November 20, 2013

Ancient DNA from Upper Paleolithic Lake Baikal (Mal'ta and Afontova Gora)

The study I mentioned in a previous post has now been made available in Nature. Two Upper Paleolithic Siberians (24-17kya) have been sequenced at low coverage. The better quality (and older) Mal'ta (MA-1) sample belongs to Y-haplogroup R and mtDNA haplogroup U, and the younger (but poorer quality) Afontova Gora (AG-2) sample appears to be related to it.

Most interestingly, there is evidence for gene flow between the MA-1 sample and Native Americans, which makes sense as these are Siberians of the period leading up to the initial colonization of the Americas. The interesting thing is that MA-1 does not appear to be East Eurasian, as proven by the test D(Papuan, Han; Sardinian, MA-1) which is non-significant, so MA-1 is not more closely related to Han than to Papuans (which is true for modern native Americans). So, it seems that the gene flow between MA-1 and Native Americans was towards Native Americans from MA-1 and not vice versa.

It is fascinating that such a sample could be found so far east at so early a time. Both Y-chromosome R and mtDNA haplogroup U are very rare east of Lake Baikal which has been considered a limit of west Eurasian influence into east Eurasia. And, indeed, both these haplogroups are absent in Native Americans, so it is not yet clear how Native Americans (who belong to Y-chromosome haplogroups Q and C and mtDNA haplogroups A, B, C, D, X) are related to these Paleolithic Siberians. The obvious candidate for this relationship is Y-chromosome haplogroup P (the ancestor of Q and R). So, perhaps Q-bearing relatives of the R-bearing Mal'ta population settled the Americas.

In any case, this is an extremely important sample, as its position in "no man's land" in the PCA plot (left) demonstrates, between Europeans and native Americans but close to no modern population.

Its closest present-day relatives are indicated in (c), with Native Americans (red) being the closest, and a scattering of boreal populations from the Atlantic to the Pacific (but not in the vicinity of Lake Baikal) next in line (yellow).

This distribution clearly related to the evidence for admixture in Europe adduced in two other recent papers, although the question of who went where and when remains to be resolved. Was MA-1 part of an intrusive western population encroaching  on east Eurasians? Or did MA-1 lookalikes arrive as first settlers in empty territory, later ceding this space to east Eurasians from, perhaps, China? Did the two mix in Siberia or did they arrive in the Americas in separate migrations and mix there? And, how does this all relate to events in Europe in the far west?

UPDATE: Razib makes an excellent point:
Also, can we now finally bury the debate when east and west Eurasians diverged? Obviously it can’t have been that recent if a >20,000 year old individual had closer affinity to western populations.
We already knew that Tianyuan was more Asian than European, so I think west Eurasians diverged from the rest >40 thousand years ago. But, Tianyuan was so early that its precise relationships to different Asian groups could not be determined. So, I'd say it's a good guess that east-west split off before 40 thousand years in Eurasia.

Nature (2013) doi:10.1038/nature12736

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

Maanasa Raghavan, Pontus Skoglund et al.

The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians1, 2, 3, there is no consensus with regard to which specific Old World populations they are closest to4, 5, 6, 7, 8. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal’ta in south-central Siberia9, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers10, 11, 12, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages5. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, 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. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians2, 13. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago14, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.

Link

264 comments:

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Tobus said...

@German:
If Tianyuan is the first wave out of America (the best surviving unadmixed examples being modern South Amerindians) and modern East Asians is the second one (the best surviving examples being Northern Amerindians), then Tianyuan will be closer to such populations as Karitiana, while modern East Asians to such populations as Na-Dene and Eskimo-Aleuts

What!? An ancient American population splits into 2 lineages, one which goes into Asia and one that stays in America. Some time later the one that stayed in America also splits, with one population staying where it is and the other going to Asia and mixing with the earlier Asian lineage... and you think the population that stayed in America will be closer to the first Asian population than the one that has admixed with them since the initial divergence?!? I suspect you've forgotten to divulge some important aspect of your speculations, because it makes no sense the way it is.

East Asians will be closer to Tianyuan than Na-Dene and Eskimo-Aleuts because they absorbed a Tianyuan-like population as they expanded from the north into south China and beyond.

So you acknowledge the effect Tianyuan admixture in regard to East Asians vs Na-dene and Eskimo-Aleuts, but not in regard to East Asians vs Karitiana? What's special about Karitiana that they possess more genetic affinity with Tianyuan after over 40,000 years of isolation than other populations with the exact same shared ancestry but who also have more recent admixture with Tianyuan's descendants?

I can't see any way to make your theory work - if Amerindians are ancestors of both Tianyuan and East Asians then East Asians should be closer to Tianyuan than Amerindians are. Since they're not, it must be the other way round - Tianyuan is ancestral to both Amerindians and East Asians.

This makes me think that the Amerindian component in Mal'ta is older than the West Eurasian component

You are more than welcome to think that if you want, but please don't state that Mal'ta "confirms the greater proximity of ancient Eurasians to modern Amerindians than to modern Eurasians" when it clearly doesn't. It's the second time now that you've intentionally misrepresented the facts by attributing them to a larger population grouping than they actually apply to. A sound theory doesn't need subterfuge and misrepresentation to gain traction - if you have to resort to misleading statements of pseudo-facts to get your point across, perhaps it's time to reassess if the point is worth making.

Eastern View said...

@Hamar Fox,

Please limit the condescending sarcasm and straight-up insults. Cut it just a bit.

"One calculator was created by Dienekes, and the other by the owner of the Harappa project."

You didn't directly link to Dienekes' of the Harppa project's data but put up a sourceless, edited version in your own Google doc, therefore warranting my comment.

The "Caucasoid" or "West Eurasian" (whatever words you used) admixture in Amerinds in Dienekes also shows up significantly in Papuan-Melanesians.

I would interpret this component as proto-Eurasian, that is, the signature leftover from when Eurasians were still splitting from Africans. This makes sense because the so-called "West Eurasian" signature splits out from the African signature at K3. So, proto-Eurasian signature can mimic West Eurasian signature.

This would mean Australasians and Amerinds and Tianyuan are more proto-Eurasian and less derived than Siberians and East Asians.

Hamar Fox said...

Eastern View,

Please limit the condescending sarcasm and straight-up insults. Cut it just a bit.

Actually, it was your own sardonic tone that prompted mine. Also, I didn't insult you.

You didn't directly link to Dienekes' of the Harppa project's data but put up a sourceless, edited version in your own Google doc, therefore warranting my comment.

I'd already linked to and talked about the calculators numerous times in the thread by then. Since you seemed so fully convinced of the inferiority of all other arguments presented in the thread than your own, I assumed you'd actually read them.

The "Caucasoid" or "West Eurasian" (whatever words you used) admixture in Amerinds in Dienekes also shows up significantly in Papuan-Melanesians.

Yes it does, which is why we need to utilise other methods to establish whether or not it's real. East Asians constitute the extreme of East Eurasian variation (not be confused with drift). But what the ADMIXTURE analyses show is that Amerindians aren't strictly equivalent to East Asians. The reasons for this could be simply that they fall short of the extreme-of-variation represented by East Asians (as I suspect is the case with Papuans), or it could mean real admixture. Or both. You stated that Amerindians and East Asians were genetically equivalent (as suggested by Raghavan et al.'s ADMIXTURE analysis). All I did was to provide evidence that this is not necessarily so.

German Dziebel said...

@Hamar Fox

"Sorry, but where is the refutation and what is it that's supposedly being refuted?... "

Yeah, we don't seem to be able to connect. I never implied that Terry refuted you. The evidence refutes what Terry picked up from you. That was the meaning of my sentence.

"This is patently false. Kalash evidence the same admixture as surrounding populations up to the point that their own component emerges, which allows them to occupy it fully."

Why what I wrote was false? Kalash became isolated, developed their own component and at a certain K level, all their previous components disappeared. But as a single population it stands out by having its own component beginning from a deeper K level than other single populations in Eurasia. This is from memory. If you are saying that Kalash are not much different from any other single population, then my memory must be faulting me. Send me a reference, if you don't mind.

"The admixture in Amerindians is absolutely equilibriated."

Amerindians are obviously older than Kalash, hence, according to some runs, their component goes all the way down to K = 2. They seem to have just as long of a time as Africans to get equilibrated. The difference is that Amerindians have been mixing with other Amerindians, while Africans likely absorbed gene flow from everywhere possible.

"Argh, You're messing with my mind. I can't tell if anything's real anymore!"

Just ask me and I'll tell you what's real and what's not.

"You seem to be making my case for me there,"

I don't think we disagree on theory, just in the way we interpret certain data.

German Dziebel said...

@TerryT


"Its first arrival in the southwest Pacific is only some 4000 years ago. Hardly the signature of 'a relic haplogroup later overrun by a host of others'."

Yes, naturally. Have you recently taken a geography class, Terry? Hg B has been present along the Pacific coast of Asia for much longer. Think of B as the mtDNA counterpart of Polynesian Y-DNA C2.

"I was sure everyone accepted by now that haploid DNA does not necessarily have a close correlation with diploid DNA."

Terry, ADMIXTURE measures diploid genes. And in the case of Mal'ta it's fully consistent with its haploid DNA results. Of course, if you delete half of my quote, you're going to arrive at a different conclusion.

"I realise science is not a democracy but you seem to represent a minority of one. The phylogeny has undergone rigorous examination..."

We inherited those phylogenies from the pre-ancient DNA age, so it's not impossible that they are flawed. The well-known problems with the molecular clock (again, actual historical evidence vs. ideal evolutionary models) reinforces this perspective. And appeal to authority doesn't count once someone brings up actual data. You need to address the latter.

"The second comment does not necessarily demand the first. If West Eurasians have no (or very little) East Eurasian genetic component while Amerindians have a significant amount we would also see that 'West Eurasians are closer to Amerindians than they are to East Asians'...."

If Amerindians admixed with a very marginal West Eurasian population very recently, this wouldn't have pulled ALL of West Eurasians closer to Amerindians.

"This explains why Amerindians have largely West Eurasian Y-DNA and mostly East Eurasian mt-DNA. They mixed."

Not at all. mtDNA X and Y-DNA Q have similar geographic signatures in the Old World, both stretching into West Asia. hg X is absent from Siberia but present in North America. Out of all Amerindian mtDNA markers, mtDNA hg A is the closest to hg X phylogenetically but it has an East Asian-Siberian distribution. mtDNA hg B has a Circumpacific distribution, is largely missing from Siberia but is phylogenetically close to West Eurasian hg U. Y-DNA C also has a Circumpacific distribution but it's present in Siberia and largely absent in West Eurasia.

If West Eurasians and East Eurasians mixed to produce Amerindians, we would have seen Y-DNA R and not Q in America, mtDNA U and not B in America, Y-DNA N and O and not C in America. Everything contradicts the mixing idea. But admixture of Amerindians into the Old World makes it easier to understand some Y-DNA and mtDNA markers shared between Siberia and America.

terryt said...

I have comments from both German and Tobus on my email but neither appear here yet.

As German appears to know a great deal about American B perhaps he would be so kind as to tell us the distribution of the Various B2 haplogroups: B2a, B2b, B2c, B2d, B2e, B2f, B2g and B2h. To the best of my knowledge B2a is centrad on the west coast of Canada. I have no idea about the others.

