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Screenshot 2016-07-04 23.33.00

One can appreciate a work of art on two levels. When one beholds the sculpted renderings of the Classical Greeks, across the distance of more than 2,000 years we can feel viscerally that they have touched something beautiful, and made it stone. To reduce this to biology, our perception maps onto to deep grooves in our evolutionary landscape of aesthetic judgments. As a savanna ape the darkness of the forest haunts us with its beauty and majesty; but we are the children of the meadows and edges of the Paleolithic pastoral. Similarly, on some level we acknowledge physical beauty when we see it, before we even think it.*

Another level of appreciation is narrower, and that is one where you have awareness of the ingenuity of technique, the deep virtuosity and fluency of execution. This aspect of understanding aesthetics is naturally delimited to those with equivalent skills, or whose skills aspire toward the plane of the masters.

Reading Iosif Lazaridis’ The genetic structure of the world’s first farmers you can evaluate on both levels. The results are broadly accessible, but the depth of the analysis is clear to anyone who has ever attempted something analogous. These papers coming out of David Reich’s lab have a certain template, but they are definitely not paint-by-numbers. For those who are interested in technical details, you have to read the supplements.

Ten years ago the insights gleaned from this preprint were only glimmers in the eyes of assorted researchers and “genome bloggers.” The problem now is one of going from the raw result, back to the dynamics which produced the result. A deep problem of inference.

To get to where we are now, and the embarrassment of copious conclusions, researchers needed three things:

1) Lots of genetic data, and methods designed to leverage that data (basically, genomics, and the statistical genetics geared toward analyzing large data sets).

2) Genetic data from time points in the human past, and not just present.

3) The technological infrastructure necessary to handle the data (from computational power to the arcane arts of the ancient DNA lab).
513EiXJjHbL._SX331_BO1,204,203,200_

What have we learned? Ancient DNA has revealed that genetic variation in the human past has been characterized by very strong discontinuities, both over time and space. What do I mean by this?

As a stylized fact it has been fashionable in some quarters to describe human variation as being overwhelmingly clinal. That is, a continuous change in gene frequencies as a function of space. One associated fact has been the expectation that gene frequencies will change over time in a similar steady and regular fashion.

Obviously there is some truth to the clinal variation in our species. If, for example, you walked form France to the Punjab, it would be difficult to establish a hard-and-fast line where there was a definite discontinuity in genes. But there could be candidates. In particular, in Central Asia there would be regions where you would find rather high frequencies of alleles more typical of East Asia, while in Afghanistan the genetic signatures of non-West Eurasian peoples of a different sort, typically found in South Asia, would start to crop up.

But these two points of discontinuity illustrate the general principle that discontinuity emerges from specific historical-demographic events. In the case of the rather high fraction of East Asian associated genes in Central Asia, this is almost certainly a product of the Turkic expansion, which occurred in starts and fits over the ~1,000 years between 500 and 1500. In South Asia, we now suspect that there was a relatively recent intrusion of West Eurasian populations, and likely some reciprocal gene flow between indigenous groups and the incomers.

These two instances point out that major disruptions in gene flow are likely correlated with major cultural disruptions. The Turkic expansion occurred in historical time, so we can inspect it and note that the decline of Iranian populations within Central Asia began during the late Sassanian period, but came to near completion with the major shocks of the Mongol period 700 years later. These were events of geopolitical note.

This is important to consider, because the older models which posit clinal variation assume that genetic change occurs through a ‘mass action’ process, whereby small family or village groups enter into a phase of demographic expansion, and literally outbreed others. This was to some extent the model implicit in the ‘demic diffusion’ theories of the expansion of the Neolithic lifestyle into Europe from the Near East, pioneered by Colin Renfew, and extended by L. L. Cavalli-Sforza and colleagues.

In a classical economic framework one can simply assume that those who practice the farming lifestyle will be in a state of land surplus on the frontier. Therefore, they will have large families, and keep expanding their range. In such a fashion individual decisions of Homo economicus can drive cultural and demographic change over large regions in relatively short time periods.

warbefore

The decisions of the many in an uncoordinated fashion can lead to the ordered patterns we see around us, with clines of variation, as well as signals of genetic expansion. As L. L. Cavalli-Sforza noted the argument here is not that most of the ancestry of modern Europeans is exogenous to the continent when using Pleistocene groups as the indigenous reference, but that the demographic wave of advance is responsible for agriculture, not cultural emulation. Even with this wave of advance model, which has been widely explored in population genetics, assimilation of native groups on the frontier means that most of the ancestry on the frontier by the end of the process could be “indigenous.”

Cavalli-Sforza’s assertions came in the wake of a series of results in the early 2000s which were interpreted to suggest that most of the ancestry of modern Europeans derives from populations resident during the Pleistocene. These results were taken to suggest that agriculture must have then spread by cultural diffusion, not demographic expansion. All Cavalli-Sforza was pointing out was that the model he was supporting was about a dynamic process, not some specific value of haplotype counting by region.

Ultimately this rearguard apologia was not necessary. It turns out that a majority of the ancestry of modern Europeans is likely exogenous to the continent over the last ~10,000 years. The earlier results which were used to support the converse were right in their results, but were misinterpreted. Additionally, I also think that the model outlined by Cavalli-Sforza and his colleagues is in some ways too elegant and stylized to be useful. If you read The War Before Civilization there are plenty of archaeological hints that there were massive inter-group conflicts during prehistory, and the arrival of farmers to the continent probably exhibited some coordination and collective action beyond the village. The 3,200 year old battle on the Baltic is probably the continuation of a long tradition in Europe, and the world, of collective action and conflict.

This is a “problem” because inter-group conflicts on a geopolitical scale are not as tractable in terms of a general model as a “wave of advance” demographic scenario where endogenous growth parameters rule supreme. Rather, demographic patterns are not due to continuous predictable dynamics, but the intersection of such parameters and contingent events. History has no guarantees, though its wheels tend toward certain favored grooves.

Twenty years ago L. L. Cavalli-Sforza wrote a book geared toward the lay audience, Great Human Diasporas. The culmination of a lifetime’s work, it surveyed what we then knew about human genetic variation with classical markers derived from contemporary populations. The tools we have today are far more precise, with hundreds of thousands of markers rather than hundreds, and DNA samples from populations thousands or tens of thousands of years in the past. Instead of simply inferring the tree of life, researchers are now constructing a lattice of relationships derived not only from the nodes visible today, but also positions within the lattice from the deep past.

The evidence which is coming back is that pre-modern populations exhibited a great deal of genetic differentiation over even small distances, and, that differentiation could persist for thousands of years. Between group proportions of variation on the order of 10% of the total variance, what you see between Europeans and Han Chinese, were not atypical for nearby peoples, even though one migrant between them per generation would have eliminated that difference in short order. This equilibrium of difference would eventually get disrupted by radical demographic turnover, as location populations went extinct or were absorbed by newcomers, who reshaped whole landscapes through their expansions. In other words, if Cavalli-Sforza were to write a book today I believe it would be titled “Great Human Disruptions and their Diasporas.”

And this isn’t just about agriculture. Ancient DNA from Pleistocene Europe indicates turnover there too. There may be meta-population dynamics which are at work on the edge of the modern human range in Eurasia. As local populations go extinct, new populations expand to occupy their territory. The ancient human landscape may have been relatively sparsely populated, diminishing opportunities for gene flow.

But this is likely not the whole story. Inter-group conflict certainly played a role, and ancient DNA has uncovered evidence of long periods of genetic distinctiveness between neighboring populations. This suggests cultural practices serving as a barrier to gene flow. We do have one case where this occurs today: India. The caste system is such that continental wide genetic distances can be found within local populations in the same region, which have coexisted for thousands of years.

So what are the results of the the Lazaridis’ paper? The figure at the top gives you a PCA-centric view. Basically, all West Eurasian populations today can be modeled to a first approximation as a mixture of four ancestral groups which flourished on the order of ~10,000 years ago. If modern genetic variation can be conceived of as an algebra, then for West Eurasia these are the four variables with differential weights you need to produce any reasonable output.

The four are:

1) Western hunter-gatherers (WHG), the indigenous populations of Europe and surrounding areas.

2) Eastern hunter-gatherers (EHG), the indigenous populations of the the northeastern fringe of Europe.

3) Western farmers, the ancestors of Early European Farmers (EEF), with roots in the zone from the southern Levant north into Anatolia.

4) Eastern farmers, who are rooted populations which flourished in the Zagros mountains of western Iran (Central Asian Farmers, CAF).

These four themselves exhibit some compound ancestry. On the order of half the ancestry of EEF and and CAF was basal Eurasian (BEu), a population which seems to have diverged from other non-Sub-Saharan Africans more than 50,000 years ago, before Neanderthal admixture. To be clear, BEu seems to be an outgroup to populations as diverse as Pleistocene European hunter-gatherers, Australian indigenous groups, and Andaman Islanders. The other half of EEF and CAF ancestry derives from two distinct sources, which explain their different positions on the PCA plot. The EEF have a WHG-like admixture. That is, some of their ancestors are nested within the broader clade which includes European hunter-gatherers, and far more distantly the Ancestral North Eurasians (ANE). Work on Pleistocene genomics indicates that there was a major increase in affinity between European hunter-gatherers and Near Easterners ~15,000 years before the present, suggesting that there was major gene flow uniting these two regions. The Near Eastern element of this movement probably fused with BEu.

Second, the CAF population, which is known from far fewer samples, seems to have shared a lot of ancestry with EHG, so the two must have shared common ancestry from related groups. It seems that the mostly likely source of this was ANE. Due to the genetic distance between ANE and WHG, the Fst between EEF and CAF was on the order of ~0.10, similar to that between Chinese and Europeans today. These two groups seem to have stumbled upon agriculture very near to each other at similar times.

Where they independent events? I suspect that they weren’t. I’m not implying here cultural diffusion. There is evidence of independent domestication of landraces in the Zagros. Rather, these two populations were part of a broader network of trade connections within a similar ecological landscape. It was not coincidental that both stumbled upon agriculture. Likely there was diffusion between the two of similar cultural precursors to agriculture. Their location in such proximity can not be coincidence, though the details are to be worked out.

Interestingly once these two populations stumbled onto agriculture they expanded in opposite directions. Why? Probably because they could. That is, both of them had high population densities and social complexity, and rather than impinging upon each other’s territories they expanded into “empty” landscape. Regions inhabited by hunter-gatherers who were easier to eliminate or assimilate. The spread of Cardial and LBK people in Europe was so fast that it is almost certain that they were all one cultural unit initially. Something similar probably applies to the CAF groups which expanded east into South Asia, and north to the steppe.

Another intriguing result in this paper is that WHG themselves seem to have had admixture from eastern populations. More precisely, the Mesolithic hunter-gatherers used in earlier analyses as “pure” exemplars of WHG turn out not to be, but exhibit some admixture with other groups. This is probably why the ANE proportion of EHG is much higher in this paper. An older sample from Bichon in Switzerland lacks the eastern admixture, and so serves as a better reference for WHG. Though not definitive, it now looks as if ANE admixture into East Eurasians (e.g., Han Chinese) has resulted in some affinity between these populations and Europeans today, going back to, but not limited to, the WHG. This is no surprise. The emergence of agriculture is not singularly new, cultural innovation seems to trigger demographic disruptions, no matter the time or place.

Though the centerpiece of this preprint is the fact that four populations are sufficient to explain the genetic variation, and demographic history, of West Eurasian populations, I think perhaps a more interesting element is the role of ANE and BEu. Neither of these groups exist in “pure” form today. We don’t know who BEu were. We don’t know where they came from. To me it is suspicious that BEu ancestry exists in about the same fractions in both EEF (at least their precursors in the Middle East) and in CAF. It does not seem that the two BEu components were very differentiated. To me that indicates that BEu may have expanded relatively recently. I also believe that BEu may have a role mediating “back to Africa” gene flow. As BEu lacks Neanderthal admixture that would explain the very low levels in most of the continent, and yet the presence of what now look to be Eurasian origin E Y chromosomal haplotypes.

