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Europe genetics

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

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

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

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

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

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

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

Image credit: yomi955

🔊 Listen RSS 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

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"