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Ancient DNA

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k8488 In The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World the archaeologist David Anthony outlines the thesis that migrations from the west Eurasian steppe during the Bronze Age reshaped the culture of Northern Europe. When Anthony published the book, which you should really read if you are interested in this topic, it was a somewhat heterodox position. Though his intellectual pedigree is of long standing, arguably going back centuries, and extending down the present with J. P. Mallory’s In Search of the Indo-Europeans, in the past few decades diffusion of different sort has been paramount. In particular, the thesis that Indo-Europeans arrived with the first agriculturalists was of late ascendant, with some support being received from phylogenetic modeling of language evolution.

Anthony’s thesis in a way was a halfway house between early modern migrationism from the Eurasian steppe the newer theories. He proposes that the influence from the steppe via the Kurgan people was due to elite dominance and cultural emulation. An analogy here might be that of Hungary, where a Ugric speaking elite eventually imparted to the people a language, but very few distinct genes.

Eventually Anthony collaborated with some geneticists, and provided samples for DNA analysis. The results ended up resulting in a resurrection of migrationism, Massive migration from the steppe was a source for Indo-European languages in Europe. From what I have heard Anthony’s reaction was one of some shock as the magnitude of the genetic change.

5156rR+E2lL._SX326_BO1,204,203,200_ That’s the high level view. But what about the details? Over the past few years I’ve highlighted work that indicates that many Y chromosomal lineages are star-shaped. That is, they underwent recent demographic expansion. Recent as in on the order of ~5,000 years ago in the past. But the Y chromosome is just one locus. I’ve always been curious about results from the X because the X also gives you good sex specific dynamics; 2/3 of the time it is spent in females, and 1/3 of the time in males.

Amy Goldberg has done so, Familial migration of the Neolithic contrasts massive male migration during Bronze Age in Europe inferred from ancient X chromosomes:

Dramatic events in human prehistory, such as the spread of agriculture to Europe from Anatolia and the Late Neolithic/Bronze Age (LNBA) migration from the Pontic-Caspian steppe, can be investigated using patterns of genetic variation among the people that lived in those times. In particular, studies of differing female and male demographic histories on the basis of ancient genomes can provide information about complexities of social structures and cultural interactions in prehistoric populations. We use a mechanistic admixture model to compare the sex-specifically-inherited X chromosome to the autosomes in 20 early Neolithic and 16 LNBA human remains. Contrary to previous hypotheses suggested by the patrilocality of many agricultural populations, we find no evidence of sex-biased admixture during the migration that spread farming across Europe during the early Neolithic. For later migrations from the Pontic steppe during the LNBA, however, we estimate a dramatic male bias, with ~5-14 migrating males for every migrating female. We find evidence of ongoing, primarily male, migration from the steppe to central Europe over a period of multiple generations, with a level of sex bias that excludes a pulse migration during a single generation. The contrasting patterns of sex-specific migration during these two migrations suggest a view of differing cultural histories in which the Neolithic transition was driven by mass migration of both males and females in roughly equal numbers, perhaps whole families, whereas the later Bronze Age migration and cultural shift were instead driven by male migration, potentially connected to new technology and conquest.

Screenshot 2016-09-30 22.33.39 The figure to the left shows the inferences made in regards to the quantitative contribution of farmer males and females, and steppe males and females, to Bronze Age European populations. In short, it looks like the population of Northern Europe derives from a fusion of males from the steppe, and native females, who themselves arose out of a group of peoples which synthesized the ancestry of European hunter-gatherers and West Asian farmers.

But one of the more interesting things about this preprint is that the admixture can’t be modeled by a single pulse event. It seems that there were repeated migrations out of the steppe over multiple generations. But, these men did not bring women, at least in large numbers. The preprint lays out the common sense reason: these were mobile groups, probably bands of men with weapons. If your game is predation on other humans, having a baggage train of women and children is not optimal.

There is a historical analog to what might have happened. Argentina is a nation where mitochondrial lineages show a lot of Amerindian heritage. But the whole genome far less. This is because of male biased migration from Europe. One generation of this would result in a mixed population, but many generations would slowly replace the whole genome.

We will never know in concrete terms what social-political organizations the Indo-Europeans set up once they conquered the plains of Northern Europe, because we don’t have writing. But it seems unlikely that we’re talking about only band or clan level scales of organization. Rather, it was likely that a ‘Indo-European commonwealth’ of some sort existed initially, predicated on domination and extraction of value from the natives. In such a fashion one can imagine Europe being a draw for enterprising males from the steppe. This could also explain likely ‘back migration’ over time, leading to ‘European’ ancestry among later steppe cultures.

 
• Category: Science • Tags: Ancient DNA, Genomics 
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pleistmap

The map and chart above is from The genetic history of Ice Age Europe, a new paper in Nature from the Reich lab (the new data has been posted). It illustrates probably the major finding of the paper, using a ~40,000 year paleogenetic transect of 51 ancient DNA samples the authors conclude that there have been at least three major population turnovers/disruptions across Pleistocene Europe. These correspond to three genetic clusters that they’ve identified in their data; the El Mirón, Věstonice, and Villabruna groups. Respectively they are the Magdalenian, Gravettian, and Epigravettian/Azilian cultures. There are also stray individuals which are harder to place, but signal other turnovers. An individual from Goyet that dates to 37,000 years ago and was presumably of the Aurignacian culture, and is somewhat sui generis. But, unlike the ~40,000 year old sample from Romania, and the ~45,000 year old Siberian, Goyet is ancestral to some later Europeans.

Screenshot 2016-05-04 00.23.42 The figure to the left is one interpretation of their results. It shows that the Goyet sample contributed substantial ancestry to the Magdalenian culture which flourished nearly 20,000 years later. But, Goyet did not contribute substantial ancestry to the Gravettian culture, which succeeded it! Rather, the Vestonice cluster which represents the Gravettians has only marginal admixture from other Pleistocene Europeans, but a notable affinity to the Konsteki sample. Intriguingly, Goyet-like ancestry can be found in the Loschbour hunter-gatherer from the Holocene.

This suggests that I was wrong in one of my predictions: I had assumed that most European hunter-gatherer ancestry dates to the Gravettian at the earliest. This is wrong. In fact, this paper suggests minimal legacy of Gravettian peoples as represented by the Vestonice cluster. Rather, earlier peoples have left their mark on modern Europeans via the Holocene “Western Hunter-Gatherers” (WHG) who mixed with incoming farmers.

There’s more. Most of Loschbour’s ancestry is not from Goyet-like groups. Rather, it is from a population with affinities to the Villabruna culture. This to some extent vindicates another prediction I made: that most European hunter-gatherer ancestry would probably date to groups which became established after the Last Glacial Maximum 20,000 years ago. That was right, as Villabruna-like affinity seems to be the dominant signal in the Mesolithic hunter-gatherers.

700px-Weichsel-Würm-GlaciationSome of the patterns above are perplexing. So at this point, I think I want to drop a conjecture which I think can be inferred from this paper, but probably will have to be explored with future results and analysis: the Villabruna cluster ~14,000 years is a product of a massive expansion of a hunter-gatherer population from the Middle East. The original papers which posited that “Early European Farmers” (EEF) were admixtures between “Basal Eurasians” (BEu) and WHG, at 40% to 60% proportions, were somewhat misleading I suspect. Rather, WHG, the Mesolithic hunter-gatherers of Europe, derive predominantly from an expansion of Middle Eastern hunter-gatherers which had larger populations in the wake of the grueling climatic regime of the Last Glacial Maximum. The WHG in EEF was not European hunter-gatherer at all, but local Middle Eastern hunter-gatherer.

The further affinities of Villabruna make a likely exotic origin obvious. As noted in the paper a Near Eastern, but not BEu, affinity of European hunter-gatherers emerges specifically with Villabruna, ~14,000 years ago. And, some individuals in this cluster likely exhibit admixture from a population related to modern East Asians. This gene flow is independent of the Middle Eastern gene flow, though I suspect that the Middle Eastern gene flow is simply an expansion of hunter-gatherers from that region, with some absorption of the local substrate. There are other explanations for why this affinity might exist (read the supplements), but other papers have indicated the possibility of this relationship, so it is probably the most likely. The Middle Eastern origin of Villabruna makes more sense of the relationship between it and “Caucasus Hunter-Gatherers” (CHG). Geographically they would have been positioned near each other.

These West Eurasian clusters form a very deep clade with the Ma’lta North Eurasian population as an outgroup, with these nested together with East Eurasians, Amerindians, and Oceanians, in comparison to BEu. But if you take a look at the tree, and consider the chronology, it seems that modern Eurasians diversified into several distinct lineages over the course of 5-10 thousand years after the Out of Africa event. Individuals on the ~40,000 year time limit are no more related to all Eurasian groups, perhaps because their lineage went extinct. Ma’lta and the North Eurasians seem to have diverged from other West Eurasians very soon after these two diverged from East Eurasians; there just isn’t that much time to allow for this, but it did happen.

By about 30,000 years ago many of the pieces were in place. Much of the demographic change we see subsequent involve a set of operations to mix and match basic elements. The patchiness and segregation of these populations is probably why ancient DNA, itself spotty and poor and seeing the landscape with precision, assigns all of Europe to a particular cluster at a particular time. There were clearly other peoples, but they are not always at accessible archaeological sights, or perhaps they had retreated into the forests as a marginal folk?

There are many other interesting aspects of this paper, such as the Neanderthal admixture. But I’ll save that for another day….

 
• Category: Science • Tags: Ancient DNA 
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Last fall while at ASHG this paper came out, Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent:

Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.

Turns out that there was a bioinformatics error which negates the magnitude of these results. Erratum to Gallego Llorente et al. 2015:

The results presented in the Report “Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent“ were affected by a bioinformatics error. A script necessary to convert the input produced by samtools v0.1.19 to be compatible with PLINK was not run when merging the ancient genome, Mota, with the contemporary populations SNP panel, leading to homozygote positions to the human reference genome being dropped as missing data (the analysis of admixture with Neanderthals and Denisovans was not affected). When those positions were included, 255,922 SNP out of 256,540 from the contemporary reference panel could be called in Mota. The conclusion of a large migration into East Africa from Western Eurasia, and more precisely from a source genetically close to the early Neolithic farmers, is not affected. However, the geographic extent of the genetic impact of this migration was overestimated: the Western Eurasian backflow mostly affected East Africa and only a few Sub-Saharan populations; the Yoruba and Mbuti do not show higher levels of Western Eurasian ancestry compared to Mota.

We thank Pontus Skoglund and David Reich for letting us know about this problem.

First, scientists are humans and mistakes happen. So respect that the authors owned up to it. On the other hand, the conclusion never smelled right to many people. I was confused by it. I asked Iosif Lazaridis at ASHG. He was confused by it. I asked Pontus Skoglund. He was confused by it.

Unfortunately the result from the bioinformatics error was emphasized on the abstract, and in the press. In The New York Times:

“The most astonishing thing is there’s quite a lot of backflow in all modern African populations,” Dr. Pinhasi said. He and his colleagues estimate that 7 percent of the genomes of the Yoruba people of Nigeria are of Eurasian origin. In the genomes of Mbuti pygmies who live in the rain forest in the Democratic Republic of Congo, 6 percent of the DNA comes from Eurasians.

Ryan L. Raaum, an anthropological geneticist at Lehman College, part of the City University of New York, called the new study “fantastic” but questioned its conclusions. If people from the Near East moved into Africa, he argued, a drastic shift in the archaeology of the region would logically follow. But no such shift occurred. It is also possible that Eurasian DNA moved into Africa earlier than 3,000 years ago, Dr. Raaum argued. Mota might have simply lived in an isolated community that never encountered people with those genes.

The best way to test the conclusions of Dr. Pinhasi and his colleagues, Dr. Raaum said, would be to gather more DNA from African fossils of the same age. If the researchers are right, they would also lack Eurasian DNA. “Then the argument starts to seem a lot more plausible,” Dr. Raaum said.

A rule of thumb in science is when you get a shocking and astonishing result, check to make sure you didn’t make some error along the sequence of analysis. That clearly did not happen here. The blame has to be distributed. Authors work with mentors and collaborators, and peer reviewers check to make sure things make sense. The idea of massive admixture across the whole of Africa just did not make sense.

If something like this happened to me I’d probably literally throw up. This is horrible. But then again, this paper made it into Science, and Nature wrote articles like this: First ancient African genome reveals vast Eurasian migration. The error has to be corrected.

 
• Category: Science • Tags: Ancient DNA, Genomics 
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000e553e_medium In 2007 a friend told me of an encounter at a seminar where L. L. Cavalli-Sforza seem to offer agriculture almost reflexively as a solution to the conundrum of signals of positive selection in the genome of humans. Basically, all paths led to agriculture. I have to say that nearly ten years later Cavalli-Sforza’s deep intuition on these issues seems to be vindicated. Agriculture was an enormously big deal.

Carl Zimmer in The New York Times has a write up of Matheison et al. (it’s in Nature), Agriculture Linked to DNA Changes in Ancient Europe. There aren’t a whole lot of surprises, as the pre-print has been around for a year or so. But, having the work written up in a newspaper allows researchers to engage in some extemporaneous speculation. Ergo, you have:

Why? Scientists have long thought that light skin helped capture more vitamin D in sunlight at high latitudes. But early hunter-gatherers managed well with dark skin. Dr. Reich suggests that they got enough vitamin D in the meat they caught.

He hypothesizes that it was the shift to agriculture, which reduced the intake of vitamin D, that may have triggered a change in skin color.

This was to some extent Cavalli-Sforza’s idea, and I’ve proposed it as well. Then there is the model of sexual selection. These theories aren’t always exclusive, and pigmentation may have multi-causal underpinnings. It is very interesting that the best methods and ancient DNA seem to be suggesting lots of very recent change and likely adaptation. But ultimately, we still have no clear idea.

