of charts. Both work in tandem for you or for anyone else who exhibits your brand of militant ignorance and latent creationism. You went as far as questioning mathematics in a crusade to combat a new scientific theory. I wish I could only use facts about the world to talk to people. But all too often I have to use facts about people who maintain beliefs about the world. Because they are not responsive to the facts about the world!

"it appears however that you really do believe there is some kind of GPS-sensor in DNA that allows it to mutate directly relative to distance."

Genetic distances match geographic distances on a global scale across all genetic systems. MA-1 shows that this trend it true for ancient samples as well, so that East Asian MA-1 is closer to Amerindians than West European LB. It doesn't matter if it's causal or just correlational. What matters is that it reflects population history.

Tobus said...

@German:
My alternative model works demonstrably better with the actual data

As demonstrated, it doesn't work at all with the actual data - it requires a deep divergence between North/South Americans that the actual data rejects, significant admixture between North/South Americans that the actual data rejects, or a population and demographic history similar to Neandertals which the actual data also rejects.

All formulas measure the same thing, namely "shared genetic history" (ancestry, admixture) between 3 populations

Not exactly, but nevertheless you are effectively claiming it measures "shared genetic history" between 4 populations, despite only 3 populations being included in the calculation. Remember that what is "shared" in one f3 stat may not be the same thing "shared" in another f3 stat with the same result, particularly if there is indirect ancestry and/or admixture involved (ie. where only part of the genome is "shared", as is the case with MA-1).

My description of your intellectual merits was just as objective as my reading of charts.

.. and just as wrong. If you think labelling someone as a "creationist bigot" and "bible-Reader" is objective then you might want to check the dictionary.


Alvah said...

@Tobus said 2-24-2014 “Yes, you would, but as we've ssen you wouldn't be able to provide an alternative model that works with the known genetic data.”

@Terryt Said;
"Neither of you have presented a single 'fact' to support your 'out of America' belief. Please do so or forget the whole thing."

Read below or go back to the beginning of this blog. Your statements regarding the facts as we have presented them(and the references to back them up), are simply bilious.

@Terryt Said;
"Is that is why two thirds of the Worlds languages are establish in the America?"

Terryt continues "That is not a 'fact'. It is a matter of classification. I am yet to see a realistic account of the relationships between the various Indigenous American languages. It is beyond belief that they are all totally unrelated. Perhaps you or German can provide us with some account of their inter-relatedness.”

That is the point; they have been in existence for so long and their diversity so great that “It is beyond belief that they are all totally unrelated.” German and I do not offer “a realistic account of the relationships between the various Indigenous American languages” except that the lack of inter-relatedness offers additional circumstantial evidence of great antiquity and that in accepting this, the problem is not in interpreting a recent “Peopling” of the Americas, but interpreting the anthropogenic reality. There is no answer except what German and I are suggesting, an autochthonous origins for Homo sapiens within the Americas, not Beringia, please.

“Greater genetic diversity” and “mutational drift equilibrium” discovered in studies of Tribal Amerindian Populations is factual, that researchers and you do not accept them at face value, is a fact. That several migrations from the Old World would continue to bring only rare Asian mtDNAs makes little sense. The interface between once isolated populations from the Americas and Asia in northeast Asia and Siberia has been articulated numerous times in this blog, whether you believe them to be factual, the fact is we are not alone in this concept, and researchers are now moving out of the America(s), step by step, by way of what they infer to as being, the American side of the Land Bridge. The both of you need please get off your high-horse and look from ground level. In time, “back-migration from the Americas” will Trump “out of Asia” and the there will be more than four players crossing this Bridge while the dummies will be left holding an empty hand.

I would agree with you that this dialog is getting know-where. Not that we are not trying.

German Dziebel said...

@Tobus

"As demonstrated, it doesn't work at all with the actual data - it requires a deep divergence between North/South Americans that the actual data rejects, significant admixture between North/South Americans that the actual data rejects, or a population and demographic history similar to Neandertals which the actual data also rejects."

You didn't demonstrate it. The actual data was in fact presented by me. And it supports out of America.

1. Amerindians have the closest demographic structure to Denisovans and Neandertals out of all modern human populations. They are consistently closer to them most Eurasians and all Africans.

2. Pan-American admixture is evident both in haploid markers and in the difference between Amerindians, on the one hand, and much more intergroup-diverse Denisovans and Neandertals.

3. African populations likely absorbed an archaic African substrate hence their "divergence" is way inflated.

"Remember that what is "shared" in one f3 stat may not be the same thing "shared" in another f3 stat with the same result, particularly if there is indirect ancestry and/or admixture involved (ie. where only part of the genome is "shared", as is the case with MA-1)."

