The coming genetic invasion of history, and the rage to come

About ten years ago I reviewed Bryan Sykes’ book Saxons, Vikings, and Celts: The Genetic Roots of Britain and Ireland. It was what it was, a product of the Y/mtDNA era. Therefore, there were a fair amount of conclusions which in hindsight turn out to be wrong. Sykes, and other genetic historians, such as Stephen Oppenheimer, have annoyed historians for years with their genetic imperialism. More frequently, genetic research has been an accent or inflection on historical work. Peter Heather has integrated some genetic results in his earlier books, though you can ignore those and still obtain the general conclusions.

The recent work on near antiquity is a hint that that is going to be blown apart. Ancient DNA in the historical period has been a slow simmer for a while now. The reason is simple: ancient DNA returns more on the investment for prehistory, where there aren’t historical documents. Until recently ancient DNA techniques were expensive in a variety of ways. The industrial process described in Who We Are and How We Got There is going to change that.

In the near future, a large number of projects are going to surface which test hypotheses and conjectures offered by historians.

You would think that testing hypotheses, generally with demographic predictions, would be something that historians would welcome. The problem is that the test will mean some scholars are going to turn out to be wrong. People who spent decades building up a particular model or understanding of the past are going to have that torn away from them.

The normal human reaction is to get defensive. But the problem is that many historians are not well trained in genetic methods. In fact, many geneticists are not well trained in the abstruse statistical methods developed by scholars in ancient DNA.

We’ve seen some of the same from archaeologists. But archaeologists had models which were, to be frank, more speculative than those historians cling to. Even if a particular historical model may be wrong, it is likely there are reasonable grounds to have held onto to that position. If ancient DNA falsifies it the reaction will be even more strident I suspect.

Of course, geneticists need the help of historians. So when the bad feelings clear I think the synthesis will get us to a better understanding of the past.

Hominins are still having sex, caught in flagrante delicto

Assuming you haven’t been sleeping under a rock, you have probably heard that a Nature paper came out on an F1 Neanderthal-Denisovan hybrid. The major new science in my opinion from the results of the genome itself is to be found in the figure above. It confirms that there was a lot of population turnover among Neanderthals, as this individual’s mother is more closely related to European Neanderthals who flourished ~40,000 years later than conspecifics from the same region 30,000 years earlier. This is not surprising in light of what we know about the genetics and paleoecology of this group, though it confirms what we know and increases our confidence.

Rather, what is surprising is that this paper was published because they found an F1. From their conclusion:

It is notable that one direct offspring of a Neanderthal and a Denisovan (Denisova 11) and one modern human with a close Neanderthal relative (Oase 1) have been identified among the few individuals from whom DNA has been retrieved and who lived at the time of overlap of these groups…In conjunction with the presence of Neanderthal and Denisovan DNA in ancient and present-day people…this suggests that mixing among archaic and modern hominin groups may have been frequent when they met.

The number of ancient genomes from these species/groups/lineages is literally in the range a handful. And among the early finds is an F1! This seems highly unlikely. It could be a fluke. Or, as inferred above, F1’s may have been very common when different hominin lineages met.

But that makes one ask: how is it that Neanderthals and Denisovans remained some genetically distinct over hundreds of thousands of years? The two reasons offered are that the lineages were geographically very distant from each other on the whole, and, that hybrid individuals had very low fitness. I think the former is the primary dynamic to focus on.

For my assertion to make sense, consider some context in the published literature and theory. From 2004 and 2011 respectively, Modern Humans Did Not Admix with Neanderthals during Their Range Expansion into Europe and Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression.

From the first paper:

…we estimate that maximum interbreeding rates between the two populations should have been smaller than 0.1%. We indeed show that the absence of Neanderthal mtDNA sequences in Europe is compatible with at most 120 admixture events between the two populations despite a likely cohabitation time of more than 12,000 y. This extremely low number strongly suggests an almost complete sterility between Neanderthal females and modern human males, implying that the two populations were probably distinct biological species.