 
• Category: Science • Tags: Ancient DNA, Genetics 
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chg1

ncomms9912-f2 Over the past few years we have seen ancient DNA researchers “carve nature at its joints” when it comes to the paleohistory of Europe after the end of the last Ice Age. In relation to this historical reconstruction we aren’t at the end of the road, but I do think that the terminus is within sight. There are only so many populations one can sample, and so many statistical constructs one can posit, before one is on the plateau of diminishing marginal returns. For example, the model of Holocene Europe being a synthesis of two very distinctive populations which merged after the last Ice Age was too simple. A model with three populations is sufficient for the vast majority of European groups. Though in these sorts of situations more complex models may be consistent with the results, the bias is to go with parsimony, and attempt some alignment with linguistic and archaeological evidence.

A new paper in Nature Communications, Upper Palaeolithic genomes reveal deep roots of modern Eurasians, fills in some gaps in the broader picture. The figure at the top of this post illustrates the modification that these authors made to the schematic of Lazaridis et al. Iosif Lazaridis himself as weighed in on Twitter:

CHG = Caucasian hunter-gatherers. More specifically, the authors of this paper analyze two subfossils from Georgia dated to ~10 to ~13 thousand years, Kotias and Satsurblia. Kotias, at ~15x coverage (that is, each position is sampled ~15 times, so you have a good sense of variation at any given position), is particularly useful. What they found is as Lazaridis reports above: CHG seem one of the primordial groups to give rise to the extant variation of modern Europeans, and Western Eurasians writ large.

The rough stylized history of the non-African populations is as such: a “basal Eurasian” (bEu) population separates off first, and then west and east Eurasians diverge, and then in the west there is a divergence between the ancestors of western hunter-gatherers (WHG) and ancient north Eurasians (ANE). The early European farmers (EEF) are compounds between WHG and bEu, with a slight bias toward WHG. The Anatolian farmers were also admixed, though biased toward bEu. The eastern hunter-gatherers (EHG) are a balanced mix between WHG and ANE, and this group fused with the CHG to give rise to Yamnaya. This brings up the question: are CHG the basal Eurasians? I doubt it. The paleodemography of the ancient Near East has been barely elucidated. It seems likely that CHG, like the Anatolian farmers, are a compound of some sort. Basal Eurasians may manifest as an allele frequency spectrum across the Middle East during this period, the remnants of a back migration from west Eurasian groups mixing with the ur-Basal Eurasians, who were the first to split off from the Out of Africa migration. In the colder and drier world of the Last Glacial Maximum (LGM) it seems likely that some of the northern hunter-gatherer populations would move into territory occupied by basal Middle Eastern groups. In addition, the Sahara had periods of extreme dryness during the Ice Age, so the ur-basal Eurasians wouldn’t necessarily have been able to withdraw to Africa.

Using G-PhoCS they inferred separation dates between the various populations. I have two issues with this. First, their mutation rate seems likely, but there is still some debate about the exact value and whether it is constant across a lineage (for this level of phylogenetic distance the assumption of constancy seems valid). Second, the confidence intervals from these results are huge. The authors report the results, and tentatively attempt to relate separation to the LGM ~20 thousand years before the present, but know that they can’t assert anything robustly. It strikes me that we know the sequence of separations between the groups better than the period of separations.

ncomms9912-f4 But one definite result is the pattern of ancestry (or shared drift) which is derived from CHG. It is high in the Caucasus, as one would expect, but also in South Asia. This is not surprising. Several papers have suggested that the West Eurasian admixture into South Asians seems to have an affinity with northern West Asians. Agriculture in South Asia began at Mehrgarh with a traditional West Asian cultural toolkit, and likely the character of the ANI-ASI admixture took root here. In Europe many researchers believe that the replacement of the hunter-gather populations in most areas was rather complete after the initial admixture event that occurred when farmers initially entered the continent, and it seems possible that the same is true in South Asia as well. There are no “Ancestral South Indians” in pure form left, and the variation in ancestry between tribes and caste groups in many areas is not very large.

dstat When you into the supplements though it all becomes much clearer. To the left you see a table of D-statistics, where the left column are Indian populations, and in the right column are the top hits, X, for these groups in terms of inferred gene flow with the tree form (Yoruba, X; Onge, Indian population). The key thing to note is that while some Indian groups have the strongest hit from the Kotias CHG sample, others, and of note the North Indian Brahmin Tiwari community, the signal from the Afanasevo is strongest. The Afanasevo are genetically basically the eastern extension of the Yamnaya. In other words, the D-statistics are showing evidence of a migration from the steppe, and a migration from West Asia. This also makes sense of supplementary figure 3, which shows non-trivial shared drift among some South Asian groups with the Swiss Bichon WHG sample. The Afanasevo would have brought this via their EHG ancestry, which was about half similar to WGH.

The evidence from uniparental (Y and mtDNA) and functional genes is also interesting. CHG carry mtDNA haplogroups H13 and K3, and Y chromosomal groups J and J2. It seems likely that the prevalence of haplogroup in H is due to post-Neolithic population replacements. The CHG contribute about half the ancestry to Yamnaya, but these two did not have haplogroup R1a or R1b. Haplogroup J2 is particularly common among caste groups in South India. All this points to the likelihood that the Dravidian languages are probably derived from agriculturalists with West Asian roots, and gives a touch more plausibility to the idea that ancient Elamite in Khuzistan may have been a distant relative of Dravidian.

Additionally, the derived light-skin variant of SLC24A5 is found among the CHG, as it is among the Anatolian farmers. The haplotype is the common one found in West and South Eurasian populations. The variant for SLC45A2 in Kotias is definitely homozygous for the ancestral variant. On the whole most South Asians do not share European light-skin variants except for SLC24A5. The exceptions tend to be groups in the Northwest, and upper castes. Exactly the same groups which likely have the strongest Afanasevo stamp.

One thing the authors note is that the Caucasus themselves have been subject to great change. It is clear that a farmer group related to EEF has mixed with the CHG descended groups. And, today the Caucasus has very high fractions of ANE ancestry in some groups, but these samples did not at all. At ASHG a few years ago a prominent population geneticist offered to me that he thought ANE might not have been the best term, as there was no strong evidence that this group wasn’t more common elsewhere. But CHG did not have ANE ancestry, despite that being very salient in modern trans-Caucasian groups. This suggests a later expansion and mixing event. From what I know ANE drift is not evident in many Indian populations, pegging the arrival of ANE-bearing groups to a later period after agriculture. Gene flow into Amerindian groups, and high ANE fractions in Central Siberia and the Altai, do point to their locus of habitation in Northern Eurasia.

Finally, let’s remember that we’re constructing the past from the slim remains which we have on hand. Ten years ago we were using extant genetic variation, because that’s all we had, and that led us astray. In the broadest sketches the inferences were right, but in many details they were misleading. Similarly, we shouldn’t think that the ancient DNA yielding populations are necessarily the direct ancestors of any modern groups. We know, for example, that Ma’lta is actually not ancestral to the ANE population which contributed to both Europeans via the EHG and Native Americans. The ANE drift of these two groups has more in common than with Ma’lta. Like the ancient Ethiopian genome there are many interesting conclusions one can derive from novel results, but to the first carving of nature’s joints is not always the best.

 
• Category: History, Science • Tags: Ancient DNA, Genomics 
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basque

There’s a new paper in PNAS, Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques. It is a nice complement to the earlier paper on an earlier Iberian Neolithic sample. These individuals all date to a later period, most ~5,000 years ago, and one ~3,500 years. Despite the media hype, the results of this paper were pretty much expected, and it’s the final nail in the coffin of the idea that the Basque language and culture are relics of Paleolithic Europe. Rather, it confirms the result that the Basque descend in large part from agriculturalists who brought the Neolithic revolution to Europe. The genetic result began to be clear as early as 2010, when PLOS BIOLOGY published A Predominantly Neolithic Origin for European Paternal Lineages. The interpretation of that paper was wrong in some of the specific detail. It is quite likely that the R1b haplogroup did not come with the first farmers, but that it was a later arrival. But, the authors were early in refuting the contention that the high frequency of this lineage among Basques was ipso facto evidence that it was a primal Paleolithic signature. In fact much of that work exhibited some circularity, with the premise that Basques were primal descendants of hunter-gatherers being the linchpin for archaeogenetic inferences which then came back around to pointing out that the intuited genetic distinctiveness of the Basques was further evidence of their uniqueness.

Screenshot - 09082015 - 10:30:26 AM The admixture plot to the left reiterate a few things I’ve been asserting of late. First, the Spanish Basque are unique in having weaker signatures of being impacted by North African gene flow and the genetic signal associated with people from the Eurasian steppe than other groups in the Iberian peninsula. This isn’t a new finding. What is interesting though is that the authors confirm through a variety of methods that the Basque have Western European hunter-gatherer gene flow which post-dates the arrival of the first farmers. The earlier paper I allude to above suggested that the Iberian Cardial individual, which predates the oldest of these samples by ~2,500 years, had hunter-gatherer ancestry which exhibited affinities with a Hungarian, and not Spanish, sample. In other words, the first European farmers were themselves a compound population to begin with. Subsequent to their expansion all across Europe they seem to have absorbed local hunter-gatherer populations. This is the resurgence of hunter-gatherer ancestry over thousands of years that David Reich has mentioned before. This was a phenomenon across much of Europe, not just in the Iberian peninsula.

Which brings us to how we go about solving this puzzle. It seems that archaeologists and anthropologists have to start tackling the issue. One possibility is that the human geography of ancient Neolithic Europe was intercalated, with hunter-gatherer populations occupying zones between the expanding farmers which were not amenable to their agricultural practices. I suspect that the Pygmy example might be informative, as this group has had a long period of symbiotic coexistence with agriculturalists. Note also that the results from earlier work suggests that the fraction of hunter-gatherer ancestry increased even before the arrival of the Eurasian Steppe populations, which changed the character of Europe’s north, and to a lesser extent south.

Finally, there’s the enigma of the Basque language. The authors of the above paper mention possible connections with Paleo-Sardinian, which predates Romance dialects on the island. And Sardinians, like Basques, exhibit strong signatures of farmer ancestry. In fact, Sardinians have more farmer ancestry than any other Europeans, likely due to marginal pre-Neolithic presence on the island. The genetic closeness of the farmer groups from Spain up into Germany in the early Neolithic indicates a rapid expansion from a small founding stock with roots in the Balkans and or Anatolia. This sort of expansion is highly likely to be accompanied by the spread of the common language and culture of these people, and in that way the Basque can actually give us some vague insight as to the cultural character of the first Neolithic people, not, the hunter-gatherers. These results reiterate that some of the ancestry of the Basques does derive from the people of Paleolithic history in a genetic sense. But perhaps more importantly, it points the likelihood that there was a massive cultural rupture between Ice Age and Neolithic Europe, and the Basque stand with the latter.

 
• Category: Science • Tags: Ancient DNA, Basque, Genomics 
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51qciM4cBhL._SX258_BO1,204,203,200_*The past after the word*

If science is hard, history is harder. Harder in that the goal is to understand what happened in ages which are fading away like evanescent ghosts of our imagination. But we must be cautious. We are a great storytelling species, seduced by narrative. The sort of empirically informed and rigorous analysis which is the hallmark of modern scholarship is a special and distinctive thing, even if it is usually packaged in turgid and impenetrable prose. It is too pat to state that history was born fully formed with the work of Thucydides (or Sima Qian). In fact Thucydides’ pretensions at historical objectivity despite obvious perspective and bias lend credence to the assertions of those who make the case that the past is fiction (in this way Herodotus may actually have been more honest). The temptation is always great to paint an edifying myth which gives succor to national pride or flatters our contemporary self-image. The fact that modern nation-states in the technological age have vigorous debates about details as to the nature of periods of history in the recent past, when the people who lived during those times are still here to bear witness, is telling in terms of the magnitude of the task before us. Fraught questions must be answered with far fewer resources.

Much of history we see only vaguely through chance and contingency, known through happenstance and the whims of our ancestors. In the West the documents which shed light upon antiquity come to us through tunnels of finite transmissions, a furious period of textual transcription in the last few centuries before 1000 A.D. The Carolingians, the Byzantines, and the Abbasids all engaged in sponsoring the capital intensive project of taking ancient texts and making copies for posterity. The vast majority of the works of antiquity we have today can be traced back to this period[1]. Biases and concerns of the elites who sponsored these projects were critical in determining the nature of the source material which serves as the foundation for our understanding of the deeper past which we take for granted today. We know how little was copied because the extant material make copious reference to a vast body of work which was circulating in the ancient world on assorted topics (and even many of the works we do have are only portions of multi-volume endeavours, such as that of Livy).

brotherhoodBut what about pushing beyond what the text can tell us, and transitioning from history to prehistory? Here is where matters become opaque and conditional upon the nature of the texts (or lack thereof). This is clear when you observe that there are very early periods of human history when our knowledge of individual actors and daily life is actually greater than later epochs due to regress of civilization, or, changes in technology which mitigated against preservation of texts[2]. The “Dark Ages” of Greece between the Mycenaeans and the Classical Greeks are the purview purely of archaeology (and even during the Mycenaean period most Linear B were of a bureaucratic nature; I do not know of narrative literature such as we have for Egypt or Babylon). For the Classical Greeks the rupture was traumatic enough that their Mycenaean past became the subject of legends. The citadels of the Bronze Age warlords were viewed as “cyclopean” works, as if only giants could have created them. Similarly, the period in Britain between the end of central Roman rule and the Christianization of the Anglo-Saxons, about two centuries, is perceived only faintly because of the paucity of written records (this also explains why this period is often utilized as the setting for historical fantasy).

9780192807281_p0_v1_s260x420 Yet when text is silent one still has material remains. Their collection and analysis are the domain of archaeology, a historical science. The fact that history as we understand it deals in the written word, and so limits its focus to the period when we have texts, is itself a historical coincidence. Ideally traditional history and archaeology should work in concert, and critically, words have a way of deceiving and misleading. Most obviously we have a major ascertainment bias in our understanding of the past when we listen only to the perspectives of those who can speak through words, because they who were literate or had access to literate professionals were a very small subset of the broader human experience. Archaeology has less of this bias, because all classes leave behind their material evidence (though if one wants textual representations of a broader cross section of the Roman populace, the novel The Golden Ass is a good place to start). An excellent illustration of this for me, as readers know, is the extended argument in the book The Fall of Rome, which brings material evidence to buttress the position that the decline and fall of the unitary Roman state in the 5th century coincided with a genuine degradation of what we might term civilization. Revisionists looking purely at textual materials have long argued that the classical view was misleading, and to reduce their argument down toward its essence, suggest that classical civilization evolved and transformed, channeling its energies into different activities (e.g., the rise of Christian theology as a successor to the classical liberal arts, see Peter Brown’s The Rise of Western Christendom). But what material remains tell us is that there was indeed an economic and demographic collapse, despite apologia that one can make as to the reshaping of high culture in texts. One may choose to weight these facts, or not, but the facts nevertheless remain, no matter how many glosses one wishes to upon them. The Rome of 600 may have had many more Christian theologians than the Rome of 400 (which was then a mainly non-Christian city), but the Rome of 400 probably had a population on the order of 10-20 times greater.

