January 09, 2014

SLC24A5 light skin pigmentation allele origin

From the paper:
Adjustment for undercounting is substantial, increasing the estimated age for the combined samples to 12.4 (95% confidence interval 7.6−19.2) kya. If mutation rates in recent humans are lower than predicted from the human-chimpanzee divergence (Scally and Durbin 2012), true ages will be even older. Our adjusted dates overlap those previously reported (Beleza et al. 2012) and are also consistent with the lower limit for the origin of A111T set by the finding that the Alpine “iceman” dated to 5.3 kya was homozygous for this variant (Keller et al. 2012).

Related:

Taking the 12.4ky estimate and multiplying by two (for the slower autosomal mutation rate) yields an estimate of 25ky, so it seems that this allele did not accompany the earliest modern human colonists of West Eurasia but emerged in some region and spread from there. It will be interesting to see (through ancient DNA) by what processes of migration, admixture, and selection this transpired.


G3 doi: 10.1534/g3.113.007484

Molecular Phylogeography of a Human Autosomal Skin Color Locus Under Natural Selection

Victor A. Canfield et al.

Divergent natural selection caused by differences in solar exposure has resulted in distinctive variations in skin color between human populations. The derived light skin color allele of the SLC24A5 gene, A111T, predominates in populations of Western Eurasian ancestry. To gain insight into when and where this mutation arose, we defined common haplotypes in the genomic region around SLC24A5 across diverse human populations and deduced phylogenetic relationships between them. Virtually all chromosomes carrying the A111T allele share a single 78-kb haplotype that we call C11, indicating that all instances of this mutation in human populations share a common origin. The C11 haplotype was most likely created by a crossover between two haplotypes, followed by the A111T mutation. The two parental precursor haplotypes are found from East Asia to the Americas but are nearly absent in Africa. The distributions of C11 and its parental haplotypes make it most likely that these two last steps occurred between the Middle East and the Indian subcontinent, with the A111T mutation occurring after the split between the ancestors of Europeans and East Asians.

Link

100 comments:

German Dziebel said...

"There is a cline of decreasing frequency of A111T in indigenous populations east of approximately longitude 75 in Central Asia, with near-absence in East Asia, Oceania, and the Americas."

Another evidence against the recent hypothesis that Amerindians carry West Eurasian admixture postulated to have occurred after Amerindians had split from East Asians.

"The precursors to C11, haplotypes C3 and C10, are common in East Asia and the New World (Figure S5)"

According to the maps, C10 is found in East Asia, PNG and Australia, while C3 is common in the New World, while rare in East Asia and absent from the Pacific. Taken at face value, this means that West Eurasians evolved from a mix of Ancient (pre-Mongoloid) East Asians/Amerindians and another group of Amerindians that left little trace in East Asia.

Kurti said...

"The distributions of C11 and its parental haplotypes make it most likely that these two last steps occurred between the Middle East and the Indian subcontinent,"

Looks to me more like between West Asia (minus Arabia) and western part of South_Central Asia (minus India).
In one word Caucasus_Gedrosia.

Kurti said...

@GermanDiezel
"Another evidence against the recent hypothesis that Amerindians carry West Eurasian admixture postulated to have occurred after Amerindians had split from East Asians."


"The C11 haplotype was most likely created by a crossover between two haplotypes, followed by the A111T mutation. The two parental precursor haplotypes are found from East Asia to the Americas but are nearly absent in Africa. The distributions of C11 and its parental haplotypes make it most likely that these two last steps occurred between the Middle East and the Indian subcontinent, with the A111T mutation occurring after the split between the ancestors of Europeans and East Asians.
"


The parental haplotypes causing for this mutation are also found in Americas and East Asians. And this mutation took place after the West and East Eurasian split. But we claimed that the Amerindians stem from a West-East Eurasian origin. But than we still don't know when exactly this mutation took place it could very well be that the West Eurasian admixture Amerindians got stems from a time when West Eurasian still hadn't developed this light skin allele.

Judging by this map it very well reminds me to the distribution of Caucasus-Gedrosia. So this mutation could have taken place as late as when the Caucasus-Gedrosia component evolved.

German Dziebel said...

Correction: "According to the maps, C10 is found in East Asia, PNG and Australia" should be read "According to the maps, C10 is found in America, East Asia, PNG and Australia"

Mark Moore (Moderator) said...

So this study claims the "Ligt skinned Gene" popped up 12.4 KYA, and even if you use a slower mutation rate it would be 2k KYA. We are also told that modern humans have been around 100KYA and OOA is at least 50K years ago and 70K is at least as likely.

Given all that, how did a mutation that just appeared that recently, presumably in one person, advance so fast that now half the planet has it? I mean imagine you are the first person 20KYA to have this mutation. Those without it have had 100K years to fill the planet, and even from an OOA perspective they have had 30-50KY to do so. How many of them are there? Millions? Tens of millions? Yet 20K later your descendents make up half the population.

On the last study I had a similar question and someone, Eurologist I believe, showed me numbers that basically said the dates were just very loose estimates and the actual date the mutation first arose could be much farther in the past. How solid are the numbers on this study?

eurologist said...

The (corrected) age estimate, distribution, and likely place of origin all are in agreement with a Gravettian expansion.

eurologist said...

Mark,

None of us, at this point, know why the Gravettian was such a transforming force - but apparently, it was. And apparently differently so in C and W Europe compared to the SE, which after LGM exhibited a very different and isolated Epi-Gravettian from the Adriatic to the Black Sea (much more closely related to the adjacent Neolithic W Asian).

German Dziebel said...

@Kurti

"But than we still don't know when exactly this mutation took place it could very well be that the West Eurasian admixture Amerindians got stems from a time when West Eurasian still hadn't developed this light skin allele."

The absolute chronology is a big issue, no doubt. But the problem is with the relative order of splits and the directionality of admixture. If you look at the maps on Fig. S5 in Canfield et al., you'll see that C3 is an almost uniquely Amerindian skin haplotype barely found in East Asia. Hence, it was likely inserted into the West Eurasian skin evolutionary path after the split between West Eurasians and East Asians but before the A111T mutation occurred. Only this interpretation puts skin data and autosomal data in sync: Amerindians admixed into an ancient West Eurasian population as supported by the presence of an Amerindian component in ancient remains from Mal'ta in the east to Loschbour and Stuttgart in the West. Not only that skin haplotype C11 is not found in the Americas but neither are mtDNA U and Y-DNA R, which are much older than the Gedrosian/Caucasus component, and this preclude any West Eurasian admixture in Amerindians.

This Amerindian admixture into an undifferentiated West-East Eurasian skin gene pool could have happened in Gravettian times or already in the Holocene. A southern, West Asian/Gedrosian origin of A111T is a possibility but I think it's just as likely it happened in the north.

About Time said...

Didn't Moorjani 2013 show that ANI separated from West Eurasia 12 kya?

Found the ref: http://dienekes.blogspot.com/2013/08/major-admixture-in-india-took-place-42.html

On the contrary, a recent study that searched for West Eurasian groups most closely related to the ANI ancestors of Indians failed to find any evidence for shared ancestry between the ANI and groups in West Eurasia within the past 12,500 years3 (although it is possible that with further sampling and new methods such relatedness might be detected).

If Gedrosia = ANI (more or less), this could make sense. Notice it's light skin, not necessarily hair/eye color.

It gets cloudy up in the Caucasus, I've heard. Light skin could still be plausible as an adaptation to agriculture (Vitamin D deficiency) in cloudy environments. Does anyone know more about cloudy areas around Caucasus/Gedrosia? @Kurti?

Slumbery said...

Mark Moore (Moderator)

You talk about this as the descendants of the carrier of the first mutated gene and the descendants of contemporary wild gene carriers were two separated populations, but they are not. You simply use a wrong model in your head.

A spread of an allele does not typically mean one group overpopulating another group.

The original carrier technically could have the entire population of the Earth as her/his descendants in less than a millennium, without "overpopulating" the contemporary non-carriers, since their descendants are common. (And all of the other genes of the original carrier may very well went extinct.)

20 or 12 kya is perfectly enough to become widely distributed for a mutation that is selected positively (by whatever selection pressure).

andrew said...

"Given all that, how did a mutation that just appeared that recently, presumably in one person, advance so fast that now half the planet has it?"

Selective advantage. Skin that is too dark at higher latitudes impairs vitamin D generation which is very important in immune function. Skin that is too light leads to skin cancer which is also deadly.

Mark for Summit/Sunnoco said...

Whether all humanity acts like one population, or if they have been in isolated groups for much of that time, the expansion of that gene just seems astounding to me. Can we cite an example of any other gene that spread from point of origin to 50% of mankind in 12-25 KY? (I think Eurologist would say these dates are wrong and it would be more like 32KYA).

Mark Moore (Moderator) said...

Regardless of whether it is viewed as the advance of a gene within a single global population, or one human group with the mutation out-competing other populations, or some of both, I find the indicated rate of expansion to be incredible.

Do we have any other example of a gene which as gone from point of origin to being present in half of all mankind in 12.4-25 KY? I think Eurologist would argue the date would be a little further back to sync with the Gravettian, but still, can we find another gene which has expanded so fast?

Kurti said...

@About Time

Gedrosia is 92% "proto" West Asian + ~8% ANI.

Yes there are allot of cloudy areas between Caucasus and Gedrosia. Especially in the mountainous Regions.

This is Hakkari in the most Southeastern corner of Turkey/Anatolia.

http://www.yuksekovahaber.com/images/other/hakkarisisaltinda.jpg

http://www.yuksekovahaber.com/galeri/images/gallery/13_30.jpg

http://www.hakkarihabertv.com/images/other/02.20130219141054.jpg

http://www.dogurehberi.com/images/haberler/hakkaride_kar_manzaralari_h311520.jpg


Trabzon in Northeast Anatolia

http://2.bp.blogspot.com/-NRB6IKpNpYI/UnZdfcnlZDI/AAAAAAAAAvg/nVgBmbWCBdc/s1600/zzzzz%2B(1).JPG

http://oguzlular.com/wp-content/uploads/2010/12/image009.jpg

Just two examples of allot more.

Fanty said...

Its still hard to digest.

So this theory says, black people will run extinct in the USA in the next 10K years, because they arent adapted to the totaly deadly envoirement.

Oh wait, yes... only black vegans. MEat eating people dont need the sun, right? :P

Thats possibly why dark skinned EUropean hunter/gatherers survived in Scandinavia where is half the year night. Because they had lots of meat.

And some middle eastern vegans came up with the white skin because its so increadable dark in the middle east (I assume that they didnt wear burkas at that time?) and they need all tricks to increase the amount of light on their skins...

right :P

eurologist said...

Skin that is too light leads to skin cancer which is also deadly.

Andrew,

But too late to have an effect in reproduction. I believe the contemporary alternative, for a while, has been destruction of folic acid (or its precursors) due to UV, in the skin.

terryt said...

"Taking the 12.4ky estimate and multiplying by two (for the slower autosomal mutation rate) yields an estimate of 25ky, so it seems that this allele did not accompany the earliest modern human colonists of West Eurasia but emerged in some region and spread from there".

It even opens the possibility of introgression of the C11 variation from an ancient population. Especially when we consider that 'The two parental precursor haplotypes are found from East Asia to the Americas but are nearly absent in Africa'.