It seems German is thinking that the remote Pacific mt-DNA B is the last gasp of a migration south through Asia from North America. What we can be fairly certain of is that Polynesian B4a1a1a is the last gasp of a migration from Taiwan, through the Philippines, along the north coast of New Guinea and out into remote Oceania. Possibly he is prepared to accept the current B phylogeny that fits this pattern?

But I presume he disputes the current B phylogeny overall, especially the single control region mutation that combines the Philippines R24, South Chinese R11'B6 and the almost 'Circumpacific' B4'5. But the current phylogeny cannot be made to fit an 'out of America' scenario.

Regarding B5, although it is spread from Japan, through SE Asia to the Admiralty Islands it is not present in America at all. Perhaps German is claiming all these R and B haplogroups are downstream mutations from B2, and they represent separate expansions into Eurasia from America. But surely it is far simpler to see the distribution as a single, gradual expansion originally from somewhere between South China and the Philippines. Especially when we consider that American B2 is just a single small twig of B4b'd'e'j.

Once again we have a single control region mutation combining B4a, B4g, B4h and B4i. That makes these 4 haplogroups equivalent to B4c and B4f as well as B4b'd'e'j. This starlike diversity probably represents a rapid expansion, but of the 7 haplogroups just some members of B4b'd'e'j could be considered 'northern'. The others are mainly centred on Vietnam but have become spread through the rest of SE Asia and southern China. Surely it is again far simpler to see the distribution as a single gradula expansion from Vietnam rather than a whole series of movements out of America. Under this Vietnam scenario the B4b1 southward movement is an isolated back movement in the otherwise gradual expansion from South China/Vietnam.

The presence of American B2's close relation, B4b1, in Hainan and the Admiralty Islands probably does indicate southward movement. But B5b2 and B4b1's presence in the Admiralties is very likely associated with the arrival of Austronesians and the development of Lapita pottery some 4000 years ago. That may place B2's arrival in America later than the other mt-DNA haplogroups.

Alashire said...

"Y-DNA R and mtDNA U are not found in America either". who told you that? Maybe you are not paying attention or any of the MTdna and Y dna boards. Maybe you should find out the facts before you repeat and repeat the same lies over and over.

" In Indigenous Americans groups, R-M173 is the most common haplogroup after the various Q-M242, especially in North America in Ojibwe people at 79%, Chipewyan 62%, Seminole 50%, Cherokee 47%, Dogrib 40% and Papago 38%. The decreasing gradient of haplogroup R-M207 from Northeastern to Southwestern North America is evidence that this results from European admixture (Malhi 2008). " in the meantime scientist have decided using the offspring from 1 million missing Asians slaves helps them find the real Native Americans.
yes it appears we are still viewed as Ignorant savages , and even neanderthal like little children we are told we don't know who we are.


German Dziebel said...

@Tobus

"please don't state that Mal'ta "confirms the greater proximity of ancient Eurasians to modern Amerindians than to modern Eurasians" when it clearly doesn't."

It clearly does. Look at Figure SI 22. Same for Tianyan, per Fu et al.: Tianyan is an ancient Eurasian sample, Karitiana are modern Amerindians. Tianyuan is closer to Karitiana than to any of the East Asians. You can't follow the data and make logical connections between different types of data - this is your problem.

"It's the second time now that you've intentionally misrepresented the facts by attributing them to a larger population grouping than they actually apply to."

I don't misrepresent facts. Especially intentionally. You are desperately trying to find a flaw in my argument to no avail. hence, you decided to go for cheap shots.

"What?!...I suspect you've forgotten to divulge some important aspect of your speculations, because it makes no sense the way it is."

I see your agony and I'm gloating at it but I wish you could spare me with your emotions. The scenario I fits the data like hand in glove. A more southerly Amerindian population (Karitiana) is closer to Tianyuan (40,000) and Malta (24,000) than modern East Asians. It's more aligned with West Eurasians and ancient East Asians. Modern East Asians are derived from a more northerly Amerindian population (Na-Dene and Eskimo-Aleuts) some 10,000 years after Mal'ta. Na-Dene and Eskimo-Aleuts are demonstrably closer to East Asians than more southerly Amerindians.

"I can't see any way to make your theory work - if Amerindians are ancestors of both Tianyuan and East Asians then East Asians should be closer to Tianyuan than Amerindians are."

Why? Tianyuan and modern East Asians are separated by some 30,000 years.




German Dziebel said...

@TerryT

"But I presume he disputes the current B phylogeny overall, especially the single control region mutation that combines the Philippines R24, South Chinese R11'B6 and the almost 'Circumpacific' B4'5. But the current phylogeny cannot be made to fit an 'out of America' scenario.

Regarding B5, although it is spread from Japan, through SE Asia to the Admiralty Islands it is not present in America at all. Perhaps German is claiming all these R and B haplogroups are downstream mutations from B2, and they represent separate expansions into Eurasia from America. But surely it is far simpler to see the distribution as a single, gradual expansion originally from somewhere between South China and the Philippines. Especially when we consider that American B2 is just a single small twig of B4b'd'e'j."

Yes. I do question the phylogeny at this node. T16189C! that initiates R24, R11'B6 and B4'5 is a back mutation to the ancestral state that undoes what supposedly happened at the formation of the whole L2'3'4'6 node. The famous 9bp deletion at 8281-8289 is found in combination with C16189 on hg L0a2, which is from the clade that's opposed to all of L1'2'3'4'5'6. Not to mention the pesky 8281-8289d on B6, which is just asking to be moved up the tree. So, the C16189B4+8281-8289d motif is ascertained in Tianyuan and is shared by "Circumpacific" Asians, South Amerindians and African foragers. B4b'd'e'j is currently defined by A827G and C15535T. But Denisova and all of Neandertals show G827, so again this lineage B4b'd'e'j is defined by a ancestral retention and only one unique innovation. Ancestral retentions are also found on L3, N (A15301G!) and R (T16223C is in fact C16223 in Denisovans, so again R is defined by just unique innovation).

I haven't checked all the B2 lineages but this kind of noise makes me question the robustness of the phylogeny. I can't say if a better phylogeny would provide support for out-of-America but I wouldn't be assumptive about the correctness of the current one.

The fact that America is missing all of the myriad of R, N and M lineages but does have 1-2 representative from each one of these major macrohaplogroups makes me think that what America has are relic lineages. If it was peopled by multiple waves of migration, why would the migrants cherry pick just 1-2 lineages out of a much greater source variety and do it multiple times? And then how did they manage to spread it so far and wide in the Americas. If America was peopled by just one migration, how come hgs B and X are so poorly attested in Siberia?

terryt said...

"I would interpret this component ['Caucasoid' or 'West Eurasian' ... admixture in Amerinds in Dienekes also shows up significantly in Papuan-Melanesians] as proto-Eurasian".

I think you're on the wrong track here. I strongly suspect that the 'Papuan' element that shows up through most of Eurasia owes its presence to the extreme likelihood that both Y-DNA MNOPS and mt-DNA R originated in a region with a 'Papuan population'. Specifically Sundland/South Wallacea. The haplogroups carried a proportion of that population as they expanded.

"We inherited those phylogenies from the pre-ancient DNA age, so it's not impossible that they are flawed. The well-known problems with the molecular clock (again, actual historical evidence vs. ideal evolutionary models) reinforces this perspective".

I repeat: the 'molecular clock' has absolutely nothing at all to do with 'phylogeny'. I'm pleased to see you actually wrote 'it's not impossible that they are flawed'. Not impossible, but very unlikely.

"mtDNA X and Y-DNA Q have similar geographic signatures in the Old World, both stretching into West Asia".

Both coming from West Asia most likely. Q is related to R, almost certainly West Asian in origin, as for X:

"hg X is absent from Siberia but present in North America".

Yes. It has almost certainly been replaced by the expansion of later haplogroups, mostly from further south in East Asia, but also seemingly with later arrivals from the west such as U.

"Out of all Amerindian mtDNA markers, mtDNA hg A is the closest to hg X phylogenetically but it has an East Asian-Siberian distribution".

As far as I'm aware mt-DNA N's diversification is starlike with no haplogroup older than any other. And X has basal representatives as far west as Egypt (X1) and so cannot in any realistic sense be called particularly 'East Asian-Siberian'.

"mtDNA hg B has a Circumpacific distribution, is largely missing from Siberia but is phylogenetically close to West Eurasian hg U".

Again, as I understand things, B is equally related to all other R-derived haplogroups, not just to U. However see above for B's closest relations. B's absence in Siberia is less a result of B being 'a relic haplogroup later overrun by a host of others'. It suggests the connection between Eurasia and America was via the Kurile and Aleutian islands. Not surprising when we consider the related southern B4b1 is definitely associated with island hopping.

"If West Eurasians and East Eurasians mixed to produce Amerindians, we would have seen Y-DNA R and not Q in America"

No. Y-DNA Q is every bit as West Eurasian as is R. Related to each other in fact.

"mtDNA U and not B in America"

We know that American mt-DNA's are mostly East Asian, which is part of the evidence for hybridisation.

"Y-DNA N and O and not C in America".

We can now be reasonably sure that Y-DNA N and O's expansions post-date the Amerindian formation. O's main expansion may be as late as the Neolithic, and N's perhaps not much older. One minute you're claiming no East Asian presence in ancient Siberia next minute you're expressing surprise at the lack of East Asian Y-DNA in America. Make up your mind.

Alashire said...

http://vnnforum.com/showthread.php?t=119918in Actually in that location they should really look slightly more north and west african because that is the part of africa our turtle island broke off of there . So it should be no shock if they look kind of European-ish.. because so does and did North Africa there in that location too.

Maybe people need to stop repeating lies as if those lies are facts just because people don't understand real History. Maybe you all should stop assuming we don't know who we are or where we came from!

Hamar Fox said...

German Dziebel,

Why what I wrote was false? Kalash became isolated, developed their own component and at a certain K level, all their previous components disappeared

Okay, we're getting a bit tangled up here. My point was that admixed populations can form their own components at certain levels of analysis, so the fact that Amerindians form their own component doesn't mean that they're not admixed. I used Kalash for what I thought was a fairly uncontroversial example of this.

Up to the K-level that Kalash appear as 100% Kalash, they have basically the same fundamental admixture proportions as, say, Pathan. This has been the case with every calculator I've seen. But it seems from what you said that we don't differ on this point, so I won't take it further.

But as a single population it stands out by having its own component beginning from a deeper K level than other single populations in Eurasia. This is from memory. If you are saying that Kalash are not much different from any other single population, then my memory must be faulting me. Send me a reference, if you don't mind.

I'm saying that they're not much different in their fundamental components from proximal populations. They are different in their intra-group relations than surrounding populations: any two given Kalash are likely to be closer cousins than any two members of all other populations that failed to have their own component before the Kalash.

The same thing is seen here:

http://www.pnas.org/content/early/2013/05/30/1306223110.full.pdf+html

On the ADMIXTURE analysis, we see a (slightly unrefined) Tunisian component at k=6, which swallows up all of the admixture that's visible at more fundamental levels. If Kalash were present, maybe they'd get a component instead, maybe at that k-level or earlier, in which case the Tunsian component would be deferred to a later k-level.

But what's important is which groups are the most internally similar and externally dissimilar, which is naturally going to be much higher in the most geographically isolated groups, bottlenecked and anciently separated populations. Representation in the dataset is also very likely a factor. Including a healthy number of aboriginal Australians in addition to the already present Papuans in an analysis may well displace Amerindians at k=4, or at least follow them swiftly.

