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David Reich’s lab has a new preprint out, Eight thousand years of natural selection in Europe, which serves as a complement to Massive migration from the steppe is a source for Indo-European languages in Europe. Where the previous work has focused on the relationships of ancient and modern populations, this research puts the spotlight on patterns of natural selection which have shaped ancient and modern populations. The method utilizes the explicit model which is supported by the previous work, that Europeans are best approximated as a three population admixture of a group represented by the hunter-gatherers of Western Europe, the first farmers which brought agriculture to Europe, and the peoples of Central Eurasia which likely brought the Indo-European languages to Europe. In the parlance of these sets of papers, WHG, EFF, and Yamnaya. Basically they have allele frequencies of these ancestral groups, thanks to ancient DNA techniques, and the frequencies in modern populations. By comparing the frequencies one can then infer if the deviations from expectation are large enough to satisfy the conditions you’d expect for a locus subject to a selective sweep of some sort which is changing proportions rapidly as a function of a given selection coefficient.

lctFirst, it is very obvious that lactase persistence in Europe has been under strong directional selection over the past 4,000 years. Even in the Bronze Age Central European samples did not exhibit frequencies of the derived variant common across Western and South-Central Eurasia on the LCT locus which is associated with persistence today. A quick survey of the 1000 Genomes data shows that this variant has wide variation in modern European populations which are phylogenetically close. The frequency in the Spanish data set is ~50 percent, but in the Tuscan Italian samples it is ~10 percent for the derived variant. In Denmark and Sweden the derived allele frequency goes up to ~75 percent (the phenotypic expression is dominant, so that means ~95 percent lactase persistence), though in the Finnish sample it is closer to the frequency of the Spanish data set. In South Asia the 1000 Genomes data as well as earlier work shows that frequencies are 25 percent or more in Northwest India, in the Punjab, where dairy culture is most pervasive. It drops as a function of distance from this zone, to 5 percent in the Southern and Eastern South Asia. The haplotype network around this particular mutation implies that it probably originated in Central Eurasia, so the varied frequencies across the Old World is suggestive of both migration and selection. Intriguingly, the lactase persistence allele is not present at appreciably frequencies in the Yamnaya. It begins to appear in cultures such as the Corded Ware Bell Beaker, though at far lower frequencies than is presently the case in this region.

But the story of lactase persistence is not entirely surprising. Its late evolutionary trajectory in relation to the rise of cattle culture and complex societies in Eurasia points to the reality that evolutionary change in the biological dimension requires a powerful cultural scaffold. That existed in the form of agro-pastoralism in Eurasia. Similar forces are at play across regions of Africa, where signatures of selection are even more evident in groups dependent upon cattle, likely because of the recency of the emergence of the trait, caught in mid-sweep.

A new face in the world?

A new face in the world?

There are few other signatures evident in these data. Three of them have to do with pigmentation, SLC24A5, SLC45A2, and HERC2. Ewen Callaway reported on the peculiarity last year that Paleolithic European hunter-gatherers may have had dark skin and light eyes. The reasoning here is that a large fraction of the complexion difference between Europeans and Africans is attributable to a derived mutation on SLC24A5, which is nearly fixed in modern Europeans. And yet ancient European hunter-gatherers on the whole were not fixed at this locus, and Western European hunter-gatherers, exhibited the ancestral variants. To get a sense of how peculiar this is the vast majority of the alleles in much of the Middle East are in the derived state, as are about half the alleles in South Asia (I am a homozygote for the derived allele for what it’s worth, and my skin is still notably brown, though obviously not extremely dark). The best available data suggests that the mutant allele emerged recently in the Middle East, and it has expanded out from that point of origin.

SLC45A2 is different in that its distribution is far more constrained to within Europe, though it is found at appreciable frequencies in the Middle East, and at lower frequencies in South Asia. The same for HERC2, though I was surprised to see that the “European” variant associated with blue eye color is actually found at a 0.10 proportion in the 1000 Genomes data in Bangladesh (I am a homozygote for the ancestral variant), the same fraction as the Punjabi sample.*

The results here seem to suggest that all these loci are under selection. The two SLC genes are under positive selection, though SLC24A5 probably got its first boost from EFF with the arrival of agriculture, and was subsequently fixed even when that group fused with the hunter-gatherers who lacked it. Curiously HERC2 is under some negative selection. Remember that all the hunter-gatherers seem to carry the derived variant, so the frequency could only but go down. But in Southern Europe it is likely being driven down in frequency, while it Northern Europe it has been maintained, or rebounded.

