Unfrying the egg

By Razib Khan | October 29, 2011 4:17 pm

Dienekes has a long post, the pith of which is expressed in the following:

If I had to guess, I would propose that most extant Europeans will be discovered to be a 2-way West Asian/Ancestral European mix, just as most South Asians are a simple West Asian/Ancestral South Indian mix. In both cases, the indigenous component is no longer in existence and the South Asian/Atlantic_Baltic components that emerge in ADMIXTURE analyses represent a composite of the aboriginal component with the introduced West Asian one. And, like in India, some populations will be discovered to be “off-cline” by admixture with different elements: in Europe these will be Paleo-Mediterraneans like the Iceman, an element maximally preserved in modern Sardinians, as well as the East Eurasian-influenced populations at the North-Eastern side of the continent.

This does not seem to be totally implausible on the face of it. But it seems likely that any “West Asian” component is going to be much closer genetically to an “Ancestral European” mix than they were to “Ancestral South Indians,” because the two former elements are probably part of a broader West Eurasian diversification which post-dates the separation of those groups from Southern and Eastern Eurasians. In other words, pulling out the distinct elements in Europeans is likely a more difficult task because the constituents of the mixture resemble each other quite a bit when compared to “Ancestral North Indians” vs. “Ancestral South Indians.”


The bigger issue which this highlights though is that the reality that many of these clustering methods are temporally sensitive. Given enough time a “hybrid” population is no longer a hybrid, but rather a new distinctive population which itself can be a “parent.” Recombination breaks apart the long range genetic physical associations which are the hallmarks of distinctive admixed ancestry on the genomic scale. That is why clustering methods easily generate a pure “South Asian” component. After at least ~3-4,000 years of continuous admixture the synthesis is now far less coarse, and the elements much more de facto miscible. And yet via other clustering techniques, such as principle components analysis, you get different results. The peculiar position of the “South Asian” individuals between Europeans and East Asians in direct proportion to their caste and regional origins becomes highly indicative of some sort of admixture event in different proportions as a function of geography and social context. The technique in Reconstructing Indian population history allowed for a resolution of this paradox by sifting through the variation and extracting out the ancestral components. The recent papers which came out on Australian Aboriginal genetics do something similar, in terms of making sense of somewhat puzzling results which are found when generating inferences from aggregate genomic variation.

Imagine how much more difficult the task would have been if the ancestral components were much closer! I suspect that’s what’s going on in Europe. I’m not privy to any big secrets, but I have heard of whispers of research groups using Sardinians as a “pure” outgroup to model the changing demographics of Europe since the arrival of agriculture. What David Reich stated at the conference was not particularly surprising to me in light of that possibility. Sardinia regularly pops out as a weird outlier in many analyses. One simple possibility here is that that’s simply a function of the fact that it’s an island, and therefore has diverged from mainland populations due to isolation from conventional village-to-village mate exchange. Another possibility, mooted by Dienekes, is that it may be a repository of European genetic variation from earlier periods, relatively unaffected by later perturbations due to demographic changes. The main reason that I can give some credit to Dienekes’ thesis has less to do with Sardinians than Basques. The French Basques in the HGDP are less atypical than the Sardinians, but in some runs they do lack a component which is most obviously classed as “West Asian,” and which other French have. In Dienekes’ own runs with a diverse array of Iberian populations this same distinction emerges.

All of this reminds us that clustering methods give us great insights into how populations are related to each other, but they don’t tell us about the details of how that relatedness came to be. It makes a great difference if an element is the outcome of relatively recent (<10,000 years) hybridization events, as opposed to having deeper roots. For example, admixture between Polynesians and Melanesians brings together two components, whatever their own prior origins, diverged on the order of 50,000 years before the present. And yet if the two groups mentioned earlier are correct than the Melanesian component itself must be decomposed into two fractions, one of which is much closer to the Polynesians than the other, our understanding of the past changes.

As I implied earlier today I think the era of wild hypothesis generation in the area of the settling of Europe over the last 10,000 years is coming to the end. The combination of more powerful analytic techniques and the emergence of ancient DNA samples with which to calibrate, peg, and check, inferences from those techniques, will probably clarify our understanding of the past to a great extent.