As for the ANE, their geographic coverage is incredible, from Western Europe all the way to the New World. It seems that as a unadmixed group they persisted into the Holocene, but in numbers they were always stretched thin. Through their amalgamation into agriculturalists they’ve persisted, but likely many of their Paleo-Siberian folkways diminished. I do believe though the R1 haplogroups on the Y chromosome likely derive from them, as it is a sister to the Amerindian Q.

There’s a lot in the paper to chew on, especially the supplements. For example, the percentages of “steppe” ancestry are non-trivial throughout South Asia. What to make of this? I think I’ll hold off until ancient DNA comes in, as it will in the next 6 months.

But, I do think ancient DNA and the model of disruptions and discontinuity supports the proposition that punctuated equilibrium as a thesis has much more validity for cultural evolution than it does for biology. Cultures exhibit inertia and a tendency toward conformity. Learning new things is difficult. Very special conditions must have existed for agriculture to “take” in the Near East, as hunter-gatherers shifted form facultative cultivation to obligate modes of production of crops. Once these cultures became farming cultures, it wasn’t easy for neighbors to easily adopt them, as cultural packages often come as a whole, with many contingent parts. The advantage of agriculture is that it extracts more yield from the ground, and population densities go up. Higher population densities means more resources in inter-group conflict, if it comes to that, and the need to expand to continue to race beyond the Malthusian limit. Once the space is occupied, a new equilibrium is reached.

And I want to reiterate, this model does not apply to just agriculture. A tweet from Spencer Wells:

New Guinea is a horticultural society, and the highlands are very densely populated. The high Fst is in line with what you see in early Holocene Western Eurasia, or in India today. But observe that the genetic differentiation is from the past 10,000 years, not the past 50,000. 10,000 years ago is when horticulture began. In all likelihood one population in the highlands began to practice this, and expanded demographically, eliminating or absorbing its neighbors. But the landscape of New Guinea sets tight limits to the range of possibilities, as the highlands of the island are a very isolated ecosystem. The genetic differentiation began once the expansion phase ceased, and groups began to struggle for existence at the Malthusian limit.

One of the insights of Lazaridis et al.’s paper is that this didn’t happen in Eurasia. The differences between EEF and CAF diminished, as the Near East saw reciprocal gene flow during the Bronze Age. The difference was not in agriculture, but post-agricultural social complexity, which allowed for the emergence of what Peter Turchin would term “meta-ethnic” identities, and complex institutions which transcend locality. In the new equilibrium state the Fst did not begin to go up as populations jostled for resources, as innovation began to gently push the production frontier outward, and foster connections of material (e.g., trade) and ideas (e.g., religion).

The whole story is not written in stone yet. The next few years are going to be interesting. China is the next frontier, and ancient DNA will open up its history soon enough. But it’s an exciting time to be witnessing the unveiling of prehistory before our eyes.

* There is a dimension of aesthetic judgement which is culturally conditional, and another which is not. I speak of the latter here.

 
• Category: Science • Tags: Genomics 
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  1. Anonymous says: • Disclaimer

    Yes.

    A word about the origin of y DNA haplotype E – a very very touchy subject amongst some quarters, for similar reasons that y DNA r1a1a is touchy amongst certain other ethnicities.

    Put bluntly E dominates Africa. If E is ultimately Eurasian – which is hotly disputed – the implication is that in ancient times Eurasians dominated Africans, a hypothesis that is very hard for some to stomach.

    However, no definitive case for a Eurasian origin of E has been tendered, so the ‘jury is still out’.

    Read More
    • Replies: @ben-canaan
    It is too early to tell. But on a more manageable timescale, detection of various E1b1b subgroups in the Natufians is also forcing an interdisciplinary reexamination of the Afroasiatic urheimat question -- will the new synthesis fall in behind the CW like it has for Indo-European?

    I always assumed that Bellwood was off-base here, what with the deep divergence of Omotic and Cushitic -- but the much stronger signal of Natufian-like gene flow (and Near Eastern technology) to North and East Africa than for the opposite is making me wonder. Not to mention, the early presence of E-Z830 (some of which is E-M123, if Genetiker is right) in Israel seriously complicates the notion of Semitic as Afroasiatic's single, late Asian offshoot.

    Then again, the Afroasiatic (and even Semitic) chronological horizon is so deep, and the nature of African-Levantine connections so potentially tangled, that ancient DNA might prove nowhere near as conclusive as in IE's case. At the least, though, it'll be helpful Epipaleolithic context for the story of E.
    , @Awale
    I think Razib was referring to Y-DNA E-M215 (E1b1b) and/or E-M35 (E1b1b's descendant) when he said it was "Eurasian". E-M35 is mostly found in populations with significant or mostly West Eurasian ancestry (Horn Africans, NW Africans, Egyptians, Greeks etc.). I doubt it's origins are in West Asia, frankly, but yeah. Is that the "E" you were referring to Razib?
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  2. Matt_ says:

    A few notes which I think you already probably know but may be clarifying for other readers:

    1) On clusters vs clines, the relative relatedness of the Anatolian Neolithic version of EEF compared to the Levant Neolithic version of EEG to European WHG and the Caucasus HG, does suggest that variation was clinal within the ancient Middle and Near East. At least by the early Neolithic / Mesolithic period.

    There seems to be similar structure within WHG as well, where the Hungarian HG sample we have seems less differentiated against EHG and Anatolia than the WHG from a similar time period from Western Europe (albeit this still seems statistically quite subtle).

    So it does seem like it could have been clinal in spatial structure of relatedness, albeit with very low differentiation within the populations that sat within those clines relative to today (and thus the very high FST differences). It seems that the question of whether the genetic structure is geographically clinal or not is distinct from the genetic differentiation relative to distance being higher or lower compared to today?

    2) I don’t know about the fst between EEF and CAF being on the order of 0.100 though. The fsts given in the paper’s supplement include:

    LevantN-Iran_N : 0.047
    Anatolia_N-Iran_N : 0.071
    Europe_EN-Iran_N: 0.071

    That’s a bit lower than the recent European-Han : 0.110.

    LevantN-Han: 0.139, Iran_N-Han: 0.123, Anatolia_N-Han: 0.133, Europe_NE-Han: 0.129

    At the same time, WHG-Iran_N: 0.126 and also WHG-Han: 0.162

    So the differentiation between Early Neolithic Near Eastern groups perhaps 0.5 as strong as between present day Europeans and Han, while between WHG and their least similar Middle Eastern relatives strong that present day Europeans and Han, with the caveat that WHG-Han differentiation also stronger compared to present day Europeans.

    Read More
    • Replies: @Shaikorth
    Fst seems to be suspectible to something here, perhaps variation in dataset sizes.

    Granot et al got 0.085 for French-Japanese and generally shorter distances for comparable stats than Lazaridis 2016 it seems. They used 660k SNP's.
    http://biorxiv.org/content/biorxiv/suppl/2016/05/25/033852.DC2/033852-1.pdf

    It isn't clear from Lazaridis paper's table S4 how many SNP's were used to differentiate Fst. If it's the same as in ADMIXTURE analysis and some formal testing, could be closer to 250k.

    In any case would be great to see Est median for the Lazaridis set.
    ReplyAgree/Disagree/Etc. More... This Commenter This Thread Hide Thread Display All Comments
  3. Shaikorth says:
    @Matt_
    A few notes which I think you already probably know but may be clarifying for other readers:

    1) On clusters vs clines, the relative relatedness of the Anatolian Neolithic version of EEF compared to the Levant Neolithic version of EEG to European WHG and the Caucasus HG, does suggest that variation was clinal within the ancient Middle and Near East. At least by the early Neolithic / Mesolithic period.

    There seems to be similar structure within WHG as well, where the Hungarian HG sample we have seems less differentiated against EHG and Anatolia than the WHG from a similar time period from Western Europe (albeit this still seems statistically quite subtle).

    So it does seem like it could have been clinal in spatial structure of relatedness, albeit with very low differentiation within the populations that sat within those clines relative to today (and thus the very high FST differences). It seems that the question of whether the genetic structure is geographically clinal or not is distinct from the genetic differentiation relative to distance being higher or lower compared to today?

    2) I don't know about the fst between EEF and CAF being on the order of 0.100 though. The fsts given in the paper's supplement include:

    LevantN-Iran_N : 0.047
    Anatolia_N-Iran_N : 0.071
    Europe_EN-Iran_N: 0.071

    That's a bit lower than the recent European-Han : 0.110.

    LevantN-Han: 0.139, Iran_N-Han: 0.123, Anatolia_N-Han: 0.133, Europe_NE-Han: 0.129

    At the same time, WHG-Iran_N: 0.126 and also WHG-Han: 0.162

    So the differentiation between Early Neolithic Near Eastern groups perhaps 0.5 as strong as between present day Europeans and Han, while between WHG and their least similar Middle Eastern relatives strong that present day Europeans and Han, with the caveat that WHG-Han differentiation also stronger compared to present day Europeans.

    Fst seems to be suspectible to something here, perhaps variation in dataset sizes.

    Granot et al got 0.085 for French-Japanese and generally shorter distances for comparable stats than Lazaridis 2016 it seems. They used 660k SNP’s.

    http://biorxiv.org/content/biorxiv/suppl/2016/05/25/033852.DC2/033852-1.pdf

    It isn’t clear from Lazaridis paper’s table S4 how many SNP’s were used to differentiate Fst. If it’s the same as in ADMIXTURE analysis and some formal testing, could be closer to 250k.

    In any case would be great to see Est median for the Lazaridis set.

    Read More
    • Replies: @M
    I think that sounds like an extreme outlier figure IRC. Although, I'm not very keen on comparing fst distances from different fst matrices, or saying the fst between population x and y *is* a certain value for that reason (there is variability from one matrix to another).

    IRC fsts tend to be relatively the same from one matrix to another, but the actual number tends to vary, e.g. Granot: Italian-Yoruba = 0.115, French-Japanese = 0.085, Laziridis: Italian-Yoruba = 0.148, French-Han = 0.128. Ratio is about 0.66-0.77 for the comparable pair. It could be more consistent though, so that is some cause for question.

    No clue if est is more or less sensitive to sample sizes. IRC that paper suggested more sensitive.
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  4. @Anonymous
    Yes.

    A word about the origin of y DNA haplotype E - a very very touchy subject amongst some quarters, for similar reasons that y DNA r1a1a is touchy amongst certain other ethnicities.

    Put bluntly E dominates Africa. If E is ultimately Eurasian - which is hotly disputed - the implication is that in ancient times Eurasians dominated Africans, a hypothesis that is very hard for some to stomach.

    However, no definitive case for a Eurasian origin of E has been tendered, so the 'jury is still out'.

    It is too early to tell. But on a more manageable timescale, detection of various E1b1b subgroups in the Natufians is also forcing an interdisciplinary reexamination of the Afroasiatic urheimat question — will the new synthesis fall in behind the CW like it has for Indo-European?

    I always assumed that Bellwood was off-base here, what with the deep divergence of Omotic and Cushitic — but the much stronger signal of Natufian-like gene flow (and Near Eastern technology) to North and East Africa than for the opposite is making me wonder. Not to mention, the early presence of E-Z830 (some of which is E-M123, if Genetiker is right) in Israel seriously complicates the notion of Semitic as Afroasiatic’s single, late Asian offshoot.

    Then again, the Afroasiatic (and even Semitic) chronological horizon is so deep, and the nature of African-Levantine connections so potentially tangled, that ancient DNA might prove nowhere near as conclusive as in IE’s case. At the least, though, it’ll be helpful Epipaleolithic context for the story of E.

    Read More
    • Replies: @Anonymous
    As a layman, I'll just add another two cents' worth.

    Haplotype E forms a clade with haplotype D. Now, haplotype D, today, is concentrated amongst east Asians, especially the Japanese.
    Perhaps the basal Eurasian DE population lived at time so very remote that the characteristic phenotypic differences between east Asians and levantine types had not even developed yet.
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  5. Davidski says: • Website

    Something similar probably applies to the CAF groups which expanded east into South Asia, and north the steppe.