The data is systematic enough to cancel this "possibility" or better to say sophism, out.

"If you think labelling someone as a "creationist bigot" and "bible-Reader" is objective then you might want to check the dictionary."

OK, I was being creative here. How do you like "science denier" and "cultural mythology ideologue"? Feel free to take a pick. But "scientist" and "high math" genius are off the table.

terryt said...

@ German:

"Amerindians have the closest demographic structure to Denisovans and Neandertals out of all modern human populations".

According to all the information I have seen that statement is completely wrong. Denisova is much more common in Papuans and Australian Aborigines.

"African populations likely absorbed an archaic African substrate hence their 'divergence' is way inflated".

I'm sure you have claimed MA-1 is admixed with something as well yet you consistently gloss over that necessity.

" How do you like 'science denier' and 'cultural mythology ideologue'? Feel free to take a pick".

I haven't yet decided which description best fits you and Alvah.

@ Alvah:

"In time, “back-migration from the Americas” will Trump “out of Asia” and the there will be more than four players crossing this Bridge"

So you admit the 'growing number of supporters' you have is just four at present.

"is factual, that researchers and you do not accept them at face value"

I wonder if there is a reason why scientists actually involved in the research do not accept your beliefs at face value.

"There is no answer except what German and I are suggesting, an autochthonous origins for Homo sapiens within the Americas"

We know for sure that is not correct. Humans do not descend from any New World monkey but from Old World apes. I'm beginning to assume you are actually a creationist and looking to discredit science.

"Read below or go back to the beginning of this blog. Your statements regarding the facts as we have presented them(and the references to back them up), are simply bilious".

I don't recall your having presented a single 'fact'. Nowhere have you presented anything other than quotes that don't actually support your claim, or you have quoted extensively from a presentation you made consisting entirely of opinions with no supporting facts.

"German and I do not offer 'a realistic account of the relationships between the various Indigenous American languages'".

with any supporting facts, or just opinions? And has any actual linguist supported your classification? Check this:

http://en.wikipedia.org/wiki/Indigenous_languages_of_the_Americas

Quote:

"There are approximately 296 spoken (or formerly spoken) indigenous languages north of Mexico, 269 of which are grouped into 29 families (the remaining 27 languages are either isolates or unclassified)".

Most of the 'others' are Californian evidently, and are extinct. South American languages remain to be classified. Because it is unlikely we can perceive language relationships beyond about 10,000 years ago and humans have been in America at least that long it is not surprising it is difficult to trace language relationships. Much work remains to be done.

"I would agree with you that this dialog is getting know-where. Not that we are not trying.

I give up. Neither of you are interested in facts supported by evidence. Just opinions based on distortion of the facts.

Tobus said...

@German:
1. Amerindians have the closest demographic structure to Denisovans and Neandertals

"Closest" doesn't necessarily mean "close" as you will well remember from your "typo".

In this case Amerindians have a population size several orders of magnitude greater than the archaics and a heterozygosity some 300% greater. Amerindian demographic structure is nothing like Neanderthals or Denisovans and much, much similar to other modern Eurasian populations. I've already pointed this out to you, your insistence on presenting this as "fact" when you known very well that it isn't true suggests dishonesty and subterfuge on your part.

2. Pan-American admixture is evident both in haploid markers and in the difference between Amerindians, on the one hand, and much more intergroup-diverse Denisovans and Neandertals.

This contradicts your own point 1 - you are now saying Denisovans and Neanderthals are very different to Amerindians demographically.

Amerindians have the lowest genetic diversity of all modern humans suggesting a recent divergence and bottleneck, and yet this genetic diversity is spread very unevenly across Amerindian sub-populations, indicating rapid expansion into unpopulated areas with little admixture between tribes. This genetic signature is impossible to reconcile with a theory of extremely deep divergence followed by extremely widespread and thorough admixture to obscure it.

I also have to question when this extensive admixture was supposed to have happened, there is no deep Amerindian divergence shown by any of the ancient or modern samples, yet in your theory it must have happened post-MA-1 for it to show up in the form of his Amerindian-but-not-East Asian affinity. So when did this supposed merge of North/South Amerindian take place?

3. African populations likely absorbed an archaic African substrate hence their "divergence" is way inflated.

"Likely" is not a fact - it's a theory or a speculation.

ADMIXTURE, PCA and f3 stats all confirm a distinct primary divergence between African and non-African populations. Unless you are suggesting that Africans are a majority non-Sapiens, archaic admixture cannot explain this lack of non-African affinity if Africans are indeed Amerindian-derived.

