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And he will be a wild man; his hand will be against every man, and every man’s hand against him; and he shall dwell in the presence of all his brethren.

- Genesis 16:12

By now you may have seen or read two important papers which just came out in Science, 2000 Years of Parallel Societies in Stone Age Central Europe, and Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity. The details have been extensively explored elsewhere. If you don’t have academic access I highly recommend the supplement of the second paper. It’s also very illuminating if you don’t have a good grasp of the nuts and bolts of archaeology (I do not). I can’t, for example, confirm whether the merging strategies of different archaeological cultures were appropriate or not, because I’m not totally clear in my own head about the nature of these distinct archaeological ‘cultures’ (quotations due to the fact that archaeologists infer culture from material remains, and so they may not be cultures in the sense we understand culture). But the overall finding is clear, in ancient Europe thousands of years ago there were multiple demographic replacements and amalgamations. The post-World War II thesis in archaeology that one could not infer changes in the demographic character from material remains (because the latter can diffuse purely through memetic means) seems to be false. The correspondence is surprisingly tight.


In its broad outlines this was clear before these papers emerged. There is very little I would change from my post The last days of Grendel. This confusing welter of societies in prehistoric Europe is hard for us to conceive of (or reconstruct with any plausibility) today, and as one of the authors of the broader mtDNA paper observes you could not infer this pattern of replacements based on modern patterns of variation. Phylogeography inferring the past from present distributions of variation clearly has limitations, because it is constrained by the necessity to adhere to parsimony in the absence of a dense enough data set. In the early aughts the argument was between scholars who adhered to a more dominant role for demographics in transferring the farming lifestyle (L. L. Cavalli-Sforza et al.) from the Neolithic societies of the Middle East to Europe, and those who pushed forward the thesis of cultural diffusion (Sykes et al.). These are obviously stylized extreme positions, but they capture the essence of the dispute in regards to how cultures transform and expand. Scholars looked at present day European and Middle Eastern populations, and compared their genetic relatedness, usually with male and female lineages (Y and mtDNA).

There was a major problem with this model: the ancient DNA we have is telling us that present population genetic distributions are poorly correlated with past population genetic distributions. And, not only are the ancient populations of Europe rather well mixed and overturned, like a well tilled field, but it seems entirely likely that those of the Middle East are too. Therefore the methodology was bound to mislead from the get-go; the premise of a few major population movements was false. But there was I believe another major lacunae in our understanding: prehistoric people were not entirely atomized. Whether one believed in the central role of demographic movements or cultural transmission, both theses seemed to posit that prehistoric human populations were mobilizing and interacting mostly on a small scale. Diffusing. This seems likely to be wrong. Or at least it misses enough of the picture that it turns out to give a false impression.

To understand what I’m getting on, consider the American migration west in the 19th century. There were multiple forces at work. First, there was a real demographic pressure in many parts of the United States. New England for example was literally at capacity. It simply had no more land for subsistence agriculture which could support a larger population beyond the Malthusian limit. There were three primary responses. A transition up the “value chain” toward industry, made possible by the natural endowments of water power available in the region. Decreased total fertility rate (related to the first). And finally, a mass migration west, first to upstate New York, but then across the Great Lakes and out even to the Pacific. To a great extent these shifts can be modeled as individual (for family/firm) dynamics. People are responding rationally to changing incentives. But this misses “higher level” structural shifts.

As we all are now well aware the United State government entered into a massive program of ethnic cleansing and pacification of the native populations of the western territories, making migration a viable option. It acquired the western seaboard states through victory in war (California) or diplomatic bluster and coordinated demographic assault (Oregon and Washington). These events are linked to macroscale cultural dynamics, encapsulated in a slogan such as Manifest Destiny. Increasing the geographic scale of the model cultural and demographic changes in Europe itself also made itself felt in the United States (i.e., European migration to places such as the Midwest were important contributors to settlement of the nation, and this migration was often due to social and political dynamics in source nations). The reality of these macroscale dynamics means that demographic shifts often occurred in pulses, in a discontinuous fashion.

Credit: dbachman

Because prehistory is defined by the lack of writing from which we can draw detailed narratives, we will always be in the dark as to the specific macroscale dynamics which resulted in the cultural and genetic shifts we infer (barring the development of time machines). But, we can at least construct a correct framework get a true flavor of the context of how humans interacted in the past. As I have stated elsewhere, I believe that once autosomal and Y chromosomal results come on line (mtDNA is more copious and so easier to extract) we will see that many of the discontinuities and shifts are actually attenuated in the female lineage. What I mean here is that the picture from these papers may actually be less radical than the real shifts truly were. In India the source populations for admixture were distinct enough that it seems clear that admixture was male-mediated. West Eurasian Y chromosomal lineages are more well represented fractionally than West Eurasian autosomal ancestry, which is more well represented than West Eurasian mtDNA. The whole zone from West Asia out toward Atlantic Europe was more of a continuum, so solid inferences will have to wait on the ancient DNA.

Finally, one last big picture aspect which I think is important to note is that the genetic distances between ancient populations across small spatial scales was very large. I suspect that with the rise of agriculture, and imperial states, we have seen a massive process of genetic requilibration across vast swaths of Eurasia in particular. Though I think we mislead ourselves if we view prehistory purely as an affair of small scale bands with vague higher order structure, it is still the fact that the scale was smaller than what came later. That leads me to conclude that population genetic diversity as a function of distance in the far past was likely greater than it has been across most of recorded history. So inferences about the character of human genetic diversity derived from contemporary variation is misleading.* The large differences between Bushmen populations may be highly representative of what was the norm in the past.

* To be clear, Fst between continental populations may be the same. But Fst over small scales may have been larger.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Anthropology, Archaeogenetics, Archaeology 
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Dienekes has a post up highlighting a preprint out of Pontus Skoglund’s group. It is titled Ancient genomes mirror mode of subsistence rather than geography in prehistoric Europe. It doesn’t seem to be online (fingers crossed that it shows up linked at Haldane’s Sieve soon). In any case I am not surprised by the broad outlines of the thesis. And, it is not as if Skoglund’s group is the only one working in this area, I have suspicions that others are finding something very similar. These results out of Europe are probably reflective of the fact that much of the model in Peter Bellwood’s First Farmers is generally correct, the emergence of an agriculture revolution in a few select world societies produced a cultural and demographic revolution.

But one can take things too far, and I think Bellwood did. The results above, and elsewhere, also confirm that there was not total demographic replacement. In many regions the agriculturalists absorbed the hunter-gatherers. Using light coverage of whole genomes Skoglund’s group inferred that the farmers who arrived in prehistoric Europe from the Middle East seem to have contributed most of the ancestry of Southern Europeans, and also match nearly perfectly the genetic profiles of farming populations in Scandinavia. In contrast, ancient hunter-gatherers in Scandinavia and prehistoric Spain resemble contemporary Baltic groups (e.g., Lithuanians, Finns, and Scanadinavians). Finally, they conclude that modern Scandinavians are slightly more close to ancient hunter-gatherers than the farmers. This implies substantial farmer admixture in demographic terms. The group notes that previous inferences of Middle Eastern admixture were compromised by the fact that modern groups often exhibit African admixture. When you look only at the non-African portion, they are a much better proxy. One reason I am curious about the preprint in full is that I believe that even removing African admixture, one might be biased by selection of ‘reference’ populations. It seems likely that there were major eruptions from Arabia in antiquity and the medieval period (inferred by comparing religious isolates such as Arab Christians with their Muslim neighbors).

Setting aside that a two-way admixture seems unlikely to be the whole story*, it does offer up a way to explore an interesting question: on what sort of genes do hunter-gatherers and farmers differ? Specifically I’m wondering about utilizing admixture mapping. In Scandinavian populations regions of the genome where there are adaptations for farming are localized should be enriched for farmer ancestry, and vice versa for hunter-gathering. In the case of Northern Europeans farmers moved up latitudinal clines, and adapted to local conditions only halting. This explains in part that it seems Iberia and parts of Western Europe have more farmer ancestry than regions of Northeast Europe which are closer to the original zone of expansion as the crow flies. Not only did the hunter-gatherers have some cultural traits which conferred benefits in the deep north, but likely there were particular adaptations in these climes which aided their survival.

I understand that admixture mapping for populations which have mixed (and frankly were not that genetically different in the first place) may be difficult. But linkage disequilibrium based methods have been pushed much further back than I could have imagined, and it has been done with South Asians in regards to “Ancestral Northern Indian” vs. “Ancestral South Indian” ancestry and genetic functionality (specifically disease risk alleles).

* In addition, I am more skeptical of a simple demic diffusion model than I was in the past. I think there may have been multiple demographic pulses, followed by equilibration phases.

(Republished from Discover/GNXP by permission of author or representative)
 
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The inimitable Joe Pickrell has dropped his Khoisan-are-part-Italian preprint onto arXiv, Ancient west Eurasian ancestry in southern and eastern Africa. I’m being glib in my characterization of the paper’s core conclusion, but there’s a reason for such a flip response: the inferences that he seems to draw from the genetic data strike me as verging on crazy. But that’s OK, what genetics is telling us is that history was a whole lot crazier than we had imagined.

Let’s back up for a moment here. For several decades now geneticists have assumed that the Bushmen of the Kalahari, the Khoisan-qua-Khoisan, Africa’s last hunter-gatherers who retain their ancestral language along with the Hadza, are the ur-humans. The basal lineage that first diverged from the rest of mankind at the cusp of the Out of Africa event. This is evident in Y chromosomal and mtDNA phylogenies, where the Bushmen and their kin harbor variants which coalesce deeply in time with those of others. And, a few years ago another group revealed the likelihood that Bushmen also are products of an admixture event in the last ~50,000 years with a distinct hominin lineage which diverged ~1 million years before the present from the main line which led up to anatomically modern humanity. Now Pickrell et al. present us with a twist which is perhaps even more astringent than a lime: in their genomes the Bushmen and their Khoisan kin, the Khoe herders, reflect an ancient admixture event with East Africans, who themselves were the outcomes of hybridizations between West Eurasians and indigenous African populations. More relevantly for my concise summation of the conclusion, the West Eurasian component does not necessarily reflect modern Middle Eastern populations, so much as Southern Europeans!

How did they infer such bizarre results? Magic? No. Basically the authors looked at patterns of linkage disequilibrium. Got it? Probably not. If you are curious, confused, and intent upon understanding the thrust of their methods in your bones, you probably need to read Loh et al. Barring that trust in the great hive-mind that is the Reich lab, or attempt to swallow my trite condensation.

If you consider a short to medium length sequence of the genome, there are genetic variants, alleles, segregating across that sequence. The frequency of these alleles vary across populations. And, there are on occasion correlations of allelic combinations, seen together across a single sequence than would be likely if the alleles across the loci assorted at random. A concrete example would be a population which is the product of a recent admixture event between Africans and Europeans. Recombination would take many generations to break apart all the associations between alleles which are diagnostic and distinctive of African and European ancestry, so long blocks of ancestry tracts could be inferred simply by phasing the genome on the individual level (i.e., you know the sequence of each homolog inherited from each parent, instead of just genotype values). There would be linkage disequilibrium within the population because particular variants would be associated with others across loci due to recent distinct ancestry at the genomic level. If you noticed that SNP 1 had an African allele, then SNP 2 located nearby in the locus is also more likely to have an African allele than expectation, until the point that linkage equilibrium is attained.

As I noted above, these associations are broken apart over time in a regular fashion by genetic recombination. Therefore, the decay in linkage disequilibrium across the genome can allow you to infer time since a putative admixture event. This works at various time depths. African Americans have long range LD because the admixture was relatively recent. To date older admixture events one must be more cunning, as the LD decays and becomes exceedingly faint as recombination hacks apart previous distinctive associations as two genetic backgrounds merge. But what about multiple admixture events and the consequent linkage disequilibrium patterns? What the authors did in the above paper was to test the fit of the data to a composite of LD curves in scenarios where it seems likely that there were two possible admixture events. And, they found multiple populations which did fit this model.

Dispensing with the technicalities, here are the results of admixture events as inferred from the LD decay curves:

The most parsimonious model that Pickrell et al. propose is simple as it is crazy.

1) An ancient initial admixture event in the environs of the Horn of Africa between a proto-West Eurasian population and a proto-Sudanic population

2) A second admixture event which occurs when a population derived downstream from event 1 encounters the ancestors of the Khoisan

Pickrell et al. infer a ~3,000 year old admixture event between West Eurasians and Africans for the Semitic populations of the Ethiopian plateau in keeping with Pagani et al.’s only marginally less crazy results. Then you have step 2, with an admixture between proto-Bushmen/proto-Khoe and the hybrid East Africans ~1,500 years ago. Let us accept these genetic results on the face of it. What they bring home to me is the power of culture. Though vastly diminished today, groups such as the Khoe Nama managed to preserve their integrity and independence down to the period of European colonialism (only being truly decimated in Namibia in the early 20th century by the Germans). A wave of Bantu farmers overwhelmed most of southern Africa, but select groups of Khoisan managed to maintain zones of habitation where they persisted with their unique cultural traditions and perpetuated their language. Some of this surely was ecology, as the vast Karoo region is not particularly amenable to the Bantu cultural toolkit. But, I also suspect that institutional and economic (e.g. cattle culture) influences that the East Africans had upon the Khoe, and perhaps even indirectly the Bushmen, also made these populations more robust to the Bantu expansion than otherwise would have been the case.

Being a preprint on arXiv, the paper of which I speak here is free to you, and copiously explained in loving detail in the supplements in terms of method and madness. I am not particularly enthusiastic about having long discussions about how these results are crazy and can not be right. They are crazy. But I know enough about the methodology here to understand the logic, and accept that the authors are grasping at something very strange and true, even if their particular interpretation and specific results may be disputable. Let me quote the paper at this point:

The hypothesis that west Eurasian ancestry entered eastern Africa through Arabia must be reconciled with the observation that the best modern proxies for this ancestry are often found in southern Europe rather than the Middle East (Supplementary Table 4). This observation can be interpreted in the context of ancient DNA work in Europe, which has shown that, approximately 5,000 years ago, people genetically closely related to modern southern Europeans were present as far north as Scandinavia [Keller et al., 2012; Skoglund et al., 2012]. We thus find it plausible that the people living in the Middle East today are not representative of the people who were living the Middle East 3,000 years ago. Indeed, even in historical times, there have been extensive population movements from and to the Middle East [Davies, 1997; Kennedy, 2008].

Think on that. If Pickrell et. al. are right do you think that the Middle East is particularly special in this regard? I will say that it comes to mind that the high consanguinity may result in strange outcomes if one is not careful with the sampling strategy (I’m thinking of the Samaritans I see in their data), though I doubt that this is an incautious group. But I do think it is plausible that some European populations are better proxies for the ancient Levantines than the modern Levantines because the latter have been washed over by multiple demographic waves (though I want to see more comparisons with Christian Arab* samples).

A second bombshell dropped by Pickrell et. al.:

We note that we have interpreted admixture signals in terms of large-scale movements of people. An alternative frame for interpreting these results might instead propose an isolation-by-distance model in which populations primarily remain in a single location but individuals choose mates from within some relatively small radius. In principle, this sort of model could introduce west Eurasian ancestry into southern Africa via a “diffusion-like” process. Two observations argue against this possibility. First, the gene ow we observe is asymmetric: while some eastern African populations have up to 50% west Eurasian ancestry, levels of sub-Saharan African ancestry in the Middle East and Europe are considerably lower than this (maximum of 15% [Moorjani et al., 2011]) and do not appear to consist of ancestry related to the Khoisan. Second, the signal of west Eurasian ancestry is present in southern Africa but absent from central Africa, despite the fact that central Africa is geographically closer to the putative source of the ancestry. These geographically-specific and asymmetric dispersal patterns are most parsimoniously explained by migration from west Eurasia into eastern Africa, and then from eastern to southern Africa.