And the second:

Recent studies have revealed that 2–3% of the genome of non-Africans might come from Neanderthals, suggesting a more complex scenario of modern human evolution than previously anticipated. In this paper, we use a model of admixture during a spatial expansion to study the hybridization of Neanderthals with modern humans during their spread out of Africa. We find that observed low levels of Neanderthal ancestry in Eurasians are compatible with a very low rate of interbreeding (<2%), potentially attributable to a very strong avoidance of interspecific matings, a low fitness of hybrids, or both.

Models are models, and they have assumptions. Don’t have the player, hate the model assumption and revisit your priors.

There are 22 ancient genomes from 40,000 years ago or before. One of them is an F1 between Neanderthals and Denisovans. And another, Oase 1, has a Neanderthal in their very recent ancestry. The sampling locations may not be totally representative. The Denisova cave is likely to be special because it’s at the nexus of the ranges of the two Eurasian archaic lineages. But with that out of the way, it seems very unlikely to me that very low fitness or very low likelihood of mating when it close contact is the reason that the lineages remained distinct. After less than half a dozen samples from Denisova, cave researchers hit on an F1. What are the chances?

And yet, if matings between the lineages occurred when they were in close contact, and they were genetically distinct nevertheless over such long periods, then that demands an explanation. Denisova hominins and Neanderthals were genetically closer than modern humans are to either. At the time that F1 was conceived the two lineages had been distinct for ~300,000 years. This is not qualitatively much longer than some modern human groups (e.g., Khoisan vs. everyone else) have been diverging. And yet, like the Denisovan-Neanderthal split, modern humans have a lot of population structure and evidence of isolation (also, note that modern humans show no evidence of reduced reproductive fitness from offspring and purification of admixture, as has been inferred for Neanderthal genomic regions in modern human genomes).

All this leads me to conclude that in Pleistocene hominins allopatry and metapopulation dynamics are the solutions to this quandary. The population density of archaic hominins was on average low, but you need to go beyond average. The distribution was possibly highly patchy and with large zones of little habitation. Gene flow across populations may have occurred, but they would run up to a wall of emptiness equivalent to the Atlantic ocean. Additionally, both Neanderthal and modern human ancient indicates a recurrent pattern of location population extinction and replacement. My hypothesis is that populations which were liminal to the range of both lineages, and so likely to have a higher load of admixture from the other lineage, were also in a marginal territory and most likely to go extinct and leave no descendants. Then, less admixed populations with larger numbers close to the core of the lineage range would repopulate the liminal region.

If the model is correct, I think the Altai was resettled by Neanderthals from the west after the Eemian interglacial.

A contrasting method to maintain genetic separation from allopatry (physical distance and barrier) are group cultural identities which maintain very strict endogamy. We see this over 2,000 years in India, where populations are co-localized but almost totally unrelated in any way you’d predict from geography. But 2,000 years is a blink of an eye geologically. The explanation for why Neanderthals and Denisovans, and various African human lineages, remained separate for hundreds of thousands of years as coherent populations despite some gene flow on the margins, has to be geology, geography and ecology. Domains where hundreds of thousands years of stasis on quite possible.

General laws of macroevolution from phylogenetics


I’ve been following the Evolution 2018 Meeting in Montpelier on Twitter. A lot of the stuff is interesting, though over my head. In biology, I began with a fascination with natural history. What we might term macroevolution today. I was that kid carrying out The Dinosaur Heresies when I was nine. But aside from the specific, broad patterns of diversification and extinction over geological time periods were clear. Over the years I wended my way through biochemistry, molecular evolution, and finally population genetics. My professional interests, therefore, have generally focused on patterns of variation on a microevolutionary scale. Stuff within species, not across species.