The data is systematic enough to cancel this "possibility"

Prove it. There are plenty of examples of populations appearing "close" on a single 3rd-party f3 axis when it is known from other data that they have no such affinity.

Feel free to take a pick.

How about we just talk about the data and leave the name calling to the kids in the playground. (And "science denier"? Honestly? You're the one denying the conclusions of mainstream science... but I guess actual scientists are "science deniers" too and you're the only one who does real science right?)

terryt said...

"So when did this supposed merge of North/South Amerindian take place?"

You're wasting your time asking such a question. Both German and Alvah steer well clear of confronting any contradictions and problems with their belief. And especially of actually having to say anything specific.

"'Likely' is not a fact - it's a theory or a speculation".

But they both specialise in confusing 'speculation' with 'fact'.

"Unless you are suggesting that Africans are a majority non-Sapiens"

From what I understand of his position that is exactly what he is suggesting. Racism?

"I guess actual scientists are "science deniers" too and you're the only one who does real science right?)"

That would appear to be his belief, but have you looked at his profile? No science in his background except for some anthropology, which he probably took to enhance his ability to manipulate groups through his advertising business, not because of its scientific element:

http://www.linkedin.com/pub/german-dziebel-ph-d/3/50b/689

German Dziebel said...

@Tobus

""Closest" doesn't necessarily mean "close""

There's a clear directionality from Africans as most different demographically from Denisovans and Neandertals down to Papuans and finally Amerindians. Amerindian are the closest. This is a pattern in the data. Predictably, as a science denier, you of course deny this.

". I've already pointed this out to you, your insistence on presenting this as "fact" when you known very well that it isn't true suggests dishonesty and subterfuge on your part."

You need to seek professional help, Tobus. It is I who pointed out to you that Amerindians don't need to be "close" to Neandertals in absolute terms but they are closer to them compared to other modern human populations. The rest is called "evolution."

"This contradicts your own point 1 - you are now saying Denisovans and Neanderthals are very different to Amerindians demographically."

How in the world can it be a contradiction?! Denisovans and Neandertals are different enough from Amerindians to allow for population amalgamation in America that obliterated more radical divergences. But we continue to see that, compared to other modern human populations, Amerindians are the closest to those Eurasian hominins.

Using your childish example: Bob lives 5 km away from Mary, Mary lives 20 km away from Jack, Jack lives 25 km away from Bob. Does it make Mary's trip to Jack's house shorter than Bob's?

"Amerindians have the lowest genetic diversity of all modern humans suggesting a recent divergence and bottleneck."

No, this suggests that Amerindians are an isolated, unadmixed population.

""Likely" is not a fact - it's a theory or a speculation."

We have craniological and genomic evidence for archaic admixture in Africa. We have genomic evidence (Neandertal and Denisovan alleles in Africa) for a migration of Eurasians to Africa. We have craniological evidence (Hofmeyr) for Eurasians in South Africa at 36,000 years. We have linguistic evidence demonstrating lack of diversity in linguistic stocks in Africa, with language being a defining characteristic of behavioral modernity. A logical conclusion is that modern humans migrated to Africa from Eurasia and absorbed a bunch of local African hominin genes. That's why Africans are genetically diverse, while Eurasians are less so. Of course we need more data, but this is the most logical model to walk around with until further data comes long.

"ADMIXTURE, PCA and f3 stats all confirm a distinct primary divergence between African and non-African populations. Unless you are suggesting that Africans are a majority non-Sapiens, archaic admixture cannot explain this lack of non-African affinity if Africans are indeed Amerindian-derived."

This "divergence" is in fact archaic admixture in Africa. The direct implication of out-of-Africa is that all of Africans are non-Sapiens because they just continued to spawn archaic lineages until finally a small subset of them experienced a bottleneck and colonized Eurasia. That's when a "symbolic revolution" occurred and allowed them to overpower Neandertals. Under out-of-America, some Africans have "archaic" genes but in general Africans derive from a Eurasian lineage (e.g., Y-DNA hg DE).

German Dziebel said...

@Tobus (contd.)

"Prove it. There are plenty of examples of populations appearing "close" on a single 3rd-party f3 axis when it is known from other data that they have no such affinity."

Your argument is circular from the get-go. That's why you'e denying Amerindian admixture in Eurasia - because it "contradicts" other "data." There's no such data, though, only your biases. Considering that f3 plots correctly group all continental samples together, it's unlikely it has any noise. Predictably, ancient Eurasian samples fluctuate between different continental groups because obviously there were migrations whereby these continental groups came about, and ancient samples provide us with glimpses of those migrations.