    They expanded into South Asia, but not really into the steppe. The uniparentals don’t match.

    After they moved into South Asia, they were mostly replaced in their own homeland by a new population moving in from the west that gave rise to the Chalcolithic population of western Iran.

    It’s likely that the ancestors of this population also moved into the steppe, probably via the Caucasus, where they acquired CHG admixture before mixing with EHG.

    But no one knows where they came from at this stage, and how much admixture exactly they contributed to the steppe pastoralists. Maybe they were the Halaf pastoralist people from the northern Levant?

    Iosif doesn’t know, but he modeled Steppe_EMBA as 57% EHG, 43% Iran Chalcolithic for now. Work in progress.

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  6. RK says:

    The bottleneck in Y-DNA diversity dating to after the initial Neolithic as discovered in Karmin et. al. finds a nice correlate in the rapid and successive changes in autosomal composition in the Near East in the Chalcolithic to Bronze Ages. Intergroup competition must have been incredibly intense.

    Hope they do a follow-up study on signs of selection in post-Neolithic genomes, since we now have the Hotu Iranian and Ganj Dareh.

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  7. One thing I have been considering with this new paper is how the dynamics of the adoption of agriculture in the Near East and East Asia now seem to be analogous. We knew that in East Asia a host of different linguistic groups at least – Sino Tibetan, Austroasiatic, Austronesian, Tai-Kadai, and Hmong–Mien – all seem to have had origins in what is now northern or central China. In addition, IIRC an upcoming paper has suggested that the ancestors of Koreans and Japanese were hunter-gatherers who basically picked up agriculture without any major outside admixture from northern Chinese. The overall model of East Asia thus seemed to be a number of different groups which independently took up agriculture in the early neolithic, later spreading into the “empty” territories surrounding. This seemed to be a different dynamic than West Eurasia, where it was presumed that there was one population which functionally swept over everything, admixing with hunter-gatherers as it went – since we knew that was the dynamic for the extensions into Europe and South Asia.

    It turns out of course, with this paper, that there were at least 2-3 divergent populations which initially took up agriculture in the Near East, which grew closer genetically with time until they formed one “race.” This is something we really should have guessed given the significant linguistic diversity among the first recorded languages in the Near East. My understanding is more ancient DNA papers are on the way from East Asia, so I suppose we will find out more soon – which is good, because it seems the major mysteries of the foundation of modern West Eurasian populations (other than who the Basal Eurasians are) are now solved.

    The Papuan paper looks fascinating, and the results honestly not too surprising. Papuans show a very broad level of phenotypical diversity from what I have read and seen from photos – even discounting more recent Austronesian admixture. Some would have no trouble passing for Sub-Saharan Africans, while others have an almost West Eurasian looking cast to their facial features – to the point that if their hair wasn’t kinky, they wouldn’t look that out of place in South Asia (Benny Wenda is a good example). Variation on the basis of height and skin tone seems to vary dramatically depending upon ethnic group as well. It would thus be no surprise at all if this pheotypical diversity was reflected in the genotype.

    As an aside, I recently read that the methods used to determine facial structure on the basis of DNA have improved dramatically. So much so that people can use these facial simulations to pick out the individual correctly 90% of the time out of a lineup. Is ancient DNA coverage good enough that we could reconstruct ancient faces in this manner? I would presume it would be explosively popular as an article in a popular science magazine like Discover or National Geographic.

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    • Replies: @RK
    The paper discovered that an Ulchi-like hunter gatherer population 9k years ago in NE Asia had similarity with Japanese and Koreans, with the remainder of their genome modeled as closest to South Chinese ethnic minorities, or Southeast Asians, which makes sense because the Neolithic package in Korea and Japan centered on Rice, in common with the South Chinese neolithic, as opposed to millet in the North China plain. So no, the tight link between demography and technology in the case of the Neolithic remains strong as ever.

    Sino Tibetan is not older than 6-7kya, Austronesian is somewhat younger. Austroasiatic farmers in multiple parts of Southeast Asia were overprinted by later Austronesians, often in protohistoric times. The Tai-Kadai languages appear to be a back-migration of Austronesians to the mainland, creating a superstrate with extensive relexification, and their spread is also very late, in the historical period for areas south of the Mekong. Koreanic appears intrusive to the Korean peninsula, which seems to have been inhabited by Japonic speakers in the earliest times. So Asia is definitely not an exception to the pattern of post-neolithic gene flow and cultural churn, and its unlikely that the features of the genetic landscape there were established in the earliest neolithic.
    , @Shaikorth
    Among other things the supplements of Lazaridis 2016 include a model fitting the East Asian metapopulation as some kind of mix between "Ancient South Eurasians" (Onge-like) and Ancient North Eurasians (Mal'ta-like) just like Native Americans. Would be a big deal if the model holds. One of the issues may be that Mal'ta now shows affinity to Onge beyond what EHG and WHG do.

    I expect the Papuan genetic situation mirrors that of Native Americans in its own way - a range of phenotypic diversity and high Fst between pops but generally all have the same composition of ancestral populations.

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  8. iffen says:

    aspire toward the plane of the masters

    More than excellent!

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  9. Excellent post. Seomwhat technical, but to serve putting genomics into (pre)historical perspective. Enjoyed this one!

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  10. Awale says:
    @Anonymous
    Yes.

    A word about the origin of y DNA haplotype E - a very very touchy subject amongst some quarters, for similar reasons that y DNA r1a1a is touchy amongst certain other ethnicities.

    Put bluntly E dominates Africa. If E is ultimately Eurasian - which is hotly disputed - the implication is that in ancient times Eurasians dominated Africans, a hypothesis that is very hard for some to stomach.

    However, no definitive case for a Eurasian origin of E has been tendered, so the 'jury is still out'.

    I think Razib was referring to Y-DNA E-M215 (E1b1b) and/or E-M35 (E1b1b’s descendant) when he said it was “Eurasian”. E-M35 is mostly found in populations with significant or mostly West Eurasian ancestry (Horn Africans, NW Africans, Egyptians, Greeks etc.). I doubt it’s origins are in West Asia, frankly, but yeah. Is that the “E” you were referring to Razib?

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  11. RK says:
    @Karl Zimmerman
    One thing I have been considering with this new paper is how the dynamics of the adoption of agriculture in the Near East and East Asia now seem to be analogous. We knew that in East Asia a host of different linguistic groups at least - Sino Tibetan, Austroasiatic, Austronesian, Tai-Kadai, and Hmong–Mien - all seem to have had origins in what is now northern or central China. In addition, IIRC an upcoming paper has suggested that the ancestors of Koreans and Japanese were hunter-gatherers who basically picked up agriculture without any major outside admixture from northern Chinese. The overall model of East Asia thus seemed to be a number of different groups which independently took up agriculture in the early neolithic, later spreading into the "empty" territories surrounding. This seemed to be a different dynamic than West Eurasia, where it was presumed that there was one population which functionally swept over everything, admixing with hunter-gatherers as it went - since we knew that was the dynamic for the extensions into Europe and South Asia.

    It turns out of course, with this paper, that there were at least 2-3 divergent populations which initially took up agriculture in the Near East, which grew closer genetically with time until they formed one "race." This is something we really should have guessed given the significant linguistic diversity among the first recorded languages in the Near East. My understanding is more ancient DNA papers are on the way from East Asia, so I suppose we will find out more soon - which is good, because it seems the major mysteries of the foundation of modern West Eurasian populations (other than who the Basal Eurasians are) are now solved.

    The Papuan paper looks fascinating, and the results honestly not too surprising. Papuans show a very broad level of phenotypical diversity from what I have read and seen from photos - even discounting more recent Austronesian admixture. Some would have no trouble passing for Sub-Saharan Africans, while others have an almost West Eurasian looking cast to their facial features - to the point that if their hair wasn't kinky, they wouldn't look that out of place in South Asia (Benny Wenda is a good example). Variation on the basis of height and skin tone seems to vary dramatically depending upon ethnic group as well. It would thus be no surprise at all if this pheotypical diversity was reflected in the genotype.

    As an aside, I recently read that the methods used to determine facial structure on the basis of DNA have improved dramatically. So much so that people can use these facial simulations to pick out the individual correctly 90% of the time out of a lineup. Is ancient DNA coverage good enough that we could reconstruct ancient faces in this manner? I would presume it would be explosively popular as an article in a popular science magazine like Discover or National Geographic.

    The paper discovered that an Ulchi-like hunter gatherer population 9k years ago in NE Asia had similarity with Japanese and Koreans, with the remainder of their genome modeled as closest to South Chinese ethnic minorities, or Southeast Asians, which makes sense because the Neolithic package in Korea and Japan centered on Rice, in common with the South Chinese neolithic, as opposed to millet in the North China plain. So no, the tight link between demography and technology in the case of the Neolithic remains strong as ever.

    Sino Tibetan is not older than 6-7kya, Austronesian is somewhat younger. Austroasiatic farmers in multiple parts of Southeast Asia were overprinted by later Austronesians, often in protohistoric times. The Tai-Kadai languages appear to be a back-migration of Austronesians to the mainland, creating a superstrate with extensive relexification, and their spread is also very late, in the historical period for areas south of the Mekong. Koreanic appears intrusive to the Korean peninsula, which seems to have been inhabited by Japonic speakers in the earliest times. So Asia is definitely not an exception to the pattern of post-neolithic gene flow and cultural churn, and its unlikely that the features of the genetic landscape there were established in the earliest neolithic.

    Read More
    • Replies: @Karl Zimmerman
    Thanks for the correction on the recent paper...I was looking around for it, but I couldn't even recall the author, so I wasn't having much luck refreshing myself on the details.

    I was not implying that East Asia didn't have genetic churn - merely that it appears that a large number of different groups took up agriculture independently in the Neolithic, and many of them survived in some form through to the present. It seems like the same general patter was also true in the Near Eastern neolithic, but there both genetic and linguistic differences tended to decrease steadily as time wore on. I suspect that the development of slavery played a major role in this - captured enemies were economically useless in mesolithic cultures, but extra labor was always useful for farmers. Two cultures of roughly similar levels of technological complexity who live alongside one another could thus raid one another periodically for women and children to add to their labor force, slowly knitting the populations together in terms of geneotype and phenotype, if perhaps not culture.
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  12. Shaikorth says:
    @Karl Zimmerman
    One thing I have been considering with this new paper is how the dynamics of the adoption of agriculture in the Near East and East Asia now seem to be analogous. We knew that in East Asia a host of different linguistic groups at least - Sino Tibetan, Austroasiatic, Austronesian, Tai-Kadai, and Hmong–Mien - all seem to have had origins in what is now northern or central China. In addition, IIRC an upcoming paper has suggested that the ancestors of Koreans and Japanese were hunter-gatherers who basically picked up agriculture without any major outside admixture from northern Chinese. The overall model of East Asia thus seemed to be a number of different groups which independently took up agriculture in the early neolithic, later spreading into the "empty" territories surrounding. This seemed to be a different dynamic than West Eurasia, where it was presumed that there was one population which functionally swept over everything, admixing with hunter-gatherers as it went - since we knew that was the dynamic for the extensions into Europe and South Asia.

    It turns out of course, with this paper, that there were at least 2-3 divergent populations which initially took up agriculture in the Near East, which grew closer genetically with time until they formed one "race." This is something we really should have guessed given the significant linguistic diversity among the first recorded languages in the Near East. My understanding is more ancient DNA papers are on the way from East Asia, so I suppose we will find out more soon - which is good, because it seems the major mysteries of the foundation of modern West Eurasian populations (other than who the Basal Eurasians are) are now solved.

    The Papuan paper looks fascinating, and the results honestly not too surprising. Papuans show a very broad level of phenotypical diversity from what I have read and seen from photos - even discounting more recent Austronesian admixture. Some would have no trouble passing for Sub-Saharan Africans, while others have an almost West Eurasian looking cast to their facial features - to the point that if their hair wasn't kinky, they wouldn't look that out of place in South Asia (Benny Wenda is a good example). Variation on the basis of height and skin tone seems to vary dramatically depending upon ethnic group as well. It would thus be no surprise at all if this pheotypical diversity was reflected in the genotype.