Isolation-by-distance is alluded to implicitly when we speak of human genetic variation as clinal. And it’s not totally lacking in utility as a null model. But I think we need to add another layer of complexity upon this parsimonious elegance of human clans eternally exchanging mates in monotonous step-wise fashion. Multiple populations over the past 10,000 years (and likely earlier!) were rocked massive demographic turmoil, as foreigners from afar amalgamated themselves upon the local substrate, and abolished the old to bring forth something new. The author of this post is himself a product of such an event. The genetic story of mankind is not just one of continuous and diffuse gene flow gradually over a landscape of small-sale societies. No, this placid background condition was periodically perturbed by an explosion of translocating peoples, likely triggered by a technological or cultural revolution of some sort. The genetic impact in many cases is too great to be anything but a folk wandering.

Unlike isolation-by-distance these patterns do not flow linearly across space, but exhibit discordant lashing patterns through ecologically fertile terrain. Rather than a mist gliding across the plains, imaging a flash flood scouring a ravine. A more gentle analogy would be that these are demographic ripples, which expand outward, temporarily distorting the calm surface of isolation-by-distance dynamics, and eventually fading back into the background and becoming the new normal. But once the ripple has faded how do we know that it was once? That is a difficult thing indeed, and these results indicate the problems inherent. It may be that the echoes of the ripple that Pickrell et al. detect issue from a source which no longer exists. Are the scions of the first farmers of the ancient Levant hidden away in the valleys of Tuscany and the plains of Tanzania? A crazy proposition also, but not necessarily a false one.

Citation: arXiv:1307.8014v1 [q-bio.PE]

* I know some Christian Arabs do not want to be called Arabs.

(Republished from Discover/GNXP by permission of author or representative)
 
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German woman, product of Mid-Neolithic?
Source: Siebbi

Yesterday I pointed to a paper which was interesting enough, but didn’t pass the smell test in relation to other evidence we have (at least in my opinion!). A primary concern was the fact that uniparental (male and female lineages) show a peculiar distribution of variation in comparison to autosomal genetic variation (i.e., the vast majority of the genome) in the case of Europe (genome-wide analysis suggest more of Europe’s variation is partitioned north-south, but Y and mtDNA results often imply an east-west split). But a secondary concern I had was that I felt the models were a bit too stylized. In particular following Cavalli-Sforza and Ammerman the authors concluded that demic diffusion better fits their results of genetic variation in Europe (as opposed to continuity of Paleolithic hunter-gatherers). This is likely correct, but these are not the only two models.

A paper out in Nature Communications, using analysis of the phylogenetics of whole ancient mitchondrial genomes, outlines my primary concern when it comes to the models being tested, Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans:

Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this ‘real-time’ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.

In other words, the mitochondrial genomic landscape of Europeans not only exhibits discontinuity with Paleolithic populations (though ~10% of Europeans, including my father-in-law, carry the U5 mtDNA haplogroup, which does seem to date to the Ice Age), but also with the “First Farmers.” In the case of this paper the focus is on Central Europe and Germany, and haplogroup H, which is modal across Europe (my wife and daughter are H1). That’s because they’ve already done work on this region and these mtDNA genotypes (see: Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities).

Probably the most arresting figure is the panel to the left. Here you have the authors perform a Procrustes analysis where they compared genetic variation of populations to geographic variation. For Europe what is striking (but unsurprising) is the correspondence between the two dimensions. What is noteworthy are the exceptions. The LBK, Germany’s first farming society (ergo, by definition early Neolithic), and the BBC, a late Neolithic culture with putative origins in Spain (this is disputed) do not align with Central Europe. Rather, LBK is shifted toward the Near East, and BBC toward Spain. The former result recapitulates what they discovered earlier. But, The “Middle Neolithic” samples are overlain upon Central Europe! This is why the authors argue that there was a disruption between the LBK and Middle Neolithic cultures (Rossen [4625–4250 BC], Schoningen [4100–3950 BC], Baalberge [3950–3400 BC] and Salzmunde [3400–3025 BC]).

Of course that’s not the end of the story. BBC arrived in the late Neolithic, presumably from Southwest Europe, and also made contributions. The mitochondrial genomic landscape of Central Europe did not freeze in the Middle Neolithic, but, it can be argued that this was a major “phase transition,” just as the shift between the Paleolithic and Neolithic was a major disruption. This is a radical change from the orthodoxy of the early 2000s. Then it was common to assert that the extant haplogroups in the Old World achieved their current distributions between the Last Glacial Maximum and the expansion in the wake of the Holocene warming. These data, along with many other points of evidence imply that in fact contemporary genomic variation is more a function of dynamics particular to the Holocene, the last 10,000 years, rather than the Ice Age.

Going back to the title of the post my contention here is that a stylized demic diffusion scneario with a wave-of-advance as one population expands into another does not model what has occurred in Europe over the past ~10,000 years. Before 2010 the argument was between those who argued that the diffusion was modest in its genetic impact, and those who argued that it wasn’t modest. But ultimately they were arguing over the margins. These results imply that diffusionary processes are not sufficient to characterize the nature of demographic turnover. Rather, there were repeated eruptions, replacements, and admixtures. It is cliche to refer to phyologeographic and archaeogenetic excavations as pealing back a palimpsest, but this actually gets to the reality that the elements of the object under study are more discrete than one might assume.

Let us posit for example an imaginary history which might explain these data.

1 – The “First Farmers” (LBK) establish nucleated settlements isolated from the hunter-gatherers, who recede and are marginalized

2 – A later culture of “Second Farmers” organized around military principles overturns the ascendancy of the “First Farmers.” Additionally, this second wave is a hybrid population, which emerged out of the synthesis of the nucleated first wave and the hunter-gatherer substrate.

3 – Finally, a subsequent series of prehistoric populations interject themselves onto the historical scene, though only inflecting the genomic landscape characterized by step 2. Like the second group these are themselves populations with diverse origins in prehistory, a syntheses of various geographical and tribal strands.

Though isolation by distance and clinal variation is important in this narrative, these dynamics are actually requilibrations after the exogenous shocks of demographic eruptions (note, a reader of this weblog outlined this model years ago in a more primitive form). Agriculture, and agricultural mass societies, were sociological shocks of a massive order, which resulted in protean shifts in the institutional and cultural fabric of diverse peoples. Like early stage innovation and business growth the “Neolithic sector” may have been characterized by rapid growth and high rates of “firm” extinction. Ultimately a series of consolidations and merges resulted in a new more stable order, as the industry entered a “mature phase.” What we term civilization.

Is that a true story? Perhaps not in the details. But I think it’s a truer story than the tales that were on offer in the early 2000s.

Addendum: It is important to note that discontinuity seems a likely story for the Y chromosomes as well (male lineages).

Citation: doi:10.1038/ncomms2656

(Republished from Discover/GNXP by permission of author or representative)
 
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Randy McDonald points me to this fascinating post, Genetic clues to the Ossetian past. In the post author outlines phylogeographic inferences one can make from uniparental lineages; maternal and paternal lines of descent. Specifically, they are in interested in the origins and relationships of the Ossete people. I assume that one reason Randy pointed me to this post is that the Ossetes are assumed by many to be the descendants or fragments of the Alans. More broadly they’re remnants of a broad array of North Iranian peoples, of whom the Scythians were the most prominent, which have been erased from the pages of history because of the expansion of the Slavs and Turks.


The main lacunae in the above analysis is that it does not cover results from autosomal studies. Some of that has been performed by Dienekes, but more is necessary for a region characterized by as much ethnographic diversity and density as the Caucasus. One peculiarity that emerges in analyses of autosomal data sets is that the Caucasus looms relatively large in a wide array of dispersed populations. For example, there is a genetic signature which ties Indo-Aryan and Caucasian populations together, and others which seem to connect the latter to some Balkan groups.

These are possible hints that the Caucasus is the “mother of nations,” and that the old idea of the “Caucasian race” may have some reality to it. But I would bet on something else: the Caucasus is not the mother of nations, but the repository of forgotten peoples. The Ossetes themselves are presumed to be just such a population. I offer up the hypothesis that one reason that disparate Caucasian populations have diverse and wide-ranging connections has less to do with outward expansion, and more to do with the fact that on the margins of the Caucasus a great range of historic genetic diversity erased by later demographic events (e.g., the Slavic and Turkic expansions from two directions in on the North Iranian peoples) is preserved, as the defeated take refuge.

(Republished from Discover/GNXP by permission of author or representative)
 
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As I’ve been harping on and on for the past few years that the patterns of contemporary genetic variation are probably only weakly tied to past patterns of genetic variation (though Henry Harpending warned me about this as far back as 2004). A major reason that scholars operated under this presupposition is the axiom that most of the variation we see around us crystallized during the Last Glacial Maximum (~20 thousand years before the present).

This may be true in some cases, but I doubt it is true in most cases. I was pointed to a classic case of this problem just today. A reader alerted me to a short paper from this spring which attempts to ascertain the point of origin of the dominant mtDNA haplogroup among the Onge tribe of the Andaman Islanders, M31a1. This is an interesting issue because some researchers proposed, plausibly in the past, that these indigenous people in the Andaman Islands represent the descendants of the first wave “Out of Africa,” who took the rapid “beachcomber” path. Understanding the key to their genetics may then unlock the key to the “Out of Africa” event. Or so we thought. It looks like the human evolutionary past was a lot more complicated than we’d presumed.

The paper is in the Journal of Genetics and Genomics. Mitochondrial DNA evidence supports northeast Indian origin of the aboriginal Andamanese in the Late Paleolithic:

In view of the geographically closest location to Andaman archipelago, Myanmar was suggested to be the origin place of aboriginal Andamanese. However, for lacking any genetic information from this region, which has prevented to resolve the dispute on whether the aboriginal Andamanese were originated from mainland India or Myanmar. To solve this question and better understand the origin of the aboriginal Andamanese, we screened for haplogroups M31 (from which Andaman-specific lineage M31a1 branched off) and M32 among 846 mitochondrial DNAs (mtDNAs) sampled across Myanmar. As a result, two Myanmar individuals belonging to haplogroup M31 were identified, and completely sequencing the entire mtDNA genomes of both samples testified that the two M31 individuals observed in Myanmar were probably attributed to the recent gene flow from northeast India populations. Since no root lineages of haplogroup M31 or M32 were observed in Myanmar, it is unlikely that Myanmar may serve as the source place of the aboriginal Andamanese. To get further insight into the origin of this unique population, the detailed phylogenetic and phylogeographic analyses were performed by including additional 7 new entire mtDNA genomes and 113 M31 mtDNAs pinpointed from South Asian populations, and the results suggested that Andaman-specific M31a1 could in fact trace its origin to northeast India. Time estimation results further indicated that the Andaman archipelago was likely settled by modern humans from northeast India via the land-bridge which connected the Andaman archipelago and Myanmar around the Last Glacial Maximum (LGM), a scenario in well agreement with the evidence from linguistic and palaeoclimate studies.


Geologically unless the Andaman Islanders’ ancestors were accomplished open ocean travelers they almost certainly did arrive via Myanmar. The inference they’re making is based on the likely false axiom that mainland Southeast Asia has been genetically stable for the past 10 to 20 thousand years . It hasn’t been genetically stable over the past 1,000 years! The authors themselves offer up a good explanation for what’s going on here in the conclusion:

In summary, by extensively studying a large number of Myanmar samples, our results failed to find any root lineage of haplogroup M31 in Myanmar, therefore suggesting that aboriginal Andamanese were unlikely originated from Myanmar, the closest region to the Andaman archipelago in geographic. Nevertheless, we still cannot completely rule out the possibility that the matrilineal landscape in Myanmar had been largely shaped by the Neolithic immigrants from the neighboring regions, addressing this issue needs extensive studying on the Myanmar populations. Significantly, our further analyses strongly suggested that Andamanese-specific M31a1 finds its origin in northeast India. Therefore, it seems that the ancient people bearing M31a root type likely had peopled the Andaman archipelago via the land-bridge connecting the Andaman archipelago and southeast Asia continent around the LGM.

Bingo! At a minimum it seems likely that the Onge have been resident in the Andaman Islands for ~10 thousand years. Therefore we should be cautious I think about making too many inferences as to whether their ancestors were resident only in Mynamar, or spanned the South China Sea to the Indus, and so forth. But, I think we can grant that they arrived via Mynamar, and were once resident in Myanmar. The disjunction between mtDNA lineages in their rather large sample strongly implies that Myanmar has seen major demographic reshaping since the ancestors of the Andaman Islanders parted ways with their mainland kin. This stands to reason. It is almost certainly likely that Myanmar was dominated by populations speaking Austro-Asiatic languages at some point in the past. These were replaced by the ancestors of the Burmans, Karen, etc. And to some extent even these have been displaced by newcomers, such as the Shan. But the Austro-Asiatic people themselves probably came from further east. If, and it’s a big if, the kin of the Andaman Islanders were the population which immediatedly predated the Austro-Asiatic groups, then there have been two linguistic shifts, likely accompanied by major genetic turnover. In fact I suspect there were probably more transitions in the past. I doubt hunter-gatherer populations were quite as static as we sometimes seem to posit, at least in the past 40 thousand years.

Here’s a table of haplogroup frequencies:

And here is how the branches of M31 are related to each other:

The Onge branch is distinct, as you might expect from an isolated island population. Using the molecular clock models they came up with a series of coalescences back to the last common ancestor (represented by the star in the figure above). I’ll quote them:

Previous work has suggested the “recent settlement” of the Andaman archipelago about 24 ± 9 kilo-years ago (kya) (Barik et al., 2008). In view of the time estimation results based on the updated phylogeny tree of haplogroups M31, peopling the Andaman archipelago would have occurred after the differentiation of lineage M31a (19.82 ± 10.01 kya) and before the divergence of M31a1 (7.96 ± 3.91 kya) (Table 2). Intriguingly, a similar result was achieved by studying the whole nuclear genome, in which the Andaman aboriginals were suggested to be originated from the potential ancestral populations of South Asian sub-continent before the admixture of ASI-ANI on the mainland (Reich et al., 2009). Noticeably, the paleoclimate evidence and data of Global Ocean Associates prepared for the office of Naval Research have showed that the sea level of Southeast Asia was about 120 m lower than that of today before 17 kya, and most of the sea level of Andaman sea was above 100 m today, supporting the existence of the potential land-bridge connecting Andaman archipelago and southeast Asia continent before the Last Glacial Maximum (LGM) (22–18 kya) ([Voris, 2000] and [Clark et al., 2009]). Taking into account the interesting distribution patterns and time estimation results of different subclades within haplogroup M31, it is likely that the ancestors of aboriginal Andamanese had arrived at Andaman arhcipelago around the LGM through the land-bridge before it was submerged with the raising of the sea level after the peak of the LGM.

They’re right that their number is in rough alignment with the results from Reich et al. The Andaman Islanders diverged from “Ancestral South Indians” on the order of a few tens of thousands of years before the present. But I wonder as the value-add of their estimate when they have a interval over ~10 years on their expectation. That being said, it seems clear that this mtDNA estimate at least pegs a lower boundary. As cultural anthropology would tell us the Andaman Islanders diverged from mainland South Asians well before agriculture. And, the arrival of “Ancestral North Indians.”

On a final note, if the Andaman Islanders arrived ~20 thousand years before the present from the South Asian mainland they don’t tell us very much about the “Out of Africa” people. They’re not “living fossils,” and it was frankly somewhat stupid probably to think they would be. Until recently the “Out of Africa” event was pegged at ~50 thousand years, at its most recent. Even assuming this date the Andaman Islanders arrived in their present location closer to the present than the point at which their ancestors left Africa. But now there is more of a tendency to accept the possibility that the “Out of Africa” event wasn’t so cut & dried in any case, and may date as far back as ~100,000 years. If so we may simply have to acknowledge that fine-grained understanding of paleodemographics will always elude us if we can’t get our hands on a sample of ancient DNA. Even among pre-agricultural peoples there was probably too much population genetic turnover for the palimpsest to be teased apart with enough subtly to read the tea leaves of the past

(Republished from Discover/GNXP by permission of author or representative)
 
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ResearchBlogging.org Seriously, sometimes history matches fiction a lot more than we’d have expected, or wished. In the early 2000s the Oxford geneticist Bryan Sykes observed a pattern of discordance between the spatial distribution of male mediated ancestry on the nonrecombinant Y chromosome (NRY) and female mediated ancestry in the mitochondrial DNA (mtDNA). To explains this he offered a somewhat sensationalist narrative to the press about possible repeated instances of male genocide against lineage groups who lost in conflicts.