German Dziebel said...

@Hamar Fox

Yes. I agree on everything. Kalash, Tunisians (now I remember) are heavily inbred. Same for Amerindians such as Karitiana and Hadza in Africa. Same for the Denisovans and even more so for the recently sequenced Altai Neandertal. This is the populational reality more typical of Mid-Pleistocene, hence I interpret Amerindians as archaic relics. I see Amerindian uniqueness as stemming all the way from K=2, per Rosenberg et al 2002 and a couple of other runs I've seen. Hence they are unadmixed within the temporal parameters of our species. If they are consistently shown to be admixed at K=2, K=3 and K=4, then I'll have to rethink it. But with more Amerindian data available it's likely to further reinforce Amerindian uniqueness.

Mal'ta is admixed, though, you have to admit it.

German Dziebel said...

@terryT

"I repeat: the 'molecular clock' has absolutely nothing at all to do with 'phylogeny'. I'm pleased to see you actually wrote 'it's not impossible that they are flawed'. Not impossible, but very unlikely."

ok, let me rephrase it: the order of the mutations in the mtDNA phylogeny is just as random as the assumptions underlying molecular clock. Whether or not the two problems are systemically related doesn't matter. They can be totally separate but they both exist. By saying "not impossible", I was just trying to put myself in the shoes of a believer like you who's taking baby steps into critical thinking. For a scientist like me, it's just obvious: without ancient DNA from archaic and AMH Africans I don't know how people can consider as proven a phylogeny that systematically ignores ancestral state attestations found in Denisovans and Sima (with or without Neandertals) and admit recurrent mutations every step of the way.

"And X has basal representatives as far west as Egypt (X1) and so cannot in any realistic sense be called particularly 'East Asian-Siberian'."

Again, look at the phylogeny: on X T16189C! C16278T! are reversals to ancestral state. 6221 is ancestral, too, as shown by the Denisovan sequences. T16189C! is highly mutable. X1'3 is defined by a highly recurrent T146C and so is X2 (T195C). The other defining site of X2 (1719) is actually in ancestral state there, as shown by both Denisovan sequences). A key X stem site 16278 is actually derived on X1 and ancestral on X2.

In a word, there's nothing "basal" about X1 and the whole node is messy. One thing is clear: it's intrusive in West Asia.

"We know that American mt-DNA's are mostly East Asian, which is part of the evidence for hybridisation."

I just gave you a whole rundown of what's actually found in the Americas and what the realities of the mtDNA phylogeny are and you just repeat your cliched ideas.

"One minute you're claiming no East Asian presence in ancient Siberia next minute you're expressing surprise at the lack of East Asian Y-DNA in America."

I'm not "claiming" that there were no East Asians in ancient Siberia. Since Raghavan et al. it's now a fact. And this fact is consistent with the lack of East Asian Y-DNA N and O and blood group B in the Americas as well as with the virtual absence of mtDNA hg X (North America-specific) and B (Mesoamerica and South America dominant) in Siberia. Hence, all the genetic similarities between Amerindians and modern East Asians are product of a back migration from the America. It's just logic, Terry. Get used to it. And your mtDNA phylogeny should follow logic and historical attestations.

German Dziebel said...

@terryT

"We know that American mt-DNA's are mostly East Asian, which is part of the evidence for hybridisation."

More on that. As I wrote earlier, North America-specific hg X and Mesoamerica- and South America-dominant hg B are barely found in Siberia. Outside of America hg X peaks in West Asia and hg B in the Circumpacific, which are widely separated and marginal Eurasian zones. The other 3 clades found in the Americas, namely hgs C, D and A, have their Amerindian-specific subclades (A2, C1, and D4h3a) turning up in Eurasia (D4h3b in China, A2a in Beringia and Western Siberia, C1a in Mesolithic Karelia and the Amur region, C1e in modern Iceland).

So, even without an overhaul of the phylogeny it's clear that mtDNA doesn't provide solid evidence for an East Asian origin of Amerindian lineages. Long-term isolation in the Americas, with a more recent backflow from the New World into Asia is a more plausible scenario.

terryt said...

"For a scientist like me, it's just obvious"

what is your background in the science of genetics then?

"And your mtDNA phylogeny should follow logic and historical attestations".

It seems you're prepared to simply alter the phylogeny to make it fit your belief.

"Again, look at the phylogeny: on X T16189C! C16278T! are reversals to ancestral state. 6221 is ancestral, too, as shown by the Denisovan sequences. T16189C! is highly mutable".

So what is your proposed phylogeny?

"Outside of America hg X peaks in West Asia and hg B in the Circumpacific, which are widely separated and marginal Eurasian zones. The other 3 clades found in the Americas, namely hgs C, D and A, have their Amerindian-specific subclades (A2, C1, and D4h3a) turning up in Eurasia"

You can talk of 'American clades' yet still insist that America is the source of those haplogroups, viz. 'Long-term isolation in the Americas, with a more recent backflow from the New World into Asia is a more plausible scenario'. How on earth do you justify that idea?

@ Alashire:

"that is the part of africa our turtle island broke off of there".

Are you really saying that humans were around when the Atlantic first formed? I think you need to learn some basic geology.

Rokus said...

It seems you're prepared to simply alter the phylogeny to make it fit your belief
The current belief is the Out of Africa paradigm, and believe it or not, a host of mtDNA mutations were introduced or taylored especially to sustain this belief. Only nowadays the full extend and fragility of this house of cards is becoming clear. What about MA-1's purported A16399G mutation while 16399G is ancestral in primates, Denisova, Sima and the Insert of chr.11, and thus actually derived in Neanderthal, LM3 and rCRS? This mutation is recurrent in L3, L4, M and P and defines U2a1 - the latter situation would thus require an intermediate flip in U to sustain the current phylogeny.
L3 (including N and M) is defined by A769G, while actually ancestral. The A15301G! backmutation in N is actually ancestral now we can compare rCRS with the genomes of Sima/Denisova. Even U's defining G12372A mutation would only flip this basepair back to what now appears to be the ancestral form, potentially turning U (or better: U2a1) the most basal modern human mtDNA haplogroup, turning L(xL3) haplogroups into nested subclades of U - or U2a1.
Unfortunately, conflicting mutations are all around. So far it seems that any phylogeny based on ancestral outgroups is as good as any. However, only the current one is heavily tainted by nothing but an ever more annoying Out-of-Africa self righteousness.

terryt said...

"The current belief is the Out of Africa paradigm, and believe it or not, a host of mtDNA mutations were introduced or taylored especially to sustain this belief. Only nowadays the full extend and fragility of this house of cards is becoming clear".

Interesting. We await developments.

Tobus said...

@German:
It clearly does. Look at Figure SI 22.

Are you saying you honestly believe, after considering all the evidence presented in the paper, that Mal'ta is closer to Amerindians than he is to Europeans and Central/South Asians?

I don't misrepresent facts. Especially intentionally.

You know that Amerindians are closer to East Asians than to Mal'ta, yet you stated that Amerindians are closer to Mal'ta than to Eurasians, even after I gave you the opportunity to correct yourself by specifying "West Eurasians" instead. You have also stated that Mal'ta is closer to Amerindians than he is to Eurasians, even though you know he has greater affinity to West Eurasians than Amerindians and your comment only applies to East Asians. You are either intelligent and intentionally used "Eurasian" to imply a fact applies to both West Eurasians and East Asians when it really only applies to one, or you are unintelligent and don't know there is a difference between East Asians and West Eurasians. I had assumed the intelligent option, but am happy to change my mind if you insist it's not intentional.

Why? Tianyuan and modern East Asians are separated by some 30,000 years.

Why? Because modern Amerindians are just as separated from Tianyuan but they don't have any of the "Second Wave" admixture with Tianyuan descendants that East Asians do... so they should be futher away than East Asians are, not closer.

Your speculation just doesn't work... if Amerindians came before Tianyuan, then East Asians would either be Amerindians with Tianyuan admixure (as you propose) or they are Tianyuan descendants, but in either case they should be *closer* to Tianyuan than the "pure" Amerindians who stayed in America. If you think about it, the only way East Asians could be further from Tianyuan in an "Americans before Tianyuan" scenario is if they had already diverged *before* the Amerindian/Tianyuan split, and had *zero* admixture with Tianyuan descendants... something completely at odds with your "Second Wave" idea.

German Dziebel said...

@Tobus

"Are you saying you honestly believe, after considering all the evidence presented in the paper, that Mal'ta is closer to Amerindians than he is to Europeans and Central/South Asians?"

You should address your concerns to Raghavan et al. Figure SI 22 is theirs and it's part of the main body of the paper.

"...you are intelligent and intentionally used or you are unintelligent and don't know..."

This is just weird. You should join the "science creep" club founded by Onur.

Once again: the issue if not that Amerindians are closer to East Asians than to West Eurasians but that they are closer to East Asians than to West Eurasians, that northern Amerindians such as Na-Dene and Eskimo-Aleuts are closer to East Asians than other Amerindians and that all of West Eurasians are closer to Amerindians than to East Asians.

"Because modern Amerindians are just as separated from Tianyuan but they don't have any of the "Second Wave" admixture with Tianyuan descendants that East Asians do... so they should be futher away than East Asians are, not closer."

I don't understand this. What second wave admixture with Tianyuan descendants?

"East Asians would either be Amerindians with Tianyuan admixure (as you propose) "

Per the data at hand, more like northern Amerindians with Tianyuan admixture, as Na-Dene and Eskimo-Aleuts are closer to East Asians than other Amerindians.

"the only way East Asians could be further from Tianyuan in an "Americans before Tianyuan" scenario is if they had already diverged *before* the Amerindian/Tianyuan split."

Or, as I have argued, if East Asians descended from northern Amerindians (or even admixed with them before admixing with Tianyuan) who in turn had derived from southern Amerindians. So the reason East Asians are pulled away from Tianyuan (although they are found in the same geographic area) relative to a population such as Karitiana (who are thousands of miles away) is because they descended from or admixed with a population such as Na-Dene.

"had *zero* admixture with Tianyuan descendants..."

This is not in the data. The data does show that East Asians are close to Tianyuan just not as close as southern Amerindians.

Tobus said...

@German:
You should address your concerns to Raghavan et al.

Raghavan etc al. aren't the ones saying that Mal'ta "confirms the greater proximity of ancient Eurasians to modern Amerindians than to modern Eurasians", you are. Figures SI 4, 5, 6, 7, 8, 9 10 and 26 from Raghavan et al. all conflict with such a statement. You should also be aware that, in order to eliminate post-Columbian admixture, for SI 22 they used an "SNP dataset masked for European
and African ancestries in Siberian and Native American populations", potentially reducing the degree of European affinity detected.

Once again: the issue if not that Amerindians are closer to East Asians than to West Eurasians...

Not sure what you think we're talking about, but the issue I raised is that twice you have used the term "Eurasian" instead of specifying "West Eurasian"/"East Asian" to create the false impression that both populations have the same genetic affinities to Amerindians/Mal'ta. Is this intentional or do you not know that they have different genetic affinities to these groups?

I don't understand this. What second wave admixture with Tianyuan descendants

This one: "Tianyuan is the first wave out of America... and modern East Asians is the second one" and "East Asians ... absorbed a Tianyuan-like population as they expanded from the north into south China and beyond."... that's you saying that East Asians are the "Second Wave" out of America and that they admixed with the existing Tianyuan population. If it were true, East Asians would be closer to Tianyuan.