But I’m still quite interested in big picture evolutionary processes. I’m not a fan of Stephen Jay Gould, but I did read the highly repetitive and prolix The Structure of Evolutionary Theory. And, I have a decent course background in phylogenetics because of where I studied (well, at least in Bayesian and ML computational methods and the big picture theory). So I followed very closely the reports of Luke Harmon’s Presidential address at the meeting this year.

After the talk came the preprint, Macroevolutionary diversification rates show time-dependency:

For centuries, biologists have been captivated by the vast disparity in species richness between different groups of organisms. Variation in diversity is widely attributed to differences between groups in how fast they speciate or go extinct. Such macroevolutionary rates have been estimated for thousands of groups and have been correlated with an incredible variety of organismal traits. Here we analyze a large collection of phylogenetic trees and fossil time series and report a hidden generality amongst these seemingly idiosyncratic results: speciation and extinction rates follow a scaling law where both depend strongly on the age of the group in which they are measured. This time-scaling has profound implications for the interpretation of rate estimates and suggests there might be general laws governing macroevolutionary dynamics.

The primary text is pretty lucid. The major figure is at the top of the post. The authors tried to check if the pattern that they saw was a statistical artifact, and they don’t think it is. Rather, they believe that the pattern is a reflection of some genuine material or dynamic processes latent in the origin and extinction of species. They conclude that “This scenario, consistent [with] our results, would imply that the scaling of rates of sedimentation, phenotypic divergence, molecular evolution, and diversification with time all might share a common cause.” More concretely, earlier in the paper they note that the K-T boundary resulted in an extinction and speciation event (for dinosaurs and mammals respectively). But these massive catastrophic shocks don’t seem to happen regularly as much as randomly.

There’s a lot to chew on in the preprint. I can’t judge the technical details, which are in the supplements. For example, I have heard of BAMM before and know some of its general principles because of my coursework, but I’ve never done this sort of analysis extensively, and so I’ve never developed a good intuition about what passes the smell test and what doesn’t. But it strikes me that this field of phylogenetics is nevertheless very accessible to those who are non-scientists but genuinely interested in evolutionary biology. I recommend you read the preprint closely if you do aver an interest in this field.

Addendum: Note that I still think that evolution is scale independent on a deep level. Should I change my mind based on this? I don’t see why.

Near universal standardized testing sends more low SES candidates to university

Most readers are probably aware that meritocratic testing for the selection of the ruling administrative class was a feature of the Chinese system for over 2,000 years. This created in China a civilian ruling coterie unified by cultured cultivation of mental rather than physical feats, similar to the Roman nobility which flourished during the first two centuries of the Empire (and persisted as a social and economic force for centuries after 200 AD, though they became progressively marginalized by the professional military class). The true crystallization of the system, which maintained itself down to 1900, occurred during the Song dynasty, around 1000 AD. The full story is told in The Age of Confucian Rule: The Song Transformation of China.

The cultural legacy of this history persists down to the modern day. Standardized testing in modern East Asia is very different in terms of the subject than in the past, but the aim is the same. To select for the best, by merit alone, in societies where inter-personal relationships still loom very large.*

This historical context is why I am somewhat dispirited by the discussion about standardized tests which is dominant among cultural elites in the United States currently. When I pointed out to someone that standardized tests were used in Britain to target lower socioeconomic students who lacked “polish” and “class”, there was a genuine surprise. But even a trivial familiarity with Chinese history and the powerful leveling influence of the examination system would have habituated people to this reality.

In the past, there were methods to select the “best” candidates without examinations in most societies. During much of the Latter Han and Tang dynasty various blood lineages, what in the west would be called nobility, dominated the ruling class. They recommended their own kith and kin. During the Yuan (Mongol) period policies of ethnic divide & rule were utilized. The British Empire was administered by broadly educated gentlemen.

The utilization of more “holistic” criteria will certainly allow for particular sorts of representative apportionment to occur which are seen as a social good, but if humans are the way they have been in the past, those with polish and pedigree will also shine more brightly in a system where human judgement and human endorsement are given more prominence.