Here is a portion of the book of Numbers in the Bible:

15 – And Moses said unto them, Have ye saved all the women alive?

16 – Behold, these caused the children of Israel, through the counsel of Balaam, to commit trespass against the LORD in the matter of Peor, and there was a plague among the congregation of the LORD.

17 – Now therefore kill every male among the little ones, and kill every woman that hath known man by lying with him.

18 – But all the women children, that have not known a man by lying with him, keep alive for yourselves.

Then there is the rape of the Sabine women. The ethnogenesis of the mestizo and mulatto populations of the New World in large part was the union between non-European women and European men. These are hard brutal myths and hard brutal facts. But do they reflect an essential aspect of the dynamics which have shaped our species’ past?

I’m not willing quite yet to add a confident weight upon this possibility, but this seems to be part at least part of the picture. You see a major disjunction on male and female lineages among South Asians for example. A new paper in PNAS adds weight to this possibility, albeit only incrementally. Ancient DNA reveals male diffusion through the Neolithic Mediterranean route:

The Neolithic is a key period in the history of the European settlement. Although archaeological and present-day genetic data suggest several hypotheses regarding the human migration patterns at this period, validation of these hypotheses with the use of ancient genetic data has been limited. In this context, we studied DNA extracted from 53 individuals buried in a necropolis used by a French local community 5,000 y ago. The relatively good DNA preservation of the samples allowed us to obtain autosomal, Y-chromosomal, and/or mtDNA data for 29 of the 53 samples studied. From these datasets, we established close parental relationships within the necropolis and determined maternal and paternal lineages as well as the absence of an allele associated with lactase persistence, probably carried by Neolithic cultures of central Europe. Our study provides an integrative view of the genetic past in southern France at the end of the Neolithic period. Furthermore, the Y-haplotype lineages characterized and the study of their current repartition in European populations confirm a greater influence of the Mediterranean than the Central European route in the peopling of southern Europe during the Neolithic transition.

First, the easy stuff. This is another datum which should make us skeptical of the idea of Neolithicization as an overwhelmingly indigenous process, spreading via cultural emulation. The Y chromosomal lineages sequenced here are very homogeneous, and seem to belong to a patrilocal kinship group. In contrast, the mtDNA lineages, which tell us about female ancestry, are much more diverse. They cover a much better sweep of contemporary European genetic diversity. The authors note that a minority of mtDNA lineages are of Middle Eastern origin, but the majority are of lineages which are presumed to have a deeper Paleolithic root, as supported by their greater variance. I think we should still be cautious of even this interpretation, but there does seem to be a notable difference in this one community between males and females which may be indicative of a particular social and cultural system.

The maps to the left show the relationship of mtDNA and Y lineages to modern patterns of European genetic variation. The darker the shading the higher proportion of lineages shared. The top figure illustrates female mtDNA, and you can see the broad correspondences between the ancient southwest French sample and modern groups. But observe the big difference in the second figure, which shows the male distributions. This is much more localized to particular regions of Iberia and Turkey. The overwhelming haplogroup in the cemetery was G2a-P15, which is rather rare in Europe today, and the region. What happened to these men? Genetic drift or population replacement perhaps. If one posits a model of long term smaller male effective populations then Y chromosomal lineages will be subject to more stochastic extinction and fixation events than mtDNA. I’m not sure if I believe this, but that is one model which doesn’t necessarily involve a conventional replacement of the male lineages a la Conan.

But the dispersal of G2a-P15 at low frequencies around the Mediterranean is also consistent with the possibility of repeated replacement of male lineages across the arc of history. This has historical precedent, the Greek colonies alonge fringes of the Mediterranean were founded by men, sometimes explicitly exiled from their home polis. They had often had to “obtain” local women to perpetuate themselves. This isn’t supposition or conjecture, but outlined in some of the texts which record how colonies were founded in the Archaic pre-Classical period. Of course we do know that these sorts of transplantations could also involve women, they seem to have in the case of the Etruscans.

Additionally, this may also be a case of male “leap-frog” migration patterns, which break apart the null model of genetic variation which is modeled by isolation-by-distance. The argument is that the expansion of farming from the eastern Mediterranean did not occur via demic diffusion by land, but rather through a process of maritime transplantation, and then subsequent expansion from the nascent nuclei. Again, we can look at the expansion of the maritime Greeks. There was no contiguous region of Greek settlement between Greece proper and “Magna Graecia” in southern Italy and Sicily. Connections were by sea, which makes sense insofar as long distance sea transport was far cheaper energetically than land migration. I see no reason why these ancient farming Diasporas couldn’t have maintained a sort of cultural continuity for centuries through ritual or regular contacts via maritime transit.

A second point in this paper is that this population seems to have lacked in totality the allele which is diagnostic of lactase persistence across much of Europe today. The authors observe that that allele has a frequency of ~43% in the modern French population (it’s dominant, so that means that ~35% of the French are lactose intolerance). I would be curious about the frequency in the south of France, as traditionally the north of France was the domain of butter, while that to the south more of olive oil (historically the south of France witnessed the preservation of the Gallo-Roman aristocracy, which explicitly adopted Frankish modes of dress in 5th century as a way to assimilate into the non-clerical administrative apparatus of the Merovingian monarchy, but maintained their cultural distinction). The authors conclude from the lack of the LP allele that the individuals buried in the cemetery were from a different migration stream than those which founded the LBK society in central Europe, and who may have invented the dairy culture.

I think the “big picture” that is shaping up is that there were multiple intrusions, eruptions, replacements, and assimilations, across prehistoric Europe, just as there were across many regions of the world. On the whole I suspect males played more of a role in this process than females, though I’m not confident that we will see a consistent pattern of female lineages in a given area being markers for the Paleolithic populations. There may have been so much shifting and layering that the original people, the oldest of old, may only be accessible via ancient DNA. Speaking of which, thank god we’re finally entering the golden age of ancient DNA! Many questions will no doubt finally be resolved.

Dienekes Pontikos also has a lot to say about this. I’m sure some of you who are more versed in mtDNA and NRY haplogroups will also offer you 2 cents!

Citation: Marie Lacan, Christine Keyser, François-Xavier Ricaut, Nicolas Brucato, Francis Duranthon, Jean Guilaine, Eric Crubézy, & Bertrand Ludes (2011). Ancient DNA reveals male diffusion through the Neolithic Mediterranean route PNAS : 10.1073/pnas.1100723108

(Republished from Discover/GNXP by permission of author or representative)
 
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The Pith: There is a very tight correlation between language and genes in the Caucasus region.

If the Soviet Union was the “The Prisonhouse of Nations,” then the Caucasus region must be the refuge of the languages. Not only is this region linguistically diverse on a fine-grained scale, but there are multiple broader language families which are found nowhere else in the world. The widespread Indo-European languages are represented by Armenians, Greeks, and Iranians. The similarly expansive Altaic languages are represented by the Turkic dialects. But in addition to these well known groups which span Eurasia there are the Northwest Caucasian, Northeast Caucasian, and Kartvelian, families. These have only a local distribution despite their distinctiveness.

On the one hand we probably shouldn’t be that surprised by the prominence of small and diverse language families in this rugged region between Russia and the Near East. Mountains often serve as the last refuges of peoples and cultures being submerged elsewhere. For example, in the mountains of northern Pakistan you have the linguistic isolate of Burusho, which has no known affinity with other languages. Likely it once had relatives, but they were assimilated, leaving only this last representative isolated in its alpine fastness. The once extensive Sogdian dialects (Sodgian was once the lingua franca between Iran and China) are now only represented by Yaghnobi, which persists in an isolated river valley in Tajikistan. How the mighty have fallen! But the mountains are always the last fortresses to succumb.

ResearchBlogging.org But the Caucasus are peculiar for another reason: they’re so close to the “action” of history. In fact, history as we know it started relatively near the Caucasus, to the south on the Mesopotamian plain ~5,000 years ago. Therefore we have shadows and glimmers of what occurred on the south Caucasian fringe early on, such as the rise and fall of the kingdom of Urartu ~3,000 years ago. The ancient ancestors of the Georgians even show up in Greek myth, as the Colchis of Medea. And this was a busy part of the world. Hittite, Greek, Roman, and Arab, came and went. The rise of Turkic resulted in the marginalization of many of its predecessors. Some scholars even argue that the Indo-European and Semitic languages families issue from the north and south fringes of the Fertile Crescent, respectively. And it isn’t as if history has skirted the Caucasians. The Georgians faced the brunt of the Mongol armies, while the Circassians have famously been present across the greater Middle East as soldiers and slaves.

Ultimately it seems that geography can explain much of the sui generis character of the Caucasus in relation to adjacent regions. The homogenizing impact of large political units such as Byzantium, Persia, the great Arab Caliphates, Russia, and the Ottomans, was dampened by the fact that the Caucasus was often administered indirectly. The cost of conquering valley after valley was presumably prohibitive, and the natives could always retreat to the mountains (as the Chechens did most recently in the 1990s).

A new paper in Molecular Biology and Evolution illuminates the genetic relationship of Caucasian peoples, both within the region, and to groups outside of it. Parallel Evolution of Genes and Languages in the Caucasus Region:

We analyzed 40 SNP and 19 STR Y-chromosomal markers in a large sample of 1,525 indigenous individuals from 14 populations in the Caucasus and 254 additional individuals representing potential source populations. We also employed a lexicostatistical approach to reconstruct the history of the languages of the North Caucasian family spoken by the Caucasus populations. We found a different major haplogroup to be prevalent in each of four sets of populations that occupy distinct geographic regions and belong to different linguistic branches. The haplogroup frequencies correlated with geography and, even more strongly, with language. Within haplogroups, a number of haplotype clusters were shown to be specific to individual populations and languages. The data suggested a direct origin of Caucasus male lineages from the Near East, followed by high levels of isolation, differentiation and genetic drift in situ. Comparison of genetic and linguistic reconstructions covering the last few millennia showed striking correspondences between the topology and dates of the respective gene and language trees, and with documented historical events. Overall, in the Caucasus region, unmatched levels of gene-language co-evolution occurred within this geographically isolated populations, probably due to its mountainous terrain.

In some ways this is a paper which would have been more in keeping with the early 2000s. It focuses on Y chromosomal markers, so the direct male lineage. This is contrast to the sort of analyses which focus on hundreds of thousands of autosomal markers across the genome. But there are some benefits to focusing on Y chromosomal lineages, which are highlighted within this paper. First, one can construct very precise trees based on the mutational distance of individuals. Haplogroups can be subdivided cleanly into haplotypes with treelike phylogenetic relationships by comparing mutational differences. Second, one can use molecular clock methodologies to peg the timing of the separation between two clades.

I don’t have a good natural grasp of the ethnography of the region, nor am I very well versed in the phylogeography of Y chromosomal lineages (at least in relation to some of the readers of this weblog), so I won’t go into specifics much (see Dienekes Pontikos’ comments). The main step forward here is the enormous sample size and fine-grained coverage of the ethnic groups across the Caucasus. In a region of such linguistic diversity and geographic fragmentation this is of the essence. They found a 0.64 correlation between variance in genes and language, and 0.60 correlation between variance in genes and geography. Because geography and language are so tightly linked in the Caucasus they couldn’t obtain statistically significant results when one variable was controlled, but language seems to be a bigger predictor than geography.

The following two maps show the distribution of haplogroups across Caucasian populations, as well as how they relate to other groups. A general affinity with Near Eastern groups is evident in this simply through inspection:

In classic fashion the authors found a very tight correlation between the phylogenetic trees generated from Y chromosomes and linguistics (the Dargins being the exception):

Many researchers, such as Marcus Feldman, assume that this sort of correspondence is a natural outgrowth of the fact that gene flow tends to be demarcated by dialect continuums. By this I mean that intermarriage between two groups all things equal is going to be favored if there is linguistic comprehensibility. In the pre-modern era before “standard” languages codified from on high this means that genes would flow from tribe to tribe, with subtle differences of dialect, which nevertheless would remain intelligible. That is until you encounter a language family barrier, where despite borrowings across the chasm intelligibility is simply not possible. In the Balkans the Slavic languages of Bulgarian and Macedonian reputedly exhibit a dialect continuum. But the barrier between these two languages and Greek is not just one of subtle shading, but deep differences. This seems to be at work in the Caucasus, where the chasm is even greater in linguistic terms (Greek and Slavic langauges are both Indo-European, though I suspect that at that level of distance there isn’t much of a difference if it was Greek to Georgian or Slavic to Azeri).

There are lots of details in the paper, ranging from a synthesis with archaeological evidence for the development of Caucasian cultural complexes derived from Near Eastern sources, to the timing of the separation between the major language families or sub-families. The weeds here are beyond me to be frank. So what can we conclude from this specific case to the generality?

At some point in the near future we’ll have thick and robust data sets like this for many regions of the world, so this may be a preview of what is to come. This is focusing on the Y chromosomal lineages, and we must remember that male mediated ancestry can exhibit consistent differences from female mediated ancestry. I no longer am very confident of the finding from comparisons of mtDNA and Y chromosomal variation that the majority of human gene flow has been female mediated because of patrilocality. But this may be at work in some areas. In general the scholars, such as Bryan Sykes, who have looked at the phylogeography of uniparental lineages tend to notice a difference between Y chromosomal and mtDNA patterns, whereby the former were subject to much clearer partitioning between groups (e.g., the Wales-England border) than the latter. The natural inference is that this is a hallmark of “man the warrior,” as male linages eliminate and marginalize each other in the “great game” of genetic competition. Over the short term in the pre-modern world there is a zero sum aspect to this, populations are relatively constant, and so for Genghis Khan to be fruitful other men must be pushed aside. This does not necessarily entail slaughter. Bonded or landless men may not reproduce their genes, or, their reproduction may be sharply diminished. A few generations of differential fertility can quickly lead to major differences in the distribution of ancestry.

Assume for example that at generation 1 population A outnumbers population B by a factor of 20. Assuming that A has a replication of 0.95 per generation and B 1.20 per generation, how many would it take for B to overtake A in total numbers? 13 generations. We have examples from the New World where Iberian Y chromosomal lineages have totally replaced Amerindian ones among the racially mixed population, while preserving Amerindian mtDNA. In areas with generations of European male migration the total genome content has become overwhelmingly male, but the mtDNA still shows the signature of the founding Amerindian population.

I am willing to be that for the Caucasus we would see much less distinction on the mtDNA if the same study was replicated with the same individuals. The major explanation for why this would not be so from my perspective would be if the original male Near Eastern groups arrived and intermarried with sharply distinctive local female lineages, and these distinctions have been preserved over time through endogamy, whether culturally conditioned (language barriers) or geographically necessitated.

Finally, on the broadest canvass these sorts of findings should make us question the contention that nationality is a totally modern invention. These language and genetic clusters clearly denote populations which have deep differences which have persisted and emerged over thousands of years. This has resulted in a “Balkan powder-keg” in our time (e.g., the Russian government backing the Ossetes against Chechens, and so on) . To some extent contemporary conflicts are rooted in the exigencies of the present. But, they often also utilize preexistent differences and allegiances which have deep time roots. Dismissing these differences as purely socially constructed epiphenomena is I think the wrong way to approach the question.