Of course one of the major issues we have when evaluating pigmentation loci and their relationship to selection is it’s not always clear if the target of selection is the trait of pigmentation, or something else which the locus modulates, and pigmentation just happens to be a salient side effect. There are many theories about why populations have become depigmented, but none of them are truly well supported in my opinion. Another question is whether we know the genetic architecture of pigmentation well enough to actually infer that these ancient populations are easily predicted in their trait character by modern models which map genotype to phenotype. In other words, were Paleolithic Europeans light skinned because of different alleles? The genetic architecture of skin color is relatively well understood in extant populations. Though it is possible, it so happens that modern Northern Europeans, and to a lesser extent Southern Europeans, harbor a substantial portion of European ancestry which is rooted in the Paleolithic. Studies in admixed African American populations, which are about ~20 percent European, indicate that the primary variants which determine complexion are the ones extant in modern populations, though it may be that there isn’t power to detect the ones from WHG, etc. Of course it could be that the lightening alleles of the Paleolithic Europeans were subject to negative selection, excepting the HERC2/OCA2 locus. But that’s not a particularly parsimonious solution from where I stand (by the way, if selection is targeting something other than pigmentation it is strange that pigmentation associated loci emerge in clusters as positive hits for selection tests).

A secondary issue in relation to pigmentation is that the Yamnaya population does not seem to have been particular fair of hair or azure of eye. The frequency of the derived HERC2 SNP is in the range of North Indian populations, while the SLC45A2 SNP is in the same frequency range as Middle Eastern groups. One might suggest that the Yamnaya are not representative of the population which was intrusive to Europe, but note that the frequencies of the alleles in question during the Late Neolithic and Bronze Age are intermediate between it and modern groups. These results imply in situ evolution within Europe over the Holocene, and down into historical times, toward the phenotype which we ascribe uniquely to Europeans. This is strange especially in light of the fact that a later eastern branch of Indo-Europeans seem to have been quite light. I don’t think we can make final inferences, but to me it is starting to look like the “Proto-Indo-European” complex of peoples was highly cosmopolitan and heterogeneous. Should we expect anything other? As the Mongols expanded in all directions their divergent tendrils were embedded in different ethnic substrate (e.g., Tatars, Khitai and Jurchen in China, Kipchak Turks in Russia, etc.).

The other major locus that showed up was one related to fatty acid metabolism, FADS1. Many tests for selection in humans and domestic animals show changes in the ability to process nutritive inputs. It seems an eminently plausible candidate phenotype to target for selection since the relationship to fitness is straightforward. Using polygenic score methods they also find that there was selection for shorter stature in early Neolithic populations in places like Spain. I think in the future one area of investigation is going to be in the domain of biological adaptations on the margin of farming populations which are put into a Malthusian pressure cooker. Humans, on average, were getting smaller until recently in comparison to their average stature during the Last Glacial Maximum. The Yamnaya people, in contrast to the Neolithic Iberians, seem to have been rather tall. Perhaps it had something to do with the nature of agro-pastoralism? (though do note that without lactase persistence they’d miss out on about 1/3 of the calories in the form of lactose sugar, though not the protein and fat)

edarmotalaBut there’s a twist which I haven’t gotten to, and that’s the one in regards to the hunter-gatherers from the Scandinavian region. Unlike the WHG samples you can see that they exhibit mixed frequencies of derived and ancestral alleles at the SLC loci. That’s peculiar, since geographically they are more distant from the core region from which EFF issued. We do know that their ancestry is somewhat exotic, as paper on Indo-European migrations pointed out that they seem to carry the same ancestral component which the Indo-Europeans brought to most of Europe, that of the Ancestral North Eurasians (albeit at far lower fractions than the EHG group which was a partial precursor of the Yamnaya population).