41hdiv6SmHL._SY344_BO1,204,203,200_ In a world without text, which is almost all of human history, the material remains are all that we have to grasp upon. Though we can attempt to glean the minds of people long gone from paintings and scratches in stone, the reality is that what they hunted with, what they ate with, and the dwellings in which they lived, are going to give us concrete information where leaps of imagination are unnecessary. Moving beyond the text can allow us to truly illuminate the vast dark oceans of human history with more than our dreams, from the dawn of our species, down to even recent periods when literacy was the privilege of the few, and the experiences of the many were dead to us. Despite this, the paintings have only a few colors on the palette, because archaeology is filled with enormous gaps in perception. Pots not cloth. Caves not tents.

Which brings us to biology, and specifically genetics, as it turns out that DNA is actually one of the material remains that one can extract from archaeological field sites. It’s a robust macromolecule, and today researchers believe that it is feasible that some information can be drawn from remains as old as 1 to 2 million years, though that’s a best case scenario. When it comes to questions of demographic change genetic insights are key, and present data in a way that allows for more rigorous analysis. As has been the case in previous posts I must now give a nod here to L. L. Cavalli-Sforza and The History and Geography of Human Genes. Cavalli-Sforza’s magnum opus reopened the book in attempting to understand history through demographics. It was the first page, and the first chapter. Prior to this before World War II there was a cottage industry which attempted to do what Cavalli-Sforza achieved in the late 20th century. But these endeavors were hobbled by two problems. First, they was not scientific, often relying upon intuition derived from their erudition (they were not hypothetico-deductive, though that’s overrated if you have lots of data). Second, the reliance upon intuition meant that many of the conclusions dovetailed rather neatly with the ideological preferences of the day, National Socialism most horrifically, but much more widely than that was a shoddiness of nationalism inflected prehistory. Scientific romance without the genocide (see Pat Shipman’s The Evolution of Racism). After World War II archaeologists reversed course and decoupled cultural evolution and change from demographic variation. Works such as the Races of Europe became anachronistic when decades before they’d have been mainstream, and there was a strong bias toward a null hypothesis that pots, that is cultural traditions, migrate, but people do not.

 

k7442 Into this intellectual climate stepped Cavalli-Sforza and his students, triggering a minefield in academic explosions (see The Human Genome Diversity Project: An Ethnography of Scientific Practice). Molecular anthropology in its earliest incarnations focused on deep time. In particular, there was a recalibration of time depth of the origin of apes and humans, where the molecular biologists clashed with paleontologists, and came out the victors (see The Monkey Puzzle for a history of these controversies). Then, there was the “Out of Africa” debate (see The African Exodus). Though these were somewhat fractious and personalized arguments, the emotions around the implications of these contests of ideas were often limited to scholars (though the scholars themselves may not have felt the fallout was limited; apparently at Stanford in the late 1990s a cultural anthropologist gave a presentation where he juxtaposed a photo of Cavalli-Sforza with Josef Mengele). What Cavalli-Sforza did was bring genetic science toward addressing more contemporary phenomena, to answer questions which come to the cusp of the present, tackling issues of relevance to living human people on the scale of nations and peoples. Over many decades his lab collected enough information from hundreds of genetic loci to arrive at the sum totality of inferences which were eventually presented in The History and Geography of Human Genes.

CosttoSequenceaGenome-e1409924136899 Let’s take a step back here. Cavalli-Sforza and his colleagues had access to hundreds of markers at best. Note that ~2% of the human genomic codes for proteins, but there are 3 billion positions in terms of bases. Today anyone who wants to pay can get millions of positions through SNP-chip services. My son has billions of positions, because he’s been whole-genome sequenced. For phylogenetic purposes you don’t need billions, millions, or even thousands, depending on the nature of the questions you have in mind. But, it puts in perspective how far we’ve come in literally 20 years. Even 5 years.

As is the nature of science there was much that Cavalli-Sforza got wrong in The History and Geography of Human Genes. But there was much that he got right, because the results were so clear and strong on particular points of contention. In short, very broad patterns on the continental level jumped out when analyzing even hundreds of neutral (that is, not subject to natural selection) markers. For example, the data confirm a gradient of genetic diversity which implies human origins from an African locus, as well as the relative homogeneity of Europe (aside from Finns, European populations have a surprisingly low between-population pairwise genetic distance in most cases). But, more subtle counterintuitive relationships were often not robust (e.g., North and South Chinese do not bifurcate in the manner that he reported in the 1990s). And, most critically for the purposes of this post inferring past demography from current phylogeographic patterns had serious limitations.

*The present as a window into the past*

downloadm511NSSGQNWL._SY344_BO1,204,203,200_ The basic idea behind historical population genetics (archaeogenetics) which was pioneered by Cavalli-Sforza at the HPGL at Stanford was to look at patterns of diversity and relatedness among modern populations, and intersect that with what was and is known about history, as well as geography, and then allow those intersections to peal back the palimpsests of human history (see his The Great Human Diasporas). Though Cavalli-Sforza focused initially on autosomal markers scattered through the genome, in the period between 1995 and 2005 there was a great deal of work using uniparental data., the markers on the Y and mtDNA. The mtDNA is passed through women only, is copious in terms of quantity on a cellular level, and has a highly mutable region of utility for molecular phylogenetics. The Y chromosome exhibited some technical difficulties in comparison to mtDNA, but with the emergence of better extraction techniques as well as a focus on highly mutable microsatellite regions, it came to be set next mtDNA as a critical tool in the forensic reconstruction of human population history. In addition, both had the virtue of being nonrecombining, so that the generation of a phylogenetic tree was not an artificiality, but a reflection of the nature of the transmission of these two regions of the genome (congenial to a coalescent framework as well).

Human_migrationIn the end this line of research often resulted in a transposition of a phylogenetic tree upon a world map, outlining patterns of human migration. It also aligned well with another line of research which explicitly modeled the expansions of humans out of Africa as a “serial founder bottleneck” process. That is, each population which left Africa progressively branched out in a unidirectional manner, resulting in reduced genetic diversity as one progressed out of Africa.

Ramachandran, Sohini, et al. "Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa." Proceedings of the National Academy of Sciences of the United States of America 102.44 (2005): 15942-15947.

Ramachandran, Sohini, et al. “Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa.” Proceedings of the National Academy of Sciences of the United States of America 102.44 (2005): 15942-15947.

In its broadest strokes this model is not without validity. It does seem that most of the ancestry of modern humans can be traced to a population which flourished around or in Africa ~50-100 thousand years ago. Much of the inter-continental racial variation that we see in extant populations does nicely fit onto a bifurcating tree-like model (e.g., Non-Africans branch off from Africans, West Eurasians and East Eurasians diverge, Amerindians branch off from East Eurasians). The problem though is that the branches themselves turn out to be brambles which turn back in on themselves, and in some cases twist with other branches, creating lineages with very diverged ancestral roots. The yield of the earliest efforts by Cavalli-Sforza and his heirs was on a very coarse continental grain, where the effects of the dynamics were so striking that they would exhibit themselves across most neutral markers without much difficulty. But, when the questions were narrower, and the temporal and spatial scope more constrained, the earlier methods were not perceptive enough to smoke out the real dynamics.

Li, Jun Z., et al. "Worldwide human relationships inferred from genome-wide patterns of variation." science 319.5866 (2008): 1100-1104.

Li, Jun Z., et al. “Worldwide human relationships inferred from genome-wide patterns of variation.” science 319.5866 (2008): 1100-1104.

By the middle years of the 2000s researchers had gone back to a focus on recombining autosomal markers. But now they had a whole human genome to compare it to, as well as SNP-chips which quickly yielded large troves of data with little effort. In 2008 a paper was published which took the origin HGDP data set collected by Cavalli-Sforza and his colleagues, and utilized the new technologies to make deeper inferences. First, instead of hundreds of markers you had 650,000 SNPs. Second, the emergence of powerful new analytic and computational resources allowed for the complemention of tree-based and PCA visualizations of genetic relationship with model-based understandings of genetic variation and population structure. By “model-based,” I mean that the algorithm posits particular parameters (e.g., “3 ancestral populations”) and operates upon the data (e.g., “650,000 SNPs in 1000 individuals”) , to generate results which are the best representation of the fit of the data to the model.HGDPme This different from PCA, which has fewer assumptions, and represents genetic variation geometrically (each axis represents an independent dimension of variation within the data). Model-based clustering is very clear and aesthetically appealing. It gives precise results. But, the model itself is not necessarily right.

Anyone who uses these methods understands their limitations. If you use PCA to project variation of the data set, then the composition of the data you input is going to influence the largest principal components. Therefore, if you are asking questions on a broader spatial scale you should be careful about the possibility that you are overloading the sample set of interest with particular populations. More data in this case might result in less insight. Similar issues crop up with model-based clustering you don’t appropriately weight the populations. Another major problem is that the models are imposing limitations which might produce false inferences (false in that they do not accurately reflect demographic history). Most simply you might ask for many more population divisions than is realistic for the demographic and genetic history of the data. Consider a data set of Irish from Cork and Nigerians from a small village. PCA would no doubt show you two very tight and distinct clusters. With a model-based framework you could look for divisions and structure beyond K = 2 (two ancestral populations). The method is devised in such way that you would get results. But, they wouldn’t be very informative, and they’d be forced. They wouldn’t be robust. The model would be a poor fit to reality.

*From model to reality*

Obviously no model captures all elements of reality. But when the model deviates so much from reality that you get a false sense of what is true then that model is not nearly as useful. Being wrong is a definite bug. Aside from model-based admixture analysis, which posits a finite number of ancestral populations which come together to produce the genetic variation in the data set, you notice that the 2008 paper also had a tree representation of genetic variation. These two together give real and substantive results that can be useful. But, they mislead to the point of falsity in many specific cases.

nihms137159f3

Reich, David, et al. “Reconstructing Indian population history.” Nature 461.7263 (2009): 489-494.

This can be illustrated by the instance of South Asians, who are about 20% of the world’s population. A 2009 paper, Reconstructing Indian Population History, utilized both the higher autosomal marker density sets and new analytic frameworks to come to some specific conclusions which resolve many confusions about the nature of the genetic history of the peoples of the Indian subcontinent. So what did we know before? If you go back to the ideas of the old physical anthropologists they observed that many South Asian groups had an affinity to the peoples of West Eurasia (Europeans and West Asians). This varied as a function of geography and caste. In other words, there was a cline to the northwest, as well as up and down the caste system. You can see it in a PCA, where Indian groups vary in distance from Europeans, while Europeans form a very tight cluster. It also shows up in admixture based analyses. There is usually a K value where a South Asian modal cluster emerges, and it is near fixation in South Indian non-Brahmins, declining in frequency as one moves toward Pakistan, or, in North India up the caste hierarchy (the residual are West Asian and European clusters, except Bengalis, who have East Asian admixture). In The History and Geography of Human Genes South Asians form an outgroup to Europeans and Middle Eastern populations using older distance measures.

So far all good. One can imagine then a cline of genetic variation, with South Asians at one end, and West Eurasians at the other. On a PCA between East Asians and Europeans South Asians usually fall in the middle, but closer to Europeans. But there have long been major problems with this model when you drilldown into the details. The mtDNA and Y chromosomes of South Asians give very different results. The former classes them as distinct from West Eurasians, with distance affinities to East Eurasians. The latter on the other hand are quite a bit more like West Eurasians. Second, South Asians exhibit a lot of variation as a function of both geography and class in terms of their relatedness to word populations. If South Asians were deeply rooted in the subcontinent, as the migration maps above would imply, then we’re talking about massive barriers to gene flow which have persisted for tens of thousands of years. An alternative explanation is that South Asians are the product of recent admixture between two very different groups, which is what is often the norm when there is a lot of inter-individual variation in ancestral components and PCA position within a putative population group (e.g., African Americans). Finally, tests of natural selection geared toward detecting very recent sweeps have indicated a commonality between South Asians and Europeans and Middle Easterners on the haplotype of SLC24A5, which implies either extreme connectedness, or, recent admixture and migration (on the margin these two models are going to be hard to distinguish, since connections are mediated through migration).

I will sidestep the technical issues at this point, and just offer up that the work on South Asians has presaged much of what we’ve learned over the past decade when it comes to the genesis of modern population structure. The puzzles about South Asian genetic variation are resolved when you admit a model where a West Eurasian population mixed with a local indigenous group with distant affinities with other East Eurasians (see Genetic Evidence for Recent Population Mixture in India). The high level of between population variance within South Asia is due to the recent nature of the admixture event and the high genetic distance between the source populations. This may actually be the story of much of the world over the last 10,000 years. Instead of a regular branching process, imagine branches that periodically fuse back together, in a reticulated pattern. Another way to conceive of it is that the last 10,000 years have been a story of the destruction of population structure accrued over the past 100,000 years. A survey of this field can be found in the review Toward a new history and geography of human genes informed by ancient DNA.

*Inference made concrete, ancient DNA*

Up until now we have been talking about increasing the power of analysis of genetic variation in existent populations. Processes like bottlenecks and positive selection leave footprints in the genomes of modern peoples. But these methods of inference have limits. And, to a great extent they necessitate a simplicity of population dynamics to allow for them to have utility in painting a portrait of the past. Researchers had to assume that the past was simple, or the methods that they had wouldn’t be able to tell them as much as they claimed. The complexity of the demographic palimpsest could never race beyond ability of the genetic methods to peel it back, so there was a ceiling on the number of layers imposed upon the model.