"The (corrected) age estimate, distribution, and likely place of origin all are in agreement with a Gravettian expansion".

Yes, but ... The final mutation seems not to have been present in the eastern ANE population that provided some of the Amerindian genetic element. Hence:

"But than we still don't know when exactly this mutation took place it could very well be that the West Eurasian admixture Amerindians got stems from a time when West Eurasian still hadn't developed this light skin allele."

Quite.

"None of us, at this point, know why the Gravettian was such a transforming force - but apparently, it was".

My guess is that it was the first group to enter previously unexploited northern Eurasia. This allowed the population to expand considerably, even back into already occupied regions to the south.

"Amerindians admixed into an ancient West Eurasian population as supported by the presence of an Amerindian component in ancient remains from Mal'ta in the east to Loschbour and Stuttgart in the West".

Most of us agree that the admixture was the other way round. Once again you are making an assumption and then trying to fit the data to that assumption.

Chad Rohlfsen said...

Here is a map of this region where it could have arisen during the LGM. This was the only region in the area that was not a desert apparently. Could this region spreading from the SW Subcontinent to Anatolia be related to the farmers and the light skin alleles that were brought to Europe?
I am not seeing how it would be Gravettian, as the Mal'ta and European samples do not have the lightening alleles.

http://en.wikipedia.org/wiki/File:Last_glacial_vegetation_map.png

Tobus said...

@Mark:Those without it have had 100K years to fill the planet, and even from an OOA perspective they have had 30-50KY to do so. How many of them are there? Millions? Tens of millions?

It's is estimated that before agriculture the total world population was less than 15M, if we assume only half(?) of these were outside Africa and only half(?) of those were in Western Eurasia - we get somewhere around 3-4 million max, possibly a lot less if you factor in glacial maxima etc... it's highly possible that a small group of light-skin-SLC24A5 carriers moved north and east into relatively uninhabited territory and were able to expand very rapidly with little or no competition from non-carriers (who were all south and west of them).

You also need to consider that nearly all the "white" SLC24A5 expansion we see today has only happened in the last few hundred years. Some of largest populations today (eg. the Americas) didn't have a single carrier 500 years ago. Remember that the world population was was under half a billion in 1500 AD. The distribution of phenotypes we see today is largely to do with migrations and expansions resulting in an extra 6.5 billion people in that very short amount of time.

Also, do you have a source for your "half the planet" claim? Doing a rough approximation I get to 3 billion people in East Asia, South East Asia and Sub-Saharan Africa before even trying to factor in the percentages of South Asia, South America and West Asia. So off the top of my head I'd have thought closer to a third than half.

Onur said...

Gedrosia is 92% "proto" West Asian + ~8% ANI.

That 8% is not ANI but the "South Asian" component, and the "South Asian" component is by no means exclusively composed of ANI. It is a composite of ASI (=Ancestral South Indian) and ANI, but mostly made up of ASI. But even the "West Asian" portion of the "Gedrosia" component includes some ASI as the "West Asian" component itself is a composite of the "Gedrosia" and "Caucasus" components:

http://1.bp.blogspot.com/-iN1EuOd52c4/UE3TT7Ka_kI/AAAAAAAAGWQ/fy53d30H2m0/s1600/_12.png

MDS plots, too, confirm the non-negligible ASI element in the "Gedrosia" component:

http://3.bp.blogspot.com/-o3aBKiyqagc/TyfglQUIlPI/AAAAAAAAEdI/LQj6qi7LE8k/s1600/1_2.png

In short, the ASI admixture of the "Gedrosia" component is obvious.

German Dziebel said...

@TerryT

"Most of us agree that the admixture was the other way round."

Most of "you" are amateurs and hence especially prone to holding uncritically accepted beliefs. The paper is plain clear that West eurasian skin gene pool derives from a mix of a unique Amerindian haplotype and a haplotype shared by "all of Eastern non-Africans."

"Once again you are making an assumption and then trying to fit the data to that assumption."

No, it's the other way around. Your prejudice against America is a source for at least part of Old World diversity stems from a 500-year-old cultural stereotype.

Kurti said...

@Onur you are like a broken recorder just copy and pasting. We had this discussion on Davidskis blog. Palisto had this discussion with you and tried to explain to you by giving examples how when Gedrosia appears in the higher K's South Asian in Iranians get weaker and the South Asian component gets more distant from other West Eurasian components.
And you have difficulties understanding the charts you are throwing through the room.

Anytime you start this debate I will simply link to your and Palistos discussion.

http://kurdishdna.blogspot.de/2013/04/kurdish-mtdna-data-ix.html

comment section.

eurologist said...

Yes, but ... The final mutation seems not to have been present in the eastern ANE population that provided some of the Amerindian genetic element.

Terry,

Of course - the first couple of waves of Siberians were also earlier than the start of the European Gravettian, and mostly associated with y-haplogroup Q. So, it is not unlikely that this transition initially only occurred in R populations (or subgroups of R), instead.

We should also keep in mind that this single mutation does not make the skin particularly fair, on its own (it occurs at a significant fraction of people who have Mediterranean, dark Mediterranean, dark W Asian, or even dark S Asian/ African skin color). As I have mentioned before, one also needs to distinguish between static skin color and adaptable (over the seasons), and perhaps take into account subtle photochemistry effects on the molecular level that don't express themselves that simply and naively as "skin tone."

Rokus said...

Amerindians admixed into an ancient West Eurasian population as supported by the presence of an Amerindian component in ancient remains from Mal'ta in the east to Loschbour and Stuttgart in the West.
As far I could verify this Amerindian component was recognized in Motala and modern Near Easterners, not in Loschbour or Stuttgart.

terryt said...

" the first couple of waves of Siberians were also earlier than the start of the European Gravettian"

Of course.

"We should also keep in mind that this single mutation does not make the skin particularly fair, on its own"

Thanks for that caution.

"The paper is plain clear that West eurasian skin gene pool derives from a mix of a unique Amerindian haplotype"

Which do you propose was the 'unique Amerindian haplotype'? As I understand things C11 arose from a hybrid between a population carrying the C3 variant and one containg the C10, neither being specifically Amerindian. You said yourself earlier, 'According to the maps, C10 is found in America, East Asia, PNG and Australia' although I think you meant C3, as the paper says, 'Although the lineage containing this haplotype must have originated in Africa, C3 is rare in Africa (1.0% in MKK) but widely distributed in East Asia, the New World, and Oceania'. Regarding C10 the authors say, 'Among these descendants is C10, which is abundant in East Asia (and the New World) but extremely rare in Africa (0.5% in LWK)'. That doesn't leave many options for an exclusively Amerindian type.

"Your prejudice against America is a source for at least part of Old World diversity stems from a 500-year-old cultural stereotype".

And your prejudice in favour stems from ...?

German Dziebel said...

@Rokus

"As far I could verify this Amerindian component was recognized in Motala and modern Near Easterners, not in Loschbour or Stuttgart."

I go by the following findings by Lazaridis et al.:

"All three hunter-gatherers and Stuttgart are genetically closer to Native Americans than
to other eastern non-Africans." (p. 9 of the main text).

"both Stuttgart and Loschbour are genetically closer to Karitiana than to Onge" (p. 74 of Suppl Mat)

Tobus said...

@German: If you look at the maps on Fig. S5 in Canfield et al., you'll see that C3 is an almost uniquely Amerindian skin haplotype barely found in East Asia

It's hard to tell exactly from the colours but that figure shows a C3 frequency of ~25-35% in America and about 10-15% in East Asia. From this information it's a very long stretch to claim this as "almost uniquely Amerindian". Table 2 from the main paper also confirms ~10% incidence throughout East Asia.

I'll also point out that the researchers say "both models for the origin of C11 imply that C3 and C10 were present in ancestors of Europeans", so there's no need to be looking for a C3 or C10 source in the first place. There is no suggestion that C11 is the result of admixture into Europeans, it's an in-situ recombination of haplotypes already existing in the population.

Onur said...

@Onur you are like a broken recorder just copy and pasting.

Copying and pasting from myself.

Palisto had this discussion with you and tried to explain to you by giving examples how when Gedrosia appears in the higher K's South Asian in Iranians get weaker and the South Asian component gets more distant from other West Eurasian components.

I told you that that is not the case, at least not in any significant degree. See my comments at David's thread:

http://bga101.blogspot.com/2013/12/eef-whg-ane-test-for-europeans.html

And you have difficulties understanding the charts you are throwing through the room.

Again, that is not the case.

Anytime you start this debate I will simply link to your and Palistos discussion.

http://kurdishdna.blogspot.de/2013/04/kurdish-mtdna-data-ix.html

comment section.


Add to that David's thread. I expressed myself pretty clearly in both threads. The rest is up to you.

German Dziebel said...

@Rokus

Also on Lazaridis's ADMIXTURE graph you can see Amerindian-related YELLOW and GREEN in all of the European ancient DNA samples including Stuttgart.

terryt said...

"If you look at the maps on Fig. S5 in Canfield et al., you'll see that C3 is an almost uniquely Amerindian skin haplotype barely found in East Asia".

That is not what the authors show in table 2 though. In fact they even show the variant as present in the Maasai. Although the dates computed in the paper do not concern variants other than C11, from the data presented it seems that the basal branch C3 may have left Africa long before any modern human OoA. In which case it may have been widespread by the time of the OoA. The reason it and C10 are virtually absent west 'of approximately longitude 75 in Central Asia' is that selection for the derived C11 has replaced the ancestral variants there. Therefore it doesn't necessarily mean:

"Taken at face value, this means that West Eurasians evolved from a mix of Ancient (pre-Mongoloid) East Asians/Amerindians and another group of Amerindians that left little trace in East Asia".

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Rokus said...

I go by the following findings by Lazaridis et al.:

"All three hunter-gatherers and Stuttgart are genetically closer to Native Americans than
to other eastern non-Africans." (p. 9 of the main text).


"both Stuttgart and Loschbour are genetically closer to Karitiana than to Onge" (p. 74 of Suppl Mat)

Don't you think this could be due to a close genetic affiliation other than admixture?
Because the paper also says this:
Loschbour and Stuttgart had little or no ANE ancestry, indicating that it was not as pervasive in central Europe around the time of the agricultural transition as it is today. (By implication ANE ancestry was also not present in the ancient Near East; since Stuttgart which has substantial Near Eastern ancestry lacks it.

Chad Rohlfsen said...

It seems strange that Some Near Easterners have more ANE than Northern Europeans. I am wondering if perhaps the Indo-Iranians were more of a pure ANE and the Indo Europeans, being more western were a hybrid WHG-ANE type. Possibly they had some minor EEF from the Northern Caucasus / Pontic Steppe.
Perhaps ANE and Basal need to be reconfigured. Perhaps a 4th population is needed.

Locrian said...

German Dziebel said : “Most of "you" are amateurs and hence especially prone to holding uncritically accepted beliefs. The paper is plain clear that West eurasian skin gene pool derives from a mix of a unique Amerindian haplotype and a haplotype shared by "all of Eastern non-Africans." “

Out of America would imply that Africans would be the most admixed with Denisovans and Neanderthals, since Africans would have had to travel through Denisovan rich Asia to get to Africa — essentially they would have had to travel the longest path. But that is not the case. Instead Amerindians are the ones who are highly admixed. So Out of America is refuted. End of story.