To be frank I think this too shall pass. So when the time comes for the dimming light to burn bright once more, here is a paper which I found very interesting from last year, ACT for All: The Effect of Mandatory College Entrance Exams on Postsecondary Attainment and Choice. The abstract:

This paper examines the effects of requiring and paying for all public high school students to take a college entrance exam, a policy adopted by eleven states since 2001. I show that prior to the policy, for every ten poor students who score college-ready on the ACT or SAT, there are an additional five poor students who would score college-ready but who take neither exam. I use a difference-in-differences strategy to estimate the effects of the policy on postsecondary attainment and find small increases in enrollment at four-year institutions. The effects are concentrated among students less likely to take a college entrance exam in the absence of the policy and students in the poorest high schools. The students induced by the policy to enroll persist through college at approximately the same rate as their inframarginal peers. I calculate that the policy is more cost-effective than traditional student aid at boosting postsecondary attainment.

Emperor Taizu would not be surprised at this result, and he died over 1,000 years ago.

The paper is open access, so read it yourself. The “natural experiment” is rather simple, though the author did have to dome some weighting of the before and after samples. The dataset looks pretty big.

* This causes major issues relating to a fixation on the test as the ultimate goal, as opposed to learning. But excessive focus on education is a “good” problem for a society to have.

Consumer Genomics in 2018, beyond the future’s threshold

In 2013 David Mittelman and I wrote Rumors of the death of consumer genomics are greatly exaggerated. This was in the wake of the FDA controversy with 23andMe, and continuing worries about DNA and privacy. Today David and I came out with a new comment in Genome BiologyConsumer genomics will change your life, whether you get tested or not.

Really transformative technology becomes beneath comment. As long as we’re having to comment about genomics, it isn’t really mainstream. But I think in 2018 it is much clearer that the 2020s will see legitimate mainstreaming. The numbers speak for themselves. I hadn’t realized in a visceral manner how much had changed since our original comment came out. It’s pretty much an order of magnitude shift.

My hypothesis for why 23andMe plateaued for a while at ~1 million is that that was the sample size which maximized the statistical power they wanted to catch loci of particular effect sizes. In the initial years, 23andMe was not just buying customers with marketing, it was subsidizing the array costs. Today Illumina SNP arrays are well under $50 (some people say less than $25) wholesale, so I think at some point in early 2017 they realized even though 10 million wasn’t worth much to them in comparison to 1 million for GWAS, they were going to lose the luster of being “market leader” to Ancestry, who were acquiring customers at a massive clip through their marketing (my understanding is that at some point Illumina was having issues processing the samples that Ancestry was returning to them it was at such high scale; higher than Ancestry had anticipated!).

Open Thread, 08/19/2018

Almost Human: The Astonishing Tale of Homo Naledi and the Discovery That Changed Our Human Story is a “deal” on Kindle. Recommended. Also, Dancing in the Glory of Monsters: The Collapse of the Congo and the Great War of Africa.

Greece’s Bailout Is Ending. The Pain Is Far From Over. Seems to me that Greece is stuck in an unfortunate equilibrium (see the employment laws).

The Big Sort: Selective Migration and the Decline of Northern England, 1780-2018.

On Twitter, I implicitly defended Steven Pinker a bit. I think The Better Angels of Our Nature: Why Violence Has Declined will be noted as one of his most important books because many people were not, and are not, aware of positive trends in the aggregate. My personal experience is that many academic biologists, especially those with ecological backgrounds, are highly pessimistic. Basically, they are stuck in the 1970s.

There are reasons to be pessimistic, and I’m not as optimistic about the future as Pinker, but we first need to accept the facts as they are.

One of the strange things over the past five years or so has been the hatred I’ve seen directed at Steven Pinker by some academics. Consider this from the classicist in the thread above: “I’ve yet to come across *any* respective expert that doesn’t think Pinker’s popular books are garbage….” Or earlier this year I saw a German researcher on my Twitter timeline declare Pinker was pro-Nazi (based on a highly edited clip)!