    As an aside, I recently read that the methods used to determine facial structure on the basis of DNA have improved dramatically. So much so that people can use these facial simulations to pick out the individual correctly 90% of the time out of a lineup. Is ancient DNA coverage good enough that we could reconstruct ancient faces in this manner? I would presume it would be explosively popular as an article in a popular science magazine like Discover or National Geographic.

    Among other things the supplements of Lazaridis 2016 include a model fitting the East Asian metapopulation as some kind of mix between “Ancient South Eurasians” (Onge-like) and Ancient North Eurasians (Mal’ta-like) just like Native Americans. Would be a big deal if the model holds. One of the issues may be that Mal’ta now shows affinity to Onge beyond what EHG and WHG do.

    I expect the Papuan genetic situation mirrors that of Native Americans in its own way – a range of phenotypic diversity and high Fst between pops but generally all have the same composition of ancestral populations.

    Read More
    • Replies: @Awale
    Don't you think David's tree-mixes somewhat contradict that "Han = ANE-like + Onge-like" model? They have all Eastern Non-Africans displaying an odd affinity for ANE:

    https://drive.google.com/file/d/0B9o3EYTdM8lQM1BINGE3V2hJczA/view
    https://drive.google.com/file/d/0B9o3EYTdM8lQZGp5VWd5M0gtTkU/view

    ?
    , @Karl Zimmerman
    Would this basically mean that Native Americans got a "double dose" of Mal'ta - one from the Proto East Asian population, and then a later one at the ethnogenesis of Amerinds? Or does this mean the at the time the proto-Amerinds came into being, nothing East Asian like was yet in existence?

    If the latter is the case, might it help to explain the hypothesis which has been bandied about that there's evidence that there was a very early OOA migration into Asia, which is reflected in part of the Austro-Melanesian ancestry today? Perhaps the ANE admixture which is shared by all Eurasians save Austro-Melanesians is causing the latter to appear more basal than they actually are.
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  13. Awale says:
    @Shaikorth
    Among other things the supplements of Lazaridis 2016 include a model fitting the East Asian metapopulation as some kind of mix between "Ancient South Eurasians" (Onge-like) and Ancient North Eurasians (Mal'ta-like) just like Native Americans. Would be a big deal if the model holds. One of the issues may be that Mal'ta now shows affinity to Onge beyond what EHG and WHG do.

    I expect the Papuan genetic situation mirrors that of Native Americans in its own way - a range of phenotypic diversity and high Fst between pops but generally all have the same composition of ancestral populations.

    Don’t you think David’s tree-mixes somewhat contradict that “Han = ANE-like + Onge-like” model? They have all Eastern Non-Africans displaying an odd affinity for ANE:

    https://drive.google.com/file/d/0B9o3EYTdM8lQM1BINGE3V2hJczA/view

    https://drive.google.com/file/d/0B9o3EYTdM8lQZGp5VWd5M0gtTkU/view

    ?

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  14. @RK
    The paper discovered that an Ulchi-like hunter gatherer population 9k years ago in NE Asia had similarity with Japanese and Koreans, with the remainder of their genome modeled as closest to South Chinese ethnic minorities, or Southeast Asians, which makes sense because the Neolithic package in Korea and Japan centered on Rice, in common with the South Chinese neolithic, as opposed to millet in the North China plain. So no, the tight link between demography and technology in the case of the Neolithic remains strong as ever.

    Sino Tibetan is not older than 6-7kya, Austronesian is somewhat younger. Austroasiatic farmers in multiple parts of Southeast Asia were overprinted by later Austronesians, often in protohistoric times. The Tai-Kadai languages appear to be a back-migration of Austronesians to the mainland, creating a superstrate with extensive relexification, and their spread is also very late, in the historical period for areas south of the Mekong. Koreanic appears intrusive to the Korean peninsula, which seems to have been inhabited by Japonic speakers in the earliest times. So Asia is definitely not an exception to the pattern of post-neolithic gene flow and cultural churn, and its unlikely that the features of the genetic landscape there were established in the earliest neolithic.

    Thanks for the correction on the recent paper…I was looking around for it, but I couldn’t even recall the author, so I wasn’t having much luck refreshing myself on the details.

    I was not implying that East Asia didn’t have genetic churn – merely that it appears that a large number of different groups took up agriculture independently in the Neolithic, and many of them survived in some form through to the present. It seems like the same general patter was also true in the Near Eastern neolithic, but there both genetic and linguistic differences tended to decrease steadily as time wore on. I suspect that the development of slavery played a major role in this – captured enemies were economically useless in mesolithic cultures, but extra labor was always useful for farmers. Two cultures of roughly similar levels of technological complexity who live alongside one another could thus raid one another periodically for women and children to add to their labor force, slowly knitting the populations together in terms of geneotype and phenotype, if perhaps not culture.

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  15. Shaikorth says:

    It does look like ANE and Onge have affinities that European HG’s do not share. Then again in the trees with Iberian Neolithic and LBK there’s over 20% edge between Dai/Han/Karitiana root and ANE immediately after Papuan/Onge have split (and then another edge for Karitiana).

    In one other set of trees ryukendo asked there’s a 16% edge between East Asians (but not Native Americans who get their specific ANE) and Euro HG/ANE branch after Onge have split off. I wouldn’t say the trees rule the ASE+ANE modeling of East Asians out, but Onge or ANE may themselves have a complicated history…

    Read More
    • Replies: @Awale
    Oh, my bad btw... I originally misread some of those tree-mixes I sent.

    In one other set of trees ryukendo asked there’s a 16% edge between East Asians (but not Native Americans who get their specific ANE) and Euro HG/ANE branch after Onge have split off. I wouldn’t say the trees rule the ASE+ANE modeling of East Asians out, but Onge or ANE may themselves have a complicated history…"

    Yeah, we ultimately need more data and ancient genomes (like ones from South Asia & East Asia), I suppose. Should be interesting to see what happens when we have those samples.

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  16. Anonymous says: • Disclaimer
    @ben-canaan
    It is too early to tell. But on a more manageable timescale, detection of various E1b1b subgroups in the Natufians is also forcing an interdisciplinary reexamination of the Afroasiatic urheimat question -- will the new synthesis fall in behind the CW like it has for Indo-European?

    I always assumed that Bellwood was off-base here, what with the deep divergence of Omotic and Cushitic -- but the much stronger signal of Natufian-like gene flow (and Near Eastern technology) to North and East Africa than for the opposite is making me wonder. Not to mention, the early presence of E-Z830 (some of which is E-M123, if Genetiker is right) in Israel seriously complicates the notion of Semitic as Afroasiatic's single, late Asian offshoot.

    Then again, the Afroasiatic (and even Semitic) chronological horizon is so deep, and the nature of African-Levantine connections so potentially tangled, that ancient DNA might prove nowhere near as conclusive as in IE's case. At the least, though, it'll be helpful Epipaleolithic context for the story of E.

    As a layman, I’ll just add another two cents’ worth.

    Haplotype E forms a clade with haplotype D. Now, haplotype D, today, is concentrated amongst east Asians, especially the Japanese.
    Perhaps the basal Eurasian DE population lived at time so very remote that the characteristic phenotypic differences between east Asians and levantine types had not even developed yet.

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    • Replies: @Razib Khan
    phenotypes we see are products of last 10,000 years. so it surely predates that.
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  17. @Shaikorth
    Among other things the supplements of Lazaridis 2016 include a model fitting the East Asian metapopulation as some kind of mix between "Ancient South Eurasians" (Onge-like) and Ancient North Eurasians (Mal'ta-like) just like Native Americans. Would be a big deal if the model holds. One of the issues may be that Mal'ta now shows affinity to Onge beyond what EHG and WHG do.

    I expect the Papuan genetic situation mirrors that of Native Americans in its own way - a range of phenotypic diversity and high Fst between pops but generally all have the same composition of ancestral populations.

    Would this basically mean that Native Americans got a “double dose” of Mal’ta – one from the Proto East Asian population, and then a later one at the ethnogenesis of Amerinds? Or does this mean the at the time the proto-Amerinds came into being, nothing East Asian like was yet in existence?

    If the latter is the case, might it help to explain the hypothesis which has been bandied about that there’s evidence that there was a very early OOA migration into Asia, which is reflected in part of the Austro-Melanesian ancestry today? Perhaps the ANE admixture which is shared by all Eurasians save Austro-Melanesians is causing the latter to appear more basal than they actually are.

    Read More
    • Replies: @Shaikorth
    Could go either way, ancient DNA from East Asia is needed for a proper answer. There are Treemix runs where Karitiana gets a double dose as you mention and some where it gets a single edge, with Dai/Han having a separate one.
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  18. Shaikorth says:
    @Karl Zimmerman
    Would this basically mean that Native Americans got a "double dose" of Mal'ta - one from the Proto East Asian population, and then a later one at the ethnogenesis of Amerinds? Or does this mean the at the time the proto-Amerinds came into being, nothing East Asian like was yet in existence?

    If the latter is the case, might it help to explain the hypothesis which has been bandied about that there's evidence that there was a very early OOA migration into Asia, which is reflected in part of the Austro-Melanesian ancestry today? Perhaps the ANE admixture which is shared by all Eurasians save Austro-Melanesians is causing the latter to appear more basal than they actually are.

    Could go either way, ancient DNA from East Asia is needed for a proper answer. There are Treemix runs where Karitiana gets a double dose as you mention and some where it gets a single edge, with Dai/Han having a separate one.

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  19. Awale says:
    @Shaikorth
    It does look like ANE and Onge have affinities that European HG's do not share. Then again in the trees with Iberian Neolithic and LBK there's over 20% edge between Dai/Han/Karitiana root and ANE immediately after Papuan/Onge have split (and then another edge for Karitiana).

    In one other set of trees ryukendo asked there's a 16% edge between East Asians (but not Native Americans who get their specific ANE) and Euro HG/ANE branch after Onge have split off. I wouldn't say the trees rule the ASE+ANE modeling of East Asians out, but Onge or ANE may themselves have a complicated history...

    Oh, my bad btw… I originally misread some of those tree-mixes I sent.

    In one other set of trees ryukendo asked there’s a 16% edge between East Asians (but not Native Americans who get their specific ANE) and Euro HG/ANE branch after Onge have split off. I wouldn’t say the trees rule the ASE+ANE modeling of East Asians out, but Onge or ANE may themselves have a complicated history…

    Yeah, we ultimately need more data and ancient genomes (like ones from South Asia & East Asia), I suppose. Should be interesting to see what happens when we have those samples.

    Read More
    • Replies: @PQ
    The models with ANE input into an ancestor of all ENA involves WHG and ANE as the final tips from a larger Basal-admixed group rooted with Iran_N; furthermore the edge shares, say, at most 3% drift with ANE vs WHG, i.e. it is not very differentiated between the two at all. Its likely that edge involves WHG and ANE being pulled closer to ENA due to the need for their non-Basal closeness to other non-Basals to be accounted for.

    Not excluding the idea that ANE and ENA have a complex history; Chad and I went to check some stats where the WHG-ANE branch are broadly symmetrical to ENA, but MA-1 is relatively close to Papuan and Onge, EHG to East Asians narrowly defined, some WHG to East Asians narrowly defined and SHG not close to any; but edges on one part of a Tree in Treemix can be compensatory adjustments for phenomena on another part.
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  20. @Anonymous
    As a layman, I'll just add another two cents' worth.

    Haplotype E forms a clade with haplotype D. Now, haplotype D, today, is concentrated amongst east Asians, especially the Japanese.
    Perhaps the basal Eurasian DE population lived at time so very remote that the characteristic phenotypic differences between east Asians and levantine types had not even developed yet.

    phenotypes we see are products of last 10,000 years. so it surely predates that.

    Read More
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  21. M says:
    @Shaikorth
    Fst seems to be suspectible to something here, perhaps variation in dataset sizes.