And this doesn’t even take into account the haplogroup tree, which by itself refutes Out of America.

Your argument id a clear case of reading Admixture as though causal direction can be read from it. But it can’t. You need to add in dates and haplogroup trees.

German Dziebel said...

@Tobus

"It's hard to tell exactly from the colours but that figure shows a C3 frequency of ~25-35% in America and about 10-15% in East Asia. From this information it's a very long stretch to claim this as "almost uniquely Amerindian". Table 2 from the main paper also confirms ~10% incidence throughout East Asia."

No matter how you describe it - almost uniquely Amerindian or else - the pattern remains and it's consistent with many other patterns uncovered to date.

"so there's no need to be looking for a C3 or C10 source in the first place. There is no suggestion that C11 is the result of admixture into Europeans, it's an in-situ recombination of haplotypes already existing in the population."

This is not the most natural explanation of the data pattern and hence requires special evidence. Neither the authors nor you have provided this evidence. As the data stands now, a haplotype common in "eastern non-Africans" (using Lazaridis's terminology) mixed and recombined with a haplotype almost uniquely Amerindian. After this event, which likely took place outside of West Eurasia, the ancestors of modern West Eurasians developed another mutation that made them look like they look today. This may have happened in the Near East or in the extreme north.

German Dziebel said...

@Rokus

"Don't you think this could be due to a close genetic affiliation other than admixture?
Because the paper also says this:
Loschbour and Stuttgart had little or no ANE ancestry, indicating that it was not as pervasive in central Europe around the time of the agricultural transition as it is today. (By implication ANE ancestry was also not present in the ancient Near East; since Stuttgart which has substantial Near Eastern ancestry lacks it."

I'm not sure I completely get your point. The way I picture it for myself is that Near East-derived agriculturalists diluted the original European (and broadly Eurasian as attested by Mal'ta) forager gene pool and reduced the Amerindian component. So there's a south to north gradient of reduction here. But there's also an east-to-west gradient in the reduction of the Amerindian component: the latter peaks in Mal'ta and progressively weakens as one goes into western Europe. The Amerindian component weakens with time and geography: the closer to America geographically and the more ancient the population sample, the closer the tie. So, the reduction in the Amerindian component in Stuttgart and Loschbour compared to Mal'ta and Motala is quite expected from an ancient out-of-America admixture angle, albeit driven by two separate genetic processes - isolation-by-distance and admixture. But we still have the Amerindian signal going on in Stuttgart, which is both western and Neolithic/Near East admixture affected.

@TettyT

"That is not what the authors show in table 2 though. In fact they even show the variant as present in the Maasai. "

Sure thing. Africa was colonized from Eurasia. The African haplotypes that the authors mistake for ancestral to modern humans are likely product of archaic admixture in Africa (hence, they are not found outside of Africa), while the trace of the Eurasian signal we see in Maasai represents the migration of Homo sapiens into Africa.

"The reason it and C10 are virtually absent west 'of approximately longitude 75 in Central Asia' is that selection for the derived C11 has replaced the ancestral variants there."

Like I pointed out to Tobus, this is a special explanation that requires special evidence. Currently, you are invoking a historical scenario whereby the data you need to support your belief went miraculously extinct.

German Dziebel said...

@ Locrian

"Out of America would imply that Africans would be the most admixed with Denisovans and Neanderthals, since Africans would have had to travel through Denisovan rich Asia to get to Africa — essentially they would have had to travel the longest path."

We have evidence for Neandertal admixture in Sub Saharan Africans. Everybody seems to have internalized this already. It means there was a migration into Sub Saharan Africa from Eurasia, as Neandertals is a Eurasian species. Fewer people have noticed that Figure S13.7 in Prufer et al. 2013 demonstrates Denisovan admixture in San and Mbuti and it's a subset of admixture sites attested in Melanesians. Contrary to what you are saying, the admixture signal decreases with geographic distance. So predictably we see Africans as less "admixed" with Neandertals and Denisovans. At the same time, Africans must be more admixed with African archaics, for which we may never have direct ancient DNA evidence, because they are consistently more diverse than Eurasians.

"End of story. "

End of your story.

"And this doesn’t even take into account the haplogroup tree, which by itself refutes Out of America."

As I pointed out multiple times on various blogs, the mtDNA tree is a mess - a relic from pre-ancient DNA times that allows for recurrent mutations to be branch defining and constantly confuses derived mutations with ancestral ones. But even if haploid trees are essentially correct, mtDNA L lineages and Y-DNA A and B lineages are African-specific and hence were likely absorbed by modern humans from African archaics after they had colonized Africa from Eurasia.

terryt said...

"The African haplotypes that the authors mistake for ancestral to modern humans are likely product of archaic admixture in Africa"

I'll grant that is possible. In fact the authors specifically state C3's presence in th Maasai is from back movement from Eurasia. But the phylogeny of the variant shows C3 derives from C2, which derives from C1. C2 and C5 are both specifically African. As is the series C4-C5, which then gives rise to C6 and C7, both widespread within and outside Africa. As a result it is difficult to see the above haplogroups as being present in Africa from admixture with ancient variants.

"Like I pointed out to Tobus, this [selection for C11] is a special explanation that requires special evidence".

Not so. It provides a far better explanation for the data than does any other explanation. As Locrian explained, 'Africans would have had to travel through Denisovan rich Asia to get to Africa' and 'this doesn’t even take into account the haplogroup tree, which by itself refutes Out of America'. But wait, there's more:

"Currently, you are invoking a historical scenario whereby the data you need to support your belief went miraculously extinct".

The paper says, 'The C11 haplotype was most likely created by a crossover between two haplotypes, followed by the A111T mutation'. The distribution map of the derived SLC24A5 variant shows a series of clines in all directions from its main concentration through much of western Eurasia. Using your explanation you somehow have to explain why all the neighbouring variants were able to invade the geographic range of the SLC24A5 variant to an equal extent, leaving a completely unadmixed region across western Eurasia. The distribution map has all indications of all these clines as being just one cline, marking the extent of an expansion of the variant over older variants of the gene.

Rokus said...

I'm not sure I completely get your point.
[…]
But we still have the Amerindian signal going on in Stuttgart, which is both western and Neolithic/Near East admixture affected.

My point: there is no Amerindian signal going on in Stuttgart (EEF). Doesn't the paper repeatedly say that Stuttgart lacks ANE ancestry?

And WHG lacks ANE as well, what comes as no surprise since EEF has enough WHG (~66%) to ‘explain away’ direct WHG influences even across the Alpes south of Stuttgart. (A smiley  because I think Lazaridis et al. are joking here)

terryt said...

German. At last I've discovered how you do 'science':

"The precursors to C11, haplotypes C3 and C10, are common in East Asia and the New World (Figure S5)"

You searched the paper and found just one map in the additional material that 'might' support your belief, ignoring all other maps and tables in the paper. Thus you were able to 'prove your point'. Not scientific in any way at all.

amarie22 said...

In the end, if your research provides a result that defies reason or just plain common sense, then that points to the need to reconsider those results? The geography of the distribution of fair skin people defies your analysis. That means, surely, that there is something wrong with your measuring tool, your math, or your basic assumptions? These results are useful only in that they provide obvious feedback that some part of your research process needs to be recalibrated before it can provide any useful answers!

German Dziebel said...

@Rokus

"My point: there is no Amerindian signal going on in Stuttgart (EEF). Doesn't the paper repeatedly say that Stuttgart lacks ANE ancestry? "

The quote I adduced above mentions that all ancient samples including Stuttgart are closer to Amerindians than to other eastern non-Africans. This means that there must be an Amerindian component in Stuttgart. This is consistent with Lipson et al. 2012 showing Amerindian-like component everywhere in Europe. The authors wrongly assume that "Karitiana has ANE ancestry," while in reality it's MA-1 that has Karitiana-like ancestry. Following their wrong assumption, they exclude Karitiana from further tests (see p. 60 of Suppl Mat) and instead postulate an "unknown hunter-gatherer population" that contributed to Stuttgart.

"Recognizing the challenge posed by the lack of accurate surrogates for the ancestral populations, we hypothesized that Stuttgart is a mixture of an unknown hunter-gatherer population that forms a clade with Loschbour and an unknown Near Eastern population (NE)."

But this "unknown hunter-gatherer population" must be Amerindian-like considering that Amerindian admixture is definitely present in Loschbour (see ADMIXTURE plot, Fig. 3).

So, in a word, the uncertainty in the admixture composition of Stuttgart is the price we all pay for the mistaken assumption by the academic authors that Amerindians are admixed, while MA-1 is a pure population. Their mistaken assumption forces them to postulate a ghost Western population, while ignoring a real Eastern population that contributed to Stuttgart.

German Dziebel said...


@terryT

"The distribution map of the derived SLC24A5 variant shows a series of clines in all directions from its main concentration through much of western Eurasia."

What are you looking at? Fig. 1 that just shows that A111T is missing in Africa, Australia, costal Asia and America but increases in frequencies as one moves into central and finally western Eurasia? Pretty consistent with my idea that a crossover between an Amerindian haplotype and an eastern non-African haplotype was followed by a mutation that took place in western Eurasia as the population movement progressed from east to west. This east-to-west movement is that very "single cline" that you misinterpret as somehow emerging in situ and sitting on top of what must be just the same Amerindian-eastern-non-African skin tone diversity. I guess you could say that the intermediary frequencies of A111T are product of admixture between West Eurasians and Sub-Saharan Africans but the intermediary frequencies of A111T in central Eurasia could be the "incipient whiteness" that posdated the mixture of the two ancestral populations (Amerindian and eastern non-African).

"You searched the paper and found just one map in the additional material that 'might' support your belief, ignoring all other maps and tables in the paper. Thus you were able to 'prove your point'. Not scientific in any way at all."

Scientists like me do read Supplemental Material. Amateurs like you tend to stick to press releases and abstracts. The distribution of C3 and C10 is critical to the problem of the origin of the Western European phenotype. The details are only given in Supplemental Material. The authors obviously chose not to foreground the Amerindian roots of one of the components that led to the emergence of the Western Eurasian phenotype. But the data is out there for the curious and critical minds to spot and evaluate.

"But the phylogeny of the variant shows C3 derives from C2, which derives from C1. C2 and C5 are both specifically African. As is the series C4-C5, which then gives rise to C6 and C7, both widespread within and outside Africa."

if you study Fig. 4, you'll notice that there's phylogenetic uncertainty around some of these nodes supported by the geographic disjunction between New World-dominant C3 and African dominant C1 and C2. Without ancient DNA and more modern samples, it's hard to say for sure where modern lineage extinction has occurred and where archaic admixture has occurred. But the exclusive African provenance of C1 and C2 is consistent with archaic admixture, while the broad distribution of C3 is consistent with the spread of a new species.

Grey said...

I think there was a sequence of multiple "Out Of" events.

Population A adapts to the tropics and stays there.

Population B moves out of the tropics into the sub-tropics, adapts to it and stays there.

Population C moves out of the sub-tropics into the mid-latitudes and expands in all direction adapting to the region they end up in creating multiple C populations.

The C population with the biggest advantage becomes the D population who drive an "Out of" event from whatever their region is.

Add lots of back-migration, rinse and repeat.

So, I think it's quite plausible there was an "Out of America" event at some point - one of many "Out of" events since the first.

.