Image credit: yomi955

CATEGORIZED UNDER: Agriculture, Anthroplogy
  • http://dienekes.blogspot.com Dienekes

    But it seems likely that any “West Asian” component is going to be much closer genetically to an “Ancestral European” mix than they were to “Ancestral South Indians,” because the two former elements are probably part of a broader West Eurasian diversification which post-dates the separation of those groups from Southern and Eastern Eurasians.

    I would not be very sure of this. If we are to judge by the mtDNA results, i.e., the only DNA for which we have comparative ancient DNA data for Mesolithic-Neolithic-modern populations, we get Fst’s between any two groups that are comparable to what we find between continental groups today.

    It is true that intra-West Eurasian Fst’s _today_ are smaller than intra-South Asian ones, but that can not only be explained by a smaller genetic differentiation of the genetic components to begin with, but also by a greater degree of gene flow. This is, again, supported by the mtDNA and Y-chromosome data that suggest a ~10-15% survival of Mesolithic mtDNA haplogroup U in Europe, compared to >50% of mtDNA macrohaplogroup M in South Asia. The evidence, as it stands, suggests a fairly comprehensive swamping of Europe, with populations from the Southwest and Northeast preserving different pre-Event components to a higher degree.

  • Onur

    David Reich:We now know in unpublished work from our laboratory that Europeans are anciently mixed just like South Asians.

    This is what I wrote in Dienekes’ relevant thread regarding these issues:

    “Without knowing what David Reich meant by “Europeans are anciently mixed just like South Asians” I am afraid we can not go beyond speculation on that issue. We do not even know what he meant by European. Maybe he meant all Caucasoids irrespective of continent and region, maybe some of them, just we do not know.

    Also we do not know the autosomal genetic analysis results of Ötzi and those of the ancient skeletons from central Europe investigated with him.”

    BTW, in the same post I also touched on the problems in the academic publication system, but I do not want to deviate from the main subject of this thread so early by quoting it.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    This is, again, supported by the mtDNA and Y-chromosome data that suggest a ~10-15% survival of Mesolithic mtDNA haplogroup U in Europe, compared to >50% of mtDNA macrohaplogroup M in South Asia

    fair point.

  • Matt (another)

    Razib: This does not seem to be totally implausible on the face of it. But it seems likely that any “West Asian” component is going to be much closer genetically to an “Ancestral European” mix than they were to “Ancestral South Indians,” because the two former elements are probably part of a broader West Eurasian diversification which post-dates the separation of those groups from Southern and Eastern Eurasians.

    Also seems likely to be a greater degree of continuous genetic exchange after separation. After Europe was “filled” by the demographic wave of advance from West Asia, I’d have imagined that they remained in more continuous (two way?) genetic exchange with the eventually-to-be-Neolithic populations of West Asia.

    Dienekes: I would not be very sure of this. If we are to judge by the mtDNA results, i.e., the only DNA for which we have comparative ancient DNA data for Mesolithic-Neolithic-modern populations, we get Fst’s between any two groups that are comparable to what we find between continental groups today.

    What about cranial clustering? Does this have as large a continental gap been Mesolithic European and contemporaneous West Asian populations? Presuming we have enough sample size to even ask the question.

    Comparing the survival of mtDna haplogroups in South Asia and Europe seems a bit dodgy. Aren’t we just basically assuming that the haplogroups in South Asia (much as we would have once assumed that the mtDna differences in Europe and the West Asia were explained by pre-Neolithic survival)?

  • http://dienekes.blogspot.com Dienekes

    >> Comparing the survival of mtDna haplogroups in South Asia and Europe seems a bit dodgy. Aren’t we just basically assuming that the haplogroups in South Asia (much as we would have once assumed that the mtDna differences in Europe and the West Asia were explained by pre-Neolithic survival)?

    Macrohaplogroup M in India is very diverse, with ages in the same order (if not older) as U5, the oldest European haplogroup. Also, unlike in Europe, there is nowhere that the Indian-specific clades within M could have come from, as they are not shared with either West Eurasians or East Eurasians. There is thus an unambiguously indigenous stratum in India; this may not necessarily derive from the _oldest_ modern humans to inhabit India, but anything other than pre-Neolithic seems impossible.

