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The Japanese as a creation of the Christian Era

The traditional model, which I’ve alluded to before on this weblog before, is that Japan is a synthesis of Jomon and Yayoi, with the latter dominant, and bringing rice-agriculture to the islands. A new paper in Science indicates it may be more complicated than that.

Ancient genomics reveals tripartite origins of Japanese populations:

Prehistoric Japan underwent rapid transformations in the past 3000 years, first from foraging to wet rice farming and then to state formation. A long-standing hypothesis posits that mainland Japanese populations derive dual ancestry from indigenous Jomon hunter-gatherer-fishers and succeeding Yayoi farmers. However, the genomic impact of agricultural migration and subsequent sociocultural changes remains unclear. We report 12 ancient Japanese genomes from pre- and postfarming periods. Our analysis finds that the Jomon maintained a small effective population size of ~1000 over several millennia, with a deep divergence from continental populations dated to 20,000 to 15,000 years ago, a period that saw the insularization of Japan through rising sea levels. Rice cultivation was introduced by people with Northeast Asian ancestry. Unexpectedly, we identify a later influx of East Asian ancestry during the imperial Kofun period. These three ancestral components continue to characterize present-day populations, supporting a tripartite model of Japanese genomic origins.

The Kofun period begins around 300 AD. The implication here is that there was a mass migration from the Asian continent less than 2,000 years ago, likely from Korea. The first agriculturalists, the Yayoi, seem to be a mix of native Jomon and individuals with strong affinities to populations in Manchuria.

Here’s a stylized representation that captures the turnover:

The Jomon are interesting because these results indicate low effective population, and, deep connections with ANE (Ancient North Eurasians). They also seem a clade deep within Northeast Asians, dating to the Pleistocene.

In any case, the authors admit that their sampling of the Yayoi is weak, so there needs to be follow-up here. If it does turn out that the Japanese are mostly Kofun-period, then I think that recalibrates our sense of its history a great deal. The Japan of the 7th century which enters into history was a very young nation.

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The echoes of greater Scythia

I’m reading The Great Indo-European Horse Sacrifice: 4000 Years of Cosmological Continuity from Sintashta and the Steppe to Scandinavian Skeid, since we now know that modern horses come from the Sintashta.

The Indo-European horse sacrifice is a pretty widespread thing. Please note the table above and its shared characteristics. Notice the references to the chariots. Chariots were clearly invented by the Sintashta. And, it seems the horses that could pull them were a special breed, the ancestors of modern domestic horses. But putatively Indo-European people expanded in Europe long before the emergence of the Sintashta in 2200-2100 BC. For example, the Bell Beakers show up in Ireland ~2500 BC. Steppe ancestry shows up ~2300 BC in Greece. Therefore, the spread of chariot-culture, and the modern horse lineages, post-date Europe’s original Indo-Europeanization.

I think this indicates that the influence of the Iranian Scythians was felt all over the Indo-European zone…

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The heavenly horses of the Sintashta

Matt pointed me to the fact that the paper that’s going to come out:

Horse domestication fundamentally transformed long-range mobility and warfare. However, modern domesticates do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling at Botai, Central Asia ~3,500 BCE (Before Common Era). Other long-standing candidate regions for horse domestication, such as Iberia and Anatolia, were also recently challenged. Therefore, the genetic, geographic and temporal origins of modern domestic horses remained unknown. Here, we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they rapidly expanded across Eurasia from ~2,000 BCE, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioral adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe ~3,000 BCE driving the spread of Indo-European languages. This contrasts with the situation in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BCE Sintashta culture.

If you have an interest in the domestic horse (I have) you are aware it’s the product of massive demographic radiation from a small founder population. With ancient DNA we now know where it started: with the Sintashta people of the Volga to the Ural steppe 4,000 years ago.

This is not totally surprising, because we know that the Sintashta were highly warlike and they invented the light war-chariot. This technology spread across the whole Old World, from Egypt to China to Ireland. In some cases, I believe that this was mediated directly by the Sintashta, the early Indo-Iranians. Not only were the Mitanni elite of Syria 3,500 years ago speaking an Indo-Aryan/Iranian language, and worshipping Indo-Aryan/Iranian gods but genetically some of them retained their steppe character. The Sintashta also had domestic dogs, but the lineage of these dogs persists only in China today. Not coincidentally, light war-chariots that are clearly copied from the Iranian-style vehicles show up in Shang China in 1200 BC.

The genetic/demographic impact won’t be visible in many areas. Perhaps Indo-Iranian mercenaries arrived in a city-state, and eventually taught the natives how to build, maintain, and utilize war chariots? This seems plausible. To this day we aren’t quite sure where the wagon was invented because it spread almost immediately over much of Western Eurasia 5,500 years ago.

We also have to remember that the “Iranian” zone of domination was far wider in antiquity than in the present. Around 500 BC Scythians were present as far east as Mongolia, as far west as Hungary, and as far south as northern Iran itself. This means that they could easily have spread the chariot within their own cultural-zone and then it was rapidly adopted by adjacent groups to the east, west, and south.

Related: check out my steppe series.