And in some ways the first "Out of" event is the least important because generally speaking as population B derives from population A and C derives from B and D derives from C and population E derives from population B etc down the line so the influence of A to B lessens with each step.

Mark Moore (Moderator) said...

OK I like thinking outside the box, even if I don't agree with German's big idea. To me, it is a necessary part of real science where even our assumptions are not above occasional question. This is the exact opposite of restrictive PC-thinking that in my view is the enemy of true scientific inquiry.

With that said, let me float another possible scenario that could explain some of this data: The ancient Amerindians started off in central Asia and spread east and west, exploiting a cold-adapted life style. Then an ice age came and basically wiped out the Eurasian population, because they either had to die or go south and compete with humans which were already there south of them.

Two groups of them were not absorbed, because they went into the New World where there were no humans to compete with or absorb them. One followed herd east across the Bering Straight. The other went England, Ireland, Greenland, Iceland, Labrador.

There are traces of them all over because they were among the humans most used to a nomadic lifestyle and most scattered by the last ice age.

terryt said...

"Scientists like me do read Supplemental Material. Amateurs like you tend to stick to press releases and abstracts".

Scientists like you have a problem though, with chronology:

"The distribution of C3 and C10 is critical to the problem of the origin of the Western European phenotype".

So apparently you accept the paper's finding that C11 arose from mixing between C3 and C10. In other words C11 didn't exist until more recently than both C3 and C10 had developed.

"Fig. 1 that just shows that A111T is missing in Africa, Australia, costal Asia and America but increases in frequencies as one moves into central and finally western Eurasia? Pretty consistent with my idea that a crossover between an Amerindian haplotype and an eastern non-African haplotype was followed by a mutation that took place in western Eurasia as the population movement progressed from east to west. This east-to-west movement is that very 'single cline' that you misinterpret as somehow emerging in situ and sitting on top of what must be just the same Amerindian-eastern-non-African skin tone diversity. I guess you could say that the intermediary frequencies of A111T are product of admixture between West Eurasians and Sub-Saharan Africans but the intermediary frequencies of A111T in central Eurasia could be the 'incipient whiteness' that posdated the mixture of the two ancestral populations (Amerindian and eastern non-African)".

From that I can only assume you are suggesting the population movement that progressed from east to west, in which the A111T formed, entered an uninhabited western Eurasia. Possible, but C11's distribution includes regions where we know that both Neandertahl and Denisovans existed at an early date, both of which have contributed genes to the modern gene pool. It is extremely unlikely that C11 moved into an uninhabited western Eurasia. What variant of C do you propose was present in western Eurasia before C11 formed?

German Dziebel said...

@Mark Moore

"OK I like thinking outside the box, even if I don't agree with German's big idea. To me, it is a necessary part of real science where even our assumptions are not above occasional question. This is the exact opposite of restrictive PC-thinking that in my view is the enemy of true scientific inquiry."

Very well.

"The ancient Amerindians started off in central Asia and spread east and west, exploiting a cold-adapted life style."

Yes. But why in Asia? America harbors 2/3 of world linguistic diversity, which is the best test to an out-of-America interpretation of the population genetic data.

German Dziebel said...

@TerryT

"What variant of C do you propose was present in western Eurasia before C11 formed?"

These days we don't need to propose anything of this sort. Just see what ancient DNA is telling us or sit tight for a couple of months and wait for it. Do we already have this info, Terry? Could you google it?

At this point the data from modern human populations is telling us that the genetic path to the West Eurasian skin color began not in Africa but in Asia and America. Unless you believe West Eurasians evolved in-situ from Neandertals.

Mark Moore (Moderator) said...

"America harbors 2/3 of world linguistic diversity, which is the best test to an out-of-America interpretation of the population genetic data."

Well I don't think linguistic diversity is as good a test of the theory as genetic diversity. And at any rate the language diversity is also explained by my hypothesis that they started in central Asia and went both east and west, picking up bits of language from other groups as they did.

In fact my idea is a BETTER fit because most of the loan words from East coast Amerindians matches up better with languages from the Med. region than with east asian languages.

The explanation I offer is the most parsimonious because I do not have to postulate that Africans are the product of admixture with unknown non-human hominems, as you do. I think our host has offered up a study which undermines the antiquity of their Y chromosomes, taking away most of the case that Africans have more non-human DNA than other groups.

terryt said...

"These days we don't need to propose anything of this sort".

Of course not because once you (German) proposed something others of us might be able to prove you wrong.

"Just see what ancient DNA is telling us or sit tight for a couple of months and wait for it. Do we already have this info, Terry?"

No. But it is absolutely obvious that the 'new' C11 must have replaced something when it formed west of the Altai/Hindu Kush mountains, and what was there before C11 is as likely to have been C10 or C3 as it is to have been anything else. In fact more likely, because that is where the mutation to C11 took place, and the homozygous form is strongly represented.

"the genetic path to the West Eurasian skin color began not in Africa but in Asia and America. Unless you believe West Eurasians evolved in-situ from Neandertals".

Your second comment doesn't follow rationally from your first at all. In fact the first comment is hardly rational. For it to be acceptable western Eurasia would have to have been uninhabited when the first step on the genetic path was taken.

German Dziebel said...

@Mark Moore

"I don't think linguistic diversity is as good a test of the theory as genetic diversity."

You don't know what you're talking about. The worldwide patterns of linguistic diversity fit well with the patterns of intergroup genetic diversity.

"my hypothesis that they started in central Asia and went both east and west, picking up bits of language from other groups as they did. "

Yours is not a scientific hypothesis but a plot for a history movie.

"In fact my idea is a BETTER fit because most of the loan words from East coast Amerindians matches up better with languages from the Med. region than with east asian languages."

There are no loanwords shared between east coast Amerindians and Mediterranean peoples. You've been reading some pseudolinguistic literature.

"The explanation I offer is the most parsimonious because I do not have to postulate that Africans are the product of admixture with unknown non-human hominems, as you do."

We have genome-wide and craniological evidence for this admixture. We know from the fossil record that archaic hominins lived in Africa. Your explanation is "parsimonious" to the extent that all data-free speculations are.

"I think our host has offered up a study which undermines the antiquity of their Y chromosomes, taking away most of the case that Africans have more non-human DNA than other groups."

Y-DNA A00, A and B lineages are low-frequency, African specific lineages and hence are likely a product of archaic admixture into a population of modern Eurasians that brought the dominant hg E ( < DE < CT) into Africa. The study that Dienekes just put up doesn't even consider this option.

German Dziebel said...

@Terry

"In fact the first comment is hardly rational."

It's just a statement of fact. The West Eurasian-specific A111T mutation occurred after the recombination of two non-African haplotypes.

"Your second comment doesn't follow rationally from your first at all. "

It was not supposed to follow from the first one. It was supposed to demonstrate that unless you believe in an independent origin of West Eurasians from Neandertals there's only one logical path for their evolution - from East Eurasian populations where C3 and C10 are found.

"Of course not because once you (German) proposed something others of us might be able to prove you wrong."

The point being that ancient DNA data is now increasingly available, so there's no need to speculate about what it might be. And ancient DNA has so far yielded strong support for my theory and a full rebuttal of out-of-Africa.

terryt said...

"It's just a statement of fact. The West Eurasian-specific A111T mutation occurred after the recombination of two non-African haplotypes".

Agreed, but you lept a yawning chasm to propose something much more than the simple facts dictate when you said, 'the genetic path to the West Eurasian skin color began not in Africa but in Asia and America'.

"unless you believe in an independent origin of West Eurasians from Neandertals there's only one logical path for their evolution - from East Eurasian populations where C3 and C10 are found".

Your path leads logically to the necessity of a total absence of humans of any sort between America and Africa until the carriers of the West Eurasian-specific A111T mutation entered West Eurasia. That is so unlikely as to be not worth considering.

"The point being that ancient DNA data is now increasingly available, so there's no need to speculate about what it might be".

But the logic of your claim here falls to the ground immediately, because you refuse to accept any currently accepted phylogenies that contradict your belief.

"ancient DNA has so far yielded strong support for my theory and a full rebuttal of out-of-Africa".

That is true only because you have consistently dismissed any research that makes your position untenable. Adopting your methodology would make it possible to prove humans originated in Antarctica. Except that at present you don't wish to 'prove' that to be so.

German Dziebel said...

@Terry

"Agreed, but you lept a yawning chasm to propose something much more than the simple facts dictate when you said, 'the genetic path to the West Eurasian skin color began not in Africa but in Asia and America'."

I just have to repeat what's just a simple fact - A111T emerged after the recombination of an Amerindian and an Asian/Amerindian haplotypes. No African haplotypes were involved. You can try to twist the facts as much as you want. I don't care. Don't assume I'm trying to "win you over." Terry, you are a liability to any theory, not an asset, hence I'd prefer if you stay with your beliefs.

"because you refuse to accept any currently accepted phylogenies that contradict your belief."

I refuse to accept phylogenies that are methodologically flawed. This has nothing to do with my beliefs. You are the one who holds "beliefs" because you don't have a scientific methodology to rely on in your judgments.

"That is true only because you have consistently dismissed any research that makes your position untenable."

No, I criticize research that is based in cultural mythology. And you are the one who tries to present myth as if it were science. Hence, as I pointed out, you are a retention from a pre-scientific worldview.

"a total absence of humans of any sort between America and Africa until the carriers of the West Eurasian-specific A111T mutation entered West Eurasia. That is so unlikely as to be not worth considering."

I never said there were no humans between America and Africa before A111T emerged. On the contrary, the data shows that the population that preceded A111T was derived from a mix of a largely purely Amerindian population and an "eastern" population that is found in America, East Asia and Oceania. It was not derived from an African population thus falsifying out-of-Africa again and again.

terryt said...

"Scientists like me do read Supplemental Material. Amateurs like you tend to stick to press releases and abstracts".

I've realised how easy it would be to 'prove' modern humans expanded from Antarctica if we use statements quite closely related to what 'scientists like German' (as opposed to almost all other scientists) have used in the recent past. I stress that I in no way believe the following to be at all justified by the actual evidence but am simply posing as a 'scientist like German':

From where did these modern humans enter America? It is often claimed human expansion through America was from south to north. We know that Australia/New Guinea and South America were the last continents to break contact with Antarctica, and Gondwanaland. Taken at face value that easily explains both the increased linguistic diversity and the similar kinship systems found in the two regions.

The absolute chronology is a big issue, no doubt. I know the currently accepted dates for Gondwanaland's breakup do not support this scenario but the ancient dating is a mess, and has been promoted by scientists whose prejudice against Antarctica as a source for at least part of Old World diversity stems from a 500-year-old cultural stereotype.

The African haplotypes that many mistake as ancestral to modern humans are likely the product of archaic admixture in Africa. Africa had broken away from Gondwanaland some time before Australia and South America had, carrying only 'primitive' and 'archaic' humans. These human types were able to move towards modernity only once the Antarctic humans had entered Laurasia and so were eventually able to reach Africa.

Scientists have failed to find evidence for this Antarctic origin because most of them are especially prone to holding uncritically accepted beliefs. They have closed minds, and are ignoring the possibility and so do not look for the evidence that must be there. As for the intense cold: we know that beech forest existed on Antarctica in the past. The dating usually given is 2 million years ago, but this date too is probably wrong.

This all proves that modern humans first emerged in Antarctica!

Thank you German.

terryt said...