Most interesting chart from Pew, How Millennials today compare with their grandparents 50 years ago.

The Nastiest Feud in Science: A Princeton geologist has endured decades of ridicule for arguing that the fifth extinction was caused not by an asteroid but by a series of colossal volcanic eruptions. But she’s reopened that debate.

“I will die here”: Death toll rises in southern India’s worst flooding in a century.

The importance of fine-scale studies for integrating paleogenomics and archaeology.

Forager-farmer transitions from East Asia to Sahul: Regional and Global Perspectives.

The Ginkgo Model of Societal Crisis.

530 House Projection.

A quantitative genetics model for the dynamics of phenotypic (co)variances under limited dispersal, with an application to the coevolution of socially synergistic traits.

The perils of intralocus recombination for inferences of molecular convergence.

The Insight is taking a break for a few weeks. Just want to note that I’m proud we have 32 episodes now! Subscribe on Apple Podcasts, Stitcher, or listen on the web.

I’ve asked people what podcasts they listen to before, but what blogs do you read? Honestly, I don’t read many anymore.

The Muslim world stands upon the shoulders of the Ummah


The two plots above are from a new working paper, On Roman roads and the sources of persistence and non-persistence in development. The basic argument is that good Roman infrastructure correlates with modern patterns of prosperity. An ingenious way the authors tested the predictive power is to contrast Europe, where carts and therefore roads, remained critical, and the Middle East and North Africa, where the rise of domestic camels rendered roads less important in the post-Roman period.

We should take these sorts of models with a grain of salt. Too often in economic history, there seems to be a tendency to search around for striking correlations, and then exclaim that this explains it all! Basically, I think some of the issues that plagued psychology and particular social psychology, are relevant here. Of course, most economists are statistically well trained, but there are limitations of data (look at how few data points they have above).

But the bigger takeaway is that historians are able to suggest deep structural reasons for the patterns we see around us today. This doesn’t mean that we should take any particular explanation as “proven” or at face value. Rather, they are interesting models and explanations in a constellation of explanations. To borrow and modify a phrase from evolutionary biology: both the proximate and the non-proximate matter.

This has been on my mind after finishing The Idea of the Muslim World: A Global Intellectual History. I’ve written a few posts on this book before, The “Clash Of Civilizations” Is A Thing, Just Not The Only Thing, and The “Islamic World” Was Not Invented By Europeans. The reason that I’ve given some thought to the book’s thesis, and decided to read it after the essay in Aeon, What is the Muslim world?, is that I thought the thesis reflects something in our current Zeitgeist, and, it was audacious.

The audacity is the tacit assertion that the idea of the Muslim world is something very recent, and emerges out of the engagement with the colonial experience. After all, how can you deny the idea that the “Muslim world” was imagined as a thing by people such has Ibn Battuta?

Let me quote in full a few portions of the last chapter:

Simplistic and ahistorical frameworks of European empires vesus non-European subaltern colonized masses must be scrapped and replaced with the history of the world as it actuall existed….

…Critically they [Muslims] talked to each other, all over the world, and to non-Muslim Asians and Africans, about solidarity against imperial domination, racism, patriarchy, and economic exploitation….

…By decolonizing (and perhaps deconstructing) our categories and conceptions of religion, civilization, and the world order, we can better confront the rising anti-Muslim racism in Europe and the United States and work in solidarity to tackkle the ongoing crsis of the unjust global order.

After having read the book I was a bit surprised that the author wants us to move beyond the simplistic dichotomy between European and non-European, because to a great extent the book operates within that framework. Since this work seems in the tradition of postcolonialism, that makes sense. The argument that I see at the heart of the book is that the “imagined Muslim world” (a phrase the author uses repeatedly) emerged as a response to the intrusion of European imperialism and that Islamic solidarity precipitated out of the context of a rising ideology of white supremacy which racialized Muslims as colored people.