41ePHetk1dL._SY344_BO1,204,203,200_ Ancient DNA was a game changer, because it did not come with these limitations. Instead of just inferring the past from the present, the past could now be inferred from the past! That is, a temporal transect in time could be generated which explicitly explored the trajectory of genetic variation across time and space. As if to recapitulate history the earliest work was with mtDNA, just as it had been with “mtDNA Eve” in the 1980s. The sequence target here is small and mtDNA is copious. The immediate upshot though is that massive discontinuities were detected. Populations replaced each other repeatedly in many regions. Pulse admixture events being inferred with novel methodologies on extant populations now could be understood to have been the natural result of migration and population change over the past ~50,000 years. Thanks to the work of researchers such as Svante Paabo and Eske Willerslev the number of samples we have from ancient DNA for humans has grown to such an extent over the past 5 years that a bright line is shining into what had been a dark cavern of prehistory.

*European man, made and unveiled*

Because of both the concentration of researchers in Europe, as well as suitable preservation conditions in Northern Eurasia, ancient DNA has totally changed how we understand the genetic history of this continent most especially. Two new papers have expanded the sample set to 170 individuals, and many major questions have now been answered, and other new questions have been triggered by perplexing results. A few years ago I was talking to Spencer Wells about the age that we are privileged to live in. Spencer is a history and genetics buff (he was one of Richard Lewontin’s last grad students). So naturally as genetic science has emerged to shed light on history we’ve tracked its developments very closely. Spencer professionally, he’s a genetic anthropologist. Many questions which in the past would have been unanswerable are now answerable. Truth is coming at us so fast that it is hard to even respond to all of it (if you wait too long to publish, everything might have changed).

Carl Zimmer’s piece in The New York Times, DNA Deciphers the Roots of Modern Europeans, is accurate as to the current state of the accelerating research in this area. This is the equivalent of having a Rosetta Stone. The ancients are now coming back to life. They speak! Everything has changed. In Nature Ewen Callway quotes a scientist stating in plain language, “Christ, what does this mean?” I’ll try and flesh out further what it means, but the papers themselves do a good job. These are first steps, but they’re very big steps. There’s only so much more to go, and truth will be at hand.

First, the two papers, Massive migration from the steppe was a source for Indo-European languages in Europe, and Population genomics of Bronze Asia Eurasia. As might be suggested by the title the latter paper has coverage of populations outside of Europe, while the former focuses on Europe. The samples sizes are 69 and 101 respectively. The first paper uses a methodology which yields many SNPs, while the latter relied upon whole-genome sequencing (variation is variation, so really this is a minor detail for the results, though it matters a lot for the working scientists who are generating the data). Both agree broadly on the major results. Additionally, there is a third work, a preprint, Eight thousand years of natural selection in Europe, which has results in line with the second paper above (it has a section on selection as well as phylogenomics).

*European genetic structure is younger than the pyramids*

51IZQjMbVlL._SY344_BO1,204,203,200_

The old debate whether Europeans are descended from farmers or hunter-gatherers was always somewhat incoherent. All humans are descended from hunter-gatherers. Rather, the issue was whether modern Europeans descend primarily from people who were resident within the continent of Europe at the end of the last Pleistocene, or, whether they descend from peoples who developed agriculture in the Middle East ~10,000 years ago. That is, did farming spread through cultural diffusion or migration? Plants or people? The answer is actually not straightforward, but, the results are not controversial today.

First, migration seems to have been the dominant dynamic which defined the spread of farming, especially early on. These first farmers who arrived in Europe were genetically very different from the hunter-gatherers of Europe’s north and west. Some of their ancestry had been isolated by long distances for tens of thousands of years before contact. The people of the Iberian peninsula today have less genetically in common with the hunter-gatherers which were present in the region when the farmers arrived than do modern Northern Europeans, who harbor a greater fraction of ancestry which derives from the Pleistocene people. The main qualifier I’d put on this though is that the farmers themselves seem to have picked up European hunter-gatherer admixture on their way out of the Middle East. The fraction is on the order of ~50%. The other component has been termed “Basal Eurasian,” because this element is an outgroup to all other Eurasians, including the European hunter-gatherers. That is, the Basal Eurasians are an outgroup to a clade that includes such as diverse populations as Andaman Islanders, Australian Aborigines, Japanese, and European hunter-gatherers.

Lazaridis, Iosif, et al. "Ancient human genomes suggest three ancestral populations for present-day Europeans." Nature 513.7518 (2014): 409-413.

Lazaridis, Iosif, et al. “Ancient human genomes suggest three ancestral populations for present-day Europeans.” Nature 513.7518 (2014): 409-413.

The figure to the left is from the paper Ancient human genomes suggest three ancestral populations for present-day Europeans. WHG = “Western (European) Hunter-Gatherers.” EEF = “Early European Farmers.” You can see that EFF is a compound. I don’t think there’s too much clarity right now with where the EEF got its WHG-like ancestry. It could have been structure in the Middle East. Or it could have been in Southeast Europe. In the supplements of Haak et al. they test a Hungarian sample, and it does seem that the EEF individuals are closer to it than the Western European hunter-gatherer samples. So there might have been structure in the ancestral European population, but the confidence here is low. And from what I can tell Basal Eurasian is still something of a mystery, almost occupying the role of “Planet X” before the discovery of Nepture. To make the patterns make sense they have to exist, but much isn’t known about them in detail. And of course there seems to be a huge lacunae right now in terms of exploring the population genetics of the Middle East in a similar fashion as has occurred in Northern Eurasia (my understanding is that Carlos Bustamante was an important person in getting Latin American populations in the 1000 Genomes; unfortunate that there wasn’t someone else to advocate for including a Middle Eastern group, since this is such an important part of the world for human history).

With all that said, if one assumes that the West Eurasian admixture in EEF was from European hunter-gatherers, then it is clearly obvious that most of the ancestry of modern Europeans can date to the Pleistocene (i.e., EEF + Yamnaya likely means more than half the ancestry is WHG-like if you look back 10,000 years). But, this proportion obscures the fact that massive migrations and population turnovers have occurred, so that a simple model of expansion out of Ice Age refuges no longer holds. Cavalli-Sforza has long argued that pure proportions of ancestry are less important than the dynamic, as population growth driven “waves of advance” will over time dilute the initial genetic signal anyway (though the final proportion of non-WHG-like ancestry is actually higher in much of Europe than Cavalli-Sforza conceded in the early 2000s). Whether the ancestry of modern Europeans derives predominantly from those of European hunter-gatherers, the idea of dominant local continuity in a given region has been thoroughly refuted. The hunter-gatherer ancestry in the British Isles, for example, may be mostly from admixture into agricultural groups far to the south and east during the initial waves of advance, not from the people who initially recolonized Northern Europe in the early Holocene.

k8488 The second demographic turnover event which has been highlighted by the papers cited so far is from the east. The migration from the steppes. This event had disproportionate, even dominant, impact across much of Northern Europe. Culturally it is often rooted in the Yamnaya complex, which gave rise to various disparate and wide ranging “daughter” societies. David Anthony’s The Horse, the Wheel, and Language surveys the archaeological terrain thoroughly. If you are interested in this topic, and haven’t read it, do read it. In this work Anthony outlines the spread of Indo-European languages via expansion of a mobile pastoralist elite. He was involved in the retrieval of some of the samples in these studies, and from what I am to understand he was personally surprised that the genetic data imply not just elite migration, but a folk wandering. Not just a band of brothers, but whole peoples on the move.

Haak, Wolfgang, et al. "Massive migration from the steppe was a source for Indo-European languages in Europe." Nature (2015).

Haak, Wolfgang, et al. “Massive migration from the steppe was a source for Indo-European languages in Europe.” Nature (2015).

Focusing on the genetics, these people seem to themselves be a compound of disparate elements. First, some of their ancestry derives from a population which Haak et al. term “Eastern Hunter-Gatherers” (EHG). And the other half derives from a population with affinities to those of the Near East, but different from that of the EEF. There is some disagreement between the two papers in Nature as to the details, but Allentoft et al. admit that they did not have EHG samples, which may have impacted their ability to detect admixture. Allentoft et al. also diverge from Haak et al. in the emphasis they place on the ancestral component among the Yamnaya which some term “Ancient North Eurasian” (ANE) based on the location of the most ancient individual of this line (see Upper Paleolithic Siberian genome reveals dual ancestry of Native Americans). What does seem clear is that this element is deeply diverged from other West Eurasian populations, on the order of ~20 to 30 thousand years. And, they contribute about half the ancestry to the EHG (the rest is WHG-like). The descendants of the Yamnaya people brought this component all throughout Europe, with the exception of the Sardinians and Sicilians, likely isolated because of their position on the Mediterranean littoral (Sicilians have later Near Eastern admixture as well). But this is not limited to Europeans, as a substantial proportion of Native American and West and South Asian ancestral heritage (at least the Kalash) also exhibit connections to this component. Allentoft et al., like Haak et al., points out that there was likely structure in this broader group. That is, the ANE themselves were diversified, with the ancestors of the element in Native Americans and Europeans different from that which contributed to the Siberian component. In fact I have talked to researchers who believe that the term “Ancient North Eurasian” is misleading, as there is little clarity on the distribution of this group (the highest inferred fractions in Eurasia are in the North Caucasus). It is feasible that the Kalash have a different ANE source than Europeans.

A key issue to note, and that confuses some people, is that the ancestry of groups such as Yamnaya exhibited commonalities with other groups across Eurasia. Therefore, if you replaced similar groups then the change in admixture components utilizing model-based programs may not be as extreme as you would think. To illustrate what I’m getting at concrete, the population transfer between Greece and Turkey during the 1920s was far more impactful as a dynamic than simple before and after admixture estimates would suggest to you (since genetically the two groups were very similar). The figure from Haak et al does not use admixture components that break out naturally, but their inferred demographic mixes taking into account the genetic character of the putative ancestral populations. The blue component refers to WHG, but WHG-like ancestry is also in both the green (Yamnaya) and orange (EEF) elements (this is why I’m saying it is likely that modern Europeans are mostly >50% WHG-like).

One temporal dimension that Haak et al emphasizes in particular, but seems clear in Allentoft et al. as well, is that non-Yamnaya ancestry slowly begins to rise again by the Bronze Age. Why? I will address that below. But, Allentoft et al. has broader Eurasian samples, including likely Indo-European populations in the trans-Ural and trans-Altai regions. In both of these areas the successor cultures had EEF-like ancestry. That is, like the Corded Ware population, and unlike the parent Yamnaya group. This strongly implies back-migration by this complex from Eastern Europe, as far east as western China, during the Bronze Age.

warbefore In The New York Times piece David Anthony states two things which puzzle me as an interested lay person without his expertise. First, he seems to think that the amalgamation of the Yamnaya and EEF-descended populations was not a warlike process. Specifically he says “It wasn’t Attila the Hun coming in and killing everybody,”. This is a useful image, but let’s be honest and note that the Huns were not primary producers, and did not aim just to increase pasturage by killing settled peoples as Genghis Khan had wanted to do (see The End of Empire: Attila the Hun & The Fall of Rome). Rather, they conquered and subordinated other barbarian groups, as well as extorted tribute from the East Roman Empire. The demographic impact of the Huns was not directly from them, but the fact that they and their successors (in particular the Avars) facilitated the migration of other groups, first, the Goths, and later the expansion of the Slavs. By the time of Attila barbarian leaders were well aware that the conquered were vital as economic producers whose capture and subjugation would allow them to engage in status competitions of conspicuous consumption. I do not believe that this was quite the case in the Copper and Bronze Ages beyond the limes of the civilized world, which was then an small archipelago of literacy in a sea of barbarism. Both the above papers indicate massive demographic disruption across Europ. Though war as we understand it is necessarily inevitable for our species, between the rise of agriculture and the modern period it seems to have been very common. It is not a coincidence that the Scandinavian Corded Ware culture are also called the Battle-Axe culture. Yes, many archaeologists believe that they were primarily a status symbols. I’m willing to bet many archaeologists are wrong. It’s been known to happen.

gokturk_empire_by_still_ates The second issue which Anthony brings up is the connectedness of the various post-Yamnaya cultures, in particular that of the earliest Indo-Europeans on the fringes of western China, 4,000 miles from their likely point of origin. The genetic characteristics of these eastern groups is also such that it is likely that there was gene flow from Europe, mediated by a common steppe culture. Anthony states that “I myself have a hard time wrapping my head around explanations for that”. This totally confuses me, because he’s a professional archaeologist, so he must know that widespread gene flow and cultural ties cross the vast swath of the Eurasian heartland is not surprising at all! To Carl Zimmer I pointed out the example of the Goturk Empire of the mid 6th century A.D., which expanded rapidly from the core Altai zone, and prefigured the later distribution of the Turkic people, from the Nile to the fringes of the Arctic sea. Language and lifestyle mediate relationships and demographic contact. The peripatetic character of steppe peoples is well known and attested from the historical and semi-historical record. Groups such as the Huns, Avars, and Alans, had inchoate origins in the heart of Eurasia, and moved back and forth along lines of cultural affinity as needed. Alans were serving under the Mongols in China in the 13th century, but 800 years earlier they had accompanied the Vandal tribe to North Africa, and maintained a separate identity there until the conquest of Justinian. It seems entirely plausible that this pattern of hyper-mobility arose with agro-pastoralism along the whole range of continuous ecological appropriateness, only ending with the rise of gunpowder empires and the crushing of the Oirat by the Manchus (with the tacit approval of Russia).