"I never said there were no humans between America and Africa before A111T emerged".

No, but your belief requires it. Unless you've changed your mind:

"the data shows that the population that preceded A111T was derived from a mix of a largely purely Amerindian population and an 'eastern' population that is found in America, East Asia and Oceania".

But hang on. You claimed the mutations that gave rise to A111T could not have happened anywhere other than in America (the genetic path to the West Eurasian skin color began not in Africa but in Asia and America). If you've now changed your mind about pre-A111T inhabitants in western Eurasia there is no reason at all why the mutations could not have happend in that region. Please try to be a little consistent.

"I refuse to accept phylogenies that are methodologically flawed. This has nothing to do with my beliefs".

I'm afraid it has everything to do with your beliefs.

German Dziebel said...

@TerryT

"This all proves that modern humans first emerged in Antarctica!"

I'm happy you found your "big idea."

"I'm afraid it has everything to do with your beliefs."

Of course not. If you read Lippold et al. 2014, you would've noticed that what used to be presented as a "proven" mtDNA phylogeny now comes with a major surprise: mhg N is upstream from a newly established L3'M node.

"You claimed the mutations that gave rise to A111T could not have happened anywhere other than in America (the genetic path to the West Eurasian skin color began not in Africa but in Asia and America)."

Yes. This is what the data suggests. I don't understand what your problem is.

"there is no reason at all why the mutations could not have happend in that region."

Oh, okay, I go it. Your twisted, pseudo-scientific imagination has taken you to an idea that Europe used to be like America in having C3 and like America, Asia and Australia in having C10, while America, Asia and Australia used to be like nothing. Then Europe became uniquely European, while America, Asia and Australia became what Europe was no more. It's a nice complement to your freshly baked out-of-Antarctica. What's your take on Atlantis, Terry?

terryt said...

Sorry. Back again. I forgot:

"I never said there were no humans between America and Africa before A111T emerged".

Well, actually, you did. Or you said the C11 mutation hadn't replaced anything else. For example this comment in response to my, 'The reason it and C10 are virtually absent west of approximately longitude 75 in Central Asia is that selection for the derived C11 has replaced the ancestral variants there':

"Like I pointed out to Tobus, this is a special explanation that requires special evidence. Currently, you are invoking a historical scenario whereby the data you need to support your belief went miraculously extinct".

Has new 'special evidence' emerged? I haven't seen it. Please bring it to our attention. Because now you're agree with Tobus and me that pre-existing haplogroups west of approximately longitude 75 in Central Asia have been replaced, presumably by selection:

"my idea that a crossover between an Amerindian haplotype and an eastern non-African haplotype was followed by a mutation that took place in western Eurasia as the population movement progressed from east to west".

Make up your mind!

Sean McClellan said...

Perhaps La Brana 1 represents a group a group of europeans you had mirgrated back to africa during glacial periods and migrated back in to europe as the glaciers retreated. Mtdna U group evolved out of M. YDNA group C6 follows that same patern as M and U MTNA only more eastward to India. La Brana's ancestors mirgrated back to the Iberian Pen from either North Afria or the Horn of Africa and mirgrated along the Northern Med back to Iberia. He still had the blue eye gene, however evolution favored darker skin being closer to the equator while in Africa

German Dziebel said...

@TerryT

""my idea that a crossover between an Amerindian haplotype and an eastern non-African haplotype was followed by a mutation that took place in western Eurasia as the population movement progressed from east to west".

Yes, this is how I would interpret the data. It's possible that C10 was introduced into Europe first and then an out-of-America migration brought C3 and the two admixed and recombined. Still later, A111T happened in West Eurasia. Or, the out-of-America migration preceded a migration from East Asia. Or the mixture happened before modern humans moved into West Eurasia. Ancient DNA will show. But the fact remains that ancient West Eurasians derived from a mix of C3 and C10 (skin genes wise), which are Amerindian and East Asian/Australian, and not from any combination of African genes. Down goes the myth that Europe was colonized from Africa.

terryt said...

"Mtdna U group evolved out of M".

No. It's from N, via R actually.

"What's your take on Atlantis, Terry?"

Probably based on some event in Mediterranean prehistory. What's your take on it? Antarctica?

"I'm happy you found your 'big idea'."

I'd be surprised if you disagree with it. The idea accounts for the two separate lines, American and East asia, you agree formed the two populations whose mixing gave rise to the C11 mutation. And it fits exactly the 'phylogenetic uncertainty around some of these nodes supported by the geographic disjunction between New World-dominant C3 and African dominant C1 and C2'.

"a 'proven' mtDNA phylogeny now comes with a major surprise: mhg N is upstream from a newly established L3'M node".

What, exactly, does that alter in any fundamental way? Most had already taken for granted that N was older than M. This just confirms it.

"Your twisted, pseudo-scientific imagination has taken you to an idea that Europe used to be like America in having C3 and like America, Asia and Australia in having C10, while America, Asia and Australia used to be like nothing".

Twisted logic? Try this:

"I never said there were no humans between America and Africa before A111T emerged. On the contrary, the data shows that the population that preceded A111T was derived from a mix of a largely purely Amerindian population and an 'eastern' population that is found in America, East Asia and Oceania".

In this statement you appear to be saying that C10 and C3 were both in western Eurasia whereas just before you were claiming neither C3 nor C10 was present there. As I keep saying: make up your mind! Surely it is obvious that both C3 and C10 were widespread but in Europe C11 evolved and selection for C11 resulted in the replacement of C3 and C10 in western Eurasia. That is what the authors suggest and it is what I have agreed with all along.

German Dziebel said...

@TerryT

"Surely it is obvious that both C3 and C10 were widespread but in Europe C11 evolved and selection for C11 resulted in the replacement of C3 and C10 in western Eurasia. "

Without ancient DNA data we don't know this. I haven't seen any direct proof of that. It's possible and there are a number of possibilities that I identified above. What we do know is that the genetic evolution for West Eurasian populations as seen through skin color genes began as a mix of Amerindian and more generic Amerindian/Asian/Australian genes. This is consistent with all the current available ancient DNA evidence from Mal'ta, La Brana, Loschbour, Motala, etc. showing a pull toward Amerindians beginning from pre-Neolithic times when West Eurasians were not "white" yet. How Europe was peopled in UP times, in how many waves and where those waves mixed, etc. is an open question.

"Try this"

I seriously don't see any lapse of logic you're imputing to me. Your logic fallacies, on the contrary, are clear and easy to identify.

"What, exactly, does that alter in any fundamental way?"

You must be kidding me: all the African L3 lineages, which are most frequent and pan-African, are now a subset of non-African genes. Just like Y-DNA hg E is a subset of non-African CT cluster. This further means that all the low frequency, African specific lineages now look more and more like introgressions from African archaics. Finally, it shows to the gullible individuals like yourself that science is not set in stone but evolves, and my theories stem from this propensity of science to evolve.

Rokus said...



"a 'proven' mtDNA phylogeny now comes with a major surprise: mhg N is upstream from a newly established L3'M node".

What, exactly, does that alter in any fundamental way? Most had already taken for granted that N was older than M. This just confirms it.

No, I don't think the Out of Africa community would ever have dared to take for granted that also African MtDNA L3 is actually a subclade of non-African mtDNA N! This is nothing short of admitting a reversed philogenetic tree to the result that mtDNA L3 actually attests an "Into Africa" migration event.

terryt said...

"Yes, this is how I would interpret the data".

Yes, now. But that is not how you saw things at the beginning of this discussion.

"It's possible that C10 was introduced into Europe first and then an out-of-America migration brought C3 and the two admixed and recombined".

On what grounds do you insist 'an out-of-America migration brought C3'? From the suggested phylogeny it is an ancient variation not found in Africa. It could have been widespread before being replaced through much of the world. Therefore not necessarily from America. That may be simply where a higher proportion has survived.

"Or the mixture happened before modern humans moved into West Eurasia".

Or once they had 'moved into West Eurasia'. One scenario is as likely as another. In fact the authors suggest the mixture happened in West Eurasia, where the selection for the later mutation occurred. Because of that I tend to accept the authors' suggestion.

"the fact remains that ancient West Eurasians derived from a mix of C3 and C10 (skin genes wise)"

Yes, we agree on that. We disagree on where and why it happened.

"which are Amerindian and East Asian/Australian"

They are only 'Amerindian and East Asian/Australian' because of selection for the C11 variant in west Eurasia. Neither variant need originally have been either Amerindian or East Asian/Australian.

"not from any combination of African genes. Down goes the myth that Europe was colonized from Africa".

Autosomal genes are different from haploid genes. I agree that C3 seems not to derive from an African form which means your critical comment of a few days ago concerning Neanderthals may be correct. It seems from research published in the last few days that Neanderthal genes advantageous to survival in the north introgressed into modern humans. Quite possibly the C3 variant was part of that introgression. It would be informative to know what the Neanderthal version was.

terryt said...

A link to more on Neanderthal admixture:

http://www.bbc.co.uk/news/science-environment-25944817

Quote:

"Researchers found that Neanderthal DNA is not distributed uniformly across the human genome, instead being commonly found in regions that affect skin and hair ... Neanderthal ancestry was found in regions of the genome linked to the regulation of skin pigmentation. 'I think what we're seeing to a large extent is the dying remains of this extinct genome as it is slowly purged from the human population' Joshua Akey University of Washington
'We found evidence that Neanderthal skin genes made Europeans and East Asians more evolutionarily fit,' said Benjamin Vernot, from the University of Washington, co-author of a separate study in Science journal".

C3 variant?

"This suggests some gene variants provided a rapid way for modern humans to adapt to the new cooler environments they encountered as they moved into Eurasia. When the populations met, Neanderthals had already been adapting to these conditions for several hundred thousand years".

That makes complete sense.

Mark Moore (Moderator) said...

German

Me: "I don't think linguistic diversity is as good a test of the theory as genetic diversity."

German: You don't know what you're talking about. The worldwide patterns of linguistic diversity fit well with the patterns of intergroup genetic diversity."

Me on that: Outside the box thinking I like, rudeness, especially when you are misinterpreting what I say, I don't. I did not say that they did not fit well, I said they would not fit AS WELL as genetic measurements. And this is clearly so. It is easier to change languages than to change genes.

Me: "my hypothesis that they started in central Asia and went both east and west, picking up bits of language from other groups as they did. "

German: "Yours is not a scientific hypothesis but a plot for a history movie."

Me on that: There you go again. I am not the first to speculate that Amerindians have a pre-Columbian European component. http://genetiker.wordpress.com/2013/12/18/admixture-analyses-of-north-american-indians/

Me: "In fact my idea is a BETTER fit because most of the loan words from East coast Amerindians matches up better with languages from the Med. region than with east asian languages."

German: "There are no loanwords shared between east coast Amerindians and Mediterranean peoples. You've been reading some pseudolinguistic literature."

Me on that: Or maybe I just mis-remembered who the European words came from. It was the Kelts... http://stevehollier.wordpress.com/2010/10/22/global-whispers-linguistic-links-between-the-algonquian-indian-language-and-gaelic/


Me: "The explanation I offer is the most parsimonious because I do not have to postulate that Africans are the product of admixture with unknown non-human hominems, as you do."