Citation: Oleg Balanovsky, Khadizhat Dibirova, Anna Dybo, Oleg Mudrak, Svetlana Frolova, Elvira Pocheshkhova, Marc Haber, Daniel Platt, Theodore Schurr, Wolfgang Haak, Marina Kuznetsova, Magomed Radzhabov, Olga Balaganskaya, Alexey Romanov, Tatiana Zakharova, David F. Soria Hernanz, Pierre Zalloua, Sergey Koshel, Merritt Ruhlen, Colin Renfrew, R. Spencer Wells, Chris Tyler-Smith, Elena Balanovska, & and The Genographic Consortium (2011). Parallel Evolution of Genes and Languages in the Caucasus Region Mol Biol Evol : 10.1093/molbev/msr126

(Republished from Discover/GNXP by permission of author or representative)
 
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Here’s the model from Wikipedia:

This hypothesises similarities between the Solutrean industry and the later Clovis culture / Clovis points of North America, and suggests that people with Solutrean tool technology crossed the Ice Age Atlantic by moving along the pack ice edge, using survival skills similar to that of modern Eskimo people. The migrants arrived in northeastern North America and served as the donor culture for what eventually developed into Clovis tool-making technology. Archaeologists Dennis Stanford and Bruce Bradley suggest that the Clovis point derived from the points of the Solutrean culture of southern France (19,000BP) through the Cactus Hill points of Virginia (16,000BP) to the Clovis point…This would mean that people would have had to move from the Bay of Biscay across the edge of the Atlantic ice sheet to North America. Supporters of this hypothesis believe it would have been feasible using traditional Eskimo techniques still in use today….

In my opinion there’s all sorts of things crazy with this model. But genome blogger Diogenes has been harping on the possibility that a low level substratum component among Northern Europeans which has affinities to Siberians and Amerindians may be a remnant of the original European hunter-gatherers. It follows then that these groups were later marginalized and absorbed by waves of farmers coming from the Middle East and south-central Eurasia. David of Eurogenes Genetic Ancestry Project has discerned the same element, which is modal among Finns among Northern European groups.


I don’t think that the “Classic Solutrean hypothesis” is viable, where Paleolithic Europeans manage to jump across the polar fringe to North America. Rather, my contention that it is not beyond the realm of possibility that a set of post-Gravettian societies spanned the northern fringe of Eurasia, and that one branch went east to populate North America. Of those that remained it may be that on the milder fringes of western Eurasia, what became Europe, they were almost totally marginalized or absorbed. Only across the great expanse of Siberia where agriculture was marginalized did this people persist down the modern day. To bring it back to the present and over romanticizing the the possibilities one might then suggest that the displacement of Amerindians in North America over the past few centuries recapitulated the marginalization of their distant cousins in Europe between 5 and 10 thousand years ago!

A major point I would like to enter into the record is that I believe that the single-demic-diffusion model is wrong for Europe. I now believe it is wrong for South Asia, where Austro-Asiatic speakers are I believe implicated in the introduction of rice agriculture to the northeast of the subcontinent. Unless programs like ADMIXTURE are saturating our pattern-matching cognitive biases a map of human variation tends to be difficult to reconcile with single population expansions in many areas (e.g., South Asia and Southeast Asia, and I believe Europe). We might not be able to make out the shape of reality very well because of the nature of palimpsest, but it is hard to reconcile the genetic variation with single-wave models. With the coming online of ancient DNA in northern Eurasia I think we’ll get a better answer of what went down in the next 5 years.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: History, Science • Tags: Archaeogenetics 
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ResearchBlogging.orgThe Pith: Over the past 10,000 years a small coterie of farming populations expanded rapidly and replaced hunter-gatherer groups which were once dominant across the landscape. So, the vast majority of the ancestry of modern Europeans can be traced back to farming cultures of the eastern Mediterranean which swept over the west of Eurasia between 10 and 5 thousand years before the before.

Dienekes Pontikos points me to a new paper in PNAS which uses a coalescent model of 400+ mitochondrial DNA lineages to infer the pattern of expansions of populations over the past ~40,000 years. Remember that mtDNA is passed just through the maternal lineage. That means it is not subject to the confounding dynamic of recombination, allowing for easier modeling as a phylogenetic tree. Unlike the autosomal genome there’s no reticulation. Additionally, mtDNA tends to be highly mutable, and many regions have been presumed to be selectively neutral. So they are the perfect molecular clock. There straightforward drawback is that the history of one’s foremothers may not be a good representative of the history of one’s total lineage. Additionally the haploid nature of mtDNA means that genetic drift is far more powerful in buffeting gene frequencies and introduced stochastic fluctuations, which eventually obscure past mutational signals through myriad mutations. Finally, there are serious concerns as to the neutrality of mtDNA…though the authors claim to address that in the methods. I should also add that it also happens to be the case that there is less controversy and more surety as to the calibration of mutational rates of mtDNA than the Y chromosomal lineages of males. Their good for determining temporal patterns of demographic change, and not just tree structures.

Here’s the abstract, Rapid, global demographic expansions after the origins of agriculture:

The invention of agriculture is widely assumed to have driven recent human population growth. However, direct genetic evidence for population growth after independent agricultural origins has been elusive. We estimated population sizes through time from a set of globally distributed whole mitochondrial genomes, after separating lineages associated with agricultural populations from those associated with hunter-gatherers. The coalescent-based analysis revealed strong evidence for distinct demographic expansions in Europe, southeastern Asia, and sub-Saharan Africa within the past 10,000 y. Estimates of the timing of population growth based on genetic data correspond neatly to dates for the initial origins of agriculture derived from archaeological evidence. Comparisons of rates of population growth through time reveal that the invention of agriculture facilitated a fivefold increase in population growth relative to more ancient expansions of hunter-gatherers.

As Dienekes notes until recently the orthodoxy was that the genetic variation of modern populations was well explained by the genetic variation of Paleolithic groups after the Last Glacial Maximum ~20,000 years B.P. In this line of thought agriculture spread often by cultural diffusion, and the first local adopters in a region would then enter into a phase of demographic expansion. Bryan Sykes’ Seven Daughters of Eve and Stephen Oppenheimer’s The Real Eve are expositions of this point of view, which really was the historical genetic mainstream. This also dovetailed with the anthropological bias of “pots-not-people,” whereby cultural forms moved through transmission and not migration. There were some dissenters, such as Peter Bellwood, but by and large the genetic evidence at least was robust enough that they could be dismissed.

So what happened? Several things. First, the sample sets of mtDNA and Y chromosomes kept getting larger. There was deeper sequencing of informative regions. Thick SNP-chip autosomal studies came to the fore, with different conclusions. Finally, ancient DNA extraction allowed scientists to compare the real lineages of hunter-gatherers in ancient Europe vs. what they had presumed were hunter-gatherer descendant lines in modern Europeans. The strong disjunction often found was indicative of a major failing in the prior assumptions of the theorists of the early 2000s: that they could infer confidently past events from the palimpsest of modern genetic variation. They couldn’t. We know that because they seem to have been wrong.

Let’s give India as an example of “what went wrong.” Here’s a paper from 2005, Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans:

Since the initial peopling of South and West Asia by anatomically modern humans, when this region may well have provided the initial settlers who colonized much of the rest of Eurasia, the gene flow in and out of India of the maternally transmitted mtDNA has been surprisingly limited. Specifically, our analysis of the mtDNA haplogroups, which are shared between Indian and Iranian populations and exhibit coalescence ages corresponding to around the early Upper Paleolithic, indicates that they are present in India largely as Indian-specific sub-lineages. In contrast, other ancient Indian-specific variants of M and R are very rare outside the sub-continent.

The Upper Paleolithic is pre-Holocene. I generally accepted this, until the the studies came out from the SNP-chips which had hundreds of thousands of autosomal markers. To be short about it Indians just seemed too close to West Eurasians if the mtDNA results were correct, and, representative. In fact, if Reconstructing Indian History is correct, about half the South Asian genome in aggregate is very close to that of West Eurasians, to the point where it seems likely to have a common ancestry in the Holocene. The mistaken inference from mtDNA may be due in part to sex-biased gene flow. That is, the South Asian exogenous genome was strongly biased toward male migration, while the deep time mtDNA substrate has tended to persist underneath all these successive layers.

Moving to the paper in question, they use a “Bayesian skyline” method to reconstruct past demographic history. Specifically, the history of the direct maternal lineage. We wouldn’t really pay attention if they didn’t have interesting results. And they do indeed.

The table is rather straightforward. They partitioned the samples they had into putative hunter-gatherer and Neolithic lineages. Notice the difference. For some of these cases we have very robust non-genetic evidence of expansion. This is true especially for the African and Southeast Asian Holocene cases. Their methods here predict exactly what we already know. So the key value add is that the methods are predicting something which is more in dispute: the demographic history of contemporary European mtDNA lineages. The concordance of the archaeological evidence of the Neolithic transition in Europe and the inferred demographic expansion of European Neolithic mtDNA lineages is striking.

The plot to the left is the curve of demographic expansion predicted from their method for Neolithic and Paleolithic lineages in Europe. The y-axis is log-scaled, so it naturally understates the explosive growth of Neolithic lineages. It comports well with what we know of how agricultural societies tend to expand and stabilize over time. During a phase of “land surplus” they enter into rapid demographic expansion, forcing the frontier of settlement out. Once the land is “filled up” we enter into the classic Malthusian “stationary state,” where the grinding misery of the peasantry becomes the lot of most. In contrast hunter-gatherer lineages didn’t experience such an explosive shift. Though pre-modern hunter-gatherer landscapes were more diversified than what we experience today, because they had access to the rich “bottom lands” and seashores now monopolized by agriculturalists, the carrying capacity of the land was generally lower for their lifestyle, and waxed and waned more gradually with shifts in ecology.

The authors also did some neat geo-visualization, if I do say so (and I’m jealous!). The two panels illustrate the spread of agriculture as inferred from archaeology, and the rate of population growth calculated from the joint information of the time of onset of a farming lifestyle in a region and the point on the “growth curve” for the Middle Eastern lineages at that time. So above you see the spread of agriculture from the eastern Mediterranean from 8000 BC to 2500 BC. Then, you see a geographical illustration of the S-shaped growth curve of the farmers. Their initial colonies experienced modest growth, but there was a transition zone in the middle of rapid expansion. Why? Perhaps there was a necessary critical mass, before the superiority of numbers began to wear down the hunter-gatherers. But this itself was a transient, as the farmer societies ran up against the limits of ecology along the northern European plain (or, perhaps just as likely, they encountered dense hunter-gatherer societies which were able to temporarily withstand their aggressive expansion on the European maritime fringe). I suspect that the models are more complex than a one-two punch, in either time or space. There were likely several pulses and distinct streams coming out of the Middle East which populated Europe.

They conclude that “Mesolithic ancestry makes up only a fraction of contemporary European genomes. U5a, U5b1, V, and 3H combined account for ≈15% of western Europeans mtDNA haplogroups.” Note that U5a and U5b are modal among the Finnic peoples of Europe. V seems widely distributed, and modal in northern Scandinavia and the western Mediterranean. I can’t seem to find easy information on 3H.

From the supplements here are the European haplgroups they selected:

We chose haplogroups associated with an origin in Near Eastern populations during the Holocene: T1, T2, J1a, K2a, and H4a. These haplogroups (T1, T2, J1a, and K) all appear to have Near Eastern founders that migrated to Europe after the Younger Dryas (2). After inspecting the haplogroup K network in Behar et al. (4), we chose the subgroup K2a, which appears to be present in the Near East (including non-Ashkenazi Jews) and European populations (but not North Africa). Haplogroup H4a is thought to have expanded throughout Europe during the Neolithic (5). However, the location of its origin is still not certain (6). Removing H4a from the Skyline analysis did not substantively change the timing of Holocene period expansion (results not shown). European haplogroups U5, V, and 3H are associated with an indigenous origin in Europe (2). Haplogroups U5a, U5b1, V, and 3H have all been attributed a TMRCA during the Last Glacial Period (2, 7–9)

Readers more well versed in the literature on mtDNA haplogroups can pick these details apart.

Where does this leave us? If this and other recent papers are correct. then the expansion of farming to Europe from the Middle East resembles the settlement of the New World far more than we may have thought! In some regions there was likely near total replacement of the substrate, perhaps like the United States. In others there was modest uptake of the indigenous substrate, as is the case in Argentina. Finally, there were regions where the indigenous hunter-gatherer substrate may have persisted to a far greater extent. I think this may be the case mostly in Baltic Europe, which combined both the possibility of relatively high hunter-gatherer carrying capacities because of marine resources and a climatic regime rather unsuitable to the initial Middle Eastern crops.

Citation: Gignoux CR, Henn BM, & Mountain JL (2011). Rapid, global demographic expansions after the origins of agriculture. Proceedings of the National Academy of Sciences of the United States of America, 108 (15), 6044-9 PMID: 21444824

(Republished from Discover/GNXP by permission of author or representative)
 
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Image Credit: Mark Dingemanse

I recall years ago someone on the blog of Jonathan Edelstein, a soc.history.what-if alum as well, mentioning offhand that archaeologists had “debunked” the idea of the Bantu demographic expansion. Because, unfortunately, much of archaeology consists of ideologically contingent fashion it was certainly plausible to me that archaeologists had “debunked” the expansion of the Bantu peoples. But how to explain the clear linguistic uniformity of the Bantu dialects, from Xhosa of South Africa, up through Angola and Kenya, to Cameroon? One extreme model could be a sort of rapid cultural diffusion, perhaps mediated by a trivial demographic impact. The spread of English exhibits this hybrid dynamic. In some areas (e.g., Australia) there was a substantial, even dominant, English demographic migration coincident with the rise of Anglo culture. In other areas, such as Jamaica, by and large the crystallization of an Anglophone culture arose atop a different demographic substrate, which synthesized with the Anglo institutions (e.g., English language and Protestant religion). The United States could arguably be held up as a in-between case, with an English founding core population, around which there was an accretion of a non-Anglo-Saxon stream of immigrants who serial adopted the Anglo culture, more or less. Sometimes this co-option of Anglo-Saxon norms may surprise. “Black English” (i.e., Ebonics) actually seems to be a genetic descendant of lower class northern English dialects. Other distinctive components of black American (e.g., “jumping the broom“) culture can also plausibly be derived back to the British Isles.

So cultural change is in the “its complicated” segment of dynamics. We have to go on a case-by-case basis. For the Bantu expansion though we have a good answer now thanks to genetics: this cultural change almost certainly was accompanied by a massive demographic migration. Thanks to Brenna Henn and company you can even run some analyses on your desktop to confirm the reality of this model. I pulled down the 55,000 SNPs from various African populations, merged with Palestinians, Tuscans, and Maya as outgroups, and pruned down to ~40,000 after removing those which were missing in more than 1% of the cases. The Hadza are also gone, as they’re such a small isolated group who always hogged up K’s all by themselves. I ran a bunch of different ADMIXTURES, from K = 2 to 12. You can see all 12 here, but let’s just focus on the 12th.

Below is a bar plot, somewhat sorted by ADMIXTURE elements. I’ve reedited some of the labels for clarity, adding regions. I’m sure some of you are ignorant of where the Brong people (Ghana) are from as I was before I looked them up. Also, please be careful about ADMIXTURE. There is a “Fulani” ancestral component below, but I’m 90% sure that’s just an artifact of recent Fulani demograhics + their unique genetic admixture.


K4, the dark green component, seems associated with Bantus and Bantu neighbors all across Africa. The lack of correspondence to geography is clearly suggestive of demographic leapfrogging. The existence of non-Bantu peoples in the wake of their migration (e.g., the Nilotic peoples in northeast Africa, the Pygmies, and the Sandawe) could be indicative of either ecological constraints on the Bantu toolkit (so the migrants simply moved around the uncongenial zones), or a later intrusion (this is often hypothesized to be what occurred to bring the Masai to Tanzania). There are no Horn of Africa samples here, but I have some 23andMe files, and I can tell you that it seems as Dienekes observed, the Sub-Saharan component among the people of Ethiopia and Somali seems singularly lacking the Bantu element. Why? My own suspicion is that this region had its own agricultural (or pastoralist) way of life which rendered them demographically robust in the face of the Bantu, who simply turned south once they reached a zone of serious cultural resistance.

But there’s more. Of course there are Fst, genetic distances, between these “ancestral” populations. You can find these, along with the frequencies, in an Excel file I uploaded. But let’s look at how the populations related to each other on an MDS plot, which visualizes the pairwise distances on a two dimensional plane. I’ve added labels this time. They should be pretty clear in terms of which K’s they correspond to.

hey

For what it’s worth, the Sandawe are presumed to be the aboriginal people of Tanzania, at least in relation to the dominant Bantu around them.