*Northern European archetypical physical characteristics are younger than the pyramids*

Spencer Wells, a new look in the world

Spencer Wells, a new look in the world

Phylogenomics is tangled and complicated still, even with all these new results. I’ve only scratched the surface above. You really need to read the papers, and their supplements, to even get a sense of what’s going on (yes, ideally you’ll know what an f3 statistic is!). But, the population genomics which give us a sense of the character of natural selection and phenotype over time is much clearer. The suite of traits which we associate with white Europeans is quite possibly very recent, as late as post-Bronze Age. White supremacist scholars of the early 20th century who posited that ancient Egypt (in fact, all civilizations) were founded by blonde Nordic people turn out to likely be wrong because these civilizations probably predate the existence of blonde Nordic people, both in their genetic structure, and in their physical type (at least in any number).

nature14507-f4 The genetic architecture of pigmentation is something geneticists know a fair amount about, because genome-wide association has been very fruitful in this area. Unlike traits such as height there is a large amount of between population variation in pigmentation. And, that variation is due in large part to a few genes of large effect. At SLC24A5 there is a SNP which accounts for around 1/3 of the melanin index difference between Europeans and Africans, using an admixed African American population to test the effect. As I have observed before SLC24A5 in its derived form is as close to fixed as you can get in Europeans. In the 1000 Genomes data set of thousands of individuals I found a few samples with a heterozygote and the ancestral copy. In the Middle East this allele is also near fixation, though not quite. As you can see from the figure I adapted from Allentoft et al., among South Asians the derived allele is also at high frequency. My whole family is a homozygote for the “European” variant. There is some suggestive evidence that this haplotype derives from the Middle East. It was only at low frequency among European hunter-gatherers[3]. But, by the Bronze Age had it gone to fixation in Europe, as well as on the Eurasian steppe.

Of more interest to me is the trajectory of SLC45A2. The derived allele is nearly fixed in modern European populations, though not nearly to the same extent at SLC24A5. In Iberian and Sardinian populations the ancestral type is in the range of ~10%. During the Bronze Age in Europe it was only at ~50% frequencies, which is in the range of modern Middle Eastern populations. It was even at lower frequency in the steppe, from which the putative Indo-Europeans migrated.

Finally, in this panel for pigmentation they included a major SNP in OCA2-HERC2 region. This locus is famous for being involved in blue-brown eye color variation, explaining 75% of the variance, and also exhibiting the third longest haplotype in the European genome. Naively projecting from these SNPs one could credibly argue that the ancient hunter-gatherers of Europe at the beginning of the Holocene were dark-skinned and blue-eyed! The Bronze Age European samples, which in this case are biased toward Northern Europeans, had a range of genetic variation equivalent to modern Southern Europeans. The people of the steppe did not seem to have blue eyes at all.

skin2

These results align perfectly with those in Mathieson et al. One thing to observe is that the Paleolithic samples, which have a much deeper time depth, are “ancestral” at all these positions. Even if the sample size is small (N =4), they’re from diverse times and places. Does that mean that they were much darker than even the Holocene hunter-gatherers of Europe? As some have pointed out we can’t just straight-line extrapolate from the genetic architecture of today to the past. Remember that Neanderthals exhibited pigmentation polym]orphism, but of a different sort. A deeper functional analysis may yield the possibility that Paleolithic Europeans had alleles which also resulted in lighter skin, but they were different ones from the ones segregating as polymorphisms today. I have already stated that I doubt much of modern European ancestry derives form before the Last Glacial Maximum. The reason that modern genetic variation in terms of predicting phenotype gives these sorts of results is that they may have arrived at the same trait value via a different set of polymorphisms. Genotype-phenotype maps derived from modern populations may be a poor predictor of the relationship 30,000 years ago. Why would one think that selection upon variation in pigmentation began at the cusp of the Holocene?

But, I do think we can predict with more confidence the nature of phenotypes for populations which are genetically much closer to modern ones. Bronze Age Europeans fit that bill. And, I know something personally about what the appearance of individuals during this period might have been based on genetic architecture: both my children exhibit a genotype profile on pigmentation loci similar to many Bronze Age Europeans. That is, they’re fixed for the derived variant of SLC24A5, and are heterozygotes at SLC45A2 and OCA2-HERC2 (my son, but not my daughter, is a heterozygote at KITLG; it does seem to make a difference in hair color). In terms of just their complexion they could pass as indigenous Southern Europeans, but definitely not Northern European.

*Culture leads genes by the leash*

Another major finding of Mathieson et al. and Allentoft et al. is that the derived allele found across West Eurasians that allows them to digest lactose sugar as adults has been sweeping up in frequency over the last 4,000 years. This allele spans a diverse array of populations, from Basques to South Asians. With pigmentation it seems that we need to consider jointly the impact of ancestry and selection (in South Asia derived SLC24A5 frequencies are definitely a function of both selection and descent). But with LCT it seems likely that selection is paramount. The predominant genetic character of Eurasia was established by the Bronze Age, but the frequency of the lactase persistent allele was still far lower. Tests of natural selection which focus on patterns of haplotype variation long detected a huge hit from LCT so this is not surprising.

51r8Ph-vcaL._SY344_BO1,204,203,200_ Intriguingly Allentoft et al. indicates that though the Bronze Age steppe populations had low frequencies of the derived allele, it seems that they did have a higher frequency than contemporary populations. This suggests that the origin of this haplotype, which spans the whole range of Indo-European speaking populations, and also into Finnic groups and the Basque, may still be attributed to the Yamnaya complex. In 10,000 Year Explosion Greg Cochran proposed the hypothesis that the favored mutation for LCT enabled the spread of Indo-European pastoralists. These results are not strong support for that direct causal relationship; rather, it strikes me that the ascendancy of the pastoralists drive the selection pressures for the allele in question. Biology did not drive culture, culture drove biology. The milk-drinking Celts and Germans encountered by Julius Caesar 2,000 years ago may still have been in the middle stages of adaptation to the agro-pastoralist lifestyle slowly being perfected by their ancestors.

*As the white man is, so shall we all be*

A new look as well

A new look as well

It is a running joke of mine on Twitter that the genetics of white people is one of those fertile areas of research that seems to never end. Is it a surprise that the ancient DNA field has first elucidated the nature of this obscure foggy continent, before rich histories of the untold billions of others? It’s funny, and yet these stories, true tales, do I think tell us a great deal about how modern human populations came to be in the last 10,000 years. The lessons of Europe can be generalized. We don’t have the rich stock of ancient DNA from China, the Middle East, or India. At least not enough to do population genomics, which requires larger sample sizes than a few. But, climate permitting, we may. And when that happens I am confident that very similar stories will be told. Using extant genetics we can already infer that modern populations in South Asia are a novel configuration of genotypes and phenotypes. The same in Southeast Asia, the Americas, and probably Africa. Probably the same in East Asia. Perhaps in Oceania. Even without admixture humans evolve in situ and changed, but with admixture the variation increases, and the parameter space of adaptation becomes richer and more flexible.

In Isaac Asimov’s later Foundation books he touched upon the existence of racial diversity in the future (from what I recall his earlier works from the pulp era were whites-only galaxies). At one point Hari Seldon encounters someone whose physical appearance seems to be East Asian, and they discuss the strangeness of people with East Asian ancestry being termed “Easterners” and those with European appearance being “Westerners.” With a loss of memory of the ancient distribution of these populations on the home planet only the shadow of a semantic recollection exists as a ghost in the galaxy-spanning Empire based out of Trantor. But of course tens of thousands of years in the future, even barring genetic and mechanical modification, it is unlikely that modern racial types will persist in any way we would recognize them.

But these results coming out of ancient DNA are telling us that what is likely to be true for the far future was also true for the recent past. White Europeans are a new type. But so are brown South Asians. Ethiopians have a recent ethnogenesis, as do most North African groups. The Bantu expansion has reshaped the face of Africa on the edge of the historical horizon. And so forth. In the big picture Young Earth Creationists are wrong, but in the specifics the idea that the sons of Noah populated the world ~5,000 years ago is not looking as crazy as it once did! Human genetic variation across Eurasia today may be mostly clinal, but in the recent past it was not. Rather, it was characteristic by sharp discontinuities and isolated local populations with diverged ancestry from their neighbors.

*And culture made man in its image*

51L3op-B8fL._SY344_BO1,204,203,200_ About ten years ago it was common in paleoanthropology to assume that human beings emerged almost fully formed ~50,000 years ago, and wiped out all the others in a genocidal wave of advance. Richard Klein advanced this model in The Dawn of Human Culture. Klein’s thesis was that some stochastic event, a mutation, resulted in the punctuation of a new species, our own. This singular genetic process allowed for the emerged of fully formed linguistic faculties in our lineage, which allowed for the development of the cultural flexibility, which made the rest of the human lineages evolutionary dead ends. It was a single and elegant story. It appealed to the principle of parsimony. The reality of “archaic” admixture was a difficulty for Klein’s model, evidenced by the fact that he voiced his skepticism of genetic claims of admixture in The New York Times after most others had moved on. For Klein a biological change explained the rise and success of our species, not a cultural one.

At the time I found the thesis compelling. We were after all a very special species. Modern Homo made it to Oceania and the New World. Something must have happened. Something big. What else could explain our rapid expansion and marginalization of other lineages? I’m a biologist, and so biology is an appealing causal mechanism.

linear

*The luck of the English facing the ocean*

At about the same time the evidence for Neanderthal admixture came out, Luke Jostins posted results which showed that other human lineages were also undergoing encephalization, before their trajectory was cut short. That is, their brains were getting bigger before they went extinct. To me this suggested that the broader Homo lineage was undergoing a process of nearly inevitable change due to a series of evolutionary events very deep in our history, perhaps ancestral on the order of millions of years. Along with the evidence for admixture it made me reconsider my priors. Perhaps some Homo lineage was going to expand outward and do what we did, and perhaps it wasn’t inevitable that it was going to be us. Perhaps the Neanderthal Parallax scenario is not as fantastical as we might think?

41z97bDZvUL._SY344_BO1,204,203,200_ Consider the case of Europe around 1600. In England and northern Germany (or what was to become northern Germany) you have two Protestant and genetically similar populations. But by 1850 it looked as if England was going to demographically overtake Germany in a broader genetic sense. James Belich’s Replenishing the Earth reviews the history of this period, when England spearheaded a demographic revolution far out of proportion to what one might have predicted in the year 1000. But by 2000 Germany, or Germans, had caught up somewhat. How? Millions of Germans migrated to the United States, starting in very large numbers in the mid-19th century, and were “picked up” by the demographic revolution which was the United States. The point is that contigencies of history, cultural and social, rather than biology, explain the trajectory of the gene pool over time. Much of the human past, and the sharp fluctuations in gene frequencies, might be driven by the long and forceful arm of culture.

In the treatment above I note that the EEF farmers who by and large replaced the indigenous hunter-gatherer groups in modern Southern Europe were themselves a compound. The hunter-gatherer ancestry within the EEF was far more successful than that of those they replaced, but the only reason that this was so was geographic coincidence. The WHG-like groups absorbed into the EEF were positioned further east, and so closer to the initial locus of expansion of Neolithic farmers. Similarly, the Neanderthal admixture into modern populations was almost certainly localized to particular groups. This is not to say that there are no biological differences between human populations which may explain a wide range of phenomena. Anyone looking at the skull of a Neanderthal and a modern human knows there are. There are also likely bio-behavioral differences between extent populations. Gene-culture coevolution is a real process, even if the details need to be worked out. But the interplay between biology and culture is complex, and in many cases cultural changes are driving the biological change, and then fixing differences which are advantageous to the “winners” (lactase persistence seems rather to be a perfect case of this). But just as in the individual case we must also remember that winning is often in part a function of being lucky. Naturally selection, generally thought of as a deterministic process, is also to some extent stochastic[4].

*From genetic islands to a roiling sea of humans*

One of the most shocking things for many of the geneticists working in the area of ancient DNA, and encountering the variation of the past, is the high level of population structure. That is, you have groups co-resident for many generations who nevertheless exhibit genetic distances of intercontinental scale. But as I stated above David Reich himself found the same results for India. And, in Africa you have long symbiotic populations, such as the pygmy groups of the Congo, and their agricultural neighbors, who are genetically very different, and have been for tens of thousands of years. Allentoft et al. dryly observe that “These results are indicative of significant temporal shifts in the gene pools and also reveal that the ancient groups of Eurasia were genetically more structured than contemporary populations.”

castesofmind About 10 years ago I read Nicholas Dirks’ Castes of Mind. Dirks is an eminent scholar who is now the chancellor of UC Berkeley. He emphasizes the power of European categories and systematization in creating the modern caste system. I don’t want to reduce his argument to a caricature. Obviously caste predates European colonialism. Dirks would admit this. But in Castes of Mind it is hard to shake the feeling that he believes that the British imposition of formalization made it what we truly understand it to be today. That caste has to be understood as a contemporary and early modern phenomenon, rather than an ancient one that was a structural feature of South Asian society.

The genetic evidence is clear now, and it paints a very different landscape. Many of the caste, even jati, boundaries we see today are thousands of years old. Endogamy long predates the British. It may predate the Aryans! Rather than the British, or Aryans, inventing caste, this form of ethnic segregation may date to the initial admixture event, to be reinvented and modified with each new population which arrives and imposes its hegemony on the subcontinent. In The New York Times David Reich states “You have groups which are as genetically distinct as Europeans and East Asians. And they’re living side by side for thousands of years.” He then he goes on to say “There’s a breakdown of these cultural barriers, and they mix,” alluding to the rise in WHG ancestry in farmer samples over time. Of course it is interesting to remember Reich’s work on India has highlighted exactly how persistent caste has been, and how it maintains genetic variation in a localized region that is often nearly inter-continental in magnitude.

We can never know if 6,000 years ago the LBK people, the first farming culture of Northern Europe, imposed a caste-like system of segregation when encountering the indigenous hunter-gatherers. Nor can we say with total confidence whether their relationship exhibited a symbiosis analogous to that between the Bantu agriculturalists and pygmies of the Congo (though do note that in these scenarios the Bantu communities are higher status, and the individual pygmies often have a semi-slave status). But, we need to look to what cultural evolutionary models and empirical results can tell us to make sense of these patterns. Ancient DNA can tell us very concretely the details of changes in allele frequencies. We can somewhat confidently reconstruct the faces and complexions of our ancestors. The questions population genomicists ask and answer in relation to animal models are relatively cleanly addressed by these data sets, assuming the sample sizes are large enough. But humans are the cultural animal par excellence, and that is the critical new variable which will require a new set of scholars to come together and create a truly multi-disciplinary understanding of the human past, present, and perhaps future. Powerful genomic techniques which produce results which have implications for the study of human history needs to leverage the full array of scholars who study human historical science.

1 – The three-fold copying is an important matter, because the different cultures had different preferences and goals. The Arab effort for example focused mostly on the philosophical production of the ancients. Without the Byzantines we would have far less of the humanistic production of Classical Greece, in particular the theatrical tradition.