German: "We have genome-wide and craniological evidence for this admixture. We know from the fossil record that archaic hominins lived in Africa. Your explanation is "parsimonious" to the extent that all data-free speculations are. "

Me on that: Sure we have evidence there were hominins, what we don't have is evidence they contributed Y chromosomes to West Africans, unless you want to go all circular reasoning on us and offer your speculation as "proof." So whose speculations are data-free again?

Me: "I think our host has offered up a study which undermines the antiquity of their Y chromosomes, taking away most of the case that Africans have more non-human DNA than other groups."

German: "Y-DNA A00, A and B lineages are low-frequency, African specific lineages and hence are likely a product of archaic admixture into a population of modern Eurasians that brought the dominant hg E ( < DE < CT) into Africa. The study that Dienekes just put up doesn't even consider this option."

Me on that: Look, I am not saying for sure you are wrong. I am saying for sure you need to be more polite, especially in espousing such a minority viewpoint on issues where there is not overwhelming evidence on either side.

What I was referring to was the link where the A00 was not 338 KYA but more like 200 KYA by other calculations. That could still be from another hominin, or one or both age estimate could be all wet. We can't HELP but speculate some given how paltry our evidence is. Still, 200 KYA makes it more likely it was from our species than 338 KYA.

I also think since then the other article our host put up, showing that for Neandertals at least, there is evidence of male sterility in hybrids. That does not necessarily say anything about what went on in Africa, but it does not FAVOR the idea of late introgression of Y chromosomes from non-human hominids into west African populations, that's for sure.

terryt said...

"No, I don't think the Out of Africa community would ever have dared to take for granted that also African MtDNA L3 is actually a subclade of non-African mtDNA N!"

Is it though:

"You must be kidding me: all the African L3 lineages, which are most frequent and pan-African, are now a subset of non-African genes".

No they're not. The most obvious conclusion to draw from that phylogeny is that the L3/N line simply split in two, with N forming outside Africa and L3 remaining within the continent. At some later stage M too left Africa. It does not follw logically that because one branch of a haplogroup reached a particular region the whole of the haplogroup must have reached that region too.

German Dziebel said...

@TerryT

"But that is not how you saw things at the beginning of this discussion."

Nothing has changed since then, I can assure you.

"On what grounds do you insist 'an out-of-America migration brought C3'? From the suggested phylogeny it is an ancient variation not found in Africa. It could have been widespread before being replaced through much of the world. Therefore not necessarily from America. That may be simply where a higher proportion has survived. "

With this frivolous logic, I'm not surprised you arrived at Antarctica as a modern human homeland. The data pattern whereby Amerindians almost uniquely "own" C3 and C3 contributed to the origin of West Eurasian skin color, fits with the autosomal data we have to date showing the presence of "Amerindian admixture" in West Eurasian-like populations from ancient Mal'ta to modern Lithuanians. The fit is pretty good, don't you think? It's only your anti-Amerindian biases that prevent you from appreciating the data for what it is.

"Quite possibly the C3 variant was part of that introgression. It would be informative to know what the Neanderthal version was."

Yes, agree this is possible.

"They are only 'Amerindian and East Asian/Australian' because of selection for the C11 variant in west Eurasia. Neither variant need originally have been either Amerindian or East Asian/Australian."

This is that special hypothesis that requires a special proof, which you don't have. As of now, the data and the logic go like this: "C10 and C3 are eastern non-African and Amerindian, respectively. They recombined to generate a Western Eurasian specific haplotype C11 that was followed by a point mutation A111T. This means West Eurasians likely originated from a mix of an Amerindian and an eastern Eurasian populations as these populations were moving westward into Europe. The point mutation on top of C11 happened already in western Eurasia."

I welcome the possibility that C3 will be detected in Neandertals. This would change the above. But in this case we'll have to grapple with the fact that Neandertals and Amerindians share unique affinity. There are already several indications that they do. For instance, it's possible that 'Amerindian admixture" in West Eurasians detected in the autosomes is that shared Amerindian-Neandertal legacy.

Kurti said...

Since Onur insists on his no sense theories let me give him another admixture calculator.

http://www.dnatribes.com/dnatribes-snp-admixture-2013-02-11.pdf

In this calculator the South Indian (ASI=Ancestral South Indian) in Kurds is 0.0%.

If the South Indian in Kurds is 0% here. How can Gedrosia which hits 28% in Kurds be part ASI. Explain that to me.

German Dziebel said...

@terryT

"The most obvious conclusion to draw from that phylogeny"

What's most "obvious" to you is usually the least scientific solution. First, the phylogeny longed touted as "proven" has changed dramatically. And it will continue to. Second, L3'N is not a clade in the current rendition. L3'M is a clade. N is a notch up. Third, N is not found in Africa and L3 or L5 are not found outside of Africa. So, the most reasonable conclusion from this phylogeny is that L3 migrated to Africa from Eurasia, while L0,L1'L2'L4 and L5 lineages were absorbed by L3 carriers from an archaic African hominin substrate that subsequently went extinct. We know from genomewide studies that there was a migration into Africa because Neandertal and Denisovan genes are there. We don't have any evidence that genes from African archaics made it into Eurasia.

@Moore

"Outside the box thinking I like, rudeness, especially when you are misinterpreting what I say, I don't."

I wasn't rude. If you want to discuss something with me, you need to at least meet basic standards of knowledge and logic. You did not. Saying "It is easier to change languages than to change genes" places you in my category of pseudoscientific trolls.

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

"I'm not surprised you arrived at Antarctica as a modern human homeland".

Perhaps English is your second language and you do not understand it very well. You certainly seem unable to read it properly. Concerning the Antarctic theory I wrote:

"I've realised how easy it would be to 'prove' modern humans expanded from Antarctica if we use statements quite closely related to what 'scientists like German' (as opposed to almost all other scientists) have used in the recent past. I stress that I in no way believe the following to be at all justified by the actual evidence but am simply posing as a 'scientist like German'"

In fact most of the sentences in the argument are only slightly adapted for those you have actually used. Through using the 'frivolous logic' of your own 'scientific' method I was able to show it was possible to prove anything at all.

The remainder of you comments in your latest contribution to this post follow your usual frivolous logic.

eurologist said...

"If you read Lippold et al. 2014, you would've noticed that what used to be presented as a "proven" mtDNA phylogeny now comes with a major surprise: mhg N is upstream from a newly established L3'M node."

As I wrote in the thread for that paper:

That is an incorrect representation of the results of the paper. There is now an L3MNUR group, which is upstream of L3M and NUR. However, the LRM-NUR and L3-M splits are only 5,000 years apart (or likely ~1/3 more, IMO) - well withing the ~20,000 years of an advantageous ooA ~125,000 - 105,000 ya time period.

L3 then simply is the surviving NE African portion of L3MNUR.

Onur said...

Since Onur insists on his no sense theories let me give him another admixture calculator.

http://www.dnatribes.com/dnatribes-snp-admixture-2013-02-11.pdf

In this calculator the South Indian (ASI=Ancestral South Indian) in Kurds is 0.0%.

If the South Indian in Kurds is 0% here. How can Gedrosia which hits 28% in Kurds be part ASI. Explain that to me.


That "South Indian" component does not equal to ASI. It is probably an ASI-majority, Caucasoid-minority composite component. According to the neighbor joining tree diagram of that admixture analysis, the closest component to the "South Indian" component is the "Indus Valley" component and those two components form a clade relative to the other components. The "Indus Valley" component is probably a Caucasoid-majority, ASI-minority composite component. Kurds possess 15.4% "Indus Valley" component, so they are expected to have non-negligible levels of ASI ancestry.

I can go on discussing this issue, but it is off the topic of this thread. So I am keeping my reply to you short.

BTW, Kurti, at a Eurogenes thread you wrote a reply to me, and I wrote a reply to your reply but it never appeared at that thread due to a technical issue at that thread. So I reposted that reply at another Eurogenes thread making an explanation of the technical issue. I am not sure whether you saw the reposted version, so I am giving you the link to the reposted version:

http://eurogenes.blogspot.com.tr/2013/12/brana-1-had-blue-eyes.html?showComment=1390124270856#c5563835104562678079

Of interest, to your statement "I am getting more and more sure that this guy is actually the Onur who is mostly of Bulgarian Turkish descend and wandering through allot of Anthro-Forums trying to spread his obsession" my reply is this:

"As I told you before, I am not that guy. My known ancestry is only 1/4 from Bulgaria (1/2 from Anatolia and 1/4 from Greece). I do not write in any forum, I only write in blogs. And I have always been on good terms with Kurds."

I hope I have made myself clear about my identity and you will from now on stop equating me to someone else. I honestly feel insulted by your this behavior. Also, as I stated, Onur is a common name in Turkey.

terryt said...

"What's most 'obvious' to you is usually the least scientific solution. First, the phylogeny longed touted as 'proven' has changed dramatically".

'Changed dramatically'? Not so, as Eurologist has just explained. 'Refined', yes.

"Second, L3'N is not a clade in the current rendition. L3'M is a clade. N is a notch up".

That's exactly what I said above. Your comprehension of English is deficient.

"Third, N is not found in Africa and L3 or L5 are not found outside of Africa. So, the most reasonable conclusion from this phylogeny is that L3 migrated to Africa from Eurasia, while L0,L1'L2'L4 and L5 lineages were absorbed by L3 carriers from an archaic African hominin substrate that subsequently went extinct".

Not only your English but your logic is deficient. How on earth do you get L3 migrating to Africa from Eurasia from the new phylogeny? That would require a haplogroup entering the vast expanse of Eurasia forming a single haplogroup branch behind while a haplogroup that entered already-occupied Africa managed to form quite a number of haplogroup branches. Doesn't make sense.

"We know from genomewide studies that there was a migration into Africa because Neandertal and Denisovan genes are there".

Yes. We know that Y-DNA R and mt-DNA M entered Africa from Eurasia.

"We don't have any evidence that genes from African archaics made it into Eurasia".

You seem to have a very racist concept of Africans. Are you disappointed that slavery was abolished?

German Dziebel said...

@TerryT

"Perhaps English is your second language and you do not understand it very well. You certainly seem unable to read it properly."

Nice try, New Zealand. Perhaps, having spent decades breeding animals, thinking has never become one of your faculties, as you clearly incapable of comprehending the various discursive means that human beings use to fight pseudoscientific biases and ad hominem attacks. Regardless of what you were trying to communicate with your Antarctic analogy, you are now an "out-of-Antarctica" guy. It's official! This is the idea your imagination would have of necessity taken you to if you hadn't stumbled on its next-of-kin - out-of-Africa.

German Dziebel said...

@Eurologist

"That is an incorrect representation of the results of the paper. There is now an L3MNUR group, which is upstream of L3M and NUR."

Yes, after re-examining that mammoth tree graph, I agree, this is more accurate. Thanks. This doesn't change the fact that L3 is now a subset of what otherwise is a non-African clade. This is precisely what we see in the Y-DNA phylogeny. And I argued multiple times that mtDNA phylogeny must be out of whack as the mtDNA and Y-DNA trees should mirror each other better than they did during the "classical" haploid research times.

"L3 then simply is the surviving NE African portion of L3MNUR."

L3 has a pan-African distribution. It's found among Khoe-San and in West Africa. The "simplest" explanation therefore is that Eurasians entered Africa through East Africa and spread across the whole continent from there. This is consistent with East Africa having the highest linguistic diversity in Africa, with all the major continental stocks (Khoisan, Niger-Congo, Nilo-Saharan, Afroasiatic) represented there. This is a perfect footprint of modern humans. All the other "L" lineages were absorbed from an archaic substrate(s) in Africa. Same for Y-DNA hgs A and B.