    Granot et al got 0.085 for French-Japanese and generally shorter distances for comparable stats than Lazaridis 2016 it seems. They used 660k SNP's.
    http://biorxiv.org/content/biorxiv/suppl/2016/05/25/033852.DC2/033852-1.pdf

    It isn't clear from Lazaridis paper's table S4 how many SNP's were used to differentiate Fst. If it's the same as in ADMIXTURE analysis and some formal testing, could be closer to 250k.

    In any case would be great to see Est median for the Lazaridis set.

    I think that sounds like an extreme outlier figure IRC. Although, I’m not very keen on comparing fst distances from different fst matrices, or saying the fst between population x and y *is* a certain value for that reason (there is variability from one matrix to another).

    IRC fsts tend to be relatively the same from one matrix to another, but the actual number tends to vary, e.g. Granot: Italian-Yoruba = 0.115, French-Japanese = 0.085, Laziridis: Italian-Yoruba = 0.148, French-Han = 0.128. Ratio is about 0.66-0.77 for the comparable pair. It could be more consistent though, so that is some cause for question.

    No clue if est is more or less sensitive to sample sizes. IRC that paper suggested more sensitive.

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  22. Matt_ says:

    Razib: There’s a lot in the paper to chew on, especially the supplements.

    I think one other thing worth mention is the finding that the Levant Neolithic (if not Natufians) seems to be responsible for West Eurasian related ancestry in East Africa.

    My view is this is a nice finding as it basically reconciles the formal statistic based evidence, which tended to find EEF as the best West Eurasian ancestor (and led to a very strong declaration from at least one blogger that the West Eurasian ancestry in East Africans was the same as the “Cardial” culture), with the ADMIXTURE analysis that found that this ancestry was best explained as a “Southwest Asian” component also common in Arabs.

    The reconciliation is the Levant Neolithic does have as it’s closest relative the Anatolia Neolithic that contributed to Europeans. Thus explaining the formal stats.

    But at the same time, Levant Neolithic has apparently less relatedness to the WHG European Hunter Gatherers than the Anatolia Neolithic does, and has a level of relatedness to WHG that’s probably more similar to Arabian populations. In a models, the paper finds a model of Anatolia Neolithic as modellable about 40% WHG, and 60% Neolithic (though I’m not sure if their model of the 33% Levant and 33% Iran Neolithic really works).

    So that explains why ADMIXTURE preferred to model East Africans with the Southwest Asian component that linked them to Arabians (lack of Euro HG ancestry / relatedness found in the Mediterranean farmers of Europe).

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  23. Shaikorth says:

    Est is more sensitive to number of SNP’s and sample size to a certain point according to the paper, but Lazaridis 2016 set has enough SNP’s and for many ancient populations enough individuals to go past that point. Interestingly Fst appears to be sensitive as well, comparing results across different matrices?

    In any case Est-median appears to correspond better to formal stats, for instance showing Native Americans closer to Europeans than Yoruba and not bloating distances between closely related but isolated populations.

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  24. Matt_ says:

    I guess the way I would think of ANE’s spread, and to put its geographic coverage into context, would be as a northern counterpart to the ENA branch, rather than comparing to the broader Upper Paleolithic European clade (basically all the samples in Fu et al 2016) from which WHG comes.

    The ANE side of the split was expanding out of Africa to the east, and there is just so much more unpopulated territory in that direction. So like the ENA branch, the descendants come to cover a very wide expanse. Possibly it seems a lot more incredible to us, because we didn’t even know this group existed until recently, while we’ve been quite familiar with the ENA branch’s expanse for a while.

    Compared to the main trunk of the ENA ancestry, that seems to me likely came from the south, through India to East Asia, ANE today has a much more marginal survival across that range. I would guess is due to northern populations suffering more population crashes, and then getting replaced by populations from the ENA branch, that adapted to cooler climates moving up through the continental East Asian climate (and perhaps the introgression of ANE variants).

    As to why the survival of ANE seems strongest through the y-chromosomal line, maybe I might tentatively guess that this is because of the increasing importance of hunting relative to gathering strategies as populations move to cooler climates. The males from ANE cultures were more preadapted, culturally / biologically, to hunting in cool climates, so their associated y-dna had better survival?

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    • Replies: @Ryukendo
    This is extremely interesting. From modern interactions between hunter gatherers and agropastoralists in the Philippines and Malaysia, the Congo, Sri Lanka, East Africa ('Dorobo' with Nilotic and Cushitic populations) and South Africa one would have thought the sex-biased gene flow and cultural influencce, e.g. language, to have occurred in one direction only, from the agropastoralists to the HGs, which always made the situations recovered from aDNA in Europe and Siberia, where the male-biased gene flow and the cultural dominance seems to be in the other direction at least some of the time, difficult to understand socially, as there was nothing to compare it to.

    This idea about facility with hunting increasing in importance towards the poles would explain a great deal due to the reasons you mentioned. Also, to generalise, in small-scale societies exchange and sharing of meat conferred tremendous status to male hunters. Probably also points to the fact that modern knowledge of HGs and their interactions is biased towards the tropics, which perhaps biases our social understanding of human prehistory towards the 'Sex at Dawn' type of egalitarian scenario with lots of divorce and independence for children, for example, and away from the harsh familial differentiation of e.g. Eskimos and Gilyaks, which may in fact come closer to the social background for the majority of the ancestors of us Eurasians.

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  25. I am actually less inclined now to associate Basal Eurasian with the spread of haplogroup E in Africa, on account of the D stats in this paper showing that Sub-Saharan Africans (Mota/Yoruba/Mbuti) are no closer to Natufians – who are half Basal – than even to EHG. A curious result in any case.

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  26. Anonymous says: • Disclaimer

    Great Post!!!

    —————————————————————————————————————–

    WHG+EHG+EEF+CAF+Exotic(East/North Asia, South Asia, Africa)=Modern Middle East amd Europe

    This is correct but it’s important to remember there’s variation within each one of the 4 ancient West Eurasian groups. All modern and ancient West Eurasians don’t have ancestry from the exact same members each one of those broad families. Exactly what the relationship members in each one of those broad families was is unknown.

    Georgians for example can’t be fit as Zagros Neolithic(CAF)+other. They clearly have lots of ancestry specifically from Caucasus hunter gatherers not only from Zagros farmers. Furthermore modern Caucasins, Anatolians, and Europeans clearly have “EEF” ancestry specifically from Anatolia(or nearby) not the Levant.

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  27. spandrell says: • Website

    Has any ancient DNA been coming out from China? I’ve only been able to find this:

    http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-13-216

    Which is interesting enough (haplotype N!), but what everybody wants to see is Yangshao vs. Longshan, Xia vs. Yi, who the hell where the Shang and where did they get their chariots, etc.

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  28. Riordan says:

    Razib,

    You know anybody who’s going to write a good, if not great, accessible (as in understandable by the sub 120 IQ masses) book about these developments any time soon? If so, when do you think they’ll publish it? Trying to keep track of all of them is headache inducing without a digestible record of some sorts.

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  29. PQ says:

    Karl,

    My point was that, the presence of multiple linguistic groups doesn’t mean that there were multiple populations taking up agriculture in East Asia, since these linguistic groups are too shallow to reach the time depths needed for the earliest neolithic. The genetic evidence–the ‘East Asian Neolithic Cluster’ is exceptionally homogeneous–seems to go against this as well.

    Likewise, linguistic diversity in Papua New Guinea is high, but ‘multiple neolithics’ are not warranted there from a genetic viewpoint.

    The presence of linguistic diversity far more closely relates to areas shielded from cultural evolution and high rates of group extinction by geographic factors, such as the Caucasus, the Southern Himalayas and Assam, the highlands of Southeast Asia, the Northwest Pacific regions in America, the Amazon, and so on. I would think linguistic diversity in the earliest periods in West Eurasia, prior to the emergence of full-fledged pastoralism and social complexity, is quite expected. In fact our null hypothesis should be why the Middle East isn’t as diverse linguistically as New Guinea, which would lead us to the conclusion that group competition and high rates of replacement were in operation since an early period in the post-neolithic Middle East, as seen in the aDNA, unlike for Papua.

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    • Replies: @Karl Zimmerman
    I think this paper shows that present day genetic homogeneity should not lead one to presume that the neolithic origins of East Asia might not have been from several genetically disparate groups. Regardless, while in general East Asia is pretty homogeneous, Sino-Tibetan, Austro-Asiatic, and Austronesian populations are genetically distinctive enough that even simple admixture runs break the groups apart upon linguistic lines pretty well. Perhaps this difference just comes down to differing proportions of Austro-Melanesian introgression or sizable periods of relative reproductive isolation during the formative years of the populations, but there is indeed still something distinctive about each one of them relative to the others.
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  30. PQ says:
    @Awale
    Oh, my bad btw... I originally misread some of those tree-mixes I sent.

    In one other set of trees ryukendo asked there’s a 16% edge between East Asians (but not Native Americans who get their specific ANE) and Euro HG/ANE branch after Onge have split off. I wouldn’t say the trees rule the ASE+ANE modeling of East Asians out, but Onge or ANE may themselves have a complicated history…"

    Yeah, we ultimately need more data and ancient genomes (like ones from South Asia & East Asia), I suppose. Should be interesting to see what happens when we have those samples.

    The models with ANE input into an ancestor of all ENA involves WHG and ANE as the final tips from a larger Basal-admixed group rooted with Iran_N; furthermore the edge shares, say, at most 3% drift with ANE vs WHG, i.e. it is not very differentiated between the two at all. Its likely that edge involves WHG and ANE being pulled closer to ENA due to the need for their non-Basal closeness to other non-Basals to be accounted for.

    Not excluding the idea that ANE and ENA have a complex history; Chad and I went to check some stats where the WHG-ANE branch are broadly symmetrical to ENA, but MA-1 is relatively close to Papuan and Onge, EHG to East Asians narrowly defined, some WHG to East Asians narrowly defined and SHG not close to any; but edges on one part of a Tree in Treemix can be compensatory adjustments for phenomena on another part.

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  31. @PQ
    Karl,

    My point was that, the presence of multiple linguistic groups doesn't mean that there were multiple populations taking up agriculture in East Asia, since these linguistic groups are too shallow to reach the time depths needed for the earliest neolithic. The genetic evidence--the 'East Asian Neolithic Cluster' is exceptionally homogeneous--seems to go against this as well.

    Likewise, linguistic diversity in Papua New Guinea is high, but 'multiple neolithics' are not warranted there from a genetic viewpoint.

    The presence of linguistic diversity far more closely relates to areas shielded from cultural evolution and high rates of group extinction by geographic factors, such as the Caucasus, the Southern Himalayas and Assam, the highlands of Southeast Asia, the Northwest Pacific regions in America, the Amazon, and so on. I would think linguistic diversity in the earliest periods in West Eurasia, prior to the emergence of full-fledged pastoralism and social complexity, is quite expected. In fact our null hypothesis should be why the Middle East isn't as diverse linguistically as New Guinea, which would lead us to the conclusion that group competition and high rates of replacement were in operation since an early period in the post-neolithic Middle East, as seen in the aDNA, unlike for Papua.

    I think this paper shows that present day genetic homogeneity should not lead one to presume that the neolithic origins of East Asia might not have been from several genetically disparate groups. Regardless, while in general East Asia is pretty homogeneous, Sino-Tibetan, Austro-Asiatic, and Austronesian populations are genetically distinctive enough that even simple admixture runs break the groups apart upon linguistic lines pretty well. Perhaps this difference just comes down to differing proportions of Austro-Melanesian introgression or sizable periods of relative reproductive isolation during the formative years of the populations, but there is indeed still something distinctive about each one of them relative to the others.

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    • Replies: @Razib Khan
    Perhaps this difference just comes down to differing proportions of Austro-Melanesian introgression

    not all of it.

    also, the Y chr looks like it burst like J or E, not R1, in east asia. i think i'll go along with the idea there were multiple nearby agriculturalists.

    in answer to ancient e. asian DNA. q fu is working on it.
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  32. Lank says:

    I thought you supported recent OOA, Razib? If modern humans migrated OOA 50-60 kya, and then back migrated shortly after that to bring basal branches of E and DE, they would have to be very similar (and with no Neanderthal) to the ancestral population left behind in Africa.