2 – Much of what is known about the diplomatic history of the Bronze Age Near East has been preserved in cuneiform tablets. Though unwieldy, this form of writing on clay tablets is obviously more robust and less dependent upon copying than parchment and papyrus which came later.

3 – I would be curious to know if it is the same haplotype as is currently common in Eurasia.

4 – New mutations will usually go extinct, even if they are favored, in the initial generations. It is only when the frequency becomes high enough due to chance that selection will inevitably drive its frequency up, perhaps to fixation.

 
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41ePHetk1dL._SY344_BO1,204,203,200_ Most readers are aware that ancient DNA has revolutionized historical inference of the past, particularly prehistory. In 15 years we’ve gone from draft genomes of one living human being, to genomes of humans who have lived tens of thousands of years ago! But by and large the ancient DNA revolution has been one of temperate and boreal climates, because of the reduced degradation of DNA in such circumstances. A new paper in PNAS opens up a sliver of a possibility of expanding the purview of this analysis, Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean:

Between 1500 and 1850, more than 12 million enslaved Africans were transported to the New World. The vast majority were shipped from West and West-Central Africa, but their precise origins are largely unknown. We used genome-wide ancient DNA analyses to investigate the genetic origins of three enslaved Africans whose remains were recovered on the Caribbean island of Saint Martin. We trace their origins to distinct subcontinental source populations within Africa, including Bantu-speaking groups from northern Cameroon and non-Bantu speakers living in present-day Nigeria and Ghana. To our knowledge, these findings provide the first direct evidence for the ethnic origins of enslaved Africans, at a time for which historical records are scarce, and demonstrate that genomic data provide another type of record that can shed new light on long-standing historical questions.

Hopefully this is just the beginning. Part of this the economics of innovation. The best ancient DNA labs are training others in their techniques. From what I’m to understand at this point there’s a backlog of remains to be analyzed. As the expertise becomes distributed labor and capital will no longer be the rate limiting step.

 
• Category: Science • Tags: Ancient DNA 
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James C. Chatters 2002 book

James C. Chatters 2002 book

By now you may have read the breaking news in The Seattle Times that Eske Willerslev’s group is going to publish genetic results on Kennewick Man. This “scoop” was obtained through the freedom of information act, which makes sense since Kennewick Man has been embroiled in political controversy since the beginning of its discovery by James Chatters in the 1990s. The issue is that morphologically the remains were not typical of contemporary Native Americans, which might cause some doubt as to the legitimacy of the social-political rights of the indigenous people of the region today. The social-political aspects have been beaten to death, and I am not particularly interested in that area. Rather, the science is more fascinating, if, somewhat less surprising in light of the results that are going to come out in the near future.

2019387254The most famous reconstruction of Kennewick Man is strange because it resembles British actor Patrick Stewart. Humans use phenotypes, morphology, to ascertain genetic relatedness when DNA is not available. In the 1990s DNA was not available. The inference by many researchers who had access to the remains was that Kennewick Man was different because his morphology may have resembled a person of European heritage. The controversy turned into such a circus that somehow Steve McNallen, arguably America’s foremost Northern European neo-pagan expositor, made claims on the remains on the same grounds as Native American people! Later scholars suggest that perhaps Kennewick Man was not so much European, as not typical of contemporary Native Americans (e.g., perhaps he was part of an early migration of basal East Eurasians related to the Jomon of Japan).

41VAznr2aiL._SX258_BO1,204,203,200_ If the Seattle Times report is correct, and I believe it is, Kennewick Man is part of the ancestral population to modern Native Americans. This should put to bed most of the political debate, since the results are likely to mollify many Native activists. But, there are still details to be fleshed out. A 2012 publication suggests that there was a secondary migration out of Eurasia, which resulted in the Na-Dene group which is common in the northern and western portions of North America. In contrast, Kennewick Man is likely to belong to the first ur-North Americans, who arrived as a relatively small population from Berengia ~15,000 years ago. This is the overwhelming majority of indigenous ancestry, and south of the Rio Grande basically the totality.*

Due for an update!

Due for an update!

The context here is important. One insight of modern ancient DNA is that there has been a great deal of population turnover over the past ~10,000 years, as well as admixture between disparate lineages. When Kennewick Man died ~9,000 years ago Europeans as we understand them did not exist genetically. All across Eurasia, Africa, and Oceania, the Holocene brought radical demographic turnover (with some exceptions such as the Andaman Islands and the deserts of southwest Africa). The New World was somewhat different, as I implied above. There were some demographic disruptions, but south of the Rio Grande, and across the eastern half of North America, the populations descend from a relatively homogeneous founder stock which arrived at the end of the Pleistocene. The fact that many remains seem “atypical” for the morphology of Native Americans is strong evidence of in situ evolution.**

Years ago a physical anthropologist told me that when you look at Amazonian natives they “looked” like Siberians. Yes, they had changed and adapted, but only somewhat. It illustrated to me the powerful constraint of limited genetic variation upon populations. Similarly, though there is variation in pigmentation among native populations in the New World, it is far less than you see in the Old World. Why? Perhaps it is a function of different (or lack thereof) of selective pressures. Or, perhaps the variation wasn’t there for selection in the first place? The history of the Old World has jumbled all our easy narratives. The New World may actually be a godsend because of the simple elegance of its demographic history.

* From my Twitter exchanges with Pontus Skoglund I believe there is some population structure in the founding “First American” group, though not a great deal.

** Admixture is an issue, but that can be obviated by genetic testing, as well as looking at early modern remains.

 
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In the post below Martin Sikora, an author on the K14 ancient DNA paper, has responded. The whole thing is worth reading:

Hi Razib,

after reading your post it I thought it would not hurt to chime in with a bit of perspective from my side, as I don’t entirely agree with some of your criticisms. Some of the reactions to our paper have caught me a little by surprise, but in retrospect it probably reflects the complexity of the story, which is something I also struggled with (and still am!).

Part of the confusion seems to be that it is assumed that since we find that K14 somehow relates to all three European ancestral proposed by Lazaridis et al., that it necessarily also has contributed these components to modern Europeans. In your post you also seem to imply that, i.e we don’t “acknowledge the possibility that K14 did not leave modern descendants, and was part of an early population which did not end up flourishing”. I actually agree with the early population part, and we also acknowledge that in our suggested model in Figure 2, which does not have a K14-related population directly contributing to modern Europeans. What one can say with reasonable certainty though is that K14 does share substantial amount of ancestry with Mesolithic Hunter-gatherers (and therefore modern Europeans by extension), but at the same time appears less close to East Asians than all Western Eurasians, so things are complex. Therefore if you take the Lazaridis et al. model as a backbone, you need some extra gene flow to account for that, be it from Basal Eurasian into K14, or some sort of basal gene flow between East Asia and early West Eurasians, post-K14 but pre-ANE/HG split. While we don’t have the resolution to be sure, our results do suggest that K14 was close to or a already somewhat down the HG branch of the ANE/HG split, which implies that those proposed components would not only have to be already somewhat differentiated by 36 kya, but also already have had mixed to a certain extent.

Regarding your take on the PCA results, I would disagree and say that these are very much what you would expect for an individual of that age. K14 is after all ~36,000 years closer to the East Asia / West Eurasia split, so it lacks a substantial amount of drift on the European branch. It is nevertheless shifted towards Europe on PC1 from the origin as expected (a bit more so than MA1 actually). Pontus Skoglund had a nice recent paper in MBE that demonstrates the same effect (see Figure 9 in doi:10.1093/molbev/msu1920). As you say, using modern variation to infer affinities of ancient samples has limitations, and PCs are often hard to interpret. In the same spirit I would also not interpret the different admixture components in K14 as itself being admixed with all those components, but rather reflecting ancestral relationship with modern populations represented by these components. The same is obviously true for the “Middle East” component, but it still implies that K14 somehow relates ancestrally to those populations whereas all other HGs including MA1 do not.

Overall, I do think that migrations played an important role, e.g. I don’t think that “Basal Eurasian” came with K14 to Central Europe or was already present back then in another way, that seems pretty clear. I would also not say that our results are necessarily a refutation of the Lazaridis et al model, but I do think they show that it seems to have been already quite complicated in the Upper Paleolithic. If you need a new migration/component for every new individual, to me this questions at least to a some extent whether one can really talk about three or any other number of discrete ancestral populations for all modern Europeans. Personally I would expect ancient samples from the Caucasus or Central Asia to yet again spring some surprises. The cool thing is that we’ll probably know soon, since many groups are adding more and more samples to the picture.

Anyways, I just wanted to share my thoughts, hope this clears up things a bit.

Btw regrading your subsequent ANE post, I can confirm that those are the Kalash. Interesting also that the correspondingly the Kalash ADMIXTURE component shows up in MA1, but is almost absent in K14 (see our Figure S20).

 

 
• Category: Science • Tags: Ancient DNA 
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credit: Alan Light

Credit: Alan Light

As you may know the actress Daryl Hannah depicted Ayla, the protagonist from Jean Auel’s Clan of the Cave Bear, in the film version. Unlike many castings Hannah was an inspired choice, as she does look like the description of Ayla in the novels. Tall, blonde, and with a high forehead (remember, there’s a lot of contrast with Neandertals in these books). Auel depicts human Neandertal interactions to such an extent that there is hybridization. In the 1980s when her series first gained traction this was not particularly a popular angle. This was the age of “mitochondrial Eve”, when replacement was a more fashionable idea (ask Milford Wolpoff about it). Even though in the details Auel may have been wrong about hwo this process played out (admixture seems to have occurred earlier on in the modern human migration out of Africa, not in northern Eurasia), overall she has admitted feeling vindicated by the work of people like Svante Paabo.

But there’s one area that is pretty important where Auel was wrong: it seems that during the Ice Age anatomically modern European humans did not fit the Nordic ideal of tall, blonde, and gracile. One reason I posted the image of the skull of K14 in the post below is that even without professional background in analysis of skeletal morphology it is visually obvious that this individual was rather robust. There’s a reason that it was apparently termed “Australoid” by earlier anthropologists. The native people of Australia and Papua are among the most robust humans alive today. In contrast other populations have gone through a great deal of gracilization, especially over the last 10,000 years. What about the coloring? I couldn’t find a reference in Seguin-Orlando et al. to any analysis of the functions of the genome, but in Anne Gibbons’ piece in Science she states that K14 was ” a short, dark-skinned, dark-eyed man.” I doubt she would say this unless she knew from the research team what the genotype of this individual was. Perhaps there is a later paper coming out on population genomics rather than phylogenomics, but these results would be consistent with other results.

One story that ancient DNA is unraveling is that of the complexity of human demographic history. There are lots of surprises in store. But a second no less important angle is that humans have adapted and changed functionally over the last 100,000 years, to the point where salient physical traits vary a great deal across both time and space.

 
• Category: Science • Tags: Ancient DNA 
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download (1) Ancient DNA has made it big time, with a write up in The New York Times by Carl Zimmer, From Ancient DNA, a Clearer Picture of Europeans Today. The primary sources of the piece are two papers published recently in Europe, Ancient human genomes suggest three ancestral populations for present-day Europeans (ungated version) and Genome flux and stasis in a five millennium transect of European prehistory. Like the earlier mtDNA work on ancient DNA what these results are suggesting is that European demographic history has been punctuated by periodic discontinuities. Here’s an important bit from the Zimmer article:

Archaeologists have found that early farming culture didn’t change drastically for the next 3,700 years. But about 4,000 years ago, the Bronze Age arrived. People started using bronze tools, trading over longer networks and moving into fortified towns.

Dr. Pinhasi and his colleagues found that the era also brought a sudden shift in human DNA. A new population arrived on the Great Hungarian Plain, and Dr. Reich believes he knows who they were: the northern Eurasians.

horsewheelbook It seems really unlikely that Europeans are special in this tendency, with broad world-wide trends as outlined in Towards a new history and geography of human genes informed by ancient DNA. For decades there have been books written about the coming for the Indo-Europeans. David Anthony’s The Horse, the Wheel, and Language is probably the best recent summation of the “they came out of the steppes” viewpoint. If there is a major update on this it now looks like the demographic impact of the Indo-Europeans was much greater than we had previous imagined. But are Indo-Europeans special? Probably not…earlier work suggested major discontinuities in Europe with the arrival of agriculture. Later in Africa you had the Bantu expansion, which replaced most of the local people. And as John Hawks points out the ancient Siberian who lived ~45,000 years ago probably comes from a group with no modern descendants. With the disappearance of the Ma’lta boy’s people ~20,000 years later from eastern Siberia it suggests that the heart of Eurasia has been roiled multiple times since the arrival of anatomically modern humans.

Addendum: I would take minor issue with the title of The New York Times piece. The picture isn’t really clearer, but cloudier. It’s just that the old clear picture was wrong, and the new cloudy picture is less wrong. Ultimately the clouds may clear, but we need more samples for that.

 
• Category: Science • Tags: Ancient DNA 
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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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180px-Spartacus_StatuePLoS GENETICS has finally published the paper which reported on the Iron Age Thracian ancient DNA results, Population Genomic Analysis of Ancient and Modern Genomes Yields New Insights into the Genetic Ancestry of the Tyrolean Iceman and the Genetic Structure of Europe. This seems to be a work which is an improvement on the margins, though it is adding solidity to a somewhat muddled picture of migrations and mixing in prehistory. It is important as the authors themselves admit that inferences from ancient DNA are constrained by the fact that we just don’t have that many samples. Basically everyone is attempting construct models predicated on the samples that we have, but that often leads us astray, even if the results themselves are trustworthy.

I should mention that the image above is of Spartacus, who was famously a Thracian. It is in Bulgaria, which covers part of ancient Thrace. But from the genetics that I’ve seen I’m rather sure now that the Slavic migrations had a very strong impact on Southeast Europe, and modern Bulgarians are far more “hunter-gatherer” than the ancient ones were. This points us to the complexity and nuance of historical-cultural memory. Bulgaria derives from the name of the Bulgars, who were Turkic. But modern Bulgarians speak a Slavic language, not ancient Thracian, and I think it is likely that they have at least as much exogenous Slavic ancestry as they do ancient Thracian (and by late antiquity in any case most people in Thrace were speaking Greek or Latin).