    >> What about cranial clustering? Does this have as large a continental gap been Mesolithic European and contemporaneous West Asian populations? Presuming we have enough sample size to even ask the question.

    Pre-Neolithic Europeans were variable, but they were mostly basically Cro-Magnoid in form, with low and broad faces and long angular skulls. Neolithic groups from southeastern Europe and the LBK represent a completely new form, with long and very high skulls, and very narrow faces. At the Bronze Age we see a proliferation of forms with the co-existence of brachycephalic and incipiently Dinaric forms such as the Bell Beakers, as well as long-skulled and narrow-faced skulls attached to both high and low vaulted braincases. In the eastern end of Europe we have survival of Cro-Magnon-like Proto-Europoids: massive, long-headed and broad-faced and especially prevalent among early Kurgan groups. The general trend is toward more gracile, higher and broader skulls attached to narrower faces, but with a lot of types deviating from the central trend.

    If anything, it is a picture of diversity, rather than of simple evolution of a population. The default position nowadays is to assume that a new skull configuration is the result of local processes, but I think that genetics will force paleoanthropologists and archeologists to revisit their old theories of substantial migration.

  • Eurologist

    As to cranial shapes, many (original, older) analyses are severely tainted by the fact that they either did not know about, or did not care that many cranial markers are heavily determined by diet. In many circumstances, diet has a stronger effect on cranial shape than heredity. I think we should be very careful about anything that that was published before researchers started to try to disambiguate between the two (i.e., ~now).

    Also, re cranial shapes: Europe has been diverse for a long time – one can make arguments for both continuity and replacement at ease – but without making progress. Without clear archaeological and DNA correlation, I simply don’t trust any cranial analysis arguments in Europe. Still, yeah, I can see some stereotypical “archaic” forms like a Baltic/ old North/Central European characterization in many places in Northern / Central Europe.

  • Onur

    Dieneke, as far as I can see, Matt’s question was about similarities and differences between pre-Neolithic crania from Europe and pre-Neolithic crania from West Asia. You seem to have skipped the West Asian part of his question in your response.

  • http://washparkprophet.blogspot.com ohwilleke

    There is good reason to think that the last big wave of European admixture, the Indo-European wave that probably started with the Bell Beaker population (although it would have been enhanced by later Greek colony, Roman expansion, and Slavic migrations, for example), would be roughly contemporaneous with or even younger than the Indo-European migration component of the ANI-ASI mix.

    Both cases also involve geography that probably led the two principal components of admixture autosomally to have a couple of layers each (at least).

    In South Asia, the ANI part of the ANI-ASI division probably reflects not just an Indo-European population, but instead, a later Indo-European population admixed with a prior Harappan population in North India that was itself genetically distinct from ancestral South India.

    In Europe, an “Ancestral European” layer probably itself reflects an admixture of a Mesolithic European layer and an early Neolithic layer.

  • http://India Indrajeet Kashyap

    Well i am a layman here & may be my english articulation somewhat clumsy but anyway
    one thing i want to ask that can these genetic differences like ANI -ASI be matched to difference in physical features of people.may be these ANI ( migration from Northwest was of mainly males ) are caucasians with dark complexion & low level agriculture skills which mixed with tribal ASI which share similar complexion but are small in height like the tribal groups of eastern India.
    Is there a closeness in mtDNA of ASI and tribal groups of eastern india (who are still isolated) but not that much in Y chromosome side. May be ASI tribals are the original inhabitants of Indian subcontinent then there was a migration of dark complexioned ANI caucasians from northwest which mixed with Tribal ASI which gives somewhat darker complexioned south Indians.
    And some what pure Tribal ASI which are still left out in less admixed form in hilly areas of central & eastern India was then influenced by the migration of Mundas through Y chromosome .Then fair complexioned Aryans and other waves came with agriculture and horses.They introduced caste system to differentiate themselves from darker skin and have slowely subjugated this hybridized ANI ASI Population through advanced agriculture and wars. And then tribals of North east arrived.

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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