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    • Replies: @Razib Khan
    i'm somewhat confused what happened.

    i think that OOA might be earlier than 50-60 btw, though expansion out of the sw corner of eurasia did happen then.

    one model that might not be crazy to me now is that there were three pops for a while, SS africans, derived non-africans, and basal non-"africans", the latter of whom may have been nested deep in africa, who knows? this would allow E to diversify in situ before mixing after the LGM?

    but honestly, i have no idea.

    I am actually less inclined now to associate Basal Eurasian with the spread of haplogroup E in Africa, on account of the D stats in this paper showing that Sub-Saharan Africans (Mota/Yoruba/Mbuti) are no closer to Natufians – who are half Basal – than even to EHG. A curious result in any case.

    it has to be very male skewed. as obviously this argument flips both ways: why aren't bearers of E in eurasia closer to SS-africans who have E?
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  33. @Lank
    I thought you supported recent OOA, Razib? If modern humans migrated OOA 50-60 kya, and then back migrated shortly after that to bring basal branches of E and DE, they would have to be very similar (and with no Neanderthal) to the ancestral population left behind in Africa.

    i’m somewhat confused what happened.

    i think that OOA might be earlier than 50-60 btw, though expansion out of the sw corner of eurasia did happen then.

    one model that might not be crazy to me now is that there were three pops for a while, SS africans, derived non-africans, and basal non-”africans”, the latter of whom may have been nested deep in africa, who knows? this would allow E to diversify in situ before mixing after the LGM?

    but honestly, i have no idea.

    I am actually less inclined now to associate Basal Eurasian with the spread of haplogroup E in Africa, on account of the D stats in this paper showing that Sub-Saharan Africans (Mota/Yoruba/Mbuti) are no closer to Natufians – who are half Basal – than even to EHG. A curious result in any case.

    it has to be very male skewed. as obviously this argument flips both ways: why aren’t bearers of E in eurasia closer to SS-africans who have E?

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  34. Lank says:

    Trying not to get ahead of myself here since formal statistics did not reveal any African admixture in Natufians (who all appear to be Y-DNA E1b1b from further analysis of the raw data of the samples who were unresolved in the paper).

    But in the Eurogenes global PCA, Natufians have an SSA pull, unlike all other ancient samples. In the Eurogenes TreeMix, they have some very basal migration edges that appear African-like. This is quite unlike the highly Basal Eurasian Iranians. Their Y-DNA is all E1b1b. ADMIXTURE shows African components in them, even when there are no mixed East African references.

    Something tells me ancient DNA from Paleolithic North Africa will reveal archaeologists were right about the African influences in Natufians, only they were not exactly like SSA. This element would then be separate from genuine Basal Eurasian, which appears to peak in Mesolithic Iran from the samples that are available.

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    • Replies: @Razib Khan
    This element would then be separate from genuine Basal Eurasian, which appears to peak in Mesolithic Iran from the samples that are available.



    but the BEu intervals there were high. so not sure that it's genuinely higher....
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  35. @Karl Zimmerman
    I think this paper shows that present day genetic homogeneity should not lead one to presume that the neolithic origins of East Asia might not have been from several genetically disparate groups. Regardless, while in general East Asia is pretty homogeneous, Sino-Tibetan, Austro-Asiatic, and Austronesian populations are genetically distinctive enough that even simple admixture runs break the groups apart upon linguistic lines pretty well. Perhaps this difference just comes down to differing proportions of Austro-Melanesian introgression or sizable periods of relative reproductive isolation during the formative years of the populations, but there is indeed still something distinctive about each one of them relative to the others.

    Perhaps this difference just comes down to differing proportions of Austro-Melanesian introgression

    not all of it.

    also, the Y chr looks like it burst like J or E, not R1, in east asia. i think i’ll go along with the idea there were multiple nearby agriculturalists.

    in answer to ancient e. asian DNA. q fu is working on it.

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  36. @Lank
    Trying not to get ahead of myself here since formal statistics did not reveal any African admixture in Natufians (who all appear to be Y-DNA E1b1b from further analysis of the raw data of the samples who were unresolved in the paper).

    But in the Eurogenes global PCA, Natufians have an SSA pull, unlike all other ancient samples. In the Eurogenes TreeMix, they have some very basal migration edges that appear African-like. This is quite unlike the highly Basal Eurasian Iranians. Their Y-DNA is all E1b1b. ADMIXTURE shows African components in them, even when there are no mixed East African references.

    Something tells me ancient DNA from Paleolithic North Africa will reveal archaeologists were right about the African influences in Natufians, only they were not exactly like SSA. This element would then be separate from genuine Basal Eurasian, which appears to peak in Mesolithic Iran from the samples that are available.

    This element would then be separate from genuine Basal Eurasian, which appears to peak in Mesolithic Iran from the samples that are available.

    but the BEu intervals there were high. so not sure that it’s genuinely higher….

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    • Replies: @Shaikorth
    The lower Neanderthal in Iran_N could be an indicator considering the intervals.

    Re: East Asian Neolithics, the ANE+ASE fits seem equally good and of similar proportion for many separate groups, could be an indicator of when their ancestors split.

    Yi, She, Kinh, Dai and Atayal have similar P-values for the Onge+MA-1 fit and each of them gets 9-10% ANE.
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  37. Shaikorth says:
    @Razib Khan
    This element would then be separate from genuine Basal Eurasian, which appears to peak in Mesolithic Iran from the samples that are available.



    but the BEu intervals there were high. so not sure that it's genuinely higher....

    The lower Neanderthal in Iran_N could be an indicator considering the intervals.

    Re: East Asian Neolithics, the ANE+ASE fits seem equally good and of similar proportion for many separate groups, could be an indicator of when their ancestors split.

    Yi, She, Kinh, Dai and Atayal have similar P-values for the Onge+MA-1 fit and each of them gets 9-10% ANE.

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  38. Ryukendo says:

    @ Razib

    If we look at ADMIXTURE at very low K, in West Eurasia we get a component peaking in the Indus, another in the Mediterranean and Levant, and another in the Baltic and Volga regions; the prior two components match very well the Natufian-Anatolian and Ganj Dareh complexes of neolithic genomes, and latter component matches well the disproportionate survival of Hunter-Gatherer lifestyles in Northern Europe and Siberia. Then in East Eurasia, we get a component peaking in Onge and Orang Asli–both hunter-gatherers in Southeast Asia; another in Ulchi/Oroqen and Nganasan, Hunter Gatherers again (the upcoming paper from the Armur may shed some light on this element of the East Asian autosome), and another encompassing all the Agropastoralists in between, from Japan to the Moluccas. This may suggest that, even if there were multiple Neolithic centres–I agree with you that the Y chromosome differences between the different Neolithic cultures is a piece of evidence towards this–they may still be much less different from each other autosomally than the neolithic genomes in in Western Eurasia.

    The components at high K in East Asia do have individuality, which suggest population movements in the past several thousand years; strange that this is not matched in the Y-DNA record though, where the star-like expansions of the most successful clades of O date back to the Neolithic instead of later. Then again, maybe the presence of J only in post-initial neolithic genomes may cause us to reevaluate the role of ‘J-like’ expansions.

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  39. Ryukendo says:
    @Matt_
    I guess the way I would think of ANE's spread, and to put its geographic coverage into context, would be as a northern counterpart to the ENA branch, rather than comparing to the broader Upper Paleolithic European clade (basically all the samples in Fu et al 2016) from which WHG comes.

    The ANE side of the split was expanding out of Africa to the east, and there is just so much more unpopulated territory in that direction. So like the ENA branch, the descendants come to cover a very wide expanse. Possibly it seems a lot more incredible to us, because we didn't even know this group existed until recently, while we've been quite familiar with the ENA branch's expanse for a while.

    Compared to the main trunk of the ENA ancestry, that seems to me likely came from the south, through India to East Asia, ANE today has a much more marginal survival across that range. I would guess is due to northern populations suffering more population crashes, and then getting replaced by populations from the ENA branch, that adapted to cooler climates moving up through the continental East Asian climate (and perhaps the introgression of ANE variants).

    As to why the survival of ANE seems strongest through the y-chromosomal line, maybe I might tentatively guess that this is because of the increasing importance of hunting relative to gathering strategies as populations move to cooler climates. The males from ANE cultures were more preadapted, culturally / biologically, to hunting in cool climates, so their associated y-dna had better survival?

    This is extremely interesting. From modern interactions between hunter gatherers and agropastoralists in the Philippines and Malaysia, the Congo, Sri Lanka, East Africa (‘Dorobo’ with Nilotic and Cushitic populations) and South Africa one would have thought the sex-biased gene flow and cultural influencce, e.g. language, to have occurred in one direction only, from the agropastoralists to the HGs, which always made the situations recovered from aDNA in Europe and Siberia, where the male-biased gene flow and the cultural dominance seems to be in the other direction at least some of the time, difficult to understand socially, as there was nothing to compare it to.

    This idea about facility with hunting increasing in importance towards the poles would explain a great deal due to the reasons you mentioned. Also, to generalise, in small-scale societies exchange and sharing of meat conferred tremendous status to male hunters. Probably also points to the fact that modern knowledge of HGs and their interactions is biased towards the tropics, which perhaps biases our social understanding of human prehistory towards the ‘Sex at Dawn’ type of egalitarian scenario with lots of divorce and independence for children, for example, and away from the harsh familial differentiation of e.g. Eskimos and Gilyaks, which may in fact come closer to the social background for the majority of the ancestors of us Eurasians.

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  40. This is a bit of an aside, but on the subject of Papuans again, I’ve never quite understood the Y DNA haplogroups in New Guinea.

    The most common groups in eastern New Guinea are branches of K2b1 – particularly M and S. K2b1 is basically only otherwise found in Sahul populations. But the sister group of K2b1 is P, which appears to be the Ancient North Eurasian haplogroup. The next group out, K1, contains N and O – which are Arctic and East Asian respectively.

    Given both the outgroup and the sister group of K2b1 seem to be North Asian in terms of origin, it seems the most parsimonious hypothesis is that K2b1 originated somewhere in Northern Asia, only migrating southward later. Perhaps all of this happened before the settling of Sahul, and K2b1 came along for the ride with the C haplogroups which ended up dominating Australia. But it also seems that two migrations would be defensible.

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    • Replies: @Megalophias
    The closest relative of P1 (QR) is P2, which is found among Philippine Negritos and on Timor. The sister to that is MS, which is found across eastern Indonesia and Sahul.

    Next is K2a/NO, but NO proper is only one branch of K2a. Pre-NO is found in South India (and was also carried by Ust'-Ishim Man and Oase-1). Also, K2*(xNO, MS), is found in western Indonesia, which must represent either some kind of pre-NO or a third branch of K2 (it has never been tested for upstream K2a markers as far as I know). Both Indonesia and India have K* that needs to be properly classified.

    So no, MS isn't nested in North Eurasian haplogroups, P1 is nested in Indonesian haplogroups.

    However, only 1 mutation links K2a and K2b, 1 links MS and P, and 2 link P1 and P2, so there's no great time depth involved. They could all just be part of the initial Upper Paleolithic expansion of F and K, with more lineages preserved in Southeast Asia than in Siberia for obvious reasons.
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  41. Sean says:

    Ultimately this rearguard apologia was not necessary. It turns out that a majority of the ancestry of modern Europeans is likely exogenous to the continent over the last ~10,000 years.

    A partial replacement 14,oooo years ago and then another in the neolithic and finally a massive near total replacement of north European men by the Indo Europeans, leaving a small at most population of hunter gatherers skulking in forests and areas unsuitable for herding or farming . Lets look at what either the women or a few HG hold outs contributed.