"the name calling to the kids in the playground."

Just stop acting childish, acknowledge your faults and flaws and I'll start calling you "Lord Tobus."

"You're the one denying the conclusions of mainstream science... but I guess actual scientists are "science deniers" too and you're the only one who does real science right?)."

Science develops and spreads unevenly across culture. Certain areas of knowledge haven't been fully colonized by scientific methodology. "Human origins research" is unfortunately one of those pre-scientific "refugias" wherein cultural ideologies rein supreme and distort facts before they are even found. Progress is slow and the majority of "academic scientists" are indeed stuck in pre-scientific world views. They spawn fans like yourself, terryT and others who are true cryptocreationists. Human origins provides a final test as to whether "science of evolution" will be capable of evolution. I agree with you - there are not too many signs that it will.

terryt said...

"The direct implication of out-of-Africa is that all of Africans are non-Sapiens because they just continued to spawn archaic lineages until finally a small subset of them experienced a bottleneck and colonized Eurasia".

That demonstrates your total lack of any scientific understanding of evolution. The groups that came out of Africa were just as much H. sapiens as the ones who remained behind. They did not suddenly become a new species.

"That's when a 'symbolic revolution' occurred and allowed them to overpower Neandertals".

After they'd mixed with them. I agree it was a subset of the out of Africa population that developed the Upper Paleolithic but you make the mistake of assuming a sudden change of species with the development of the UP. It was a change of culture and technology, not a genetic change. I was certainly under the impression that culture was your strong point. It seems you are as ignorant of that as you are of biological evolution.

"A logical conclusion is that modern humans migrated to Africa from Eurasia"

Correct. As shown by the haplogroup evidence which you so quickly dismiss. You seem to believe that every single migration involves the whole population. How on earth would that be possible? It would leave no-one behind.

"Science develops and spreads unevenly across culture".

Certainly it is yet to reach you.

Tobus said...

@German:
Amerindian are the closest. This is a pattern in the data. Predictably, as a science denier, you of course deny this.

I don't deny it at all - I simply point out that Americans are the "closest" to Denisovans in the same way the London is the "closest" UK capital to Timbuktu. You're insinuation that this "closeness" means that Amerindians are somehow like Denisovans demographically is like saying that London is more like Africa than the UK just because it's a tiny bit closer than any other UK capitals.

Using the relative term "closest" to imply "closeness" in an absolute sense is semantics, and since you are continuing to do it when you are well aware there is no actual correlation I can only assume you are being intentionally misleading. Is you theory really so weak that you need to resort to this kind of misdirection to support it?

To get back to the facts, are *you* denying that Amerindians are much, much closer to Eurasians in this respect, and thus (following the logic you applied to Denisovans) much closer to Eurasians in demographic structure?

Bob lives 5 km away from Mary, Mary lives 20 km away from Jack, Jack lives 25 km away from Bob. Does it make Mary's trip to Jack's house shorter than Bob's?

Nope and I never said it did... tell me though, would you say Mary lives in Bob's neighbourhood or Jacks?

No, this suggests that Amerindians are an isolated, unadmixed population.

That's not what science says: "This observation is consistent with previous findings, suggesting a strong bottleneck followed by a recent and rapid expansion in Native Americans" (Tishkoff 2009). You're not one of them "bible-carryin' science deniers" are you?

A logical conclusion is that modern humans migrated to Africa from Eurasia and absorbed a bunch of local African hominin genes.

Yet this logical conclusion if refuted by the latest genetic evidence. Go back to the drawing board and see if you can come up with an alternative conclusion (hint, read some conclusions that science has come up with).

The direct implication of out-of-Africa is that all of Africans are non-Sapiens because they just continued to spawn archaic lineages until finally a small subset of them experienced a bottleneck and colonized Eurasia

Where do you get this nonsense! Can you show me a single published source that says only Eurasians are sapiens? Africans and non-Africans are clearly the same species which is a good indication that any archaic admixture in Africans (and/or non-Africans) is only a small part of the genome... and hence not the primary cause of African/non-African divergence.

That's why you'e denying Amerindian admixture in Eurasia - because it "contradicts" other "data." There's no such data, though

Amerindian admixture into MA-1 is explicitly ruled out by the pattern of archaic and modern genetic affinities shown in various data, so the gene flow went from MA-1 into Amerindians. This isn't just my opinion, it's what science says too: "we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World." (Rhagavan 2013) - you wouldn't be "denying science" again would you?

"Human origins research" is unfortunately one of those pre-scientific "refugias" wherein cultural ideologies rein supreme and distort facts before they are even found.