There’s obviously some truth to this. The Idea of the Muslim World benefits from outlining the argument and then supporting it with facts. Lots of facts. Perhaps the most surprising assertion made by the author (to me) is the preeminence of South Asian Muslims in international discourse in the period between 1850 and 1950. The author argues that this was due to demographic and economic heft, as well as the fact that South Asian Muslims were embedded within a powerful British Empire. Though they were a subordinate people, the monarchy had to take into account Muslim concerns, and the overrepresentation of Muslims in the Indian army was also something that was relevant when it came to force-projection.

I don’t know enough about the details of Indian Islam in relation to West Asian Islam during this period to judge this as a valid assertion or not. But, there are other aspects of the work which left me confused and unconvinced. For example, the author asserts that sectarian divisions between Shia and Sunni Muslims were generally minimal, leaving us with the perception that conflict along sectarian lines is a feature of very late modernity (that is, the late 20th century). But during the 17th century and 18th century both Iran and India saw massive forced conversions on sectarian lines. In Iran, it was the transformation of what had been a predominantly Sunni region to a uniformly Shia one. In India, the Mughals, in particular, Aurangzeb, targeted “heretical” Muslim groups, in particular, Ismaili Shia. In Crossing the Threshold and Mullahs on the Mainframe the authors both argue that substantial numbers of Ismaili Muslims were forcibly converted to Sunni Islam (or in some cases, the more acceptable Twelver Shia sect, which is dominant in Iran, Iraq, and Lebanon, as well as some parts of South Asia).

The point I’m making is that Islamic sectarianism has had multiple phases of salience and relevance, before abating. Though I agree with the author of  The Idea of the Muslim World that “Islamic fundamentalism” is actually a very modern development, it is also important to understand that these modern ideological movements draw upon much older thinking and precedents. For example, the popularity of Ibn Taymiyyah among many Sunni radicals is important to understand and entirely unsurprising, especially in light of the fact that Ibn Taymiyyah lived during a time when the Muslim world as he understood it was under threat from non-Muslims.

Fundamentally, the author’s observations that Muslims repeatedly sided with non-Muslims against other Muslims due to their own self-interest does not negate the power and depth of the Islamic world. The reality is that these “meta-ethnic” universal loyalties are always at tension with situational interests. History is filled with Hindus in Muslim armies, Protestants marching with Turks against Catholics, and Muslim bodyguards of Catholic monarchs (Frederick II). But Muslim and Christian are not arbitrary and imaginary constructs. These identities have important predictive power over the long run.

The final chapter was at some tension with the rest of the book, because it foregrounded values and views which were clear within the subtext of the book, but which were not prominent. That is, the author has a particular view on current geopolitics and justice, and seems to be suggesting that his scholarship might help in forwarding this project. I bolded the part about “patriarchy” in the quote because I don’t think modernist Muslim intellectuals in the earl 20th century had problems with patriarchy in a way we’d understand it today. True, many favored the education of women and even equal political rights for women, but I don’t think that that’s the way “patriarchy” is defined today in “social justice” circles in 2018.

An attempt to take historical facts, and leverage them for current social and political concerns, often results in these sorts of anachronisms. For example, I have heard people who support gay rights speak as if anti-homosexual legislation derived from the colonial period invented and created prejudice against homosexuality in non-European societies, when the reality is that that prejudice was already there, albeit with modifications and variations. Consider, that Pashtun tolerance of pederasty does not imply that Pashtun society is not homophobic.

The Idea of the Muslim World is a decent book in light of its intellectual tradition, which I disagree with. That is, the author marshals evidence in support of his thesis, rather than engaging in argumentative bluster. But I do have to say that it seems that in the 40 years since Edward Said’s Orientalism was published the field of postcolonial studies hasn’t really made any big conceptual breakthroughs. Rather, scholars seem to be using the same tools on different topics and coming to similar general conclusions.