    Hair/ eye colour, a minor gene for lighter skin, all seem very much concentrated in Europe, where the hair/ eye colour genes originated in indigenous Europeans over ten millennia ago . A lot of these genes relatively recently must have been re-flourishing in Europe, especially north Europe. There is also an absence in Europe of something with enough of an advantage to be massively favoured elsewhere (East Asians EDAR variant has a profound effect on chin shape).

    It looks, to me at least, feasible that selection for an affect on appearance operated. The hair / eye colours seem to have been favored in north Europe starting when conquering Indo Europeans who lacked the eye hair colours arrived and killed almost all conquered men men and many of the women. The resultant mixed European male / conquered women population rapidly became white, possibly because a white skin was selected for as a care-eliciting trait .

    It seems to me that the thing for northern hunters with a Y-chromosome, as main family provider (in winter at least), is monogamy. In the north men would have reduced their reproductive fitness by trying to start and provide for another family. North agriculture would be tough and also have that limited food drawback. A limited sex drive is not an advantage in the tropics, because the second wife can often get by gathering or garden agriculture . Northern HG men had a handy adaptation for farming there. I suppose the post conquering Indo Europeans had their pick of women, but also a steadily growing problem of not being able to support multiple families. Some had to go, and that is where I think white skin as such got off the launch pad.

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    • Replies: @Razib Khan
    It seems to me

    just cite peter frosts' paper of interest. he's clearer than you, and you are just recycling his ideas like you do incessantly.
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  42. @Karl Zimmerman
    This is a bit of an aside, but on the subject of Papuans again, I've never quite understood the Y DNA haplogroups in New Guinea.

    The most common groups in eastern New Guinea are branches of K2b1 - particularly M and S. K2b1 is basically only otherwise found in Sahul populations. But the sister group of K2b1 is P, which appears to be the Ancient North Eurasian haplogroup. The next group out, K1, contains N and O - which are Arctic and East Asian respectively.

    Given both the outgroup and the sister group of K2b1 seem to be North Asian in terms of origin, it seems the most parsimonious hypothesis is that K2b1 originated somewhere in Northern Asia, only migrating southward later. Perhaps all of this happened before the settling of Sahul, and K2b1 came along for the ride with the C haplogroups which ended up dominating Australia. But it also seems that two migrations would be defensible.

    The closest relative of P1 (QR) is P2, which is found among Philippine Negritos and on Timor. The sister to that is MS, which is found across eastern Indonesia and Sahul.

    Next is K2a/NO, but NO proper is only one branch of K2a. Pre-NO is found in South India (and was also carried by Ust’-Ishim Man and Oase-1). Also, K2*(xNO, MS), is found in western Indonesia, which must represent either some kind of pre-NO or a third branch of K2 (it has never been tested for upstream K2a markers as far as I know). Both Indonesia and India have K* that needs to be properly classified.

    So no, MS isn’t nested in North Eurasian haplogroups, P1 is nested in Indonesian haplogroups.

    However, only 1 mutation links K2a and K2b, 1 links MS and P, and 2 link P1 and P2, so there’s no great time depth involved. They could all just be part of the initial Upper Paleolithic expansion of F and K, with more lineages preserved in Southeast Asia than in Siberia for obvious reasons.

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  43. Matt_ says:

    @ Ryukendo

    More differentiation of West Eurasian components at lower K, does seems to show up best on ADMIXTURE panels that are quite lopsided in sample number towards West Eurasia, but I think still true and shows up with more balanced composition between East and West Eurasia. I think you would expect that if, further down the route out of Africa you get a wider geographical spread of closely related clades (as West Eurasia is to Africa, is to East Asia, is to the Americas), not amazingly strong drift in East Asia (unlike the Americas) and along more climatic phenotypic adaptation within a clade (as is the case in the relatively closely related clade that moved into the Americas).

    Although the fst based differentiation between populations even within the East Asian mainland do still seem like they can be quite strong. Big tables of fst that include both plentiful West Eurasian-West Eurasian comparisons and East Asian-East Asian are hard to find. However there was one from http://www.cell.com/ajhg/fulltext/S0002-9297(11)00488-5 – “Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia”. Some of the distances like Dai-Han are comparable to French-Sardinian (0.008) or Dai-Japanese at 0.019 comparable to French-Bedouin or Georgian-Sardinian or Russian-Sardinian.

    That could be because the samples there are from minorities with unusual drift history, or because there is some strong differentiation between regional populations that doesn’t fall into big clusters as it is distinct to the individual populations (IRC East Asian populations usually seem to fall as unadmixed with relatively long individual branches in treemix).

    Of course you could cross check this with the est measure Shaikorth talks about also.

    Re: comments on interactions between HG and agropastoralists, I was kind of thinking more of the pre-Neolithic replacement of ANE by East Asian groups in Siberia, which seems like a process that was partially complete by the time the proto-Americans left for the Americas, then happened further, but that is an interesting extension to the Neolithic era.

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    • Replies: @Shaikorth
    Est-median between South Han and Japanese was in Granot's supplements, it's 0.365. Comparable distances from West Eurasia are French-Kargopol Russian 0.319, Bergamo-Tuscany 0.245 and Bergamo-Orcadian 0.455. Cambodian-Mongola is > 0.6 and comparable to Kalash-Balochi.

    OTOH even Dai-Japanese allele sharing distance (should correspond to IBS) is considerably shorter than something like French-Tuscan or French-Orcadian (Behar et al 2010. supplements). This is probably caused by East Asians being more homozygous in general.
    , @Ryukendo
    My main point was not that there were more or less components in East Asia or West Eurasia, this is affected by which populations are represented in the dataset, I get this, more referring to the fact that, in ADMIXTURE runs with purely West Eurasians or purely East Asians, at K=3 two components are captured by Neolithics in purely West Eurasian runs but at K=3 only one component is captured by a putative Neolithic group in East Asian runs. At K=4 the Neolithic group in E Asia splits into one dominating Ami and another in NE Asians, but the two components are not that differentiated from fst measures unlike in W Eurasia and some of that differentiation may come from Onge-like ancestry in the Ami/SE Asian component. As no of K increases, all the 'East Asian' components all have low fst with each other, forming a single clade when forced onto trees, but the West Eurasian components typically split into the West Med/SW Asian-like ones and the Gedrosia/Caucasus like ones, from both fsts and their forced fitting onto a tree.

    I'm not sure how homozygosity dating back to first colonizations and movements of very old clades would affect ADMIXTURE, interesting issue. It does seem like higher Ks would be dominated by recent drift in minor allele freqs in a smaller set of loci and be more informative of more recent events though.

    Btw thanks for the fst and est convo, and the interesting figures elicited, this is probably caused both by different drift histories/diversity and admixture between divergent clades, e.g. I expect cambodian to be admixed with an Onge-like substrate, maybe division/subtraction style analyses could help here a bit as well?

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  44. Shaikorth says:
    @Matt_
    @ Ryukendo

    More differentiation of West Eurasian components at lower K, does seems to show up best on ADMIXTURE panels that are quite lopsided in sample number towards West Eurasia, but I think still true and shows up with more balanced composition between East and West Eurasia. I think you would expect that if, further down the route out of Africa you get a wider geographical spread of closely related clades (as West Eurasia is to Africa, is to East Asia, is to the Americas), not amazingly strong drift in East Asia (unlike the Americas) and along more climatic phenotypic adaptation within a clade (as is the case in the relatively closely related clade that moved into the Americas).

    Although the fst based differentiation between populations even within the East Asian mainland do still seem like they can be quite strong. Big tables of fst that include both plentiful West Eurasian-West Eurasian comparisons and East Asian-East Asian are hard to find. However there was one from http://www.cell.com/ajhg/fulltext/S0002-9297(11)00488-5 - "Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia". Some of the distances like Dai-Han are comparable to French-Sardinian (0.008) or Dai-Japanese at 0.019 comparable to French-Bedouin or Georgian-Sardinian or Russian-Sardinian.

    That could be because the samples there are from minorities with unusual drift history, or because there is some strong differentiation between regional populations that doesn't fall into big clusters as it is distinct to the individual populations (IRC East Asian populations usually seem to fall as unadmixed with relatively long individual branches in treemix).

    Of course you could cross check this with the est measure Shaikorth talks about also.

    Re: comments on interactions between HG and agropastoralists, I was kind of thinking more of the pre-Neolithic replacement of ANE by East Asian groups in Siberia, which seems like a process that was partially complete by the time the proto-Americans left for the Americas, then happened further, but that is an interesting extension to the Neolithic era.

    Est-median between South Han and Japanese was in Granot’s supplements, it’s 0.365. Comparable distances from West Eurasia are French-Kargopol Russian 0.319, Bergamo-Tuscany 0.245 and Bergamo-Orcadian 0.455. Cambodian-Mongola is > 0.6 and comparable to Kalash-Balochi.

    OTOH even Dai-Japanese allele sharing distance (should correspond to IBS) is considerably shorter than something like French-Tuscan or French-Orcadian (Behar et al 2010. supplements). This is probably caused by East Asians being more homozygous in general.

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  45. @Sean

    Ultimately this rearguard apologia was not necessary. It turns out that a majority of the ancestry of modern Europeans is likely exogenous to the continent over the last ~10,000 years.
     
    A partial replacement 14,oooo years ago and then another in the neolithic and finally a massive near total replacement of north European men by the Indo Europeans, leaving a small at most population of hunter gatherers skulking in forests and areas unsuitable for herding or farming . Lets look at what either the women or a few HG hold outs contributed.

    Hair/ eye colour, a minor gene for lighter skin, all seem very much concentrated in Europe, where the hair/ eye colour genes originated in indigenous Europeans over ten millennia ago . A lot of these genes relatively recently must have been re-flourishing in Europe, especially north Europe. There is also an absence in Europe of something with enough of an advantage to be massively favoured elsewhere (East Asians EDAR variant has a profound effect on chin shape).

    It looks, to me at least, feasible that selection for an affect on appearance operated. The hair / eye colours seem to have been favored in north Europe starting when conquering Indo Europeans who lacked the eye hair colours arrived and killed almost all conquered men men and many of the women. The resultant mixed European male / conquered women population rapidly became white, possibly because a white skin was selected for as a care-eliciting trait .

    It seems to me that the thing for northern hunters with a Y-chromosome, as main family provider (in winter at least), is monogamy. In the north men would have reduced their reproductive fitness by trying to start and provide for another family. North agriculture would be tough and also have that limited food drawback. A limited sex drive is not an advantage in the tropics, because the second wife can often get by gathering or garden agriculture . Northern HG men had a handy adaptation for farming there. I suppose the post conquering Indo Europeans had their pick of women, but also a steadily growing problem of not being able to support multiple families. Some had to go, and that is where I think white skin as such got off the launch pad.

    It seems to me

    just cite peter frosts’ paper of interest. he’s clearer than you, and you are just recycling his ideas like you do incessantly.

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    • Replies: @Sean
    Not demographic continuity as Peter says, and there was disruption and massive replacement of Europeans it seems. I understood Peter to be saying Europeans' hair and eye colours plus white skin are simply due to them being mainly descended from indigenous ice age ancestors of the north European plain. But DNA studies show they aren't even though their hair and eye colours are extremely common now.

    The light /diverse hair and eye colours, must have exploded at the the Indo European conquest. We know the Indo Europeans enslaved the conquered women, who tended to meet grisly fates such as being sacrificed several at a time at funerals. The white skin look apparently took over around the time of the Indo European conquest and that's why I think it something to do with eliciting care and provisioning of wives in a merciless hierarchical, patriarchal Indo European society where women's status was lowered by unending conquest, and concubinage of captured females .

    While using original ideas of Peter about the ice age, I explain the current blue eyes and blonde hair appearance of Europeans as the result of a second coming of sexual selection. Fully white skin is a little different but appeared very suddenly after the Indo Europeans turned up and imposed disruption of a very special type.

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  46. Sean says:
    @Razib Khan
    It seems to me

    just cite peter frosts' paper of interest. he's clearer than you, and you are just recycling his ideas like you do incessantly.