The past is complex and doesn’t fit into a solid narrative. And yet the weirdest aspect of the Scandinavian samples is that they carry the East Asian/Native American variant of EDAR at appreciable frequencies! The figure to the right illustrates this. In blue you have the focal SNP (dark is homozygote, light is heterozygote, dark circle means only one allele was retrieved). In the Chinese from Beijing population (CHB) the derived variant is at high frequency. In the sample of Northwest Europeans from Utah (CEU) it is not present. You can confirm these findings in the 1000 Genomes and elsewhere. In European EDAR of the East Asian form seems only to be found in Finland and associated populations. Using ALDER the authors conclude that admixture occurred on the order of 1 to 2 thousand years before the present, from an East Asian-like group (in the Indo-European paper they found this source best matched the Nganasans of North Central Siberia). An interesting fact which also comes out of this finding is that the haplotype that the derived SNP arose against is relatively common in Northern Europe. The arrows in the figure point to individuals who carry the ancestral SNP, but exhibit the same haplotype which is dominant in East Asia (and also among the Scandinavian hunter-gatherers with the derived variant). The authors state that “The statistic f4(Yoruba, Scandinavian hunter-gatherers, Han, Onge Andaman Islanders) is significantly negative (Z=-3.9) implying gene flow between the ancestors of Scandinavian hunter-gatherers and Han so this shared haplotype is likely the result of ancient gene flow between groups ancestral to these two populations.” Though in earlier work on these data sets they left open the possibility of gene flow between Eastern and Western Eurasia during the Paleolithic as a way to explain some results, it was not offered as a result for the Scandinavian hunter-gatherers. I do not know what to think of the fact that the haplotype that the derived East Asian SNP arose in is common in Northern Europe (though without the derived SNP, which is likely only present in a few populations due to recent Siberian admixture). Could it be that ancient gene flow from Western Eurasian Paleolithic people occurred into East Asian populations, and that then this haplotype accrued the mutation which later swept to near fixation? If that is the case I’m curious about haplotype networks, as Northern Europeans should be more diverse when it comes to the haplotype in question.

In the near future we’ll probably have better and more numerous whole genome sequences of ancient samples. Some of the confusions engendered by this work will be cleared up, as better data renders paradox crisply coherent. The preprint is free to anyone, and I invite readers to dig deeply into it. Though the results yielded only a few positive signals of selection, they’re subtle and complex in their implications. I certainly haven’t thought through everything….

* The fraction of blue eyes is MUCH higher among Punjabis than Bengalis in my experience. It goes to the point that blue eyes likely expresses against the genetic background found in Europeans, where there are other depigmenting alleles near fixation.

• Category: Science • Tags: Europeans, Population Genetics, Selection 
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Citation: Nature 513, 409–413 (18 September 2014) doi:10.1038/nature13673

Citation: Nature 513, 409–413 (18 September 2014) doi:10.1038/nature13673

Ancient human genomes suggest three ancestral populations for present-day Europeans has finally be published in journal, Nature. This is important as a validation and confirmation of the strange results which were reported therein. One simple finding which I haven’t commented on in too much detail is how clearly Europe as a biogeographic entity is distinct from the Near East genetically. Arguably, it’s more than a cultural construct. Europeans share descent in part from an ancient lineage which dates to the late Pleistocene, and is not shared with those outside Europe (haplogroup I-M70 in Y chromosomes). To an extent this isn’t totally surprising, as water barriers are often incredibly good at allow for populations to drift apart due to lack of reoccurring gene flow (even ones as narrow as the Straits of Gibraltar and the Bosporus). On the other hand there is arguably more continuum with populations in Northeast Asia, though much of that is relatively recent in vintage (e.g., many of the Central Asian Turkic groups occupy a position between west and east Eurasia, but they are relatively recent admixtures).

Finally, this paper leaves a lot of unanswered questions, which I suspect will be answered soon:

Several questions will be important to address in future ancient DNA work. One question concerns where and when the Near Eastern farmers mixed with European hunter-gatherers to produce the EEF. A second question concerns how the ancestors of present-day Europeans first acquired their ANE ancestry. Discontinuity in central Europe during the late Neolithic (~4,500 years ago) associated with the appearance of mtDNA types absent in earlier farmers and hunter-gatherers raises the possibility that ANE ancestry may have also appeared at this time. Finally, it will be important to study ancient genome sequences from the Near East to provide insights into the history of the basal Eurasians.

One thing to note about “basal Eurasians” is that they claim that it shares “drift” with all other non-Africans. This implies that they were not post-Out-of-Africa migrants from Sub-Saharan Africa, but shared in a common Out-of-Africa history with the other populations of the world. I hope that deeper study of non-European populations might be able to get us a better sense of where basal Eurasians shake out.