(Republished from Discover/GNXP by permission of author or representative)
 
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To the left you see a zoom in of a PCA which Dienekes produced for a post, Structure in West Asian Indo-European groups. The focus of the post is the peculiar genetic relationship of Kurds, an Iranian-speaking people, with Iranians proper, as well as Armenians (Indo-European) and Turks (not Indo-European). As you can see in some ways the Kurds seem to be the outgroup population, and the correspondence between linguistic and genetic affinity is difficult to interpret. For those of you interested in historical population genetics this shouldn’t be that surprising. West Asia is characterized by of endogamy, language shift, and a great deal of sub and supra-national communal identity (in fact, national identity is often perceived to be weak here). A paper from the mid-2000s already suggested that western and eastern Iran were genetically very distinctive, perhaps due to the simple fact of geography: central Iran is extremely arid and relatively unpopulated in relation to the peripheries.

But this post isn’t about Kurds, rather, observe the very close relationship between Turks and Armenians on the PCA. The _D denotes Dodecad samples, those which Dienekes himself as collected. This affinity could easily be predicted by the basic parameters of physical geography. Armenians and Anatolian Turks were neighbors for nearly 1,000 years. Below is a map which shows the expanse of the ancient kingdom of Armenia:

Historic Armenia was centered around lake Van in what is today eastern Turkey. The modern Republic of Armenia is very much a rump, and an artifact of the historic expansion of the Russian Empire in the Caucasus at the expense of the Ottomans and Persians. Were it not for the Armenian genocide there may today have been more Armenians resident in Turkey than in the modern nation-state of Armenia,* just as there are more Azeri Turks in Iran than in Azerbaijan. Many areas once occupied by Armenians are now occupied by Kurds and Turks. But a bigger question is the ethnogenesis of the Anatolian Turkish population over the past 1,000 years.

Dienekes has already shed light on this topic earlier, adding the Greek and Cypriot populations to the mix as well as Turks and Armenians. The disjunction between Kurds and the Armenian-Turk clade suggests to us that Turks did not emerge out of the milieu of Iranian tribes in the uplands of southeast Anatolia and western Persia. Like the Armenians the Kurds are an antique population, claiming descent from the Medes, and referred to as Isaurians during the Roman and Byzantine period.

Below is a reformatted K = 15 run of ADMIXTURE with Eurasian population. I’ve removed the labels for the ancestral components, but included in populations which have a high fraction of a given ancestral component. The geographical labels are for obscure populations. I’ve underlined the four populations of interest:

First, let’s get out of the way the fact that Turkish samples have non-trivial, though minor, northeast Asian ancestry. The Yakut themselves are a Turkic group situated to the north of Mongolia. The more southerly and central Asian affinities the nomadic ancestors of the Anatolia Turks may have picked up in their sojourns over the centuries between their original homeland in east-central Siberia and Mongolia and West Asia. The rest of ancestry is rather typical of northern West Asian groups. In particular, Armenians! Here is the ancestral breakdown for the four groups I want to focus on using Dienekes’ labels:


Population Greek Cypriots Turks Armenians
West Asian 37.6 54.1 47.2 56.3
Central-South Asian 5.3 8.6 18.2 18.4
North European 25.1 5.6 12 12.3
South European 27.4 20.8 9.4 8.4
Arabian 3.4 8 4.3 3.4
Altaic 0.3 0 2.6 0.1
East Asian 0.3 0.2 2.2 0
Central Siberian 0.1 0.2 1.4 0.2
Chukchi 0 0 1.1 0.2
South Indian 0 0.1 0.8 0.3
Nganasan 0.1 0 0.4 0.2
Koryak 0.1 0 0.2 0.1
East African 0 0.4 0.1 0
West African 0 0 0.1 0
Northwest African 0.3 1.9 0.1 0

And now the correlations between the populations by ancestral components:


Greek Cypriots Turks Armenians
Greek * 0.863 0.823 0.813
Cypriots * * 0.941 0.946
Turks * * * 0.997
Armenians * * * *

Let’s remove the East Eurasian and African components, and recalculate the proportions by taking what remains as the denominator:


Population Greek Cypriots Turks Armenians
West Asian 38.1 55.7 51.8 57.0
Central-South Asian 5.4 8.9 20.0 18.6
North European 25.4 5.8 13.2 12.4
South European 27.7 21.4 10.3 8.5
Arabian 3.4 8.2 4.7 3.4

And the recomputed correlations:


Greek Cypriots Turks Armenians
Greek * 0.747 0.640 0.647
Cypriots * * 0.901 0.908
Turks * * * 0.999
Armenians * * * *

With all the ~0 ancestral components which were common across these four populations removed the correlations have gone down. Except in the case of the Armenian-Turk pair, because I’ve removed the ancestries which differentiate them.

So what’s a plausible interpretation? A straightforward one would be that the Muslim Turk population of Anatolia has a strong bias toward having been assimilated Armenians, rather than Greeks. The cultural plasticity of Armenians in late antiquity and the early medieval period was clear: individuals of ethnic Armenian to origin rose the pinnacles of the status hierarchy of the Orthodox Christian Greek Byzantine Empire. The Macedonian dynasty of the Byzantines under which the civilization reached its mature peak were descended from Armenians who had resettled in Macedonia. Just as plausible to me is that eastern Anatolia as a whole exhibited little genetic difference between Greeks and Armenians, and the former were wholly assimilated or migrated, while the Armenians remained. One way to test this thesis would be type the descendants of Greeks who left eastern Anatolia during the population exchange between Greece and Turkey in the 1920s. But the difference between Greeks and Cypriots also points us to another possibility: perhaps the Greeks of Greece proper (as opposed to Anatolia) were much more strongly impacted by the arrival of Slavs? One need not necessarily rely solely on the Scalveni migrations either, water tends to be a major dampener to conventional isolation-by-distance gene flow, so the Greek mainland may always have been subject to more influence from the lands to the north.

Whatever the details of ethnogenesis may be, it will be interesting to see how things shake out as we increase sample sizes and get better population coverage. These results may be due to regional selection bias. One might expect that the descendants of Rumelian Turks be more “European” than Anatolian Turks. But, these data do seem to suggest on face value that Armenians are the population which Anatolian Turks have the most genetic affinity with.

* My main hesitation would be that Armenians are a very mobile population, and their numbers within a modern Turkey may have declined simply through emigration, just as those of Christian Arabs have over the 20th century.

(Republished from Discover/GNXP by permission of author or representative)
 
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School girls in Hunza, Pakistan

A few days ago I observed that pseudonymous blogger Dienekes Pontikos seemed intent on throwing as much data and interpretation into the public domain via his Dodecad Ancestry Project as possible. What are the long term implications of this? I know that Dienekes has been cited in the academic literature, but it seems more plausible that this sort of project will simply distort the nature of academic investigation. Distort has negative connotations, but it need not be deleterious at all. Academic institutions have legal constraints on what data they can use and how they can use it (see why Genomes Unzipped started). Not so with Dienekes’ project. He began soliciting for data ~2 months ago, and Dodecad has already yielded a rich set of results (granted, it would not be possible without academically funded public domain software, such as ADMIXTURE). Even if researchers don’t cite his results (and no doubt some will), he’s reshaping the broader framework. In other words, he’s implicitly updating everyone’s priors. Sometimes it isn’t even a matter of new information, as much as putting a spotlight on information which was already there. Below is a slice of a bar plot from Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation. It uses STRUCTURE with K = 7. To the right of the STRUCTURE slice are two plots of individual data on French and French Basque from the same HGDP data set using ADMIXTURE at K = 10 from Dodecad.

fbasq


Repeated runs and higher K’s make it clear that the French Basque lack a “West Asian” aspect which other French, and Iberians as well, have. Some of this is clear in the paper I referenced above as well…the key is you have to look at the supplements at K = 6. Because the Basque are the only native non-Indo-European speakers in Western Europe, their origin and relationship to nearby populations has always been of interest (they also have the highest Rh- frequency of world populations). Granted, the French Basque are very similar genetically to the French as a whole. But, it is obviously highly informative that they lack an ancestral component in totality which seems to exist at low but consistent levels across Western European populations. The only other European population at K = 15 who lack the West Asian component in totality are Finns (the Lithuanians come very close).

This is all preamble to a discussion of a post Dienekes put up today, A solution to the problem of Indo-Aryan origins. Remember that Dienekes has been “playing” with ADMIXTURE for only a few months. To claim to have found a ‘solution’ to a problem as intellectually and politically intractable and explosive as this is rather bold. The crux of the matter is that at a certain confluences of K’s and population sets Dienekes has discovered a distinctive signature of ancestry which seems to be modal on the north slope of the Caucasus, and spans India and Europe. He terms this “Dagestani,” due to the fact that among a population sample from this province in Russia this ancestral component is overwhelmingly dominant. The patterns of Dagestani admixture in Europe and India are curious and suggestive.

1 – In Europe the frequencies are low, but irregularly distributed (excepting around the North Caucasus). Scandinavians and British have appreciable fractions, Finns and Southern Europeans do not. Here’s Dienekes:

Interpreting this pattern is not easy, but it does seem that this component seems to have a V-like distribution, achieving its maximum in Caucasus and its environs, then undergoing a diminution, and achieving a secondary (lower) frequency mode in NW Europe.

The surprising appearance of the homonymous Dagestan component in India suggests a widespread presence of a common ancestry element. The West Asian element, by comparison seems to have a more normal /-like distribution around its center in Anatolia-Caucasus-Iran region. It does reach the Atlantic coast, but is lacking in Scandinavia and Finland, and also in India itself.

2 – South Indian Brahmins have appreciable fractions, but non-Brahmins in the same region do not. In contrast, those who come from Indo-Aryan speaking backgrounds do seem to have Dagestani ancestral components, irrespective of other aspects of ancestry. For example Pakistanis don’t have that much more Dagestani than South Indian Brahmins or Gujaratis. Also compare the relatively narrow window of Dagestani ancestry variance among Dodecad South Asians (I’m DOD075). DOD088 is from what I recall a Reddy from Andhara Pradesh, a non-Brahmin but non-low caste. It is interesting that they have a high proportion of “Pakistan,” but no Dagestani. I have ~10% Dagestani, but no Pakistani.

Below is K = 10 for a selection of populations. Dienekes has now included in two non-Indo-European speaking Pakistani populations: the Brahui (Dravidian) and Burusho (linguistic isolate in the mountains of Pakistan):
dages

Some general patterns are evident. The light blue is indicative of generic “Indian” ancestry. It is not found in appreciable proportions outside of subcontinental populations (or those of recent subcontinental origin). The same with the red, and light orange. For your reference the dark orange is a “Northern European” component, modal in Lithuania. The light and dark Green are both East Asian components. The dark blue is a “West Asian” component modal in Georgia, and prominent across Europe with declining as a function of distance from the eastern shore of the Black Sea (this is surely the West Asian which distinguishes the French from the French Basque). I believe that the light purple dominant in the Brahui and the light red dominant in the Burusho probably form as a compound the aforementioned Pakistani component. The dark purple is the Dagestani.

587px-Dravidische_SprachenFirst, a word on the Brahui. These are a group of tribes who reside in northern Balochistan in Pakistan. A small number are even to be found in Afghanistan. Historically they have had close relations with the Baloch, an Iranian speaking cluster of tribes who totally envelop the Brahui. The Brahui do speak a Dravidian language, of a family dominant in South India and found in isolated regions of Central and Eastern India. There are two broad models for the existence of a Dravidian language in Pakistan. The first is that the Brahui are remnants of more widely spoken Dravidian languages which date back to the Indus Valley civilization. The second is that the Brahui arrived during the medieval period from another region of South Asia where Dravidian languages were more common. Assuming either model, it has long been presumed that their involution by the Baloch has had a strong impact on the Brahui genetically; the two groups are very close. This is evident in Dienekes’ results as well. But observe that the Baloch are the group which seems more cosmopolitan in ancestry than the Brahui. If the Brahui were Dravidians from deep in India it seems that they would have a greater residual component of India-specific ancestry (light blue and orange). This is not so. In fact the Baloch have more of the Indian ancestral component than the Brahui. The Brahui component is found across Pakistan, and into India, albeit at lower proportions. Naturally, the Baloch have the second highest fraction. I believe these results should shift us toward the position that the Brahui are indigenous in relation to the Baloch, and that the Baloch ethnic identity emerged through the shift of a Brahui substrate, as evidenced by the greater cosmpolitanism of the Baloch. Additionally, Dienekes observes that the Brahui have a lower proportion of the Dagestani component than most other Pakistani groups, and several Indo-Aryan groups in India proper.

The Burusho are event more interesting than the Brahui. Unlike the Brahui the Burusho are very isolated in the mountainous fastness of Baltistan in northern Pakistan. Additionally, their language, Burushashki, is a linguistic isolate. Others of the class are Basque and Sumerian. In general it is assumed that linguistic isolates were once part of broader families of languages which have gone extinct. Burushashki probably persists in large part because of the geography which its speakers inhabit. Mountainous areas often preserve ethnic and linguistic diversity because the terrain allows for the persistence of local variety. I believe it is plausible that the Burusho have been far more isolated than the Brahui. This seems to show up in the ADMIXTURE plot, the Burusho have a greater proportion of their modal ancestral component than the Brahui. Additionally, the Burusho have even an smaller component of Dagestani than the Brahui.

Below is a chart Dienekes constructed ordered by proportion of Dagestani for his South Asian populations. Next to it I’ve placed a chart from a PCA which has some of the same population samples. Compare & contrast:

pcadag

The PCA is looking at between population variation in totality. So naturally the Dagestani component isn’t going to be predictive of that. Rather, it speaks to the possibility which Dienekes is mooting: that the Dagestani component spread in the India subcontinent with the Indo-Aryans specifically, overlying the local resident substrate. In South India this meant that Brahmins brought this, mixing with the indigenous Dravidian population. In Pakistan the Indo-Aryan, and Iranians, were overlain on a substrate which were the ancestors of the Burusho and Brahui. The dominant signal of genetic relationship has to do with the substrate, not the Indo-Aryans. So that’s what’s going to show up on the PCA. In other PCA plots the model where South Indian Brahmins are a linear combination of a Pakistani-like population and a Dravidian population becomes clearer. But when you look at ancestry using something like ADMIXTURE you have the potential to tease apart different components, and so uncover relationships which may have been obscured when looking at aggregate variation.

dieDienekes’ model seems to post three steps in rapid succession ~4,000 years ago. A background variable which must be mentioned is that one must account for the Mitanni, a dominant Syrian power circa 1500 BC where a non-Indo-European language was the lingua franca, and yet a definite Indo-Aryan element existed within the elite. Indo-Aryan specifically because the Indo-European element within the Mitanni was not Iranian, but specifically Indo-Aryan. An easy explanation for this is that the Indo-Aryan component of the Indo-Iranian branch of the Indo-European languages crystallized outside South Asia, and independently reached Syria and India. In Syria it went extinct, while in India it obviously did not. By Dienekes’ model the Mitanni would be rather closer to the urheimat of the Indo-Aryans.