Or, as I have argued, if East Asians descended from northern Amerindians... the reason East Asians are pulled away from Tianyuan ... relative to a population such as Karitiana ... is because they descended from or admixed with a population such as Na-Dene.

So where did the Na-Dene come from and why are they further from Tianyuan? You are now speculating is that both Tianyuan and nothern Americans are descended from southern Americans and that northern Americans are further from Tianyuan than southern ones... are you saying northern Americans diverged pre-Tianyuan and somehow southern Americans migrated through them without admixing to get into Asia?

This is not in the data. The data does show that East Asians are close to Tianyuan just not as close as southern Amerindians.

Exactly my point. For your speculation to work East Asians must either be closer to Tianyuan (a post-Tianyuan MCRA with Amerindians plus subsequent Tianyuan admixture), or they must have diverged earlier and not admixed (Amerindian/Tianyuan MCRA closer than East Asian/Tianyuan MCRA and no post-Tianyuan geneflow into East Asians). Neither of those are supported by the data, so your speculation doesn't work - Amerindians are not the ancestors of Tianyuan.

Hamar Fox said...

No doubt to be reported by Dienekes before long, but there's a new paper from the Reich lab:

http://biorxiv.org/content/early/2013/12/23/001552

Some general points:

It basically affirms Raghavan et al.'s interpretation, with Amerindians being the product of admixture between two diverged Eurasian populations.

It also adds the interesting fact that there seems to have been two Eurasian hunter-gatherer populations ancestral to modern Europeans (one represented by MA-1 and AG, and the other by La Brana and some others), with a Neolithic element constituting a third.

The two hunter-gatherer populations seem to be closely related (descended from a common ancestral population with no additional admixture), though only one is directly related to Amerindians. Both are equally related/unrelated to other world populations, again with the exception that the MA-1 'ANE' population was more related to Amerindians than the W. European hunter-gatherers were. The lack of an 'Amerindian' component in analyses of La Brana seem now to be explained (credit to Rokus there).

The farmer populations were less related to other Eurasian populations than were the two hunter-gatherer populations because they derived a portion of their ancestry (~40%) from an earlier Eurasian population that didn't share as much common ancestry with all other Eurasians as the ancestors of the HGs (and 60% of the farmer DNA) did before splitting off. This explains, IMO, why some W. Eurasian components are closer to E. Eurasian components than others, even where admixture seems unlikely.

The ANE proportions in modern W. Eurasians are basically as expected, and they map quite well onto affinity with MA-1, though Sardinians appear to have virtually none (despite being moderately related to MA-1), while Greeks and one of the two Basque populations (Pais Vasco) have more than, for example, the English (who have a higher 'Amerindian' score in Dienekes' ADMIXTURE runs than the other two).

The ADMIXTURE analysis is similar in what it shows to Raghavan's. Interestingly, many Amerindian populations show significant W. Eurasian ancestry, although Karitiana still show none, while W. European populations show no non-W. Eurasian ancestry either, so one of those results obviously has to give, and ADMIXTURE, as before, is in itself inconclusive.

MA-1 seems to have been a better representative of the HG ancestry in non-European W. Eurasians than the La-Brana like W. European mesolithics, whose influence doesn't seem to extend much beyond Europe.



German Dziebel said...

@Hamar Fox

"It basically affirms Raghavan et al.'s interpretation, with Amerindians being the product of admixture between two diverged Eurasian populations."

The paper mentions this in passing. It's about admixture in Europe, not America. What's important is that it reaffirms Patterson et al. 2012's conclusion.

"Two Upper Paleolithic Siberian samples project beyond the variation of Europeans
on the second PC (Fig. 2A), suggesting that they may be derive from the Ancient North Eurasian
(ANE) population previously shown to have contributed to Europeans4, 5"

And: "One of the inferred admixture events is the ANE gene flow into both Europe6 and the Americas6 that has previously been documented."

This is different from Raghavan, as I've already pointed out. Considering that the best living representation of ANE are Amerindians, we can safely consider that the data is consistent with a backflow out of the Americas into Europe.

"The two hunter-gatherer populations seem to be closely related (descended from a common ancestral population with no additional admixture), though only one is directly related to Amerindians."

No, the paper actually says: "All three hunter-gatherers and Stuttgart are genetically closer to Native Americans than to other eastern non-Africans" (p. 9, SI 12.5).

"Interestingly, many Amerindian populations show significant W. Eurasian ancestry, although Karitiana still show none..."

Karitiana, Surui and Piapoco stay pure through all the K levels. At K=4 and K=5 we can see Amerindian GREEN admixed into Siberia and Europe. At K=3 northern Amerindians are a mix of southern Amerindians at K=2 and southern Amerindians at K=3, not of West Eurasians and East Asians. In the New World we find pure BLUE, pure YELLOW and a mix of both. This suggests that Amerindians predate the split between East Asians and West Eurasians, contra Raghavan et al.

Also of note:

"Karitiana, on the other hand appear generally closer to present-day west Eurasians than all other ENA [eastern non-African) populations." (SI, p. 70).

German Dziebel said...

@Tobus

"Raghavan etc al. aren't the ones saying that Mal'ta "confirms the greater proximity of ancient Eurasians to modern Amerindians than to modern Eurasians", you are."

But they are showing it clearly at SI 22. It's a more precise way to measure genetic proximity than PCAs. Same for Tianyuan and Karitiana vs. modern East Asians. The new paper by Lazaridis et al. further confirms this (see my comment at Hanar Fox) when it comes to the ancient European samples. So you have Tianyuan, Mal'ta, Stuttgart, Loschbour and Motala all supporting my inference.

"the issue I raised is that twice you have used the term "Eurasian" instead of specifying "West Eurasian"/"East Asian" to create the false impression that both populations have the same genetic affinities to Amerindians/Mal'ta. Is this intentional or do you not know that they have different genetic affinities to these groups?"

You are trolling now. Like I said, the issue you're raising is irrelevant to this discussion at this point. What's important is that you've consistently suppressed the data indicating the proximity of Amerindians to all of West Eurasians to the exclusion of East Asians, the data indicating the special proximity of northern Amerindians to East Asians and the proximity of Amerindians to ancient Eurasian samples that pre-date modern East Asians.

"You are now speculating is that both Tianyuan and nothern Americans are descended from southern Americans and that northern Americans are further from Tianyuan than southern ones... are you saying northern Americans diverged pre-Tianyuan and somehow southern Americans migrated through them without admixing to get into Asia? "

You're very incoherent, so I don't know for sure where I should be correcting your nonsense. Northern Amerindians diverged before East Asians, would-be modern East Asians migrated to Asia to mix with Tianyuan. They are likely closer to Tianyuan than northern Amerindians but not as close to Tianyuan as southern Amerindians. Of course, southern Amerindians just survived better in South America but they used to be much more widespread and northerly (likely coastal) in their distribution in the New World, so they didn't need to jump over anybody to get to East Asia the first time.

"East Asians must either be closer to Tianyuan (a post-Tianyuan MCRA with Amerindians plus subsequent Tianyuan admixture)."

Northern Amerindians, again.

""Neither of those are supported by the data, so your speculation doesn't work - Amerindians are not the ancestors of Tianyuan."

Karitiana are the closest among living people to Tianyuan. Tianyuan pre-dates genetically (and chronologically) all of modern East Asians. This means that Karitiana is less derived than modern East Asians. These are facts and logic. The origin of Tianyuan from an American antecedent is a hypothesis and, as I said before, we need ancient DNA from the Americas to test it. But in light of Raghavan et al.'s data, Tianyuan cannot be ancestral to Amerindians unless it's shown that it's also ancestral to West Eurasians. The data doesn't bear out the latter, hence it's likely that Tianyuan is a New World offshoot.

Eastern View said...

So, according to Reich, Near Easterners are a mix of people more related to East Eurasians and a basal Eurasian population.
And since modern Europeans are admixtures of farmers and hunter-gatherers, that makes Europeans admixtures no matter which way you look at it.

Eastern View said...

I've been saying all along that early Eurasians split on the Iranian plateau. Those that went west were Basal Eurasians and those that went east were "East Eurasians". It's just time to decided whether to identify with the Basal or the East Eurasian and get out of this identity crisis.
(I'm half teasing.)

Hamar Fox said...

Eastern View,

I've been saying all along that early Eurasians split on the Iranian plateau. Those that went west were Basal Eurasians and those that went east were "East Eurasians". It's just time to decided whether to identify with the Basal or the East Eurasian and get out of this identity crisis.

Inoorrect (again). There's no basal Eurasian vs. East Eurasian. Various figures show what the actual relationships seem to be at this point. Clearly East Eurasians are irrelevant in the formation of any of the three fundamental components identified, which would have developed the same way even if East Eurasians had never existed. There's no ambiguity in the paper on that point. You should try reading the paper sometime.

German Dziebel,

This is different from Raghavan, as I've already pointed out. Considering that the best living representation of ANE are Amerindians, we can safely consider that the data is consistent with a backflow out of the Americas into Europe.

No, if you read the paper, they explicitly state that MA-1 is a better representation of 'ANE' than modern Amerindians.

No, the paper actually says: "All three hunter-gatherers and Stuttgart are genetically closer to Native Americans than to other eastern non-Africans" (p. 9, SI 12.5).

The the closer relationship between ANE and Amerindians is the only global relationship that differs between the two HG populations. I haven't yet read all of the SI, but the above quote is fine by me, since it supports what I've argued previously that admixture from one of these populations into another would automatically draw all of these populations closer to the admixed one.

Tobus said...

@German:
But they are showing it clearly at SI 22. It's a more precise way to measure genetic proximity than PCAs.

If you want to take a single graph which a panel that will underestimate European affinity and ignore the 8 others that disagree with you then that's your call. Just don't expect anybody else to accept the conclusions you draw from it, and maybe think twice before you call others "biased and self-serving".

Like I said, the issue you're raising is irrelevant to this discussion at this point

Not to me it isn't, which is why I raised it in the first place. Although your insistence on changing the subject makes me feel I've made my point somewhat.

Northern Amerindians diverged before East Asians, would-be modern East Asians migrated to Asia to mix with Tianyuan. They are likely closer to Tianyuan than northern Amerindians but not as close to Tianyuan as southern Amerindians

I understand what you are hypothesising, but it implies that northern Amerindians had already diverged from the southern Amerindian lineage before Tianyuan - otherwise they'd have the exact same ancestral relationship to Tianyuan as southern Amerindians do. Is it part of your speculation that the north/south Amerindian split had already occurred before the Amerindian/Tianyuan split? If not, please explain why your theory assumes north Amerindians are further from Tianyuan than southern Amerindians?

Northern Amerindians, again.

Again, when in your speculation did these northern Amerindians diverge from southern Amerindians - before or after Tianyuan?

Tianyuan cannot be ancestral to Amerindians unless it's shown that it's also ancestral to West Eurasians

"Cannot"? Raghavan gives a perfectly good explanation for this - "Amerindian" represents an East Asian/West Eurasian hybrid.... if Tianyuan is ancestral to some 70-80% of Amerindian DNA and Mal'ta is ancestral to the rest, then, contrary to your statement, Tianyuan is ancestral to Amerindians without being ancestral to West Eurasians.

Rokus said...