Ignore the dates. They are a moving target.

terryt said...

"you are now an 'out-of-Antarctica' guy. It's official!"

OK. But I can't understand how you would disagree with me as I used exactly your arguments to support my claim. In fact often quoted you directly.

"This doesn't change the fact that L3 is now a subset of what otherwise is a non-African clade".

How on earth do you come to that conclusion? L3MNUR apparently simply split in two. You are proposing that L3MNUR emerged from Africa, then a single branch of it (NUR) was left behind in uninhabited-by-anything-like-it Eurasia, but failed to expand for quite some time. Meanwhile the other branch (L3M) re-entered an already-occupied Africa and instantly diversified considerably. My decades spent breeding animals tells me that makes no ecological sense at all.

"And I argued multiple times that mtDNA phylogeny must be out of whack as the mtDNA and Y-DNA trees should mirror each other better than they did during the 'classical' haploid research times".

On what grounds do you assume that? We know from more recent times that the two haploid lines can be remarkably different.

"L3 has a pan-African distribution. It's found among Khoe-San and in West Africa".

But much of that 'pan-African distribution', especially in South Africa, is a product of more recent expansion, with farming. L3 looks to have been originally primarily a Sahelian haplogroup, spread from Ethiopia to Birkina Faso. Presumably it was the presence of a similar habitat outside Africa that allowed haplogroups related to L3 to expand from Africa.

terryt said...

Further to my previous comment. German wrote:

"L3 has a pan-African distribution. It's found among Khoe-San and in West Africa. The 'simplest' explanation therefore is that Eurasians entered Africa through East Africa and spread across the whole continent from there".

But the 'Eurasian' entry did not require L3 to have come from outside Africa, merely to be a vector for expansion within Africa. Check out Dienekes' latest post:

http://dienekes.blogspot.co.nz/2014/02/west-eurasian-ancestry-in-eastern-and.html

A couple of quotes from the abstract:

"Here we use genome-wide genetic data to show that there are at least two admixture events in the history of Khoisan populations (southern African hunter–gatherers and pastoralists who speak non-Bantu languages with click consonants). One involved populations related to Niger–Congo-speaking African populations, and the other introduced ancestry most closely related to west Eurasian (European or Middle Eastern) populations. We date this latter admixture event to ∼900–1,800 y ago and show that it had the largest demographic impact in Khoisan populations that speak Khoe–Kwadi languages".

'900–1,800 y ago' is far more recent than even German would claim for L3's original expansion.

"we also find evidence for two admixture events in the history of Kenyan, Tanzanian, and Ethiopian populations, the earlier of which involved populations related to west Eurasians and which we date to ∼2,700–3,300 y ago".

Perhaps we're getting closer with that date?

German Dziebel said...

@terryT

"How on earth do you get L3 migrating to Africa from Eurasia from the new phylogeny? "

Just like several authors argued that Y-DNA hg E migrated to Africa because it's nested within the Eurasian CT (CDEF) clade. And you in fact supported it in a number of forum discussions.

"Yes. We know that Y-DNA R and mt-DNA M entered Africa from Eurasia."

And now we know that hg M and hg L3 are sister clades. So, L3 logically entered Africa just like M1 did.

"You seem to have a very racist concept of Africans?"

African "archaics" is an accepted term for pre-modern human hominin populations. Just like Neandertals and Denisovans are spoken about as populations behind "archaic introgressions" in Eurasia.

But you are missing a bigger point: out-of-Africa theorists forgot that they need to furnish some evidence for the "Africanness" of Eurasian populations. The only way to do this, without falling into circular arguments, is to find genes from African archaic hominins outside of Africa. They would've been carried out by the expanding modern human populations who had previously admixed with them within Africa. Since African archaics are African-specific species, just like Neandertals and Denisovans are Eurasia-specific species, one would have been justified in considering an out-of-Africa migration "proven." But in reality it's a migration into Africa that's now a proven fact, not a migration out of Africa.

So, as you can see, I have plenty of logic and enough command of the English language to say something meaningful. You, admittedly, can chirp in English but you have nothing of value to say.

terryt said...

"And now we know that hg M and hg L3 are sister clades. So, L3 logically entered Africa just like M1 did".

We've 'always' known M is a sister clade to all the L3s, not to L3 as a whole. M is just one of the several L3 clades, equal to L3a (Ethiopia), L3b'f (Across Sahel to Birkina Faso), L3c'd'j (across Sahel and into Kenya), L3e'i'k'x (across Sahel and into SW Asia) and L3h (across sahel and into Tanzania). From that we see that M is the odd one out and so it is extremely unlikely that its presence outside Africa indicates the 'origin' of the whole set. It is especially unlikely when we consider that just the downstream mutation M1 entered Africa. And then only a very small proportion of that haplogroup.

"Just like several authors argued that Y-DNA hg E migrated to Africa because it's nested within the Eurasian CT (CDEF) clade. And you in fact supported it in a number of forum discussions".

I am actually yet to be convinced that E is anything other than African in origin. What we may be seeing is that DE became spread through the African Sahel and out into the grassland steppe of Eurasia. D and E represent mutations from the opposite ends of the geographic range. At some subsequent time the haplogroup suffered extinction through the regions intermediate between Africa and Eastern Eurasia.

"The only way to do this, without falling into circular arguments, is to find genes from African archaic hominins outside of Africa. They would've been carried out by the expanding modern human populations who had previously admixed with them within Africa".

How can you expect any African group who emerged into Eurasia to carry a fully representative sample of African genes? This is especially surprising considering your previous comment:

"African 'archaics' is an accepted term for pre-modern human hominin populations".

But you place every African that lacks Eurasian element into the archaic category.

"I have plenty of logic and enough command of the English language to say something meaningful".

But what you say is still rubbish. Certainly of no value at all.

German Dziebel said...

@terryT

"But I can't understand how you would disagree with me as I used exactly your arguments to support my claim."

Are you now claiming that Antarctica has the greatest linguistic diversity in the world? Just like I indeed do for America.

"You are proposing that L3MNUR emerged from Africa..."

No. Why? Your decades of breeding animals has affected your comprehension of humans. L3MNUR emerged from Eurasia. Populations that carried L3 and M1 migrated into Africa.

"On what grounds do you assume that?"

Again, the comprehension of human speech is difficult for you, Terry. Just like pan-African Y-DNA hg E is a subset of the Eurasian clade, pan-African mtDNA hg L3 is a subset of the Eurasian clade.

"But much of that 'pan-African distribution', especially in South Africa, is a product of more recent expansion, with farming."

Do you have a reference? L3 is found in Hadza who are foragers (Tishkoff 2007). But I agree that the pan-African provenance of Y-DNA hg E is more salient than that of mtDNA L3. Hg E is abundant across South and East Africa, foragers and farmers alike. However, this is normal as sex-biased gene flow has been reported from several regions. E.g., Munda's genetic connection to other Austroasiatic speakers in SE Asia is noticeable in its Y-DNA makeup but not in its mtDNA makeup. Munda are Indian in their mtDNA but SE Asian in their Y-DNA. Y-DNA proves to be more reflective of their origin.

German Dziebel said...

@TerryT

"We've 'always' known M is a sister clade to all the L3s, not to L3 as a whole."

That's a big change. But you are obviously in denial.

"I am actually yet to be convinced that E is anything other than African in origin."

The fact is mtDNA L3 is a subset of non-African haplogroups should help you on this difficult mental journey.

"But you place every African that lacks Eurasian element into the archaic category. "

Stop your hysteria. Out-of-Africa theorists put all Africans in a pre-Eurasian stage of genetic evolution, again making them closer to the African "archaics." My model is much more progressive than out-of-Africa: I just have different hominin populations mixing with each other, with some of them surviving (modern humans), others (African archaics, Denisovans, Neandertals, etc.) going extinct post mixing.

"Certainly of no value at all."

For an individual with an archaic worldview.

terryt said...

"Are you now claiming that Antarctica has the greatest linguistic diversity in the world? Just like I indeed do for America".

Has no-one told you that Antarctica is now a frozen continent? You should read more. And I though you claimed a high linguistic diversity for New Guinea as well. Doesn't a migartion from Antarctica fit exactly with your claims?

"Just like pan-African Y-DNA hg E is a subset of the Eurasian clade, pan-African mtDNA hg L3 is a subset of the Eurasian clade".

That is complete rubbish. E is no 'subset' of a Eurasian clade but a 'brother' to a Eurasian clade. That tells us nothing about where their ancestral haplogroup originated. And 'pan-African mtDNA hg L3' is even less 'a subset of the Eurasian clade'. L3 is primarily an African clade with just M being non-African according to the paper you are quoting. As a result 'your comprehension of humans' is non-existent.

"L3 is found in Hadza who are foragers (Tishkoff 2007)".

Since when have Hadza been South African though. And we have numerous examples of farmers turning to foraging whne conditions change.

"Hg E is abundant across South and East Africa"

And West Africa.

German Dziebel said...

@TerryT

"Has no-one told you that Antarctica is now a frozen continent? You should read more. And I though you claimed a high linguistic diversity for New Guinea as well. Doesn't a migartion from Antarctica fit exactly with your claims? "

I like your thinking here. Could you develop it a bit more and start a blog about it? This would channel your energy into a productive pursuit.

"E is no 'subset' of a Eurasian clade but a 'brother' to a Eurasian clade."

E is a subset of CT which includes D, F and C - all Eurasian.

"L3 is primarily an African clade with just M being non-African according to the paper you are quoting."

But both of them are part of a clade that includes U, N and R, all of which are Eurasian. So this makes L3 a subset of a Eurasian clade just like African and West Asian hg M1 is a subset of hg M, which otherwise has Eurasian distribution.

"Since when have Hadza been South African though. And we have numerous examples of farmers turning to foraging whne conditions change. "

Not Hadza's case.

""Hg E is abundant across South and East Africa"

And West Africa."

You got it! It's pan-African.

terryt said...

"E is a subset of CT which includes D, F and C - all Eurasian".

Absolute rubbish. E is a subset firstly of DE and only then with CT. And CT is a subset of BT, in turn a subset of A1b. Of the whole collection just CF and D are found beyond Africa, and exclusively so. I agree it is 'possible' that E originated outside Africa but the distribution of its own subgroups suggests otherwise.

"You got it! It's pan-African".

But check out the distribution of its various clades. None are 'Eurasian' except for very derived ones. It first formed E1 and E2. E2 is especially present in West Africa and E1 could also have originally been West African. E1a is definitely West African leaving just E1a clades in East Africa, but even here we have many basal West African clades.

"But both of them are part of a clade that includes U, N and R, all of which are Eurasian".

Again absolute rubbish. U, N and R remain a single haplogroup within the new phylogeny you are so enthusiastic about. This enthusiasm in spite of your continued denial of any relevance in constructed phylogenies. Once more we see your incredible inconsistency, using data willy-nilly depending on what you wish to 'prove'.

"So this makes L3 a subset of a Eurasian clade just like African and West Asian hg M1 is a subset of hg M, which otherwise has Eurasian distribution".