An aspect of his model which I do not understand is why it has to be Indo-Aryan, instead of Indo-Iranian. The South Asian population which the Dagestani component is modal, the Pathans, are Iranian, not Indo-Aryan. Additionally, this model seems to not speak in detail to the existence of the Dagestani element among Europeans. Here is a sorting of European populations (with Iranians included) by the Dagestani component:


Population Dagestan
Urkarah 93
Lezgins 47.9
Stalskoe 38.7
Adygei 16.4
Orcadian (Orkney) 12.6
Georgians 12.4
White_Utahns 11.2
Iranian 10.9
Scandinavian_D 10.2
Armenian_D 9.9
German_D 9.1
Turks 8.8
Armenians 8.4
French 7.9
Hungarians 7.5
Russian_D 6.3
Spanish_D 4.6
North_Italian 4.5
Spaniards 4.4
Romanian 4.1
Finnish_D 4.1
Russian 4
Greek_D 3.8
Portuguese_D 3.6
Tuscan 3.5
Tuscans 3.4
Lithuanians 2.9
S_Italian_Sicilian_D 2.8
Belorussian 2.5
Cypriots 2
Sardinian 1.5
French_Basque 0.7

There is here a strange pattern of rapid drop off from the Caucasus, and a bounce back very far away, on the margins of Germanic Northwestern Europe. This to me indicates some sort of leapfrog dynamic. A well known illustration of this would be the Ugric languages. The existence of Hungarian on what was Roman Pannonia is a function of the mobility and power of Magyar horseman, and their cultural domination over the Romance and Slavic speaking peasantry (their genetic impact seems to have been slight). No one believes that Germanic languages are closely related to Indo-Aryan (rather, if there is structure in Indo-European beyond Indo-Iranian, Celtic, etc., it would place the Indo-Iranian languages with Slavic). So what’s going on? I think perhaps the Dagestani component is part a reflection of the common Indo-European origin in that region. For whatever reason that signal is diminished in much of the rest of Europe. Perhaps Southern Europe was much more densely populated when the Indo-Europeans arrived. Additionally, it seems highly likely that in places like Sardinia, much of Spain, and Cyprus, Indo-European speech came through cultural diffusion (elite emulation) and not population movement. Or perhaps we’re seeing the vague shadows of population admixtures on the Pontic steppe, where distinct Germanic and Indo-Iranian confederations admixed with a common North Caucasian substrate.

Going back to India, let’s revisit the model of a two-way admixture between “Ancestral North Indians,” who were genetically similar to Europeans and West Asians, and “Ancestral South Indians,” who were closer to, but not very close to, East Eurasians. The ANI & ASI. The ASI were probably one of the ancient populations along the fringe of southern Eurasia, all of whom have been submerged by demographic movements from other parts of Eurasia over the past 10,000 years, excepting a few groups such as the Andaman Islanders and some Southeast Asian tribes. The model was admittedly a simplification. But taking that model as a given, and accepting that the Dagestani element is in indeed Indo-Aryan, we can infer that the ANI were not Indo-European. It is notable that the South Indian Brahmins have elevated fractions of both the Brahui and Burusho modal components. This is probably indicative of admixture of the Indo-Aryan element in the Indus Valley, prior to their expansion to other parts of India. I assume one of the languages spoken was Dravidian, though if ancient Mesopotamia was linguistically polyglot at the dawn of history I would not be surprised if the much more geographically Indus Valley civilization was as well.

arai
Aishwarya Rai

The irony is that today when someone refers to a “Dravidian” physical type, they’re not talking about someone who looks like a Pakistani. They’re talking about someone who looks South Indian, where most Dravidian languages are spoken. But combining the inference from Dienekes’ model and the previous two-way admixture model, you reach the conclusion that lighter skin and more West Asian features among South Asians may be more due to Dravidian-speaking ancestors in the Indus Valley, not Indo-Aryans! It goes to show the wisdom of differentiating linguistic classes from biological ones when discussing historical population genetics. Unfortunately wisdom most of us interested in these topics do not show, alas.

As I like to say, interesting times….

Note: If you leave a comment, please don’t be smarter-than-thou in your tone. I have stopped publishing those sorts of comments because the reality is that most of them have not been that smart or informed. At least by my estimation. If you actually are smarter than the average-bear, and impress me with your erudition and analysis clarity, I’ll probably let your comment through no matter your attitude. But I wouldn’t bet on it if I were you, so show some class and humility. Most of us are muddling through.

Image Credit: Georges Biard, iStockPhoto

(Republished from Discover/GNXP by permission of author or representative)
 
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Ainu in 19th century Hokkaido, and rice paddies


Unlike some islands Japan has a long history of human habitation. More interestingly, under the Jomon culture the Japanese archipelago was home to one of the earliest, if not the earliest, societies which used pottery. The Jomon do not seem to have been intensive agriculturalists. Rather, with a widespread marine littoral they likely maintained extremely high population densities, and at least semi-sedentary habitation patterns, simply through a hunting & gathering mode of production. Pacific Northwest Amerindians are likely a good analogy. They also relied on a dense stock of marine life to maintain population densities of a high level and a sedentary lifestyle.

About 2,000 years ago the Yayoi people arrived in Japan. The first Yayoi settlements are in northern Kyushu. These people brought intensive agriculture, in particular rice agriculture, to the Japanese archipelago. The general assumption is that the Yayoi are the precursors of the Japanese who entered into the international system of East Asia during the Tang dynasty in the second half of the first millennium. The Ainu of Hokkaido are presumed to be the descendants of the remaining Jomon people, maintaining a hold in the northern island because of its ecological unsuitability to Japanese agriculture.

The question is: what proportion of the ancestry of modern Japanese is Jomon/Ainu, and what proportion is Yayoi? The dynamics here are nicely constrained by the fact that Japan is a relatively isolated island system. The Yayoi seem to have arrived at one discrete moment in history, and rapidly expanded in ~1,000 years to all the main islands of Japan, though the full settlement of Hokkaido commenced in the 19th century. Interestingly, parts of northern Honshu seem to have had a distinct post-Jomon culture down to ~1000 AD.

Conveniently the HapMap has both Japanese and Chinese samples, but often there hasn’t been too much focus on the differences between these two groups because they’re very close in a global context when compared to the Yoruba or Europeans. In more recent analyses of East Asian groups the coverage seems to be better with various Chinese ethnic groups, but relatively few samples from Siberian populations. The latter are critical because the supposition is that these are the groups which would have the most affinities with the Jomon, due to the culture and contacts of the Ainu which evident during the modern period.

Dienekes most recent post on K = 15 ancestral components in ADMIXTURE clarifies some issues in this regard. There are multiple Han Chinese and Japanese samples, as well as a wide range of East Asian and Siberian groups. I’ve reedited and formatted K = 15 a bit, with the aim of focusing on the relationships of the Japanese in particular.


japan

First, it is reasonable that the Denver and Singapore Chinese sample would have a greater proportion of the orange “Southeast Asian” component, Han in the United States are mostly from southern regions of China. Notice that the Japanese don’t have this component at all. The Japanese have more of the light gray component, which is modal among the Nganassan of the Arctic coast of Central Siberia. Unlike the Chinese the Japanese also have the blue component which is modal in Eastern Siberia, and also found in many North American groups (many omitted). Finally, it is interesting that the Japanese have the light yellow component in both of the samples Dienekes ran through ADMIXTURE. Going through his spread sheet, here’s are some of the populations sorted by this component (number 13):


Population 13
Melanesian 99.99
Paniya (South Indian tribe) 6.18
Malayan 2.85
North Kannada 1.44
Malay, Singapore 1.34
Sakilli (South Indian) 1.02
Japanese 0.71
Japanese #2 0.7
Papuan 0.56
Cambodians 0.53
Ethiopians 0.51
Yizu 0.48
Ket 0.41
Uygur 0.39
Yakut 0.08
Chinese, Beijing 0.06
Chinese, Singapore 0.03
Chukchi 0.03

This is basically Melanesian. Strangely, though at low proportions, the Japanese have much more of this than mainland Chinese, or most East Asians period. They’re in the same range as Cambodians, and topped only by maritime Southeast Asians and Indians. I find this interesting because Japanese Y chromosomes are often of haplogroup D, also common among the Ainu. This lineage spans various isolated regions of eastern Eurasia, such as the Andaman Islands. The implication is that D is a relict of a large set of populations which have slowly been absorbed by expansions of other groups. Additionally, some physical anthropologists have observed similarities in the morphology of the remains of the Jomon people and Australian Aborigines. I am inclined to chalk that up to the general robustness of non-farming populations, but it is something to consider.

But my primary point about writing this post was to offer some judgment as to the provenance of the modern Japanese. I think that looking at these results, and also keeping in mind other results on East Asian genetics, I’m of the mind that Japan looks to be a classic case where farmers totally marginalized hunter-gatherers. In other words, the modern Japanese are predominantly descendants of farmers from the Korean peninsula who arrived ~2,000 years ago. The alternative is that the Jomon were more similar to mainland East Asians in Korea and China than they were to Siberian peoples, which seems unlikely if the Ainu give us any clue as to the culture of the Jomon. This seems more implausible in light of the fact that the Japanese do seem to have some affinities to Siberian people, to a greater extent than the northern Chinese of Beijing (Beijing is a large city, so likely this sample has people who are descendants of ‘reverse colonists’ from the South as well).

If this inference is correct then it is an amazing instance of demographic expansion and replacement. In much of the civilized world intensive farmers replaced extensive farmers in fertile regions in prehistoric times. Or at least during periods when textual evidence is thin on the ground. In contrast, in Japan the process persisted right up until the margins of written history. Additionally, we can peg the arrival of the Yayoi culture very well chronologically because of the discontinuity. Assuming 25 years per generation, in 40 generations the Yayoi had totally extirpated the post-Jomon cultures across all of the Japanese islands except Hokkaido. And, it is notable that the Jomon are generally judged to have been a relatively numerous for hunter-gatherers. Their longevity in Japan as a continuous culture also attests to their success. This narrow specific case may have larger implications for the demographic-genetic patterns we see in the rest of the world.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Ainu, Archaeogenetics, Genetics, Genomics, Japan, Jomon 
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I decided to take the Dodecad ADMIXTURE results at K = 10, and redo some of the bar plots, as well as some scatter plots relating the different ancestral components by population. Don’t try to pick out fine-grained details, see what jumps out in a gestalt fashion. I removed most of the non-European populations to focus on Western Europeans, with a few outgroups for reference.

Here’s a table of the correlations (I bolded the ones I thought were interesting):

W Asian NW African S Europe NE Asian SW Asian E Asian N European W African E African S Asian
W Asian * -0.01 -0.18 0.04 0.81 0.59 -0.64 0.39 0.2 0.04
NW African * * 0.19 -0.16 0.23 -0.09 -0.19 0.26 0.67 -0.11
S European * * * -0.38 -0.03 -0.27 -0.42 -0.11 -0.02 -0.36
NE Asian * * * * -0.06 0.5 0.26 -0.04 -0.1 -0.07
SW Asian * * * * * 0.21 -0.62 0.74 0.59 -0.13
E Asian * * * * * * -0.27 0.08 0 0.14
N European * * * * * * * -0.34 -0.28 -0.31
W African * * * * * * * * 0.86 -0.04
E African * * * * * * * * * -0.07
dodenorthdodsouthdodswasiandodwestscatternorthwestscattersouthnorthscattersouthwestscatterwestasiansouthwest

(Republished from Discover/GNXP by permission of author or representative)
 
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pc1
Synthetic map

In the age of 500,000 SNP studies of genetic variation across dozens of populations obviously we’re a bit beyond lists of ABO blood frequencies. There’s no real way that a conventional human is going to be able to discern patterns of correlated allele frequency variations which point to between population genetic differences on this scale of marker density. So you rely on techniques which extract the general patterns out of the data, and present them to you in a human-comprehensible format. But, there’s an unfortunate tendency for humans to imbue the products of technique with a particular authority which they always should not have.

ResearchBlogging.org The History and Geography of Human Genes is arguably the most important historical genetics work of the past generation. It has surely influenced many within the field of genetics, and because of its voluminous elegant visual displays of genetic data it is also a primary source for those outside of genetics to make sense of phylogenetic relations between human populations. And yet one aspect of this great work which never caught on was the utilization of “synthetic maps” to visualize components of genetic variation between populations. This may have been fortuitous, a few years ago a paper was published, Interpreting principal components analyses of spatial population genetic variation, which suggested that the gradients you see on the map above may be artifacts:

Nearly 30 years ago, Cavalli-Sforza et al. pioneered the use of principal component analysis (PCA) in population genetics and used PCA to produce maps summarizing human genetic variation across continental regions. They interpreted gradient and wave patterns in these maps as signatures of specific migration events. These interpretations have been controversial, but influential, and the use of PCA has become widespread in analysis of population genetics data. However, the behavior of PCA for genetic data showing continuous spatial variation, such as might exist within human continental groups, has been less well characterized. Here, we find that gradients and waves observed in Cavalli-Sforza et al.’s maps resemble sinusoidal mathematical artifacts that arise generally when PCA is applied to spatial data, implying that the patterns do not necessarily reflect specific migration events. Our findings aid interpretation of PCA results and suggest how PCA can help correct for continuous population structure in association studies.

A paper earlier this year took the earlier work further and used a series of simulations to show how the nature of the gradients varied. In light of recent preoccupations the results are of interest. Principal Component Analysis under Population Genetic Models of Range Expansion and Admixture:

In a series of highly influential publications, Cavalli-Sforza and colleagues used principal component (PC) analysis to produce maps depicting how human genetic diversity varies across geographic space. Within Europe, the first axis of variation (PC1) was interpreted as evidence for the demic diffusion model of agriculture, in which farmers expanded from the Near East ∼10,000 years ago and replaced the resident hunter-gatherer populations with little or no interbreeding. These interpretations of the PC maps have been recently questioned as the original results can be reproduced under models of spatially covarying allele frequencies without any expansion. Here, we study PC maps for data simulated under models of range expansion and admixture. Our simulations include a spatially realistic model of Neolithic farmer expansion and assume various levels of interbreeding between farmer and resident hunter-gatherer populations. An important result is that under a broad range of conditions, the gradients in PC1 maps are oriented along a direction perpendicular to the axis of the expansion, rather than along the same axis as the expansion. We propose that this surprising pattern is an outcome of the “allele surfing” phenomenon, which creates sectors of high allele-frequency differentiation that align perpendicular to the direction of the expansion.

The first figure shows the general framework with which they performed the simulations:

pcab1

You have a lattice which consists of demes, population units, all across Europe. They modulated parameters such as population growth (r), carrying capacity (C), and migration (m). Additionally, they had various scenarios of expansion from the southwest or southeast, as well as two expansions one after another to mimic the re-population of Europe after the Ice Age by Paleolithic groups, and their later replacement by Neolithic groups. They modulated admixture and introgression of genes from the Paleolithic group to the Neolithics so that you had the full range where the final European were mostly Neolithic or mostly Paleolithic.

Below are some of the figures which show the results:

[nggallery id=25]

allesurAs you can see the strange thing is that in some models the synthetic map gradient is rotated 90 degrees from the axis of demographic expansion! In this telling the famous synthetic map showing Neolithic expansion might be showing expansion from Iberia. Perhaps a radiation from a post-Ice Age southern refuge?

One explanation might be “allele surfing” on the demographic “wave of advance.” Basically as a population expands very rapidly stochastic forces such as random genetic drift and bottlenecks could produce diversification along the edge of the population wave front. The reason for this is that these rapidly expanding populations explode out of serial bottlenecks and demographic expansions, which will produce genetic distinctiveness among the many differentiated demes bubbling along the edge of expansion. Alleles which may have been at low frequency in the ancestral population can “fix” in descendant populations on the edge of the demographic wave of advance. This is the explanation, more or less, that one group gave last year for the very high frequencies of R1b1b2 in Western Europe. With this, they overturned the classic assumption that R1b1b2 was a Paleolithic marker, and suggested it was a Neolithic one.

Here’s their conclusion from the paper:

A previous study showed that the original patterns observed in PCA might not reflect any expansion events (Novembre and Stephens 2008). Here, we find that under very general conditions, the pattern of molecular diversity produced by an expansion may be different than what was expected in the literature. In particular, we find conditions where an expansion of Neolithic farmers from the southeast produces a greatest axis of differentiation running from the southwest to the northeast. This surprising result is seemingly due to allele surfing leading to sectors that create differentiation perpendicular to the expansion axis. Although a lot of our results can be explained by the surfing phenomenon, some interesting questions remain open. For example, the phase transition observed for relatively small admixture rates between Paleolithic resident and Neolithic migrant populations occurs at a value that is dependent on our simulation settings, and further investigations would be needed to better characterize this critical value as a function of all the model parameters. Another unsolved question is to know why the patterns generally observed in PC2 maps for our simulation settings sometimes arise in PC1 maps instead. These unexplained examples remind us that PCA is summarizing patterns of variation in the sample due to multiple factors (ancestral expansions and admixture, ongoing limited migration, habitat boundary effects, and the spatial distribution of samples). In complex models such as our expansion models with admixture in Europe, it may be difficult to tease apart what processes give rise to any particular PCA pattern. Our study emphasizes that PC (and AM) should be viewed as tools for exploring the data but that the reverse process of interpreting PC and AM maps in terms of past routes of migration remains a complicated exercise. Additional analyses—with more explicit demographic models—are more than ever essential to discriminate between multiple explanations available for the patterns observed in PC and AM maps. We speculate that methods exploiting the signature of alleles that have undergone surfing may be a powerful approach to study range expansions.