 
• Category: Science • Tags: Ancient DNA 
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How Europeans became Europeans is a big question, in large part because Europeans (i.e., “whites”) are still what an ideology in disrepute would term the herrenvolk of the world. But this reality, the truth of which sows discord in any discourse, does not need to negate the fact that the question itself is of interest, and today is eminently answerable. Europe has a long history of archaeology and its climate is mild-to-frigid in a manner which might aid in preservation of subfossils. For decades archaeologists have debated whether the ancestors of modern Europeans were farmers or hunters. It seems quite likely that the real answer is both, and, it’s complicated.

But the Gordian knot of history’s inscrutable veil is now be shredded by Thor’s hammer of Truth. More literally Pontus Skoglund has another paper out in in Science (how many times will I type that?), Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers. If you don’t have academic access, the supplements are quite rich.

ancientDNA The panel to the left shows the where and when of the samples. The key is that some of these are farmers and some of these are hunter-gatherers (as inferred by their cultural association). They’ve been examined before with more primitive techniques, but this latest paper ups the ante, even granting genomic coverage as relatively modest by current standards. The authors reiterated that there was a massive genetic difference between the first farmers who arrived in Sweden ~5,000 years ago, and a native hunter-gatherer tradition. The F st was on the order of 0.05. To get a sense of scale the maximum F st for modern Europeans is between Finns (a highly drifted group) and southern Italians (a highly admixed group with significant Near Eastern ancestry), at ~0.01. The F st between modern Europeans and modern East Asians is on the order of ~0.10. In other words, two contemporaneous ancient populations in Sweden which were in near proximity for many generations had a genetic distance on the order of half the distance of Eurasia today. In fact this F st is familiar to me. A few years ago at ASHG an Indian group had a poster which talked about the fact that coexistent South Asian groups (castes, jatis, etc.) within a region might have an F st as incredibly high as…0.05! Obviously I’m not saying that ancient Sweden was characterized by caste, but I am asserting that genetic distinctiveness in Europe on the cusp of full agriculture within a local region probably mirrored modern India, where occupation and community identity are as informative as geography.

treemix So why the huge genetic distance? The figure to the left gives a clue as to why. The farmers from Sweden, represented by Gokhem2, have more “hunter-gatherer” admixture than Otzi the Iceman. Ajvide58 has significant “Ancestral North Eurasian,” which is also found in the New World (Anzick1 is a Clovis individual from Montana). What is of note is that both the European farmers have a component with a red shading that has previously been termed “Basal Eurasian,” in that it forms an outgroup in the non-African phylogenetic tree to populations from West Eurasia, East Eurasia, and Australasia. Because it is such an outgroup it no doubt had a large genetic difference from the others, and a high F st value. Even ~25% contribution, as in the case of Gokhem2, might have been enough to introduce enough diverged drift to generate a great deal of allele frequency difference.

pc Many of the results in this paper were prefigured earlier. For example, it turns out that modern Swedes are closer to the hunter-gatherers than they are to the farmers. The PC plot to the right has northern Europeans at the top and Middle Eastern populations at the bottom. To the right are Finnic groups, with the Sami off the chart (I reedited it). All the ancient hunter-gatherers are outside of the contemporary distribution. One thing to remember is that the ancient individuals were projected upon the variation of modern populations. Therefore I suspect this plot understates how distinctive the ancient groups were. Second, it seems likely that modern Finnic populations are relatively intrusive latecomers to the Nordic scene, as the ancient hunter-gatherers have no particular affinity for them. Rather, if there is one population which resembles the hunter-gatherers from Gotland it is Lithuanians. This is not surprising. I have always held that the last region of Europe to be touched by the farmers from the Near East was the eastern Baltic. It is somewhat ironic that this area, and the Lithuanians precisely, were the last continental Europeans to be Christianized in the 14th century.*

So we’ve established that modern Swedes, and therefore modern Scandinavians, are descended more from the hunter-gatherers than the farmers who brought agriculture to the north. But it is in the functional genome where there’s a twist on the story: the farmers may have looked physically more like modern Swedes than the hunters. That’s because at two SNPs which are fixed (in SLC24A5) or nearly fixed (in SLC45A5) in modern Europeans yield matches to the farmers and not the hunters. These two SNPs are among the strongest quantitative trait loci for pigmentation in Europeans. Without them it seems unlikely that the hunter-gatherers would have been recognized as what we’d term “white.” An immediate objection to this is that the ancient hunter-gatherers had a different genetic architecture for pigmentation, so that their lightening alleles were different. Perhaps, but observe that we’ve already stated that the preponderance of the ancestry of modern Swedes is from these hunter-gatherers, and from what we know the genetic architecture in this population is not particularly surprising. Substituting the ancestral allelic variant at this loci tends to make these individuals darker (that is, through mixed marriage with non-Europeans). One could construct more complex scenarios of gene-gene interactions, but I think at this point we know where the parsimony lay.

With the large genetic distance, as well as the fact that the hunter-gatherers exhibited minimal gene flow from the farmers, and, likely a very salient physical difference, it seems plausible that we have the ingredients for inter-group conflict or at least an uneasy coexistence. Though it seems unlikely that the story of Grendel is an allegory recollecting this far distant time, it might not be far off from the truth in terms of how the farmers and hunter-gatherers interacted. Eventually the two groups congealed, but it took thousands of years.

Finally, let’s get back to the truly exotic fact lodged within these new papers: that there was a group of Basal Eurasians. The Basal Eurasians were further from the hunter-gatherers of Europe than the hunter-gatherers of Europe were from the ancestors of Australians or East Asians. Like the “Ancient North Eurasians” it seems likely that this is a “ghost population,” with no modern exemplars. No doubt as I write this there are papers which are being written or conjectured as to their relationship to populations outside of Europe, as it seems that the Middle East is one area where a deeper probe of possibilities is necessary. But perhaps it is to this group of Basal Eurasians that we owe the innovation of agriculture? Like shadows in our past their cultural impact is strong, but their identity as a distinct people has been eroded away by thousands of years of admixture and the flux and flow of peoples.

Citation: Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmer, Pontus Skoglund, Helena Malmström, Ayça Omrak, Maanasa Raghavan, Cristina Valdiosera, Torsten Günther, Per Hall, Kristiina Tambets, Jüri Parik, Karl-Göran Sjögren, Jan Apel, Eske Willerslev, Jan Storå, Anders Götherström, and Mattias Jakobsson, Science, DOI:10.1126/science.1253448

* The Sami were Christianized later, but the Sami were not at all part of the European system, as the Lithuanians actually were. The Sami are analogous to various indigenous groups, or Jews. In Europe, but not of it.

 
• Category: Science • Tags: Ancient DNA 
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admixture

Citation: Towards a new history and geography of human genes informed by ancient DNA, Joseph Pickrell, David Reich, doi: 10.1101/003517

440px-PazuzuDemonAssyria1stMilleniumBCEThere were giants in the earth in those days; and also after that, when the sons of God came in unto the daughters of men, and they bare children to them, the same became mighty men which were of old, men of renown.

- Genesis 6:4

Joe Pickrell and David Reich have put up a preprint at BioRxiv, Towards a new history and geography of human genes informed by ancient DNA. Since it’s a preprint at BioRxiv you can 1) read it for free 2) comment on it. It is a magesterial review of “where we are,” though close readers of this weblog may not find much that is new in their survey of the empirical results which are coming out of human population genomics and ancient DNA analysis. In regards to this let me highlight two sentences. First, it is now clear that long-range migration, admixture and population replacement have been the rule rather than the exception in human history. Second, the serial founder effect model is no longer a reasonable null hypothesis for modeling the ancient spread of anatomically modern humans around the globe. For the second I’m thinking in particular of Sohini Ramanchandran’s 2005 paper, Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa, though the model is older than that obviously, as is made clear in the acknowledgments. For the massive ground that the paper covers when it comes to the latest findings it is highly concise, and I commend it to anyone wishing to dive into this exploding literature. Pickrell & Reich show how the analysis of dense marker data sets with more powerful techniques has allowed for the teasing apart of the interlaced layers of the historical genetic palimpsest. But, the complement to this has been the development of the field of paleogenomics, which allows for the explicit analysis of ancient genomes. Another section of the preprint touches upon the technological changes which are allowing for more and more DNA analysis of ancient samples. In particular they point out that rather than focusing on sequencing very rare pristine remains the near future may be in looking at known SNPs on a larger number of samples, because the technical challenges for such typing are far lower.

Credit: Maulucioni

Credit: Maulucioni, Haplogroup R

The preprint is focused on the genomic aspects of this research because the authors are statistical geneticists, but it does not hesitate in offering up a host of historical and archaeological hypothesis which might be tested in the next few years. Also, they do not take a definitive position on the role of long distance migration and punctuated admixture events, as opposed to more continuous gene flow (though the methods which analyze contemporary populations seem to be better at detecting the former). So I will hazard a general model. It seems that root of what is driving these demographic changes are cultural changes. And cultural changes over the past ~30,000 years have been very fast and punctuated, and have accelerated. To given an example, the cultural chasm between a Egyptian in 500 AD as opposed to one in 500 BC would be far greater than that between two that lived in 500 BC and 1500 BC. Whether the word “revolution” is necessary for cultural adaptations such as the acquisition of agriculture, it seems clear that these were shifts in lifestyle which radically changed the local human demographics, as some populations entered into a phase of rapid population expansion in a condition of land surplus (e.g., farmers can extract many more calories per unit of land than hunter-gatherers, so the first farmers invariably encounter massive land surplus and operate at the higher boundary of productivity). Basically Peter Bellwood’s model in First Farmers captures many of the broad features of what occurred in the Holocene to produce ubiquitous admixture we see in the map at the top of this post (the methods pick up the strongest signals, and so usually underestimate admixture). Small group of individuals acquired a cultural adaptations which resulted in a winner-take-all scenarios of demographic expansions until a new equilibrium was attained repeatedly over the past 20,000, and especially 10,000, years. These the primary layers in the palimpsests that geneticists are teasing apart. Additionally, I will add the proviso that I suspect these long distance leapfrogs often became strongly male-biased in the genetic signal. It would be totally unsurprising to me if haplogroup R has its origins in the North Eurasian population which has left a legacy in Native Americans and Europeans.

Archaeologists and historians are going to be reluctant to shift from a dominant position which is skeptical of migrationism. Part of this is due to an ideological bias which emerged after World War 2. It is also simply the fact that the statistical methods employed by the newest batch of researchers are abstruse and difficult for outsiders to decrypt (though I find the methods in Ancient Admixture in Human History comprehensible after a close reading, so it’s not impossible). But archaeologists and historians are essential in constructing plausible models which can explain the genetic patterns we see around us. The motive engine for these changes are cultural phenomena, and cultural researchers are the ones who can shed the most light on the possibilities.

 
• Category: Science • Tags: Ancient DNA, Human Genomics 
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Palearctic ecozone

Palearctic ecozone

pca21.40.43

Citation: Nature (2014) doi:10.1038/nature12960

After reading the supplements of the La Brana hunter-gatherer paper I have a few extra thoughts in a very general sense. One result you see on PCA plots with Europeans is that the La Brana sample (along with the Swedish hunter-gatherers) are shifted toward modern Northern Europeans, and to some extent even Finns. Obviously this is noteworthy because they don’t cluster with modern Spaniards (even Basques). But when you plot them on a world-wide distribution you see something else: the La Brana individual is the most shifted toward Asians of any of the European samples (this includes British, Iberians, Utah whites, Finns, and Tuscans). This isn’t due to cryptic East Asian ancestry. Rather, it’s that Paleo-Siberian ancestry which can be found in many West Eurasians and Native Americans. This is in contrast with the Luxembourg hunter-gatherer which is dated ~1,000 years earlier than the La Brana individuals. I don’t know if the dates are reliable enough, but it seems plausible enough that there may have been events of demographic change on the scale of 1,000 years in ancient Europe.

dstat

Citation: Nature (2014) doi:10.1038/nature12960

To get a better sense they used D-statistics to estimate possible admixture/relatedness between Mal’ta and various populations. A negative value indicates more drift shared between H2 and H1 (admixture, gene flow, common ancestry, etc.). Sardinians are a European floor for “Ancestral North Eurasian” (ANE), which the Mal’ta individual represents. La Brana is statistically significantly more related to Mal’ta than all tested populations except for Orcadians and Russians. It is more shifted, but not to a statistically significant degree in those cases. The main qualification I want to add here is that Lazaridis et al. have reported that there is a “Basal Eurasian” population which has admixed across Western Eurasia, and increases the distance between Mal’ta and the populations with which it has mixed. The farmers which introduced agriculture to Europe seem to have brought this element, and it is found at a high fraction in the Caucasus, explaining the value for the Adygei. In fact the Adygei have more not less ANE than Northern Europeans. Since the La Brana individuals likely lack Basal Eurasian that could be affecting the D-statistics, inflating the implied ANE in the La Brana.

With all that qualification, it does seem that these La Brana individuals have genetic affinities with populations as far afield as Central Siberia, and the New World (via these Siberians). Additionally, like the other ancient European hunter-gatherers it exhibits signs of reduced genetic diversity compared to modern populations. What are we to think of this? In the broad view this is really not that surprising. 400,000 year old Iberian hominins seem to have had affinities to populations which were later found in Siberia. The Neandertals, from the Altai to Spain, seem to be surprisingly similarly and genetically homogeneous. Eurasian wolves have also gone through a population bottleneck during the Pleistocene. What this suggests to me is that the Palearctic ecozone has been characterized by a high degree of population mobility, and, extinction. Ancient DNA is sampled from northern locations due to likelihood of preservation, but these regions are also on the settlement frontier, and it wouldn’t be surprising to me that the populations are going to be characterized by low effective population sizes because they’re expanding rapidly from small founding groups.