Completely fawlty logic once more. M1 is in fact a subset of M, yes. And M has an otherwise Eurasian distribution. Therefore M1 almost certainly moved from Eurasia to Africa. But you completely miss the boat with its relationship with L3. What you should have said is, 'M is a subset of L3, which otherwise has an African distribution'.

terryt said...

Sorry. I missed German's earlier comment:

"That's a big change [M is a sister clade to all the L3s, not to L3 as a whole]".

Please explain. In what way is it 'a big change'? M is just one branch of the six L3 clades. L3 is not 'one clade' within M. Nothing has changed. That is how the haplogroup has long been seen.

"The fact is mtDNA L3 is a subset of non-African haplogroups should help you on this difficult mental journey".

OK. Please explain how it is that you see L3 as 'a subset of non-African haplogroups'. It doesn't make sense.

"Out-of-Africa theorists put all Africans in a pre-Eurasian stage of genetic evolution"

No they don't. How do you come to that conclusion? They see Africans as being 'in a pre-Eurasian stage of technological evolution'. But many non-Africans also remained in that state until quite recently. You are conflating technological evolution with genetic evolution.

"I just have different hominin populations mixing with each other"

And so does every other geneticist. That is hardly 'proof' that humans came from America.

"My model is much more progressive than out-of-Africa"

And doesn't make sense. How did humans reach America in the first place? Via Antarctica, I suppose.

German Dziebel said...

@terryT

"M is just one branch of the six L3 clades. L3 is not 'one clade' within M."

In the new version, M and all of L3 are sister lineages within the broader M'L3'N'U'R. In the old version, M and N are a subset of L3, R is a subset of N, U is a subset of R. So all those supposedly downstream lineages representing the "colonization of Eurasia" from Africa got pulled up in the new version.

I think you are just not looking at the new tree.

"No they don't. How do you come to that conclusion? "

It's funny how scientists have managed to fool people like you for such a long time. In the "classic" version of the mtDNA tree. L0 is African-speciifc and basal to the rest of the human tree, L1'2'4'5 are next to split and they are African specific, too. L3 is also African specific only two of L3 lineages, namely M and N - - which are also most recently derived - are Eurasian. So effectively the Eurasian lineages are several steps removed from the root of the human tree and all of Africans are closer to it. And the root of the human tree is most immediately derived from an African archaic tree, for which we have no direct evidence but which must have existed if we believe in Darwinian evolution. So in this model all modern Africans are closer to archaic Africans than Eurasians.

terryt said...

"I think you are just not looking at the new tree".

I wasn't able to access it until recently and so I was basing my comments on youronservations along with those of others.

"In the new version, M and all of L3 are sister lineages within the broader M'L3'N'U'R. In the old version, M and N are a subset of L3, R is a subset of N, U is a subset of R. So all those supposedly downstream lineages representing the 'colonization of Eurasia' from Africa got pulled up in the new version".

Yes. I see that M and L3 are 'sister' lineages rather than M being a single clade within L3. And that could indicate L3 entered Africa from Eurasia. In other words N'U'R and L3'M may have formed outside Africa from some sort of L2 that had left the continent. But M and L3 are not 'sister lineages within the broader M'L3'N'U'R'. We have N'U'R and L3'M forming separate clades perhaps, as you claim, outside Africa. Then L3 and M form separate clades with, perhaps, L3 moving back into Africa. The 'new' tree still has 'R is a subset of N, U is a subset of R'. In other words N, R and U form sequentially, not forming single lineages within M'L3'N'U'R, in fact not even within N. We still have basically just two lineages outside Africa: M and N. As a result we can't expact M'L3'N'U'R to have moved very far from that continent before L3 moved back in. Perhaps as far as what we now know as 'The Fertile Crescent'.

"In the 'classic' version of the mtDNA tree. L0 is African-speciifc and basal to the rest of the human tree, L1'2'4'5 are next to split and they are African specific, too. L3 is also African specific"

And that is still so in the 'new' version of the tree. No change there.

"only two of L3 lineages, namely M and N - - which are also most recently derived - are Eurasian".

That is also still the case in the new tree. The only difference is we now have N and M on separate branches within the tree.

"effectively the Eurasian lineages are several steps removed from the root of the human tree and all of Africans are closer to it. And the root of the human tree is most immediately derived from an African archaic tree".

True.

"for which we have no direct evidence but which must have existed if we believe in Darwinian evolution".

We have the evidence of the tree itself, as well as ample evidence for ancient human ancestors in Africa. Something we do not have at all for America. Unless you do not accept Darwinian evolution?

"So in this model all modern Africans are closer to archaic Africans than Eurasians".

They are closer to early modern humans than are Eurasians although you seem to be ignoring the considerable gene flow and mixing that has always been occurring during our evolution. Haplogroups are not always precise indicators of diploid genes. In fact Dienekes has recently posted a paper on the subject of admixture in Africa. I presume you've seen it.

German Dziebel said...

@TerryT

"We have the evidence of the tree itself, as well as ample evidence for ancient human ancestors in Africa. Something we do not have at all for America."

We have hominin fossils in Eastern Eurasia and we don't have them in America. But we're talking about modern humans, a new species. A new species requires isolation. America provided this isolation precisely because there were no hominins there. Once speciated in America, modern humans migrated back to the Old World some 60-50,000 years ago. There they admixed with Old World hominins, most extensively in Africa.

"In fact Dienekes has recently posted a paper on the subject of admixture in Africa."

Here you go.

"They are closer to early modern humans than are Eurasians."

You're not going to wiggle yourself out of a mouse trap, Terry. Under out-of-Africa modern Africans are closer to archaic African hominins than modern Eurasians. This is the age-old racist myth of primitive Africans who are ultimately closer to chimps than non-Africans. Alternatively, under out-of-America, many Africans carry "archaic" genes but this is immaterial and not "race-forming," as this is not ancient descent but recent admixture by a population that speciated in a continent devoid of in-situ "archaic" hominins.

terryt said...

"We have hominin fossils in Eastern Eurasia and we don't have them in America. But we're talking about modern humans, a new species. A new species requires isolation. America provided this isolation precisely because there were no hominins there. Once speciated in America, modern humans migrated back to the Old World some 60-50,000 years ago".

The problem for that argument is that we don't have evidence for any humans in America anything like 60-50,000 years ago. However I'm sure you will like this link:

http://www.pasthorizonspr.com/index.php/archives/02/2014/near-east-crossroad-of-the-palaeolithic-now-questioned

Quote:

"If this new research is correct, the story may need to be rewritten about the early movement of our ancestors and exactly how they left Africa. Instead of colonising the Levant then moving into Europe, they may have first settled in the central Asian steppes before turning west".

But it still makes 'out of America' extremely unlikely.

terryt said...

"But we're talking about modern humans, a new species. A new species requires isolation. America provided this isolation precisely because there were no hominins there".

On what grounds are you dismissing Australia as the point of origin then? For a start we can be reasonably confident humans reached there something approaching 60,000 years ago. And it was empty of humans before then. And is is isolated. And, most convincingly, Australia has very basal Y- and mt-DNA haplogroups under the usually-accepted phylogenies, unlike America.

"Once speciated in America, modern humans migrated back to the Old World some 60-50,000 years ago"

Again we have apparently basal members of the widespread Y-DNA MNOPS and mt-DNA R prestn very near Australia. In fact possible originating near that continent. Australia fits your theory far more closely than does America.

"Under out-of-Africa modern Africans are closer to archaic African hominins than modern Eurasians. This is the age-old racist myth of primitive Africans who are ultimately closer to chimps than non-Africans".

No. It is what the accepted phylogenies say. And any admixture has certainly removed any apparent closer connections to chimps. We are very sure that pre-human species were present in Africa and that something close to Homo erectus first evolved there. What we don't ywet know is where 'modern' humans evolved, or even if they were that much different from 'archaic' humans.

German Dziebel said...

@TerryT

"On what grounds are you dismissing Australia as the point of origin then? "

Feel free to build a case for Antarctica and Australia.

"The problem for that argument is that we don't have evidence for any humans in America anything like 60-50,000 years ago. "

Why would this be a problem? We have thousands of years ahead of us to find everything we need. You can't use archaeology as a source for hypotheses of human evolution. The archaeological record changes all the time and we have older and older signs of human activity in the Americas every 5-10 years. What archaeology is telling us is that there's no archaeological culture in the Old World that can be considered a source for the earliest New World cultures.

"But it still makes 'out of America' extremely unlikely."

I don't care how "unlikely" it seems to you. The very notion of likelihood is inapplicable here. out-of-America is a testable hypothesis built on unmistakable interdisciplinary patterns and as the new data comes in, we'll test it against it. So far ancient DNA and genomics holds a new promise for out-of-America and a bleak future for out-of-Africa.

"No. It is what the accepted phylogenies say."

Terry, you treat phylogenies as if they were the Bible. You are religious believer who found a new sacred text to worship.

terryt said...

"Feel free to build a case for Antarctica and Australia".

Either region has as much evidence going for it as does your out of America theory.

"So far ancient DNA and genomics holds a new promise for out-of-America and a bleak future for out-of-Africa".

So far ancient DNA and genomics have completely failed to produce a single piece of evidence for your theory.

"Terry, you treat phylogenies as if they were the Bible".

That is better than grossly distorting them to make them fit a particular theory, in the manner you do.

"You are religious believer who found a new sacred text to worship".

And you are not such a person? 'Faith' is the only 'evidence' you have ever provided.

German Dziebel said...

@terryT

"Either region has as much evidence going for it as does your out of America theory. "

Just like all creationists, you're denying the evidence that favors evolution.

"And you are not such a person? 'Faith' is the only 'evidence' you have ever provided."

Jus like all creationists, you can see only 'faith' around you and you believe that all the epistemological differences are differences in religious beliefs.

terryt said...

"Just like all creationists, you're denying the evidence that favors evolution".

And just like all creationists, you're denying the evidence that does not fit your belief.

"Jus like all creationists, you can see only 'faith' around you"

Just like all creationists your whole theory relies totally on faith. You argue consistently to the effect that absence of evidence does not mean evidence of absence, exactly as do those who like to believe Solomon was a real king with a huge kingdom.

German Dziebel said...

@TerryT

"And just like all creationists, you're denying the evidence that does not fit your belief."

I don't have beliefs, I have theories and hypotheses and I've never denied any piece of evidence. I only question the models.

"You argue consistently to the effect that absence of evidence does not mean evidence of absence..."

This is logic, not faith. And time proves that my logic is correct: e.g., 10 years ago we had no idea Denisovans even existed and what we have from them now is only a pinkie and a tooth. But their impact is huge.

terryt said...

"I don't have beliefs"

Your support of an out of America scenario can only be described as a 'belief', supported only by 'faith'.

"I have theories and hypotheses and I've never denied any piece of evidence".

You seem to be confusing 'theories and hypotheses' with 'beliefs'. As for 'never denied any piece of evidence' you have spent most of your time at Dienekes' blog denying evidence. You certainly cocnsistentl;y deny the validity of constructed haplgroup phylogenies with providing the slightest piece of evidence supporting any alternative.

"And time proves that my logic is correct"

On the contrary. Mal'ta, for one, proves your theory was incorrect although you refuse to see it, not to mention the currently accepted haplogroup phylogenies. And how does the existence of Denisovans support your out of America beleif? To me the existence of Denisovans was noy unexpected.

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