What’s the big picture here? In the textbook Human Evolutionary Genetics it is asserted that synthetic maps never became very popular compared to PCA itself. I think this is correct. But, the original synthetic maps have become prominent for many outside of genetics. They figure in Peter Bellwood’s First Farmers, and are taken as a given by many pre-historians, such as Colin Renfrew. And yet a reliance on these sorts of tools must not be blind to the reality that the more layers of abstraction you put between your perception and comprehension of concrete reality, the more likely you are to be led astray by quirks and biases of method.

In this case I do think first-order intuition would tell us that synthetic maps which display PCs would be showing gradients as a function of demographic pulses. And yet the intuition may not be right, and with the overturning of old orthodoxies in the past generation of inferences from the variation patterns in modern populations, we should be very cautious.

Citation: Olivier François, Mathias Currat, Nicolas Ray, Eunjung Han, Laurent Excoffier, & John Novembre (2010). Principal Component Analysis under Population Genetic
Models of Range Expansion and Admixture Mol Biol Evol

(Republished from Discover/GNXP by permission of author or representative)
 
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After linking to Marnie Dunsmore’s blog on the Neolithic expansion, and reading Peter Bellwood’s First Farmers, I’ve been thinking a bit on how we might integrate some models of the rise and spread of agriculture with the new genomic findings. Bellwood’s thesis basically seems to be that the contemporary world pattern of expansive macro-language families (e.g., Indo-European, Sino-Tibetan, Afro-Asiatic, etc.) are shadows of the rapid demographic expansions in prehistory of farmers. In particular, hoe-farmers rapidly pushing into virgin lands. First Farmers was published in 2005, and so it had access mostly to mtDNA and Y chromosomal studies. Today we have a richer data set, from hundreds of thousands of markers per person, to mtDNA and Y chromosomal results from ancient DNA. I would argue that the new findings tend to reinforce the plausibility of Bellwood’s thesis somewhat.

The primary datum I want to enter into the record in this post, which was news to me, is this: the island of Cyprus seems to have been first settled (at least in anything but trivial numbers) by Neolithic populations from mainland Southwest Asia.* In fact, the first farmers in Cyprus perfectly replicated the physical culture of the nearby mainland in toto. This implies that the genetic heritage of modern Cypriots is probably attributable in the whole to expansions of farmers from Southwest Asia. With this in mind let’s look at Dienekes’ Dodecad results at K = 10 for Eurasian populations (I’ve reedited a bit):


neolith

Modern Cypriots exhibit genetic signatures which shake out into three putative ancestral groups. West Asian, which is modal in the Caucasus region. South European, modal in Sardinia. And Southwest Asian, which is modal in the Arabian peninsula. Cypriots basically look like Syrians, but with less Southwest Asian, more balance between West Asian and South European, and far less of the minor components of ancestry.

Just because an island was settled by one group of farmers, it does not mean that subsequent invasions or migrations could not have an impact. The indigenous tribes of Taiwan seem to be the original agriculturalists of that island, and after their settlement there were thousands of years of gradual and continuous cultural change in situ. But within the last 300 years settlers from Fujian on the Chinese mainland have demographically overwhelmed the native Taiwanese peoples.

During the Bronze Age it seems Cyprus was part of the Near East political and cultural system. The notional kings of Cyprus had close diplomatic relations with the pharaohs of Egypt. But between the end of the Bronze Age and the Classical Age Cyprus became part of the Greek cultural zone. Despite centuries of Latin and Ottoman rule, it has remained so, albeit with a prominent Turkish minority.

One thing notable about Cyprus, and which distinguishes it from mainland Greece, is the near total absence of a Northern European ancestral component. Therefore we can make the banal inference that Northern Europeans were not initially associated with the demographic expansions of farmers from the Middle East. Rather, I want to focus on the West Asian and Southern European ancestral components. One model for the re-population of Europe after the last Ice Age is that hunter-gatherers expanded from the peninsular “refugia” of Iberia and Italy, later being overlain by expansions of farmers from the Middle East, and perhaps Indo-Europeans from the Pontic steppe. I have a sneaking suspicion though that what we’re seeing among Mediterranean populations are several waves of expansion out of the Near East. I now would offer the tentative hypothesis that the South European ancestral element at K = 10 is a signature of the first wave of farmers which issued out of the Near East. The West Asians were a subsequent wave. I assume that the two groups must correlate to some sort of cultural or technological shift, though I have no hypothesis as to that.

From the above assertions, it is clear that I believe modern Sardinians are descendants of that first wave of farmers, unaffected by later demographic perturbations. I believe that Basques then are a people who emerge from an amalgamation of the same wave of seafaring agriculturalists with the indigenous populations preceding them (the indigenes were likely the descendants of a broad group of northern Eurasians who expanded after the end of the last Ice Age from the aforementioned refugia). They leap-frogged across fertile regions of the Mediterranean and pushed up valleys of southern France, and out of the Straits of Gibraltar. Interestingly, the Basque lack the West Asian minority element evident in Dienekes’ Spaniards, Portuguese, as well as the HGDP French (even up to K = 15 they don’t shake out as anything but a two way admixture, while the Sardinians show a minor West Asian component). Also, the West Asian and Southern European elements are several times more well represented proportionally among Scandinavians than Finns. The Southern European element is not found among the Uyghur, though the Northern European and West Asian one is. I infer from all these patterns that the Southern European element derived from pre-Indo-European farmers who pushed west from the Near East. It is the second largest component across much of the Northwestern Europe, the largest across much of Southern European, including Greece.

A second issue which First Farmers clarified are differences between the spread of agriculture from the Near East to Europe and South Asia. It seems that the spread of agriculture across South Asia was more gradual, or least had a longer pause, than in Europe. A clear West Asian transplanted culture arrived in what is today Pakistan ~9,000 years ago. But it does not seem that the Neolithic arrived to the far south of India until ~4,000 years ago. I think that a period of “incubation” in the northwest part of the subcontinent explains the putative hybridization between “Ancient North Indians” and “Ancient South Indians” described in Reconstructing Indian population history. The high proportion of “Ancestral North Indian,” on the order of ~40%, as well as Y chromosomal markers such as R1a1a, among South Indian tribal populations, is a function of the fact that these groups are themselves secondary amalgamations between shifting cultivators expanding from the Northwest along with local resident hunter-gatherer groups which were related to the ASI which the original West Asian agriculturalists encountered and assimilated in ancient Pakistan (Pathans are ~25% ASI). I believe that the Dravidian languages arrived from the Northwest to the south of India only within the last 4-5,000 with the farmers (some of whom may have reverted to facultative hunter-gathering, as is common among tribals). This relatively late arrival of Dravidian speaking groups explains why Sri Lanka has an Indo-European presence to my mind; the island was probably only lightly settled by farming Dravidian speakers, if at all, allowing Indo-European speakers from Gujarat and Sindh to leap-frog and quickly replace the native Veddas, who were hunter-gatherers.

Note: Here is K = 15.

* Wikipedia says there were hunter-gatherers, but even here the numbers were likely very small.

(Republished from Discover/GNXP by permission of author or representative)
 
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A new paper in The New Journal of Physics shows that a relatively simple mathematical model can explain the rate of expansion of agriculture across Europe, Anisotropic dispersion, space competition and the slowdown of the Neolithic transition:

The front speed of the Neolithic (farmer) spread in Europe decreased as it reached Northern latitudes, where the Mesolithic (hunter-gatherer) population density was higher. Here, we describe a reaction–diffusion model with (i) an anisotropic dispersion kernel depending on the Mesolithic population density gradient and (ii) a modified population growth equation. Both effects are related to the space available for the Neolithic population. The model is able to explain the slowdown of the Neolithic front as observed from archaeological data

The paper is open access, so if you want more of this:
fareq

Just click through above. Rather, I am curious more about their nice visualization of the archaeological data:


euroneolithic

Note how much variance there is in terms of the rate of change of the clines. As I’ve observed before there was a “break out” of the LBK farmers into Central Europe nearly 7,000 years ago, but it took much longer to close the gap between the farms on the frontier and the sea. This is well known from the archaeology, as there seems to have been a pause of ~1,000 years across much of the north European plain. On the scale of 10,000 years that’s not much time, but that’s about 40 generations. In Frisia it looks like the spreading of farming stopped for nearly ~2000 years!

Why the abatement of the spread of farming? I think the authors of the above paper are correct in their acceptance of the conventional wisdom of greater Mesolithic densities in Northern Europe. But I think perhaps a better description might be maritime Northern Europe. We often imagine early farmers displacing hunters and gatherers of game and herb, but what if in much of the world the main clash numerically was between dense populations oriented toward the sea, and those who were depended on the land? About seven years ago a study came out which argued for a rapid transition from seafood to meat in the diets of early Britons, Why Did Ancient Britons Stop Eating Fish?:

When cattle, sheep, pigs, and wheat arrived on the shores of Great Britain about 5,000 years ago, fish quickly fell off the Neolithic menu, according to an analysis of human bones scattered throughout the island.

“Farming really took off in Britain during the Neolithic. The main questions concerning the speed of change relates to how quickly Mesolithic peoples adapted—or otherwise—to the new farming methods and/or the spread of farming into Britain by new farming communities,” he said.

The research by Richards and colleagues Rick Schulting at Queen’s University Belfast and Robert Hedges at the University of Oxford tracks the shift in diet by examining the dietary signature stored in the bones.

They find that the shift was rapid and complete at the onset of the Neolithic. “Marine foods, for whatever reason, seem to have been comprehensively abandoned,” the researchers conclude in the September 25 issue of the journal Nature.

“We determined that after the introduction of domesticates, as well as the other artifacts associated with the Neolithic, the isotope values showed that marine foods were not used anymore,” he said. “We then infer that this is a switch from wild foods such as fish and shellfish to the new domesticates that arrive at this time.”

Richards said there are three plausible reasons why the British abandoned seafood from the beginning of the Neolithic: the domesticated plants and animals presented a steady source of food; the shift was forced by a climate change; or cultural pressure.

In the early 2000s the idea of wholesale rapid demographic replacement was not in the air. I think we need to put that back on the table. Here is the chart on isotope ratios from the 2003 paper:
culwar

Notice the sharp discontinuity. Richards et al. in 2003 interpreted this as a rapid cultural acquisition of the Neolithic lifestyle ~2500-3000 BC. They note in the media reports that later Britons, for example at the time of the Roman conquest, seem to have utilized fish a bit more in their diet than these early Neolithics. This stands to reason, much of Britain is not too far from the sea. To me the very sharp drop in marine consumption is indicative more of a food taboo, than a practical shift. Obviously farmers would primarily be subsistent on grain, but there’s no necessary reason to avoid meat or fish, but as it happens in many parts of the world societies preserve and perpetuate exactly such norms. These norms may have spread through cultural diffusion, for example through an adoption of a new religion. Or, the norms may have been brought by a new group which arrived in large numbers and replaced the indigenous population.

Here is an equivalent chart from Denmark from an earlier paper by the same group:

denmark

800px-Saami_Family_1900pacnortWhen we think of peoples who aren’t farmers, we often think of marginalized nomadic or semi-nomadic groups. Many of the remaining hunter-gatherers such as Bushmen, as well societies which supplement their conventional lifestyle with a lot of hunting & gathering, such as the indigenous peoples of Siberia or the Sami of northern Scandinavia, occupy territory which is simply not viable for conventional agriculture. But this was not so in the past. Before the farmers arrived the rich bottom-lands were occupied by hunters & gatherers, of fish, game, grain, and nuts. In certain ecologies, such as around productive estuaries one could imagine enormous aggregations of these peoples. Additionally, it seems likely that a sedentary lifestyle predates farming. A good contemporary analog for what ancient Northern Europe may have been like was the Pacific Northwest before the European settlement. These native tribes were relatively affluent because of the abundance of salmon runs, and engaged in lavish signalling, such as with their famous potlatches. Seeing as how there are Atlantic salmon runs in places like Norway and Scotland one can make even closer correspondences perhaps!

Stonehenge-GreenAs I have stated before just because we have no written records of this period, we can not assume that these were necessarily the fragmented and scattered “small-scale societies” which we’re familiar with today. There may have been ideologically motivated political coalitions and alliances which broke down along ethnic and cultural lines. In the paper above the authors argue that there is evidence that a climatic constraint, crops which do not have a good yield in cooler or warmer temperatures, is a weak hypothesis. If so I wonder if it is a bit too pat to simply model the dynamics as a diffusive “bottom up” process. Seems plausible enough for much of Europe where Mesolithic populations were thin on the ground because of local carrying capacity, but I suspect that the encounter between dense agglomerations of farmers and fishermen resulted in an inevitable ramp up of political integration and consolidation, as villages and tribes had to coordinate together because of a positive feedback loop of conflict.

Image Credit: Lordkinbote, Mactographer

(Republished from Discover/GNXP by permission of author or representative)
 
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uyghurboy
Uyghur boy from Kashgar

Every few years a story crops up about “European-looking” people in northwest China who claim to be of Roman origin. A “lost legion” so to speak. I’ll admit that I found the stories interesting, amusing, if implausible, years ago. But now it’s just getting ridiculous. This is almost like the “vanishing blonde” meme which always pops right back up. First, let’s quote from The Daily Mail,* DNA tests show Chinese villagers with green eyes could be descendants of lost Roman legion:

For years the residents of the remote north western Chinese village of Liqian have believed they were special.

Many of the villagers have Western characteristics including green eyes and blonde hair leading some experts to suggest that they may be the descendants of a lost Roman legion that settled in the area.

Now DNA testing of the villagers has shown that almost two thirds of them are of Caucasian origin.

The results lend weigh to the theory that the founding of Liqian may be linked to the legend of the missing army of Roman general Marcus Crassus.
Enlarge

In 53BC, after Crassus was defeated by the Parthians and beheaded near what is now Iran, stories persisted that 145 Romans were captured and wandered the region for years.

As part of their strategy Romans also hired troops wherever they had conquered and so many Roman legions were made up not of native Romans, but of conquered men from the local area who were then given training.

250px-Statue-AugustusLet’s start from the end. The last paragraph indicates a total ignorance of the nature of military recruitment during the late Republic. In the year 110 BC the Roman army was composed of propertied peasants. These were men of moderate means, but means nonetheless. They fought for the Republic because it was their duty as citizens. They were the Republic. Due to a series of catastrophes the Roman army had to institute the Marian reforms in 107 BC. Men with no means, and who had to be supplied with arms by the Republic, joined the military. This was the first step toward the professionalization of the Roman legions, which naturally resulted in a greater loyalty of these men to their leaders and their unit than the Republic. Without the Marian reforms Sulla may never have marched on Rome. By 400 AD the legions were predominantly German in origin, and supplemented with “federates,” who were barbarian allies (though alliances were always subject to change). But in 53 BC this had not happened yet. The legions who marched with Crassus would have been Roman, with newly citizen Italian allies in the wake of the Social War. The legions of the Julio-Claudians were probably still mostly Italian, a century after Crassus (service in the legions, as opposed to the auxiliaries, was limited to citizens, who were concentrated among Italians). So that objection does not hold.


But really, do we need the Roman hypothesis? Those big blonde Romans? Here’s one section of the piece: “Archaeologists discovered that one of the tombs was for someone who was around six foot tall.” Because of issues of nutrition the Roman soldiers were notoriously short relative to the Celts and Germans (who had more meat and milk in their diet). Perhaps they had the potential for greater height, which they realized in the nutritional surfeit of…China?