[...] would-be modern East Asians migrated to Asia to mix with Tianyuan. They are likely closer to Tianyuan than northern Amerindians but not as close to Tianyuan as southern Amerindians. Of course, southern Amerindians just survived better in South America but they used to be much more widespread and northerly (likely coastal) in their distribution in the New World, so they didn't need to jump over anybody to get to East Asia the first time.`
No, this doesn't explain how northern Amerindians moved away from a common Amerindian source into "the special proximity of northern Amerindians to East Asians". According to your scheme, Tianyuan shared a much older ancestry with southern Amerindians but how you think this can be reconcilated with home-grown northern Amerindian divergence and distances to an outgroup like Tianyuan that per definition should remain equal? Or do you imply a more recent immigration event into Northern America you still didn't tell us about?
Moreover, I miss the indication that Tianyan-modern East Asian relatedness became skewed by more recent events, like may have been the case in northern America and for sure in northern Eurasia.
Hence, I think it is much more likely that Tianyuan was a pre-East Asian hybrid between a founding northern Eurasian population and a local archaic population. Evidence of both components can be found all over. This would result in a single hybrid component that by it's nature can't be measured in MA-1, even though Amerindians might show varying degrees of relatedness regarding their common source.

Hamar Fox said...

Aha, I've just had a look at the high-res ADMIXTURE analysis, and the W. European HGs have a clear Amerindian signal, so if La Brana were included they should too. So I wasn't wrong in saying that admixture signals appear in unrelated but similar populations, and it now explains why populations with little to no ANE but some WHG are still part of the 'Amerindian' cline in many analyses.

German Dziebel said...

@Hamar Fox

"No, if you read the paper, they explicitly state that MA-1 is a better representation of 'ANE' than modern Amerindians."

I said "living Amerindians." Mal'ta is an ancient population. But even there, Russians, Finns and Mordvinians fall outside of that pattern having an extra amount of Karitiana-specific admixture.

"admixture from one of these populations into another would automatically draw all of these populations closer to the admixed one."

Sorry, I'm not following it. Which population is admixed into which?

Rokus said...

Ahh, U2a1 was a typo. I meant U5a1 being the most basal mtDNA haplogroup, based on the genotypes of Sima de los Huesos and MA-1.

Hamar Fox said...

German Dziebel,

Sorry, I'm not following it. Which population is admixed into which?

I'd previously argued that populations like Druze, Mozabite etc. were pulled toward Amerindians (or, rather, Amerindians were pulled toward them) because, despite not being directly related to MA-1, they were fundamentally related to him through a general W. Eurasian-ness, which I believed already existed by that time.

The fact that EEF also are more related to Amerindians than to other E. Eurasians generally supports my earlier interpretation. I'm not going to deny that certain details can also be interpreted your way, but, because I don't think your theories are tenable overall, they're not the interpretations I make.

German Dziebel said...

@Tobus

"If you want to take a single graph which a panel that will underestimate European affinity and ignore the 8 others that disagree with you then that's your call."

It's not just me who prefers graphs derived from f-statistics to PCAs. Comp.: "PCA is a powerful technique for measuring genetic similarity, but its interpretation in terms of history is difficult, as gradients of variation due to admixture may arise under a variety of different histories." (Lazaridis 2013).

"Raghavan gives a perfectly good explanation for this - "Amerindian" represents an East Asian/West Eurasian hybrid.... if Tianyuan is ancestral to some 70-80% of Amerindian DNA and Mal'ta is ancestral to the rest, then, contrary to your statement, Tianyuan is ancestral to Amerindians without being ancestral to West Eurasians."

Raghavan is blatantly wrong as I showed earlier. There's no Western Eurasian admixture in pure Amerindians such as Karitiana but there's an Amerindian admixture in Mal'ta and to a lesser degree in other West Eurasian populations. This is what's in the data across the board.

"otherwise they'd have the exact same ancestral relationship to Tianyuan as southern Amerindians do."

It doesn't matter when northern and southern Amerindians diverged relative to Tianyuan. What matters is that modern East Asians are derived from a different population than Tianyuan. They only admixed with Tianyuan. And hence we see a) quite specific similarities between Amerindian and East Asian genetics (and Amerindians arguable expressing some key East Asian traits stronger than East Asians themselves) and clear break between pre-Mongoloid East Asians and modern East Asians in the Holocene but 3) don't see East Asians in Siberia until much later than Mal'ta, the likely source for East Asians is North America.

@Rokus

"No, this doesn't explain how northern Amerindians moved away from a common Amerindian source into "the special proximity of northern Amerindians to East Asians". "

We are talking about the last glacial age. There must have been some geographic isolation factor going on in North America at that time that generated the genetic specificity of Na-Dene and Eskimo-Aleuts. So it's likely drift and not admixture that pulled them away from the general Amerindian source.

"Hence, I think it is much more likely that Tianyuan was a pre-East Asian hybrid between a founding northern Eurasian population and a local archaic population."

Amerindians are definitely related to a northern Eurasian population you're talking about, but when it comes to facts, Fu et al.'s Table 1 puts Han ahead of Sardinian and French when it comes to genetic similarity with Tianyuan. And Karitiana is still the closest.

German Dziebel said...

@Hamar Fox

"I'm not going to deny that certain details can also be interpreted your way, but, because I don't think your theories are tenable overall, they're not the interpretations I make."

You are free to continue to believe that the Sun rotates around the Earth because the opposite is "untenable overall." But, mind you, science is in the details, which you're brushing aside in favor of your bird's eye view biases.

" fundamentally related to him through a general W. Eurasian-ness"

What are you talking about? Amerindians are extreme East Eurasians. Closest to Mal'ta, closest to Tianyuan. How can the Druze be related to them through a general W. Eurasianness? Unless Amerindians are basal Eurasians (close to Tianyuan and Druze at the same time), which would make a whole lot of sense when it comes to the data.

Rokus said...

We are talking about the last glacial age. There must have been some geographic isolation factor going on in North America at that time that generated the genetic specificity of Na-Dene and Eskimo-Aleuts. So it's likely drift and not admixture that pulled them away from the general Amerindian source.
Even so drifted population A should keep the same genetic distance like any other member B-Z of the same unadmixed population with regard to an outgroup. There is no way that one subgroup will differentiate more from the ancestral group than any individual member. Hence, Tianyuan can't be more similar to southern Amerindians than to northern Amerindians, especially since Tianyuan is much older than the Last Glacial Age.

Fu et al.'s Table 1 puts Han ahead of Sardinian and French when it comes to genetic similarity with Tianyuan. And Karitiana is still the closest.
Sure, Karitiana has more of the ancestral European component than the Tianyuan hybrid had. Still, the local archaic component in Tianyuan is best preserved in Karitiana. The low distance between Han and Papuans probably suggests the existence of a third, more southern archaic element that however didn't affect Kiritiana or Tianyuan. I don't see how migration arrows can solve this equation equally elegant.

German Dziebel said...

@Rokus

"Even so drifted population A should keep the same genetic distance like any other member B-Z of the same unadmixed population with regard to an outgroup. There is no way that one subgroup will differentiate more from the ancestral group than any individual member. Hence, Tianyuan can't be more similar to southern Amerindians than to northern Amerindians, especially since Tianyuan is much older than the Last Glacial Age."

Fu et al. didn't conduct/publish a comparison between Tianyuan and Na-Dene, so I don't know for sure but considering that East Asians are pulled toward Na-Dene and they are less Tianyuan than Karitiana, I just deduced that Na-Dene must have diverged from southern Amerindians/Tianyuan. Na-Dene contain the same autosomal component as Karitiana (and the same haploid lineages as found further down south but at different frequencies). Admixture happens between diverged populations. So they diverge before admixture can happen.

"The low distance between Han and Papuans probably suggests the existence of a third, more southern archaic element that however didn't affect Kiritiana or Tianyuan."

I agree. There could have been several distinct archaic populations in old East Asia with which the incoming Amerindian-looking East Asians admixed.

"Sure, Karitiana has more of the ancestral European component than the Tianyuan hybrid had. Still, the local archaic component in Tianyuan is best preserved in Karitiana. ...I don't see how migration arrows can solve this equation equally elegant."

Could you re-phrase your solution to the situation? I'm not 100% following it now.

Hamar Fox said...

German Dziebel,

How can the Druze be related to them through a general W. Eurasianness?

I said they were related to MA-1 through a general W. Eurasianness. If Druze are related to MA-1, and MA-1 admixed into Amerindians, then Amerindians will be related to Druze. MA-1 has no direct affinity with the Druze, but he seems to have been connected to them on some basic level.

Think of a newly-discovered island with two genetically identical tribes inhabiting it, each on the other side of an insurmountable wall, which neither tribe can or tries to breach.

Say some Irish stop by and mix with one tribe but not the other. 500 years later, the two tribes are genetically analysed. The admixed tribe is unsurprisingly more related to the Irish than the unadmixed tribe. But the admixed tribe is also more related to the French, to the Germans, to the Italians, to the Poles, Greeks, Turks, Armenians, Moroccans, Saudis, Saami, Pakistanis etc. than the unadmixed tribe. Maybe, if the Irish are closer to Han (or insert any other population) than this hypothetical island population is, the admixed population will also be more related to the Han than the unadmixed tribe is. It's all a sliding scale based on not just the admixing population but the wider relationships of said admixing population relative to the relationships of the to-be-admixed population.

terryt said...

"The low distance between Han and Papuans probably suggests the existence of a third, more southern archaic element that however didn't affect Kiritiana or Tianyuan".

I am very much inclined to agree with that idea. I'm sure there was some southern population that contributed to Papuans but contributed very little to any other population.

"Even so drifted population A should keep the same genetic distance like any other member B-Z of the same unadmixed population with regard to an outgroup. There is no way that one subgroup will differentiate more from the ancestral group than any individual member. Hence, Tianyuan can't be more similar to southern Amerindians than to northern Amerindians, especially since Tianyuan is much older than the Last Glacial Age".

Exactly.

"modern East Asians are derived from a different population than Tianyuan. They only admixed with Tianyuan".

German, I agree with you. Tianyuan represents just a proportion of the modern 'East Asian' gene pool. Modern East Asians most probably descend largely from a more westerly population than was present in Tianyuan 40,000 years ago. It is possible Tianyuan didn't even have the EDAR370A mutation.

"Na-Dene contain the same autosomal component as Karitiana (and the same haploid lineages as found further down south but at different frequencies)".

But different clades of those 'same haploid lineages'.

"hence we see ... clear break between pre-Mongoloid East Asians and modern East Asians in the Holocene"

Yes. The big expansion of the East Asian phenotype through China, and points north and south, post-dates Tianyuan, and Mal'ta. The East Asian phenotype's movement south is probably as late as the Neolithic even.

"but 3) don't see East Asians in Siberia until much later than Mal'ta, the likely source for East Asians is North America".

The second comment here does not necessarily follow from the first. The more obvious conclusion is that a 'Mal'ta' population was present in Siberia before any 'East Asian' population was able to enter the region. Haplogroup evidence supports such a conclusion. I realise you totally dismiss haplogroups but I feel you do that because such evidence does not fit what you want to believe. I've just finished reading a paper on possible hybridism between two species of Pterodroma (petrel) species that uses mt-DNA as evidence. We also have many interesting and influential studies on the mt-DNA phylogeny of cattle, dabbling ducks and so on. Are you claiming that all conclusions in all these studies are completely false? Or do you believe humans are somehow completely different from all other species?