Finally, this has some implications for our model of population assimilation and replacement. It seems that modern Europeans are a synthesis of disparate strands which have co-mingled over the past 10,000 years. One element, the majority element in the north and east, are hunter-gatherers which descend from the early West Eurasian settlers of the northwest. These were the Ice Age inhabitants of Europe. Likely they had long had connections across the latitudes of the Palearctic zone. One thing that we are seeing with the pigmentation genes is that these Western European hunter-gatherers were very different from modern Europeans. If about ~50% of the ancestry of Western Europe derives from these populations, then we’re confronted with the possibility that several of these loci have experienced nearly complete selective sweeps after an admixture event. This is not impossible, but, another option is presented us when we consider that the far north has long been a conveyor belt of peoples. Eastern cousins of the Western hunter-gatherers, could have brought whole-genome affinities into modern Europeans similar to these ancient individuals. But these may already have changed in their modal phenotype. The paper’s supplements reports that the Y chromosome of the La Brana seem to be ancient branch of haplogroup C, which is dominant in Eastern Eurasia. A possible connection to the Mal’ta people? Perhaps. But it is important to note that very low frequencies of this haplogroup still exist in Southern Europe. So the hunter-gatherers are likely not gone in toto. But combined with the mtDNA evidence of massive changes, this may point to later Bronze Age demographic shifts, being masked by the wide scope of genetic homogeneity in Eurasia.

Obviously the picture is still only partially formed. But it’s nice to have the past being painted so vividly.

 
• Category: Science • Tags: Ancient DNA 
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Citation: Nature (2014) doi:10.1038/nature12960

Citation: Nature (2014) doi:10.1038/nature12960

Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European:

Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe…The adoption of farming, stock breeding and sedentary societies during the Neolithic may have resulted in adaptive changes in genes associated with immunity and diet4. However, the limited data available from earlier hunter-gatherers preclude an understanding of the selective processes associated with this crucial transition to agriculture in recent human evolution. Here we sequence an approximately 7,000-year-old Mesolithic skeleton discovered at the La Braña-Arintero site in León, Spain, to retrieve a complete pre-agricultural European human genome. Analysis of this genome in the context of other ancient samples suggests the existence of a common ancient genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic. The La Braña individual carries ancestral alleles in several skin pigmentation genes, suggesting that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Moreover, we provide evidence that a significant number of derived, putatively adaptive variants associated with pathogen resistance in modern Europeans were already present in this hunter-gatherer.

The headlines about this individual having dark skin are well founded, like the Luxembourg hunter-gatherer the sample has ancestral “non-European” copies of most of the major loci which are known to have large effect sizes (SLC24A5, which is now fixed in Europeans, SLC45A2, which is present at frequencies north of 80% in most of Europe, and KITLG, a lower frequency variant known to have a major impact on skin and hair). Additionally, this individual is related to the Ma’lta individual, just like the Swedish hunter-gatherers, but unlike the Luxembourg male (which did predate the Spanish samples by 1,000 years). Lots of functional stuff is in this paper too. Seems like immune adaptations aren’t just a function of agriculture.

One thing I want to note is that I’m not sure how much of the shift toward Finns of the Swedish and Spanish hunter-gatherers is due to Paleolithic European ancestry, vs. admixture with “eastern” elements. Since the Finns seem to have more recent East Asian ancestry excess paleo-Siberian in the Mesolithic samples may shift them in the same direction. The eastward since of the La Brana individuals is really obvious in the world wide PCA, they are farther toward East Asians than any other modern Europeans.

 
• Category: Science • Tags: Ancient DNA 
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Ancient DNA figure

Citation: Ancient human genomes suggest three ancestral populations for present-day Europeans

Note:
Purple text included by author of this post

At some point you have no doubt encountered trees of the sort you see to the left. They are incredibly useful visualizations of historical relationships between lineages. Breeding populations. The metaphor of the tree of life was co-opted almost immediately by evolutionary science in the 19th century. On the orders of tens of millions to billions of years the idea of diverging and bifurcating lineages is accurate to a great extent in terms of depicting the dynamics of natural history. But even on this scale the tree masks facts which are not of trivial importance. Horizontal gene transfer means that even very sharply delineated branches of the tree of life may share commonalities across wide regions of the genome. The smaller the value which defines the last common ancestors of two putative lineages, the muddier the image reflected through the lens of the tree becomes. And yet the tree visual metaphor persists when comparing populations which are rather close genetically in an evolutionary sense because of its plain utility. Trees are thick in L. L. Cavalli-Sforza’s History and Geography of Human Genes, which paints the broad and rich landscape of human populations only diverged over the past few tens of thousands of years, our own species.

This is not to ignore the self-evident fact that tips of the branches can eventually converge. Geneticists have long acknowledged, and leveraged, recent admixture between populations long separated by time and space. No one denies that African Americans coalesced out of the relations of black slaves and white settlers. Or that the population genetic landscape of Latin America can not be understood without taking into account the varied quanta of African, European, and Amerindian ancestry which defines particular locales. The reality of admixture in these cases was attested to historically, is visible in a straightforward phenotypic sense, and, can be detected using a small number of classical markers.

What has has changed over the past 10 years, and in particular the past 5 years, has been the analytic fruit born of high density marker sets. By this, I mean rather than the hundreds of markers which L. L. Cavalli-Sforza and colleagues had access to, modern statistical geneticists can extract patterns out of hundreds of thousands of markers, and often whole genomes. This allows for researchers to detect more subtle or distant events which have been erased slowly by the effects of time. To my mind the seminal paper which heralded a paradigm shift was 2009′s Reconstructing Indian History. In this publication the authors concluded that South Asians, ~20% of the world’s population, are themselves a synthetic population, derived from two primary ancestral groups. One group, “Ancestral North Indians,” (ANI) has close affinities with West Eurasians (Europeans, Middle Easterners, etc.). Another group, “Ancestral South Indians” (ASI) has distant affinities with East Eurasians. In fact nearly all Indian subcontinental populations (there are exceptions) can be modeled as a two-way admixture, with various proportions of these two ancestral populations (also see Genetic evidence for recent population mixture in India for an update). The big take home was that the admixture had been thorough and deep enough so that standard clustering techniques (e.g., PCA) could not allow one to infer that South Asians were a synthetic group, ~2,000 to ~4,000 years post-dating an amalgamation event. One major stumbling block was that no close proxy existed for ASI, which was totally absorbed into what became South Asians. But the authors made use of the fact that Andaman Islanders were sufficient substitutes for the purposes of inferring the dynamics of the admixture (they diverged ~20 to ~30,000 years before the present from ASI). Using these methods the same group also came to similar conclusions about Amerindians in Reconstructing Native American population history. Another research group concluded the same for populations in the Horn of Africa, Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool. And even stranger results can be found deeper in Africa, Ancient west Eurasian ancestry in southern and eastern Africa.

More recently there has been the finding that an ancient Siberian boy seems to be representative of a population related to West Eurasians which contributed a substantial proportion of the ancestry of the first settlers of the New World. These results were prefigured by intriguing hints in the genome-wide studies as well as uniparental lineages. The power in this case is that internal nodes in the tree of life which were once only inferred from descendants, can now be examined directly with ancient DNA. There are limitations to time and locale. DNA degrades exponentially, and even in the best of cases it seems that the edge of preservation will be on the order of 100,000 to 1 million years. Additionally, cold and dry climates are naturally going to be highly enriched for samples, because tropical wet climates are amenable to rapid degradation of biomolecules of any sort.

A_large_blank_world_map_with_oceans_marked_in_blue To me a major implication is that over the next ten years the natural history of Pleistocene metazoans of some size and numbers across the Palearctic shall be illuminated to a much greater degree than we could have imagined. First in line will be humans and dogs, and later this will expand to assorted other lineages, such as bison and elk. And it is the human part of the jigsaw which is at the heart of a recent preprint posted on bioArxiv, Ancient human genomes suggest three ancestral populations for present-day Europeans. Since it is a preprint I won’t repeat much that you can read for yourself. I want to emphasize though that you really should read the supplements if you want more than spare conclusions. As the title states the authors conclude that overall you require at minimum three ancestral populations over a post “Out-of-Africa” time scale to model the dynamics of the emergence of Europeans. Though there were hints of this utilizing results from extant populations, the presence of ancient DNA truly pushed the ability to draw conclusions over the edge. That is because it seems that few of these ancient populations exist in “pure” form. One of the major shortcomings of drawing conclusions from distributions of populations in the present about the past is that interactions and admixtures were far more thoroughgoing than researchers had imagined.

The figure (modified) at the top of this post lays out the findings. In the preprint the authors arrive at the simplest model which can explain the most data. They acknowledge freely that there are likely modifications and elaborations on the edges and margins, and that the data might be explained by more complex models, but the key outcome is that they have rejected more parsimonious models which were once ascendant in regards to the ethnogenesis of Europeans. Ten years ago (see Seven Daughters of Eve) some researchers were presenting a cartoon model of hunter vs. farmer, as if these were two distinct options for the origins of all Europeans. But it turns out even the more nuanced and realistic models which posit varied degrees of genetic and cultural assimilation and interaction were false. Which seems clear from these data, and the ancient DNA, is that a substantial minority fraction of the ancestry of Europeans derives from a third population of northern Eurasian provenance.

Vision1 Going back to the lack of parsimony, to the left you see a model of diversification outside of Africa that many had in mind until recently. In this framework a small population of northeast Africans left that continent 50 to 100 thousand years ago, and populated the rest of the world. One group moved east, and gave rise to the populations of eastern Eurasia, as well as Australasia and the New World. Another branch moved north and west, and gave rise to Europeans and and Middle Easterners. The rest of population history might be modeled then as admixtures and rearrangements of this original diversification. In this scenario South Asians are an admixture of West Eurasians and an extinct branch of East Eurasians, explaining their affinities to both great branches of humanity. The divergent nature of Australians might simply be an artifact of their long term isolation in Oceania, rather early on in the diversification of East Eurasians. This model was already difficult to square with genetic data, but it could be shoehorned. Or at least I thought it could, because I did so myself.

Vision2 The simplest form of the new model complexifies the topology considerably. Now there is an early branch off of a Eurasian population prior to the diversification of West and East Eurasians, and within the western clade there is a separation between a North Eurasian group, and West Eurasians proper. Putting the focus on Europeans, they may be thought of as a complex admixture between Basal Eurasians, West Eurasians, and North Eurasians. The Basal Eurasian component is mediated by “Early European Farmers,” EFF, who seem to be a hybrid between this group and West Eurasian hunter-gatherers. The North Eurasian component seems to be both ancient and recent. Ancient because some Swedish hunter-gatherers had it (though the Central European one lacked it), and recent because the EFF populations which evident ancient Near Eastern ancestry lacked it, suggesting that it was not as widely present across western Eurasia as it is now. In fact, it is present in high fractions across many Middle Eastern populations, especially the Caucasus. Though the authors studiously avoiding speculating, it is clearly intriguing to them that the North Eurasian component is so widespread, and, that it is likely that it expanded relatively recently. Like the Denisovans the pesence North Eurasian DNA from the far north may simply be a function of biased preservation.

How the authors inferred the existence of Basal Eurasians is rather convoluted, and outlined in the supplements. In many ways this is the only simple model which fulfills all the conditions of their data. The key finding is that the European hunter-gatherers, both Central and Northern, were equally genetically closer to all East Eurasians than EFF. This sort of symmetrical relatedness implies that it is not admixture, but reflecting an ancient, but more recent than the outgroup, bifurcation in the phylogenetic tree. The EFF distance from East Eurasians is a function of the earlier divergence of their Basal Eurasian ancestry. The nature of the Basal Eurasians is left somewhat opaque. One can posit many scenarios of ancient population structure in the Near East, or migrations back and forth between these region and Africa. More data, and especially ancient DNA from the Near East, would clarify the model (unfortunately modern Near Eastern populations are high admixed).

Citation:  Mallick et al.

Citation: Mallick et al.

Though I have focused on phylogenetics, the authors had enough marker density to draw some functional conclusions. In particular they found that the Central European hunter-gatherer had some of the distinctive pigmentation mutations common to Europeans (and lesser extent other West Eurasians), such as at the OCA2-HERC2 ‘blue eye’ locus, as well as SLC45A2. But what was shocking to me is that the hunter-gatherer was fixed for the ancestral homozygous state at SLC24A5. To most of you that might not mean anything, but SLC24A5 is almost always homozygous in the derived state in modern Europeans. The HapMap data set as 329 alleles at this SNP for Europeans, whites of Northwest European heritage and Tuscans from Italy. There is only one copy of the ancestral alleles in the whole data set. Assuming that the result is not a genotyping error of some sort, a homozygote at this locus implies to me that the evidence for a strong selective event in this region (it has a long haplotype) within the last ~10,000 years is correct. The widespread distribution outside of Europe of the derived variant of SLC24A5 means we may not be looking at an originally ‘European’ allele, even if it is fixed in Europeans today. No doubt there will be much more in terms of our understanding of functional and population genetics through the window which ancient DNA allows us to view the past.

There are so many details, and so little time. Because it is a preprint you really should read the whole thing (several times). You are part of the revision process in some sense. But I think the general finding that the past is much more complex than we’d imagined will stand the test of time. On some level everyone understood that the trees illustrating genetic relationships on species which exhibit evidence of extensive gene flow were stylized representations which elided a great deal. But in the case of humans thanks to ancient DNA we see just how much that representation masked. Admixture events were collapsed back into the tree to such an extent that it may have been grossly simplified, and our understanding of past demographic events were sorely lacking in realism. We know this about humans across Northern Eurasia because they’ve been extensively studied, and, we have ancient DNA. Unfortunately due to climate we may never have ancient DNA from the tropics, or from many organisms due to the constraints of preservation (e.g., fish?). But I think that we need to update our null hypotheses. This may mean we give up some cherished models which explain things in a neat fashion, but obscure complexity which is truer to reality is preferable to elegant models which lead us to falsity. Perhaps we should finally end our love affair with the beautiful tree, and admit the virtues of a rambling graph.

Citation: Ancient human genomes suggest three ancestral populations for present-day Europeans.

Addendum: I’ve seen references in internet discussions to affinities in Admixture plots of MA1 (the Siberian boy). Please remember that because we only have one MA1 individual that individual will be forced to be a combination of populations generated from the groups where we have many individuals. So some of the strange and intriguing results are just nonsense, as the algorithm is trying to find the best fit to confusing conditions.

 
• Category: Science • Tags: Ancient DNA, Population Genetics 
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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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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"