Anyway, there’s a straightforward explanation for the “Chinese Romans”: they’re out of the same population mix, roughly, as the Uyghurs. Before the year 1000 AD much of what is today Xinjiang was dominated by peoples with a European physical appearance. Today we call them Tocharians, and they spoke a range of extinct Indo-European dialects. It seems likely that there was also an Iranian element. The archaeology is rather patchy. Though there were city-based Indo-Europeans, it is clear that some of them were nomadic, and were among the amorphous tribes that the ancient Chinese referred to as the “Rong and Di.” The Yuezhi and Wusun were two mobile groups who left China in the historical period and are recorded in the traditional annals.

Meanwhile, between 500 AD and 1000 AD the Indo-European substrate of the Tarim basin was absorbed by Turkic groups coming from Mongolia. They imposed their language on the older residents, but genetically assimilated them. The modern Uyghurs are a clear hybrid population. In the papers published on the Uyghurs they shake out as about a 50/50 West/East Eurasian mix. But the DODECAD ANCESTRY PROJECT has them in the sample, and here’s how they break down by a finer grain:
uad

Uyghurs are the third population from the bottom. Below them are the Yakut and Chinese. The Yakut are the northernmost Turkic people, and the Turkic element which settled in Xinjiang and assimilated the Tocharians was from the north. The Chinese-like element may simply be that the proto-Uyghurs were already admixed with the Han populations, or, that that element has a geography-conditional cline where the Yakuts are at an extreme. In any case, the other components of Uyghur ancestry are not East Asian. Like many European popualtions the Uyghurs have a West Asian and Northern European aspect, but they lack the South European ancestry. This is important, because it is dominant in both the Tuscans and North Italians. If the “Roman Chinese” are genuinely Roman, they will have this specific southwest European ancestry, which will put them at a distinction from the Uyghurs.

As it is, I don’t think that’s what’s going on. On the order of 4,000 years ago the domestication of the horse allowed for the expansion of Indo-European populations from east-central Eurasia across the steppe. Eventually they they also percolated into the underpopulated zones between the taiga and the highlands around the Himalayan massif. I believe that these were the groups which introduced nomadism and agriculture to the Tarim basin, and their genetic and cultural impact was a function of the fact that they simply demographically swamped the few hunter-gatherers who were indigenous to the region.

In the period between 1000 BC and 1000 AD the flow of people reversed. The expansion of the Han north and west, and the rise of a powerful integrated state which could bully, and could also be extorted, changed the dynamics on the steppe and in the oasis cities beyond. The vast swaths of Central Asia which were Indo-European in speech became Altaic in speech. But many of these populations absorbed the Indo-European groups, and came out genetically admixed. A clear residual of West Eurasian admixture can also be found among peoples who presumably never interacted much with Indo-Europeans, such as the Mongols, though at lower levels.

The villagers of Liqian are a different part of the story. Clearly substantial numbers of “barbarians” were assimilated into a Han identity on the northern frontier. In the case of tribes such as the Xianbei and Khitan they even did the assimilating themselves, through top-down sinicizing edits. In areas like Gansu these elements contribute a greater proportion of the ancestry, and just as the Uyghur are Turkic speaking, and yet have equal portions of West and East Eurasian ancestry, so the people of Liqian are Chinese speaking, and have equal portions of West and East Eurasian ancestry.

I find it curious that the piece above didn’t mention Uyghurs at all. No idea if politics was involved, but I won’t be surprised if I get some angry Han and Uyghur comments because of what I’m saying here (I’m not totally clear what these sorts of commenters are angry about really, they’re usually pretty inchoate).

Addendum: East and West Eurasian ancestry seems pretty equitably distributed among the Uyghurs. But the number of genes which code for racially salient traits are far smaller than the total set which can be used to estimate ancestry. So within a large enough population allelic combinations across loci will segregate so that some individuals exhibit a “pure” ancestral phenotype. What colloquially might be termed a “throwback.” This little boy comes strikingly close.

* I am aware of the reputation of this newspaper. Nevertheless, it’s being picked up by the international press and some blogs, so I’m going to address it.

Image Credit: Gusjer

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: History, Science • Tags: Archaeogenetics, China, Genetics, Genomics, Uyghurs 
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uzbekmanThere’s a new paper out in The European Journal of Human Genetics which is of great interest because it surveys the genetic and linguistic affinities of two dozen ethno-linguistic groups from the three Central Asian nations of Uzbekistan, Kyrgyzstan, and Tajikistan. This is what the Greeks referred to as Transoxiana, and the Persians as Turan. Originally inhabited by peoples with close cultural affinities with those of Persia, indeed, likely the root of the peoples of Persia, by the historical period Turan developed a distinctive identity as a frontier or march. It was in Turan where the Turk met the Iranian (a class which included non-Persian groups, such as the Sogdians), from the pre-Islamic Sassanians down to the present day. It is a region of the world which has a very ancient urban culture, cities such as Merv, as well as peoples that were only recently nomads, forcibly made sedentary by the Soviet regime.

To add another twist to the picture many of the ethno-linguistic groups which we are familiar with today and which serve as the cores of the new Central Asian nations only came into being within the last few centuries, with a particular “push” from Russian Imperial and Soviet ethnologists who were tasked with fleshing out national identities with which the center could negotiate. A “Tajik” is after all simply part of the Persian-speaking residual population of Central Asia, spreading down into Afghanistan. The carving out of an independent Tajikistan out of the Central Asian landscape is as much a creation of the modern age as the state of Israel. The “Uzbek” identity was once simply that of the ruling caste of Transoxiana who came to power after the decline of the Timurids. Today it is an appellation which brackets the settled Turkic speaking peoples of Uzbekistan and beyond.

ResearchBlogging.org Into this near Gordian knot of history and ideology walk the naive and well-meaning geneticists. There is no great objection one can make to the genetics within the paper, but the historical framework and some of the assertions are peculiar and tendentious indeed. It’s a problem which starts within the abstract. In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations:

Located in the Eurasian heartland, Central Asia has played a major role in both the early spread of modern humans out of Africa and the more recent settlements of differentiated populations across Eurasia. A detailed knowledge of the peopling in this vast region would therefore greatly improve our understanding of range expansions, colonizations and recurrent migrations, including the impact of the historical expansion of eastern nomadic groups that occurred in Central Asia. However, despite its presumable importance, little is known about the level and the distribution of genetic variation in this region. We genotyped 26 Indo-Iranian- and Turkic-speaking populations, belonging to six different ethnic groups, at 27 autosomal microsatellite loci. The analysis of genetic variation reveals that Central Asian diversity is mainly shaped by linguistic affiliation, with Turkic-speaking populations forming a cluster more closely related to East-Asian populations and Indo-Iranian speakers forming a cluster closer to Western Eurasians. The scattered position of Uzbeks across Turkic- and Indo-Iranian-speaking populations may reflect their origins from the union of different tribes. We propose that the complex genetic landscape of Central Asian populations results from the movements of eastern, Turkic-speaking groups during historical times, into a long-lasting group of settled populations, which may be represented nowadays by Tajiks and Turkmen. Contrary to what is generally thought, our results suggest that the recurrent expansions of eastern nomadic groups did not result in the complete replacement of local populations, but rather into partial admixture.

In my initial comment on this paper in a link round-up I wondered what the authors were thinking making such a comment: anyone who knows Central Asians would see on their faces that the Turks did not completely replace the local populations. The image above is of an Uzbek man, who does not exhibit any visible “Mongolian” features. This is not the norm, but is not unheard of. Even populations which are presumed to have less Iranian admixture, such as the Kazakhs, exhibit a range of physical types. It would be one thing if this reference was an isolated peculiarity, but there are other comments within the paper which indicate to me that the research group’s familiarity with the non-genetic literature is cursory at best. They refer to Huns as having “brought the East-Asian anthropological phenotype to Central Asia.” There is no clear definite foundation for this assertion. Unfortunately historians do not have a clear idea what the ethno-linguistic character of the Huns was. By the time Roman observers encountered them the Hunnic horde seems to have been predominantly German, with a Iranian (Alan) secondary component, the Huns themselves being a small elite (Attila’s name itself may be Gothic). In light of subsequent eruptions into Europe of Turkic and Ugric nomads it is easy to slot the Huns into this exotic category, but the primary literature makes it clear that you can’t ascertain their ethnic character from the contemporary sources (the “White Huns” of Central and South Asia had no real connection to the Huns of Europe).

Near the end of the paper they say something really peculiar: “The Westernized view of westward invasions usually emphasizes the extreme violence and cruelty of the hordes led by Attila the Hun (AD 406–453), or that from the Mongolian empire led by Genghis Khan. However, our results somehow challenge this view and rather suggest that these more recent expansions did not lead to the massacre and complete replacement of the locally settled populations….” It is true that European observers of the Mongol expansion did not have a sanguine attitude. But the idea that Mongols were genocidal exterminationists really comes to us via the Islamic historians, for whom the Mongol conquests were totally shocking and a literal world-turned-upside-down moment. The Mongol conquests did seem to result in a decline in population between Mesopotamia and Transoxiana. Whole cities in Central Asia were depopulated. There is an assumption that the Mongol conquests marks the turning point where Central Asia passed from being a predominantly Iranian world with a Turkic military elite (which was to be the nature of Iran proper until the 20th century) to a Turkic world with a large Persian minority. Though the military conquests of the Mongols were important punctuating events, I do not believe that scholars today would assume that they produced an ethnic shift in toto. On the contrary, the null hypothesis is generally against migrationism.

With those preliminaries out of the way, what’s going on with the genetics? Below are the less interesting tables & figures. The first is important because it has the abbreviations which they use. Basically anything that starts with a “T” are Indo-Iranian Tajiks, and everything else is Turkic, except LUzn LUza, who are Indo-Iranian Uzbek nationals, but I presume would be ethnic Tajiks in Uzbekistan (this stuff is really confusing in regards to labels, because as I said the national categories are to some extent ad hoc impositions on more ancient identities which don’t always follow the European language = nation formula). The second image is a figure which shows the sampling of locations, as well as pie charts with ancestral quanta. The third image is a table which shows that Indo-Iranians are genetically more varied than Turks. While the fourth is a STRUCTURE plot which I reedited to zoom in on peoples of interest for this study, as well removing some of the lower K’s. Remember that each K is a putative ancestral population. As Dienekes notes since they used only 27 microsatellite markers across their 26 populations, the plot may inflate minor ancestral contributions.

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Of more interest is the correspondence analysis, which is conceptually similar to principal component analysis. The variate inputs are allele counts. I’ve obviously reedited the figure a bit, and added some labels (yeah, I ended up thinking that rotating after I’d added some labels was best, sorry). Note the clear color-coding of Turkic vs. Iranian Central Asian groups.

turkiraneurasian

There’s a clear separation linguistically between Iranian speaking and Turkic speaking groups in Central Asia. Some of the Turkic groups are close to Iranian groups, closer than to other Turkic groups, but still the two broad sets have a coherent identity. Undergirding the linguistic variation is classical geographic variation. The eastern Turkic groups seem the least impacted by the Iranian substrate which was dominant before the arrival of Turks, while the Turcoman group sampled from western Uzbekistan seems to have been the most genetically “Iranized.” In a world wide context the central position of Central Asians is not surprising. Interestingly the Iranian groups of Central Asia seem to overlap rather well with the Indo-Iranian groups from the HGDP data set. In contrast, the Turkic groups are distributed along a linear axis from East Asians to the Iranian cluster. This is the same pattern evident among African Americans as individuals. It’s a two-way admixture, with different dosage degrees by population as a function of history and geography (I presume you’d see the same pattern if it was broken down on individuals with a SNP-chip).

admixMoving to the explicit admixture estimates, the labels leave something to be desired. The shaded area is for Turkic speakers. The very last group, TJY, indicates the Yagnobis of Dushanbe. I happen to know offhand that the Yagnobis are reputed to be descendants of the Sogdians, having preserved their language and Zoroastrian religion relatively late in history before switching to Tajik and Islam. Like many ethno-linguistic relics these people preserved their independent identity after the Arab conquest, which saw the decline of Sogdian influence on the Silk Road, by taking refuge in isolated regions. It is no surprise then that this group shows the least East Asian admixture of all the Iranian samples, as they were isolated from many of the social and historical processes which were operative in Transoxiana after the conquest by the Arabs, and the later pushing in of the zone of Turkic hegemony after the fall of the Samanids.

These admixture estimates definitely put the spotlight on the role of Central Asia as a nexus of sorts. In the archaeology and history it is clear that Central Asia has been affected by peoples of European, South Asian, Middle Eastern, and East Asian origin. Central Asia itself has been the mother of empires, famously the seat of Timur, but also the original base of what later became the Abbasid dynasty. At one point the Caliphate was split between western and eastern factions and there was a possibility that the capital would be relocated from Baghdad to the Central Asian city of Merv! I do not believe that the Arabs had a strong genetic impact, nor was there a large South Asian migration in recent periods into Central Asia. So the admixture estimates adduced for these groups may be due to the natural cline in allele frequencies which are found in different peripheral Eurasian populations. Frequencies which are naturally intermediate in Central Asia. The main caveat is that it is probable that local conditions will vary a great deal. In contrast we have strong reason to suspect that the East Asian component arrived relatively recently with the Turks, and we see that its aspect is most evident among the groups which were nomadic within living memory, the Kazakhs and Kyrgyz. These two ethnicities, which are really compounds of several tribes or “hordes,” were only marginally integrated into sedentary Islamic society where the Tajik element would be prominent (shamanism among many of these tribes only disappeared under the influence of the Islamic missionaries sponsored by Russian Empire). I think this pattern is reinforced by what we saw in the correspondence analysis, where the Turkic groups exhibited a linear distribution toward East Asia, while the Iranian ones were placed where you’d expect them geographically. Finally, I want to note that Dienekes observes that using South Asians as a Central Asian population source is strange since South Asia is more appropriately thought of as a demographic sink for Turan. True, but the HGDP populations are strongly biased toward groups with relatively little indigenous South Asian ancestry, with the Sindhi being the only Indo-Aryan speakers within the set. So I think that objection is mitigated by these factors. Rather, the Iranian-speaking Pakistani groups serve as proxies for the original Central Asian Iranian substrate, from which both they and the Tajiks presumably derive.

Moving back to the Turk vs. Iranian distinction, the authors note that the Turkic groups exhibit a strong degree of genetic homogeneity on the Y chromosomal lineages. This points to the possible manner in which the East Asian genetic element spread in Central Asia, not necessarily just through population displacement, but also through polygamy and the high reproductive fitness of particular “super-male” lineages. The children of elite Turkic men who took Iranian wives presumably adopted the culture of their fathers, including the linguistic identity. This may have been particularly easy in Central Asia because they did not have to repudiate their maternal heritage in totality, as Persian culture still had great status and currency. If we partition the ancestry into “East Eurasian” and “West Eurasian” components the Turkic groups have much more of the latter than the Iranian ones have of the former. That stands to reason as the Turks were newcomers, and an elite which the locals would wish to assimilate to if they had the opportunity. In contrast, the shift from Turk to Iranian may have been rarer, and a switch which individuals would wish to avoid since the latter did not have the same level of temporal power. Over ~1,500 years gene flow does occur between the groups, and even the Yagnobis have appreciable East Asian ancestry. Eventually the linguistic differences would probably be dwarfed by the geographical ones, but currently we’re taking a snapshot of a “transient.”

It’s complicated. And one has to be very careful about using terms like “Turk” in a localized context, vs. a more international one. The Turks of Turkey are overwhelming derived from the same source populations as their Balkan (because of Rumelian Turks), Iranian, and Armenian, neighbors. The decline in East Asian fraction is evident even in this sample, as the Turcomans from western Uzbekistan have the least eastern ancestry of any of the groups. But this paper is an excellent within into a critical geographical hinge of genetic variation and historical tumult (though one must set aside some of their tacked-on historical speculations).

Citation: Martínez-Cruz B, Vitalis R, Ségurel L, Austerlitz F, Georges M, Théry S, Quintana-Murci L, Hegay T, Aldashev A, Nasyrova F, & Heyer E (2010). In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations. European journal of human genetics : EJHG PMID: 20823912

Image Credit: Wikimedia

(Republished from Discover/GNXP by permission of author or representative)
 
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"