As I thought - you consider yourself the sole provider of true knowledge in this area... I sure hope you have a science degree, wouldn't it be embarrassing if the self-proclaimed sole fountain of all scientific fact had only studied humanities!

German Dziebel said...

@Tobus

"You're insinuation that this "closeness" means that Amerindians are somehow like Denisovans demographically."

It's not an insinuation. It's a statement of fact. Amerindians are the best approximation of Mid-Pleistocene population structure among modern humans. That's why geneticists use them as a model for a mid-Pleistocene ancestral human population. They just incorrectly place this ancestral human population in Africa instead of where it belongs - in America.

"To get back to the facts, are *you* denying that Amerindians are much, much closer to Eurasians in this respect, and thus (following the logic you applied to Denisovans) much closer to Eurasians in demographic structure?"

Amerindians are clearly a modern human population but the fact that they are the closest to Neandertals and Denisovans suggests that their low intragroup diversity is not a product of a recent bottleneck but rather a retention from a mid-Pleistocene demographic realities - small, drifting, fissioning-and-fusioning demes. The fact that Amerindians are followed by Papuans in this regard confirms that it's not a recent artifact but an ancient systematic pattern.

"would you say Mary lives in Bob's neighbourhood or Jacks?"

It's about who lives in whose neighborhood. It's about who came first into the 'hood and how the neighborhood formed over time.

"That's not what science says: "This observation is consistent with previous findings, suggesting a strong bottleneck followed by a recent and rapid expansion in Native Americans" (Tishkoff 2009). You're not one of them "bible-carryin' science deniers" are you?"

Don't confuse "science" with "scientists." Tishkoff et al. are mistaken as century-old linguistic and ethnological evidence and growing and solid (genome-wide and ancient DNA) genetic data shows. It's not their fault that they believe in a paradigm that was introduced without sufficient data to inform science. But they should've noticed back in the 1980s that America has become the most diverse (intragroup) continent since 1492 and it became such because of recent admixture, not ancient divergence.

"Amerindian admixture into MA-1 is explicitly ruled out by the pattern of archaic and modern genetic affinities shown in various data, so the gene flow went from MA-1 into Amerindians. This isn't just my opinion, it's what science says too."

It's an opinion, as you correctly pointed out, and it's inconsistent with the data. It doesn't matter how prevalent an opinion is.

"you wouldn't be "denying science" again would you?"

You are the one who's been denying the science behind f3 stats. I'm a scientist who thinks other scientists are wrong but I don't question the methodologies. And if question the methodology (as in the methodology of building haploid trees), I suggest an immediate alternative (root them in Denisovan sequences to see which sites are ancestral and which ones are derived).

"I sure hope you have a science degree, wouldn't it be embarrassing if the self-proclaimed sole fountain of all scientific fact had only studied humanities!"

I have 2 doctorates from two top schools in two great countries of the world. Tishkoff et al. are no match for that. Anthropology is the best of science and the best of humanities. Think of a crossover SUV - aren't they great? They handle like a sedan but have the power of a truck. What you call "science" is a big ass gas guzzler that's impossible to maneuver.

German Dziebel said...

@Tobus (contd.)

"Where do you get this nonsense! Can you show me a single published source that says only Eurasians are sapiens? "

Are you going to have another hysterical fit because your pre-set ideas about the world are collapsing under the weight of my critique?! I can show you plenty of published articles that say that we descended from "Adam" and "Eve". Not everything published in a scientific journal should be taken literally, but also if something is not published in a scientific article, it doesn't mean it's not real. There's always an overt message and then a logical conclusion from a picture that's being painted. The story went like this: The so-called "Anatomically modern humans" couldn't exit African because Neandertals blocked their way and killed them off in the Levant. 50,000 years later AMH became "behaviorally modern humans" or underwent a "symbolic revolution" and only then managed to leave Africa and dominate over Neandertals in West Eurasia. At the same time, mtDNA lineages supposedly showed a bottleneck at the exit from Africa, so only a small group of now-behaviorally modern humans left Africa. So, no African lineages are now found outside of Africa, while Africans are composed of multiple layers of African-specific lineages (L0, L0'1, L1'2, etc.) that stayed behind. So effectively ancient African were portrayed as "non-behaviorally modern" and closer to "African archaics" than Eurasians, while ancient non-Africans as "behaviorally modern" and further removed from "archaics" than Africans.

terryt said...

"I sure hope you have a science degree, wouldn't it be embarrassing if the self-proclaimed sole fountain of all scientific fact had only studied humanities!"

Ain't that the truth!!!

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