In the end, it’s all about goblin-kind.

Alpha is finally almost here

I’ve wondered whatever happened to Alpha, the film about a Solutrean boy? It was supposed to come out much earlier in the year, but they pushed it back to August. So it will be competing with Crazy Rich Asians this weekend. Not sure if I’ll end up catching it, but it seems like they are making the new trailer a bit more “feel good.”

I do have to admit: it’s strange to realize that for the vast majority of our species’ existence we were just hunters, like the ones depicted in this film. Unfortunately I doubt they’ll illustrate much about Soultrean society, even if conjectural, because the film is mostly about a lone boy with a tamed wolf.

Open Thread, 08/14/2018

Weekly book recommendation, Power and Plenty: Trade, War, and the World Economy in the Second Millennium.

V. S. Naipaul has died. I never read his fiction. Perhaps I should. Suggestions? People always talk about A House for Mr. Biswas.

Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations. ” We propose that it is time to contemplate the inclusion of polygenic risk prediction in clinical care, and discuss relevant issues.” Totally honestly, this is happening way faster than I had assumed it would.

Relatedness disequilibrium regression estimates heritability without environmental bias. A blog post on the topic: Relatedness disequilibrium regression explained.

Large-scale whole-genome sequencing of three diverse Asian populations in Singapore. Han (Southern) Chinese, Malays, and Indians (mostly Tamil).

Can Amazon Maintain the Spirit of ‘The Lord of the Rings’? I doubt it. One thing to remember is that George R. R. Martin was a screenwriter in Hollywood for a period. His writing is a more natural translation to modern visual media.

Only the Truth Will Prevent Harm. Sarah Haider. Enough said.

Deep Reads: How I learnt to love population genetics.

Important preprint. Expected patterns of local ancestry in a hybrid zone.

Salt and heart disease: a second round of “bad science”?

Last year, The Witchwood Crown was published. Haven’t read it. Any good?

Live not by the haplogroup alone

In The population genomics of archaeological transition in west Iberia the authors note that “the population of Euskera speakers shows one of the maximal frequencies (87.1%) for the Y-chromosome variant, R1b-M269…” In the early 2000s the high frequency of R1b-M269 among the Basques, a non-Indo-European linguistic isolate, was taken to be suggestive of the possibility that R1b-M269 reflected ancestry from European hunter-gatherers present when farmers and pastoralists pushed into the continent.

The paper above shows that the reality is that the Basque people have higher fractions of Neolithic farmer ancestry than any other Iberian people. Additionally, they have lower fractions of the steppe pastoralist ancestry than other Iberian groups. This, despite the fact that we also know from ancient DNA that R1b-M269 does seem to have spread with steppe pastoralists, likely Indo-Europeans.

Obviously the relationship between Y chromosomes and genome-wide ancestry is complex. The pattern here for the indicates that Indo-European male lineages were assimilated into the Basques. Perhaps the Basque were matrilineal? One can’t know. But, these men did not impose their culture. Instead, they were assimilated into the Basque. This is entirely not shocking. There history of contact between different peoples in the recent past shows plenty of cases where individuals have “gone native.” In some cases, many individuals.

I was thinking this when looking at South Asian Y chromosome frequencies. Though R1a1a is correlated with higher castes and Indo-European speakers, its frequency is quite high in some ASI-enriched groups. I suspect that the period after 2000 BC down to the Common Era witness a dynamic where particular patrilineal societies were quite successful in maintain their status over generations. Additionally, the ethnogenesis of “Indo-Aryan” and “Dravidian” India was occurring over this period, in some cases through a process of expansion, integration, and conflict. It seems some pre-Aryan paternal lineages were assimilated into Brahmin communities. For example, Y haplogroup R2, whose origin is almost certainly in the Indus Valley Civilization society.

Some population genetic models are stylized and elegant. They have to be to be tractable. But we always need to remember that real history and prehistory were complex, and exhibited a richer and more chaotic texture.