German Dziebel said...

@ Hamar Fox

Your general West Eurasianness has to "live" in some modern populations more than in others. You're saying that Druze and Mozabites are pulled toward Amerindians via Mal'ta, but many other West Eurasians should be pulled way more toward them than the Druze. Why singling Druze out? There's a special connection between Druze and northern Amerindians on the mtDNA side (higher than normal frequencies of hg X), so I thought there was something special about the two autosomally.

Plus a hypothetical West Eurasian population should have other components that emerged post-West Eurasianess. We don't see those in Amerindians. Ancient West Eurasianness couldn't have been put in a test tube and sent to Mal'ta who in turn waited for East Asian-derived Amerindians to be passing by in order to pass that test-tube along.

Rokus said...

"Sure, Karitiana has more of the ancestral European component than the Tianyuan hybrid had. Still, the local archaic component in Tianyuan is best preserved in Karitiana. ...I don't see how migration arrows can solve this equation equally elegant."

Could you re-phrase your solution to the situation? I'm not 100% following it now.

According to Fu et al. (2012)'s Table 1, Tianyuan's chromosome 21 is virtually as close to Han as to Sardinians, while only Karitiana have a better match. However, Karitiana themselves make a better match with French and Sardinians than with Tianyuan, suggesting part of the Karitiana similarity with Tianyuan might be due to an ancient "European" component. This component may have been once all pervasive in the east, as e.g. attested by the Old Man of Upper Cave 101 near Peking whose orbits are relatively low and rectangular, not unlike the European Cro Magnon 1 skull that is about the age of Mal’ta boy. Since this component "also" postdated Tianyuan, a progressing admixture process would help explaining why modern East Asians are slightly more similar to Europeans than Tianyuan. There may be a huge dating problem here, since in China archaic types often postdate Tianyuan, or otherwise different phenotypes may have coexisted there for a long time, obfuscating the precise details of this process. It's clear Tianyuan is not altogether "archaic", it's a hybrid that already carries a presumably local archaic component. Since Karitiana is most similar to Tianyuan, I suggest the archaic component in Tianyuan is slightly better preserved in Karitiana than e.g. in modern Han. This may be due to progressive "European" admixture in East Asia like in Karitiana, combined with the growing influence of more southern admixed local types that didn't reach Amerindian populations.

I gather you'd preferably called the archaic component in Tianyan "American", and the second archaic component of modern East Asians "North American"? Unfortunately we can't check this in the table with a North Amerindian specimen, all we see in East Asia is that Dai (south) are slightly more divergent from Kiritiana than Han (north), and the Papua are significantly more divergent. The Papuan population is more in agreement with and admixture between ancient Europeans and, unlike Tianyuan, the second "southern" archaic component in East Asians. I'm afraid this would supply contradictory evidence for a North American origin of this component.
Or was it the reverse, that old local Cro Magnoid specimens represent the non-Amerindian archaic popuations? This does not change that Tianyuan was strongly admixed with a local archaic component that progressively diluted, not an ancient Amerindian prototype.

German Dziebel said...

@Rokus

Thanks - now it's clear.

"However, Karitiana themselves make a better match with French and Sardinians than with Tianyuan, suggesting part of the Karitiana similarity with Tianyuan might be due to an ancient "European" component."

"This component may have been once all pervasive in the east, as e.g. attested by the Old Man of Upper Cave 101 near Peking whose orbits are relatively low and rectangular, not unlike the European Cro Magnon 1 skull that is about the age of Mal’ta boy."

UC 101's Amerindian and Circumpacific affinities have been noted multiple times. Often it appears the closest to ancient Lagoa Santa in Brazil. See, e.g.., Hubbe et al. 2011. Paleoamerican morphology in the context of European and east Asian late Pleistocene variation: implications for human dispersion into the new world.

UC 101's date it uncertain and ranges between 12,000 (Kamminga 1992) -30,000 YBP. But it's clear that it predates "Mongoloids." UP Europeans are not as close to UC 101, although all of them form a cluster in contrast to a) Mongoloids, b) modern African blacks, 3) modern Europeans, on the one hand, and AMH in Africa, on the other.

UC 101'a special proximity to Lagoa Santa parallels the special proximity of Tianyuan to Karitiana.

In a word, the data doesn't bear out the special connection between pre-Mongoloids in Asia and West Eurasians to the exclusion of Amerindians. It doesn't quite fit to argue that West Eurasians admixed more into Karitiana than into East Asians, and hence Tianyuan is more like Karitiana because if that happened Tianyuan would've been closer to West Eurasians than to Karitiana. An admixture of Karitiana into West Eurasians, on the one hand, and into ancient East Asians still seems to be the strongest - albeit unusual - option.

"I gather you'd preferably called the archaic component in Tianyan "American", and the second archaic component of modern East Asians "North American"? "

yes.

"Unfortunately we can't check this in the table with a North Amerindian specimen, all we see in East Asia is that Dai (south) are slightly more divergent from Kiritiana than Han (north),"

I agree we need something else to explain the greater proximity of Karitiana to Han than to Dai. And a reasonable option I have is the admixture of northern Amerindians into ancient East Asians (=modern East Asians) AND within the New World into southern Amerindians such as Karitiana. That this is indeed what happened is suggested by the fact that the dates for Clovis-type points become younger as one goes north into Alaska (and arguably, into Ushki and Uptar in NE Asia) and into South America (fishtail points).

This seems to me to be the "best of all worlds" option to explain the simultaneous proximity of Amerindians to a) ancient and modern West Eurasians and to b) ancient and modern East Eurasians.

German Dziebel said...

@TerryT

"The second comment here does not necessarily follow from the first."

The second comment derived from the first THREE.

" Haplogroup evidence supports such a conclusion. "

I showed you that it doesn't.

"But different clades of those 'same haploid lineages'."

Na-Dene and Eskimo-Aleuts share not just A with the rest of Amerindians but A2. This confirms their common descent. Y-DNA is consistent with it with C3a shared between Na-Dene and a slew of other North American populations. Hg A2a is also found in Siberia supporting the idea of a back migration.

"Are you claiming that all conclusions in all these studies are completely false? Or do you believe humans are somehow completely different from all other species?"

We have much more data on the evolution of humans and hominins than any other taxa. hence, what we learn from the former should be applied to the latter, not the other way around. I don't deny the notion of a haplogroup, but the methodology of connecting the haplogroups together into a hierarchical order, the lack of site ancestral state verification through ancient hominin DNA and the abundance of recurrent mutations in mtDNA haplogroups are untenable.

Rokus said...

It doesn't quite fit to argue that West Eurasians admixed more into Karitiana than into East Asians, and hence Tianyuan is more like Karitiana because if that happened Tianyuan would've been closer to West Eurasians than to Karitiana.
Instead, my position is this: West Eurasian (or rather Cro Magnoid phenotype) admixtures introgressed more into the ancestors of Karitiana than into East Asians since Tianyuan.
I agree that Kiritiana may represent Tianyuan better than East Asians, and Lagoa Santa in Brazil most likely gives us an impression of how this resemblance once looked like - probably slightly more Cro Magnoid than Tianyuan. However, I would like to draw your attention on the genetic triangle defined by the proximity of Sardinians with Han and Tianyuan on one side and the proximity of Sardinians with Dai and Papuans on the other side. Since Sardinians only have an ancestral relation with Amerindians (0.8% ANU, Lazarindis et al.Table S12.7), this affinity on chromosome 21 can't be due to Amerindian backmigrations - not even from Siberia. Some pre-Amerindian Upper Paleolithic population must have expanded into all of these areas (North, Central and East Asia, Oceania and the Americas) in expansion waves that actually can't be distinguished from initial AMH expansions. The nature of this triangle, considering apparent local admixtures as explained in my previous answer, excludes Kiritiana but favours modern Sardinians as the closer surviving relatives of these people.

terryt said...

"We have much more data on the evolution of humans and hominins than any other taxa. hence, what we learn from the former should be applied to the latter, not the other way around. I don't deny the notion of a haplogroup, but the methodology of connecting the haplogroups together into a hierarchical order, the lack of site ancestral state verification through ancient hominin DNA and the abundance of recurrent mutations in mtDNA haplogroups are untenable"

Sounds as though you do believe that all conclusions in all those studies are completely false. You really do have a closed mind. Or do you believe that God created humans but all other species evolved?

"all we see in East Asia is that Dai (south) are slightly more divergent from Kiritiana than Han (north), and the Papua are significantly more divergent".

All of which makes complete sense. The southern China Dai population is preseumably an mixture of 'East Asian' (Mongoloid) with an older 'Papuan' population from the region. This 'Papuan' element is not present in Kiritiana, who are more closely connected with northern Chinese, who have more of the 'East Asian' (Mongoloid) element than do the Dai. And the Papuans have virtually no East Asian element apart from a small amount along the northern coastline of New Guinea and in Austronesian-speaking regions of Melanesia.

"I agree we need something else to explain the greater proximity of Karitiana to Han than to Dai".

See above, although as that explanation doesn't fit your belief system I presume you will dismiss it.

"This does not change that Tianyuan was strongly admixed with a local archaic component that progressively diluted, not an ancient Amerindian prototype".

Quite. The presence of mt-DNA B suggests Tianyuan was part of a northerly movement, possibly from as far south as SE Asia. It had become admixed with the East asian element however.

"UC 101'a special proximity to Lagoa Santa parallels the special proximity of Tianyuan to Karitiana".

So, German, it remains to be seen whether B is ancient in America or arrived after the other mt-DNAs. By the way, you are still to inform us of mt-DNA's subgroups in America.

Tobus said...

@German:
It's not just me who prefers graphs derived from f-statistics to PCAs.

I'm am pleased that you defer to Lazaridis, but the quote you provided doesn't say he prefers f-stats to PCAs, it says PCA's are excellent at showing who is closer to whom, but not so great at showing us where this affinity comes from.

Raghavan is blatantly wrong

... and yet Lazaridis agrees with him. Are we only considering Lazaridis and expert when he agrees with you?

There's no Western Eurasian admixture in pure Amerindians such as Karitiana

By "pure" I assume you mean has a solid colour in ADMIXTURE. We know that Amerindians have low genetic diversity and that they have been isolated with very low admixture since divergence. This is exactly the kind of thing that ADMIXTURE will pick up - but it doesn't mean the Amerindian component is unadmixed. Consider the possibility that the "Amerindian" component is formed from a mixture of ancient East Asian and West European DNA. The subsequent bottleneck and isolation in America would makes it any easy target for ADMIXTURE and it would show up early... and because it contains some West Eurasian alleles this "early" component would also show up in some West Eurasian populations. What we see in the ADMIXTURE results is exactly what we'd expect to see if Amerindian is a "Tianyuan-lie/Mal'ta-like" hybrid.

It doesn't matter when northern and southern Amerindians diverged relative to Tianyuan. What matters is that modern East Asians are derived from a different population than Tianyuan. They only admixed with Tianyuan.

It certainly does matter, in fact it completely undermines your speculation of an Amerindian ancestry for Tianyuan. In such a scenario the East Asian lineage (whichever "different population" this is) must have diverged *before* Tianyuan otherwise East Asians would be closer to Tianyuan than Amerindians are (recent East Asian/American MCRA plus Tianyuan admixture). But if they did diverge before then East Asians would be *further* from Amerindians than Tianyuan is, not closer (due to the more recent Tianyuan/American MCRA).