• Category: Science • Tags: Europeans 
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Raptus_EuropaeI’ve mentioned the preprint Ancient human genomes suggest three ancestral populations for present-day Europeans several times, but I thought that I would highlight that there has been a substantial revision as of April 5th. One section I think points to possible future results, and where we are now. The authors conclude (before the methods): Three questions seem particularly important to address in follow-up work. Where did the EEF obtain their WHG ancestry? Southeastern Europe is a candidate as it lies along the path from Anatolia into central Europe. When and where the ancestors of present-day Europeans first acquire their ANE ancestry? Based on discontinuity in mtDNA haplogroup frequencies, this may have occurred ~5,500-4,000 years ago in Central Europe. When and where did Basal Eurasians mix into the ancestors of the EEF? An important aim for future work should be to collect DNA from additional ancient samples to illuminate these transformations As is clear from their results to a first approximation to be genetically European entails ~20 on the order of 10 percent ANE ancestry. If the admixture in most of Europe dates to 5,500 to 4,000 years ago, then it is possible that the basic historical framework which serves as the backdrop for the Epic of Gilgamesh was contemporaneous with the emergence of populations which we would recognize as European! I am rather doubtful as to the power of ancient myths rooted in the Bronze Age to give us deep insights about prehistory, mostly because the myths themselves are often sprawling enough that they can be “fit” to a host of diverse scenarios. But, it does suggest that it is possible that Greek myths which date back to the Bronze Age may actually be somewhat informative, even if by chance, of the origins of the peoples and places of antiquity.

• Category: History • Tags: Europeans, Genetics, History 
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Screenshot - 090614 - 19:56:13

Screenshot - 100614 - 01:23:00 David Reich’s talk at SMBE 2014 has come and gone, and it seems like from the reports on Twitter that it was a synthesis of the results in their bioRxiv preprint from last fall, Ancient human genomes suggest three ancestral populations for present-day Europeans, and the ancient DNA samples from Samara in Russia. The major takeaway being that genetically modern Europeans are by and large an admixture between three very distinct population groups, which fused together only during the Holocene (last ~10,000 years). A stylized variant of the model is represented in the figure I’ve taken from the bioRxiv preprint.

But a question that’s nagged me is how realistically to take the proposition that some of these nodes are genuinely distinct populations separated by barriers to gene flow, as opposed to being part of a broader continuum of genetic variation? For example, populations separated by water barriers such as those of Sahul almost certainly exhibited enough attenuated gene flow so that drift could work to shift their allele frequencies away from the populations of Sundaland. On the other hand, it seems reasonable to me that genetic variation on the broad plain from western Europe to the Urals in northern Europe may have been mostly clinal, with each population exchanging genes with the next, from the Atlantic to the fringes of Siberia. Some have argued that the Paleo-Siberian population which has been termed “Ancient North Eurasian” (ANE) is only part of a cline across Eurasia which extends out toward the European hunter-gatherers (to be clear, I’m skeptical of this because the genetic distance seems too great, but who knows how rapidly genetic distance increased as a function of distance in the Pleistocene?). On the other hand one might posit regions of extremely low population density during the Pleistocene due to inclement conditions in many regions so that various ancestral groups may have been isolated enough to drift apart due to more conventional genetic isolation (for example, it seems to me that the ancestors of groups such as the Han Chinese have been isolated from western Eurasians for ~40,000 years, unless you count relatively recent fusions such as the Uygurs and the peoples of Turkestan more broadly).

And yet some discussions I’ve had recently (on Twitter) have made me clarify my thoughts and admit that for some purposes it really doesn’t matter whether ANE was part of a genetic continuum or not in relation to European hunter-gatherers. The reason is that I believe that the human past was characterized by many powerful demographic sweeps which we are beginning to comprehend due to the power of ancient DNA. If the expansions occur from specific narrow geographic zones, and overwhelm a huge area adjacent, then whether the genetic variation is characterized by clines or not is irrelevant, as it will look like a discontinuous replacement in regions far from the core point of origination.

This brings me to a major update in my own personal views on these sorts of dynamics. I recently read Richersen, Boyd, and Heinrich’s Gene-culture coevolution in the age of genomics. It’s a good overview of the intersection of the fields of cultural evolution and genomics, but too often it struck me that the authors were keen on ascertaining how genomics could illuminate problems in cultural evolution, without considering the converse. That is, what can our understanding of cultural evolutionary process tell us as to what patterns of genomic variation we should see around us? Modern human genomics has a surfeit of data, and population genetic theoretical machinery of yore is being drafted to hammer away at the massive rich empirical seams, but in the domain of paleodemography a model of culture is probably more informative in allowing us to gain an expectation of the distribution of dynamics. More concretely cultural and economic factors are clearly critical in understanding why a few nations of western Europe* entered into massive settlement of the New World after 1492, and others did not. Obviously we’ll never have historical records from 50,000 years in the past, but a better understanding of the processes of cultural evolution might allow us to judge whether rapid archaeological transitions signal demographic shifts, or not. And these then might serve as an interpretative framework for genomic results.

* I specify western Europe because the genetic distances here are small, and the major settler nations, the British and Iberians, are not particularly clustered together.

• Category: Science • Tags: Ancient DNA, Europeans, Genomics, Human Genomics 
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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

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