    Not demographic continuity as Peter says, and there was disruption and massive replacement of Europeans it seems. I understood Peter to be saying Europeans’ hair and eye colours plus white skin are simply due to them being mainly descended from indigenous ice age ancestors of the north European plain. But DNA studies show they aren’t even though their hair and eye colours are extremely common now.

    The light /diverse hair and eye colours, must have exploded at the the Indo European conquest. We know the Indo Europeans enslaved the conquered women, who tended to meet grisly fates such as being sacrificed several at a time at funerals. The white skin look apparently took over around the time of the Indo European conquest and that’s why I think it something to do with eliciting care and provisioning of wives in a merciless hierarchical, patriarchal Indo European society where women’s status was lowered by unending conquest, and concubinage of captured females .

    While using original ideas of Peter about the ice age, I explain the current blue eyes and blonde hair appearance of Europeans as the result of a second coming of sexual selection. Fully white skin is a little different but appeared very suddenly after the Indo Europeans turned up and imposed disruption of a very special type.

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    • Replies: @Razib Khan
    maybe. much of what you say is pretty speculative, and it looks like selection for lighter pigmentation has continued even after the initial period (e.g., see the british isles paper) long after some of the things you describe. ultimately, you have no evidence so it's hard to say concretely.

    also, you tend to be vague on the genetics, which is unfortunate. you should fix that.

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  47. @Sean
    Not demographic continuity as Peter says, and there was disruption and massive replacement of Europeans it seems. I understood Peter to be saying Europeans' hair and eye colours plus white skin are simply due to them being mainly descended from indigenous ice age ancestors of the north European plain. But DNA studies show they aren't even though their hair and eye colours are extremely common now.

    The light /diverse hair and eye colours, must have exploded at the the Indo European conquest. We know the Indo Europeans enslaved the conquered women, who tended to meet grisly fates such as being sacrificed several at a time at funerals. The white skin look apparently took over around the time of the Indo European conquest and that's why I think it something to do with eliciting care and provisioning of wives in a merciless hierarchical, patriarchal Indo European society where women's status was lowered by unending conquest, and concubinage of captured females .

    While using original ideas of Peter about the ice age, I explain the current blue eyes and blonde hair appearance of Europeans as the result of a second coming of sexual selection. Fully white skin is a little different but appeared very suddenly after the Indo Europeans turned up and imposed disruption of a very special type.

    maybe. much of what you say is pretty speculative, and it looks like selection for lighter pigmentation has continued even after the initial period (e.g., see the british isles paper) long after some of the things you describe. ultimately, you have no evidence so it’s hard to say concretely.

    also, you tend to be vague on the genetics, which is unfortunate. you should fix that.

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  48. Ryukendo says:
    @Matt_
    @ Ryukendo

    More differentiation of West Eurasian components at lower K, does seems to show up best on ADMIXTURE panels that are quite lopsided in sample number towards West Eurasia, but I think still true and shows up with more balanced composition between East and West Eurasia. I think you would expect that if, further down the route out of Africa you get a wider geographical spread of closely related clades (as West Eurasia is to Africa, is to East Asia, is to the Americas), not amazingly strong drift in East Asia (unlike the Americas) and along more climatic phenotypic adaptation within a clade (as is the case in the relatively closely related clade that moved into the Americas).

    Although the fst based differentiation between populations even within the East Asian mainland do still seem like they can be quite strong. Big tables of fst that include both plentiful West Eurasian-West Eurasian comparisons and East Asian-East Asian are hard to find. However there was one from http://www.cell.com/ajhg/fulltext/S0002-9297(11)00488-5 - "Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia". Some of the distances like Dai-Han are comparable to French-Sardinian (0.008) or Dai-Japanese at 0.019 comparable to French-Bedouin or Georgian-Sardinian or Russian-Sardinian.

    That could be because the samples there are from minorities with unusual drift history, or because there is some strong differentiation between regional populations that doesn't fall into big clusters as it is distinct to the individual populations (IRC East Asian populations usually seem to fall as unadmixed with relatively long individual branches in treemix).

    Of course you could cross check this with the est measure Shaikorth talks about also.

    Re: comments on interactions between HG and agropastoralists, I was kind of thinking more of the pre-Neolithic replacement of ANE by East Asian groups in Siberia, which seems like a process that was partially complete by the time the proto-Americans left for the Americas, then happened further, but that is an interesting extension to the Neolithic era.

    My main point was not that there were more or less components in East Asia or West Eurasia, this is affected by which populations are represented in the dataset, I get this, more referring to the fact that, in ADMIXTURE runs with purely West Eurasians or purely East Asians, at K=3 two components are captured by Neolithics in purely West Eurasian runs but at K=3 only one component is captured by a putative Neolithic group in East Asian runs. At K=4 the Neolithic group in E Asia splits into one dominating Ami and another in NE Asians, but the two components are not that differentiated from fst measures unlike in W Eurasia and some of that differentiation may come from Onge-like ancestry in the Ami/SE Asian component. As no of K increases, all the ‘East Asian’ components all have low fst with each other, forming a single clade when forced onto trees, but the West Eurasian components typically split into the West Med/SW Asian-like ones and the Gedrosia/Caucasus like ones, from both fsts and their forced fitting onto a tree.

    I’m not sure how homozygosity dating back to first colonizations and movements of very old clades would affect ADMIXTURE, interesting issue. It does seem like higher Ks would be dominated by recent drift in minor allele freqs in a smaller set of loci and be more informative of more recent events though.

    Btw thanks for the fst and est convo, and the interesting figures elicited, this is probably caused both by different drift histories/diversity and admixture between divergent clades, e.g. I expect cambodian to be admixed with an Onge-like substrate, maybe division/subtraction style analyses could help here a bit as well?

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    • Replies: @Matt_
    Ah, thanks for the explanation, I understand better what you are talking about now. IIUC: at any given K for a panel of West Eurasians / East Asians, fewer components emerge in East Asia that can be putatively linked to any Neolithic archaeological expansion, and closer fst differentiation between those that can be linked to a Neolithic expansion when they do emerge.

    I can't really judge personally on that, as I'm not sure I've personally seen any runs of purely West Eurasian populations and purely East Asian populations of a comparable sample size / breadth of geography to make a comparison, and definitely not with the fsts between components from those that are published (and I'm pretty sure I have less knowledge of the Neolithic archaeology to boot), but I'll take your comment on that on board.
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  49. Matt_ says:
    @Ryukendo
    My main point was not that there were more or less components in East Asia or West Eurasia, this is affected by which populations are represented in the dataset, I get this, more referring to the fact that, in ADMIXTURE runs with purely West Eurasians or purely East Asians, at K=3 two components are captured by Neolithics in purely West Eurasian runs but at K=3 only one component is captured by a putative Neolithic group in East Asian runs. At K=4 the Neolithic group in E Asia splits into one dominating Ami and another in NE Asians, but the two components are not that differentiated from fst measures unlike in W Eurasia and some of that differentiation may come from Onge-like ancestry in the Ami/SE Asian component. As no of K increases, all the 'East Asian' components all have low fst with each other, forming a single clade when forced onto trees, but the West Eurasian components typically split into the West Med/SW Asian-like ones and the Gedrosia/Caucasus like ones, from both fsts and their forced fitting onto a tree.

    I'm not sure how homozygosity dating back to first colonizations and movements of very old clades would affect ADMIXTURE, interesting issue. It does seem like higher Ks would be dominated by recent drift in minor allele freqs in a smaller set of loci and be more informative of more recent events though.

    Btw thanks for the fst and est convo, and the interesting figures elicited, this is probably caused both by different drift histories/diversity and admixture between divergent clades, e.g. I expect cambodian to be admixed with an Onge-like substrate, maybe division/subtraction style analyses could help here a bit as well?

    Ah, thanks for the explanation, I understand better what you are talking about now. IIUC: at any given K for a panel of West Eurasians / East Asians, fewer components emerge in East Asia that can be putatively linked to any Neolithic archaeological expansion, and closer fst differentiation between those that can be linked to a Neolithic expansion when they do emerge.

    I can’t really judge personally on that, as I’m not sure I’ve personally seen any runs of purely West Eurasian populations and purely East Asian populations of a comparable sample size / breadth of geography to make a comparison, and definitely not with the fsts between components from those that are published (and I’m pretty sure I have less knowledge of the Neolithic archaeology to boot), but I’ll take your comment on that on board.

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    • Replies: @PQ
    Some of these analyses are done by quite obscure hobbyists, often quite some time ago. Most others don't focus on the HUGO PASNP dataset because its overlap with other datasets is quite poor.

    Here is fsts between some components by Diogenes Artemis:
    http://4.bp.blogspot.com/-I9bLmnKcUtY/Te0_m4cl14I/AAAAAAAAAKY/w1vg_6YUb_E/s1600/Screenshot-2.png
    The dark blue, red, light green and dark green are the "Austroasiatic", "Northeast Asian", "Hmong-Mien", and "Austronesian" components, which have fsts hovering around .05 with each other. This is approximately the same as between multiple 'Bantu" components in his intra-African runs.

    By a blogger from the Philippines:

    http://1.bp.blogspot.com/-2of7N2PmkIw/UmIJT81VglI/AAAAAAAAAcI/KLmw0z5OT-I/s1600/SILANGAN11SL90007KU2GP.19.Fst.JPG

    http://4.bp.blogspot.com/-8Fkc2gRdka4/Uk95yU-fKlI/AAAAAAAAAb4/FO1saQoum3E/s1600/image002.png

    While the divergence between the West Eurasian components, 4 of them, is around .5, the divergence between the 3 East Asian components is only ~.25, only the Siberian/N Asian component is around .5 distance away. Also notice how W Eurasian components are bifurcated into the Mediterranean-W Asian distinction, which we have a better idea now as to the ultimate causes, but East Asian agriculturalists are in a single branch:
    http://2.bp.blogspot.com/-RHaCKCcUNCo/Uk95yRJcFUI/AAAAAAAAAbs/UPUrXasHkMI/s1600/image001.png
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  50. Very interesting article. Thank you.

    My only comment is that I would like to see more of this type of content, not necessarily on genetics or science alone, but of intellectual relevance. The political rants that dominate the posts published at Unz (and the ensuing comment threads) are most often inane and tiresome.

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  51. PQ says:
    @Matt_
    Ah, thanks for the explanation, I understand better what you are talking about now. IIUC: at any given K for a panel of West Eurasians / East Asians, fewer components emerge in East Asia that can be putatively linked to any Neolithic archaeological expansion, and closer fst differentiation between those that can be linked to a Neolithic expansion when they do emerge.

    I can't really judge personally on that, as I'm not sure I've personally seen any runs of purely West Eurasian populations and purely East Asian populations of a comparable sample size / breadth of geography to make a comparison, and definitely not with the fsts between components from those that are published (and I'm pretty sure I have less knowledge of the Neolithic archaeology to boot), but I'll take your comment on that on board.

    Some of these analyses are done by quite obscure hobbyists, often quite some time ago. Most others don’t focus on the HUGO PASNP dataset because its overlap with other datasets is quite poor.

    Here is fsts between some components by Diogenes Artemis:

    The dark blue, red, light green and dark green are the “Austroasiatic”, “Northeast Asian”, “Hmong-Mien”, and “Austronesian” components, which have fsts hovering around .05 with each other. This is approximately the same as between multiple ‘Bantu” components in his intra-African runs.

    By a blogger from the Philippines:

    While the divergence between the West Eurasian components, 4 of them, is around .5, the divergence between the 3 East Asian components is only ~.25, only the Siberian/N Asian component is around .5 distance away. Also notice how W Eurasian components are bifurcated into the Mediterranean-W Asian distinction, which we have a better idea now as to the ultimate causes, but East Asian agriculturalists are in a single branch:

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  52. PQ says:

    The runs span populations from Siberia to papua, and include all the ‘negritos’ in between as well, so I think the representation should be quite good. The philipino blogger created a Jinuo component, i.e. a Sino-Tibetan one! I think this is the only run where I’ve seen such a thing.

    This is RK by the way, posting from a different name from a different network, sorry for multiple monikers.

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  53. […] Razib Khan maps out the great human disruptions. […]

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