An "Amerindians before Tianyuan" supposition just doesn't fit the facts and so can be discarded... Tianyuan must be ancestral to Amerindians and not the other way around.

German Dziebel said...

@Rokus

"Since Sardinians only have an ancestral relation with Amerindians (0.8% ANU, Lazarindis et al.Table S12.7), "

The trick here is that Amerindians are closer to all three of the ancient reference populations in Table S12.7 than any other modern population. ("All three hunter-gatherers and Stuttgart are genetically closer to Native Americans than
to other eastern non-Africans.") So, we can't identify Karitiana exclusively with ANE. The Amerindian component is present across West Eurasia (consistently with haploid data) in addition to East Eurasia.

"Some pre-Amerindian Upper Paleolithic population must have expanded into all of these areas (North, Central and East Asia, Oceania and the Americas) in expansion waves that actually can't be distinguished from initial AMH expansions. "

I agree that there was this population. I just identify it with ancient Amerindians. Otherwise, how else can we get special proximity between Karitiana and Tianyuan in the East, Karitiana and Mal'ta in the North and Loschbour, Stuttgart and Motala in the West? Not to mention Yuzhnyi Olenyi Ostrov for which we have only haploid data This is consistent with Fu et al. where Karitiana gets the shortest distance from Tianyuan, Han, Dai, Sardinians and French.

It's possible that human genome gets pulled away from this Amerindian-derived core in the Sahul, Africa and maybe Near East, but this is all going to be due to archaic admixture (Denisovan, African archaics and West Asian Neandertals).

"West Eurasian (or rather Cro Magnoid phenotype) admixtures introgressed more into the ancestors of Karitiana than into East Asians since Tianyuan."

From this I can infer that you don't believe Amerindians is an offshoot of East Asians. What's the parent population of Amerindians, in your view?

terryt said...

Can't resist this little one at German:

"Na-Dene and Eskimo-Aleuts share not just A with the rest of Amerindians but A2 ... Hg A2a is also found in Siberia supporting the idea of a back migration".

Interesting that you call on mt-DNA haplogroups when you think it might support your belief. The trouble is that the above is fairly convincing evidence that you are wrong. Hg A2a is only just present in Siberia, only in the very far northeast. While I agree it might indicate a migration from America into East Asia it is far from convincing evidence that any other haplogroups did so. And that idea is especially unlikely when we consider that in America A2a is basically an Eskimo/Na-Dene haplogroup, and is a just one of the 6 basal branches within A2. The others are A2b, A2r, A2s, A2z and the hugely diversified A2 everything else. So many haplogroups in it the compilers reached Z, and started again: A2aa, A2ab, A2ac etc.

And there are those who claim little work has been done on Native Americans. Get real.

Rokus said...

The trick here is that Amerindians are closer to all three of the ancient reference populations in Table S12.7 than any other modern population. ("All three hunter-gatherers and Stuttgart are genetically closer to Native Americans than to other eastern non-Africans.")
As a matter of fact this also has the reverse result that West Eurasians are most likely a source population to Native Americans.

I just identify it with ancient Amerindians. Otherwise, how else can we get special proximity between Karitiana and Tianyuan in the East, Karitiana and Mal'ta in the North and Loschbour, Stuttgart and Motala in the West? [...] This is consistent with Fu et al. where Karitiana gets the shortest distance from Tianyuan, Han, Dai, Sardinians and French.
Again, this relatedness works both ways - except for the proximity with Han that must be due to the East Asian component in Amerindians (not to be confused with MA-1).

It's possible that human genome gets pulled away from this Amerindian-derived core in the Sahul, Africa and maybe Near East, but this is all going to be due to archaic admixture (Denisovan, African archaics and West Asian Neandertals).
Then why the genetic distances with South East Asia/Oceania are much less variable when compared with Sardinians? Papuans are closer to Sardinians than to Karitiana. Compared with Sardinians the Papuans are just 1.3% more divergent than Dai (285 differences more), while compared with Karitiana Papuans are 10.3% more divergent than Dai (2079 more differences, this is 7.3 times more!). Hence your suggestion this anomaly in Karitiana differences with Papuans can be explained by archaic admixtures is invalid. Actually, this is quite impelling counter evidence for an Ameridian identity of the AMH source population, and rather supports affinity with a Sardinian-like AMH component.

I figure less parsimonious Out of America explanations are still open, like Amerindians that migrated first to Europe before they continued to Oceania? I only hope here you won't repeat the same anti-Popper mistakes of the Kurganists, Orientalists and ROA parties.

"West Eurasian (or rather Cro Magnoid phenotype) admixtures introgressed more into the ancestors of Karitiana than into East Asians since Tianyuan."

From this I can infer that you don't believe Amerindians is an offshoot of East Asians. What's the parent population of Amerindians, in your view?

I think Amerindians have two parent populations, one derived from West Eurasians and the other derived from an already heavily admixed local archaic component in northern East Asia. I don't think I say anything new here.

German Dziebel said...

@terryT

You make absolutely no sense. Why don't you study the evidence first and then contribute. I can't even react to what you just wrote.

German Dziebel said...

@Rokus

"Papuans are closer to Sardinians than to Karitiana."

But Papuans are closer to Karitiana than to French. How is it possible if French and Sardinian are closer to each other than to other populations?

Sardinians are an anomaly here. If you have supporting evidence from other studies, please send a link.

"Hence your suggestion this anomaly in Karitiana differences with Papuans can be explained by archaic admixtures is invalid."

We do have enough evidence in support of Denisovan admixture in Papuans followed by Dai and Karitiana. This may create the observed divergence between Karitiana and Papuan. Sardinians can hardly be closer to Papuan considering that Europeans tend to have less of that admixture than Amerindians and SE Asians. French in Fu follow this pattern nicely.

" I only hope here you won't repeat the same anti-Popper mistakes of the Kurganists, Orientalists and ROA parties."

I don't understand exactly what you mean here. I do postulate a single source for anatomically and behaviorally modern humans, not a patchwork of admixtures only. This is what unites my thinking with OOA. But I do see several instances of admixture that pulls Old World populations away from the source, in line with some of the multiregional thinking.

Eastern View said...

Rockus, if you understood physical anthropology a bit more, you'd see that Upper Cave 101 has a long broad face and have the exact opposite facial contour of Jomon or Cro-Magnon. Some of the common features all three share are long-headedness (front-to-back, not up and down), deep square eye-sockets, and robustness. But these are archaic traits shared by all pre-Neolithic people. They have no meaningful phylogenetic use.

For a better idea, see these pictures

Cro-magnon (approximated) by this actor: http://z.about.com/d/movies/1/0/5/p/7/jrhd18b.jpg

pure Jomon: http://imageshack.us/a/img480/4221/marainiainu45bk.jpg

Upper Cave 101 (approximated by this Taiwanese aboriginal):
http://www.roc-taiwan.org/public/Data/24218234453.jpg

terryt said...

"As a matter of fact this also has the reverse result that West Eurasians are most likely a source population to Native Americans".

But there is no way German or Eastern View are going to consider that possibility for a moment. They each have a justified scepticism of haplogroup phylogeny but their faith is ADMIXTURE analyses is touchingly childlike.

"I think Amerindians have two parent populations, one derived from West Eurasians and the other derived from an already heavily admixed local archaic component in northern East Asia. I don't think I say anything new here".

That is what all of us, except for German and Eastern View, understand the evidence to demonstrate.

"You make absolutely no sense. Why don't you study the evidence first and then contribute. I can't even react to what you just wrote".

Read it again then. From the perspective that humans may not have emerged from America, although I realise that perspective is so heavily imprinted in your psyche it will be impossible for you to do so.

Rokus said...

"Papuans are closer to Sardinians than to Karitiana."

But Papuans are closer to Karitiana than to French. How is it possible if French and Sardinian are closer to each other than to other populations?
This is not so difficult, the difference of just 662 mutations extra between French and Papuans probably comes from the 794 mutations that French share with Han (compared with Sardinians). Sardinians are known for being an isolated group, that preserved some old features.

Sardinians are an anomaly here. If you have supporting evidence from other studies, please send a link.
No, not an anomaly. They are conservative. This became clear in the studies on Ötzi. BTW, be aware that "conservative" does not always means "closer to Papuans", since Tianyuan is both conservative and much further away from Papuans. The same probably applies to Karitiana, equally without this same result of closer relatedness.

We do have enough evidence in support of Denisovan admixture in Papuans followed by Dai and Karitiana. This may create the observed divergence between Karitiana and Papuan.
Indeed. However, your problem is why Karitiana diverge more from Papuans than Sardinians.

Sardinians can hardly be closer to Papuan considering that Europeans tend to have less of that admixture than Amerindians and SE Asians. French in Fu follow this pattern nicely.
Still, this is what Fu et al. published in their Table 1:
Sardinian-Papuan 21,968 nucleotide differences in chromosome 21
Karitiana-Papuan 22,210 nucleotide differences in chromosome 21
The latter despite the proximity of East Asian populations like Han, that over time could have passed some of their Karitiana-shared nucleotides to Papuans.

I do postulate a single source for anatomically and behaviorally modern humans, not a patchwork of admixtures only.
Maybe there was a single node of expansion within a much more complicated patchwork. However, the patchwork of relatedness that show Fu et al. is straightforward enough to single out at least one possible node of expansion that wasn't Amerindian.

German Dziebel said...

@Rokus

"However, your problem is why Karitiana diverge more from Papuans than Sardinians."

It's not just my problem. It's everybody's problem, as there's no easy explanation for it under the current theories either.

If you follow Fu's values for Sardinian vs. African and French vs. African, you'll see that Sardinians are not systematically pulled toward Africans vs. French. Only Mandenka is closer to Sardinians than to French, which is likely an effect of some late gene flow between southern Europe and west Africa. If Sardinians were "conservative," then, at least under the mainstream model, they would have been closer not just to Papuans but to SSAfricans, too. But they are not. Hence, it's the special connection between Sardinians and Papuans that needs to be explained.

From (Lipson M, Loh PR, Levin A, Reich D, Patterson N, Berger B (2013) Efficient moment-based inference of admixture parameters and sources of gene flow. Mol Biol Evol 30, 1788-1802) we know that all of Europeans were subject to Amerindian-like gene flow, not just northern Europeans: "Notably, we confirm a
signal of ancient admixture in European populations—including previously undetected admixture in Sardinians and Basques—involving a proportion of 20-40% ancient northern Eurasian
ancestry."

This is consistent with Lazaridis's finding that all of ancient European samples (Loschbour, Motala and Stuttgart) are pulled toward Amerindians. It means that Sardinians did get affected by Amerindian gene flow, so Fu's data needs to be interpreted with this fact in mind. In the light of the recent Sima de los Huesos study, it seems reasonable to attribute the proximity of Sardinians to Papuans through the observed special affinity between Sima and Denisovans.

So, from an out-of-America perspective, the instances of special divergence of populations from the Amerindian (=anatomically and behaviorally modern humans) core as well as instances of special affinity between such geographically widely separated populations as Sardinians and Papuans (to the exclusion of Amerindians) can be explained as "archaic" admixture in the Old World sometimes reflecting population affinities predating the spread of anatomically and behaviorally modern humans across the Old World.

"Maybe there was a single node of expansion within a much more complicated patchwork. However, the patchwork of relatedness that show Fu et al. is straightforward enough to single out at least one possible node of expansion that wasn't Amerindian."

See above.

Rokus said...

"If Sardinians were "conservative," then, at least under the mainstream model, they would have been closer not just to Papuans but to SSAfricans, too."

No, this is not the mainstream model. Mellars (2006):

Recent research has provided increasing support for the origins of anatomically and genetically ‘‘modern’’ human populations in Africa between 150,000 and 200,000 years ago, followed by a major dispersal of these populations to both Asia and Europe sometime after ca. 65,000 before present (B.P.). However, the central question of why it took these populations 100,000 years to disperse from Africa to other regions of the world has never been clearly resolved.

Fu's table indeed seems to reflect this 100,000 year gap, since Africans appear too divergent from Eurasian populations to be recognized as "basal" or "conservative" with respect to the apparent Cro Magnoid expansions that are the subject of this discussion. So far we don't have a consistent picture of the origin of Cro Magnon: they suddenly dominate Eurasia in the earliest Upper Paleolithic, while in Africa there is a dearth of Cro Magnoid finds of this same period. Just the Hofmayr skull in South Africa could be considered closely related to the Eurasian AMH specimen, though more recent African phenotypes strongly diverge what indeed seems to confirm the genetic gap.

"it's the special connection between Sardinians and Papuans that needs to be explained."

I already did: apparently West Eurasia was an important AMH expansion node. This also corresponds to Lazaridis'observations:
"Every eastern non-African population except Native Americans is genetically equally close to Loschbour, Motala12, and MA1",
and:
"All three hunter-gatherers and Stuttgart are genetically closer to Native Americans than to other eastern non-Africans."

The latter probably means that Amerindian isolation prevented genetic dilution of this event, without achieving the same central position of AMH expansion as attested in Sardinians.

"It means that Sardinians did get affected by Amerindian gene flow"
I already told you that for Sardinians the ANE component was 0.8%, that's all there is. Lipton et al. (2012) published their assertions without the knowledge of an ancestral West Eurasian relatedness of Amerindians as supplied by MA-1, their estimation is now obsolete. Besides, what makes you think this could ever contribute to Sardinians being closer to Papuans than Amerindians themselves?

"In the light of the recent Sima de los Huesos study, it seems reasonable to attribute the proximity of Sardinians to Papuans through the observed special affinity between Sima and Denisovans."
Actually, Sima was quite basal to modern humans, much more so than Denisovans. Both hominines are separated by a gap of 350,000 years and the resemblances are reminiscent of a shared development that was too short and old to be possibly responsible for the same nucleotide differences in chromosome 21 measured in Papuans. No, I don't think this is reasonable to assume.
In Raghavan's Figure SI 12 you can see that MA-1 was slightly affected by Denisovan DNA, suggesting the AMH admixture already happened in Siberia. West Eurasia was not affected. Part of the proposed "local archaic" component responsible for the nucleotide differences in chromosome 21 of Papuans may indeed be Denisovan, though in this comparison the actual source of nucleotide differences is irrelevant: it suffice to say these differences are probably due, at least partly, to archaic admixture.

German Dziebel said...

@No, this is not the mainstream model.

That Australia and PNG were peopled during the first wave of migration out of Africa is pretty mainstream. This would create a special proximity between Papuans and Africans. I agree with you that there's no evidence for it and sometimes Mellars and others may even acknowledge problems with it but overall it remains mainstream thinking. (Mainstream in contradistinction to yours and mine.)

"apparently West Eurasia was an important AMH expansion node."

I like alternative models even if they are different from mine.

"I already told you that for Sardinians the ANE component was 0.8%, that's all there is. Lipton et al. (2012) published their assertions without the knowledge of an ancestral West Eurasian relatedness of Amerindians as supplied by MA-1, their estimation is now obsolete. "

Amerindian admixture is in Sardinians, whether it's significant or not. We'll see what future studies will show. One thing to remember is that Amerindian admixture is broader than ANE in Lazaridis. This may be why it's so low in Sardinians - Amerindian admixture is diluted by several different later gene flows into Western Europe.

"Besides, what makes you think this could ever contribute to Sardinians being closer to Papuans than Amerindians themselves?"

No, my thinking was that "archaic admixture" in Europe contributed to the proximity between Papuans and Sardinians and to the dilution of the Amerindian component.

"Actually, Sima was quite basal to modern humans, much more so than Denisovans. Both hominines are separated by a gap of 350,000 years and the resemblances are reminiscent of a shared development that was too short and old to be possibly responsible for the same nucleotide differences in chromosome 21 measured in Papuans. No, I don't think this is reasonable to assume. "

We just obtained the data documenting special proximity between Sima and Denisovans. let's not jump to conclusions. I'm just going by face value here.

You need something else besides a single-study Sardianian-to-Papuan link to offset the growing evidence in favor Amerindians being basal to the rest of Eurasians (save archaic admixture here and there). But I'm fully open to your alternatives.

"In Raghavan's Figure SI 12 you can see that MA-1 was slightly affected by Denisovan DNA, suggesting the AMH admixture already happened in Siberia. "

I'm traveling right now and don;t have Raghavan in front of me. But thanks for the reference - I'll review when I come back. Do you think we can make a connection between the "Papuan" component in MA-1 ADMIXTURE profile and the Denisovan "component" fron Fig. SI 12?

terryt said...

"I like alternative models even if they are different from mine".

Obviously.

"the growing evidence in favor Amerindians being basal to the rest of Eurasians (save archaic admixture here and there)".

So what level of Amerindian mixture do you propose is present in Papuans?

Rokus said...

@EV, about understanding the issue and your impertinent unsourced "view":

The hypothesis that UC material may represent members of an as yet undifferentiated
early modern human population that expanded across Eurasia in the Late Pleistocene, was rendered obsolete with the recent discovery that also archaic hominines contributed to modern populations. Hence, Cro Magnoid - or European early modern humans (EEMHs) - features regain their phylogenetic usefullness, and we need another explanation why all investigations suggest a close link of the Chinese Upper Cave finds (and some others) with Upper Paleolithic European samples.

"Opposite facial contours"? Instead I highlighted short faces. Here is a more extense list of similarities. Harvati 2009:
PC 2, which reflects supero–inferiorly tall, anteriorly projecting faces, retreating frontal squama, heavy browridges with projecting glabella, and narrow, sagittally rotated zygomatic regions. Modern specimens score low on this axis, reflecting supero–inferiorly short faces, with light browridges and a flatter glabella, steeply rising frontal squama, and broader, coronally rotated zygomatics. Both Upper Cave specimens fall well within the range of modern human variation along this axis, showing similar scores to most Upper Paleolithic Europeans.

Indeed there is a close relation between the Upper Cave finds and European finds. Harvati 2009:
Particularly striking is the finding that, out of a large sample of modern human specimens, UC 101 was closest neighbor in the shape of its vault (as measured by Procrustes distance) to Predmostí 3, while UC 103 was nearest to Mladec 1 in the shape of its face.
[...]
It is interesting to note that, in their recent publication of the early modern human remains from Tianyan cave, Zhoukoudian, Shang et al. (2007) reported a close resemblance in the dental morphology of this specimen with that of Upper Paleolithic specimens from Arene Candide, Dolní Vestonice, and Mladec, a result very similar to the one reported here. These features and other "archaic"-like traits described by Shang et al. (2007) for Tianyan might also be interpreted as retentions of ancestral modern human morphology, rather than the result of admixture with local archaic populations.
[...]
The present analyses also fail to reveal strong affinities between the UC specimens and any of the recent human samples measured.
[...]
The Upper Cave specimens also do not show particular resemblances to archaic human fossils

Obviously, Harvati was not focussed on finding local archaic influences in Tianyuan, Upper Cave or any other Upper Paleolithic AMH specimen. Instead, he confirmed the link with Cro-Magnoids that you for some reason fail to acknowledge.

Rokus said...

"Do you think we can make a connection between the "Papuan" component in MA-1 ADMIXTURE profile and the Denisovan "component" fron Fig. SI 12?"

I think we can, and actually Figure SI 9 might give a hint into this direction.
Also the newly discovered YDNA MP grouping suggests a close connection that involves West Eurasians/Amerindians and Papuans.

German Dziebel said...

@terryT

"So what level of Amerindian mixture do you propose is present in Papuans?"

Rosenberg et al. 2002 have it nicely depicted in a STRUCTURE graph: Papuans have less Amerindian admixture than East Asians but slightly more than West Eurasians who in turn have more of it than Africans.

Alashire said...

"mtDNA hg B is likely a relic haplogroup later overrun by a host of others. It survived in its more or less pristine frequencies on both sides of the Circumpacific region".

Its first arrival in the southwest Pacific is only some 4000 years ago. Hardly the signature of 'a relic haplogroup later overrun by a host of others'.

so what exactly are you all doing with the fact that there is clear B's turning into U5 or visa-versa or we have clear proof that B comes from U5 or visaversa because North America has B's with both 270 and 217 so are they changing into B's or into U5's ? . sojust maybe the tree is messed up . What is sure is that no one knows why Mtdna mutates and no one knows how old this cr'p has been going on by looking at mtdna anyway . If there is a real reason it mutates due to unknown stresses in certain locations then all your clocks and your theories of origins are BS at best.

terryt said...

"What is sure is that no one knows why Mtdna mutates".

We do know that mt-DNA mutates though. You seem surprisingly worked up over the currently-accepted phylogenies. One gets the impression the reason for that is primarily because it conflicts with what you would like to believe. My problem is that I can't work out what it is that you want to believe.

"all your clocks and your theories of origins are BS at best".

The identification of haplogroups has certainly helped our understanding of several species' evolution, sometimes offering surprises. For example, despite being indistiguishable visually, American and Eurasian mallards have distinct mt-DNA lines. Similarly for Eurasian and American bison. In both cases unexpected, but logical, connections occur from outside the immediate species.

"and no one knows how old this cr'p has been going on by looking at mtdna anyway"

But surely we all know that mt-DNA is not the full answer. Nor is Y-DNA. And the two lines are often surprisingly distinct in their association and spread. It follows that aDNA is complicated as well. Ultimately each individual is the temporary combination of individual genes, each with separate origins. Genes, including haplogroups, do tend to travel in sets though. Over time these sets get broken up through hybridism.

"sojust maybe the tree is messed up"

Under the currently-accepted phylogeny B is part of a complex of R-derived haplogroups centred on SE Asia/South China, and U is a separate western R-derived set of haplogroups. The order of R's branching has not yet been determined. At present it is diversification is presented as 'starlike'.

"the fact that there is clear B's turning into U5 or visa-versa or we have clear proof that B comes from U5 or visaversa because North America has B's with both 270 and 217 so are they changing into B's or into U5's ?"

Perhaps U is part of that B set. To me it seems less likely that B is part of the U complex though. But if we can determine whether B is derived from U, or U from B, we can perhaps discover if R's movement was westward or eastwards. We know R is relatively common in South Asia and so we can be reasonably sure the route was through there.

"sojust maybe the tree is messed up"

If U derives from B the route was westward, if B derives from U, eastward. Which direction do you favour?

sidoroffs said...

Kristiina,

"Udmurts have considerably more N1c (58%) and less R1a (10%). According to my old papers, Udmurts also carry a high frequency of K, of which I would really like to know what it is. If the Udmurts are the closest match to the Mal’ta boy, we should take into account their main haplogroups:
N1c 58%, K 25%, R1a 10%"

Don't the Udmurts have N1b (N-P43)?

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