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Not all causes are treated equal

Over on Twitter the eminent population geneticist Molly Przeworski has an important and lauded thread up:

The thread has been widely re-tweeted and quote-tweeted by biologists. This prompted a response by a prominent sociologist, who quoted this from Kathryn Paige Harden’s discussion with Sam Harris:

What Harden is alluding to is that heritability within populations is not portable necessarily to between populations. In less sophisticated hands, this is almost used as an incantation. In my review of Harden’s book I said the following:

The biological reason that this extrapolation founders is that human populations differ, and those differences matter. The genetic architecture of intelligence may vary between populations so that predictions from the markers in one population are poorly predictive of variation in another, in line with the general concerns for GWAS portability…Harden points out correctly that population structure exhibits different layers of granularity and continuity. Perhaps a prediction trained on British samples is poorly predictive in Pakistanis. But what about Iranians? If it is poorly predictive in Iranians, what about in Bulgarians? The ability to infer within and between-group heritability is conditional on what you mean by “group,” and that is to some extent a subjective choice guided more by heuristics and instrumental utility than idealistic differences between races.

To be entirely frank I think Harden was on solid ground as a behavior geneticist with psychological training who relied on what population geneticists say publically all the time about heritability and group differences. The issue is that I do not believe population geneticists were entirely candid about the deep texture of their assumptions, beliefs, and expectations. They wanted to be left alone to do their research, and so relied on a mantra to make people leave them alone, and now that mantra taken so literally is coming back to haunt them. One reason Prezworski’s thread got a lot of attention is privately this is the sort of intuition and sense that’s widely understood, but the issues are subtle, so to outsiders people just leave it off with the quick quips about portability. A friend told me “Molly doing this is like a goddess descending to Earth to speak to mere mortals so it will get a lot of attention.”

The real issue though is that some are now rather perturbed that Harden and behavior geneticists are trying to shield their study of psychological trait heritability from charges of racism by separating the discussion of between and within-group differences by implicitly reifying “population.” Additionally, some geneticists are quite unhappy at the discussion of heritability when it comes to psychological characteristics, so what was a convenient mantra to have people leave them alone is now coming back to haunt them, as it’s opening up avenues for research that they’re not comfortable with, are not interesting in, and believe are possibly dangerous. To be candid if I was Harden I’d be a bit peeved since all she’s doing is repeating what a lot of authorities in the field have been writing and saying for decades.

Nevertheless, if you take a look at the people who re-tweeted and commented on Przeworski’s thread it’s pretty much everyone. The high and mighty, all the way to the low. It was positively re-tweeted by people who are very skeptical of the study of heritability in psychological characteristics in humans (to be charitable). And, it was positively re-tweeted by me. Since so many people liked it and re-tweeted it, I can tell you it was re-tweeted by people who are actually quite open to and interested in the study of psychological characteristics in humans, within and between groups, without divulging confidence (I checked who commented and re-tweeted and liked).

So what’s going on? Prezworski’s group has published several papers in this area (for example, The evolution of group differences in changing environments), and one of the upshots for many is that there’s a lot less certainty about the heritability of many traits and its utility for polygenic risk scores even within groups because of uncorrected confounds. Some people took from this that polygenic risk scores are useless (not necessarily Prezworski and her group!). But when I talked about these findings with Amit Khera, who works on polygenic risk scores relating to cardiovascular disease, he was actually happy about these results. Why? Because he wanted to correct any confounds there were. He viewed these results not as a death knell for polygenic risk scores, but as a way to make them better, more accurate, more precise. He’s a medical doctor who is trying to help people in their health decisions. All he cares about is greater effectiveness. He’s not invested in a particular result, he’s invested in outcomes (OK, at least ideally, but I talked to him and his enthusiasm seemed genuine).

This is almost certainly why people who think polygenic risk scores are useful, and heritability in psychological characteristics are real, and vary widely in human populations, re-tweeted the Prezworski explainer. I myself did for this reason. My own current belief is there’s good evidence for heritability for a lot of behavioral traits, and that polygenic risk scores can be useful, at least on the margin. But we need to get better, and to do that, we need to explore all the subtle distinctions and details in relation to environmental and genetic variation. This is no guarantee. Perhaps the skeptics of polygenic risk scores will be correct (I doubt it, but who knows). But we’re not at the point where we can settle that question right now. More science needs to be done.

Finally, we need to address the magic of genes. People put a lot of stock in genes for various ideological reasons. But the reality is a lot of environmental factors taken for granted by many (e.g., shared home environment) are a lot less clear and well understood than genes are. And yet the skeptical takes don’t rain down on social science inferences and correlations. Mostly because they’re not seen as insidious because they’re environmental. But causes are causes. When there is a great deal of environmental variation in an outcome that doesn’t mean that you can control it, or you even know what it is. A lot of what is in the “E” in the ACE model is mysterious. Many focus on genes because they’re clear and distinct.

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Open Thread – 9/12/2021 – Gene Expression

Adrian Wooldridge has a new book out, The Aristocracy of Talent: How Meritocracy Made the Modern World. The juxtaposition between the terms aristocracy and meritocracy is amusing.

Obviously, I’ve had less time for this weblog due to other things, like my Substack. Please check out Among Afghans: jewel of the dragon if you haven’t. I post correspondence from a reader here there at the end, so it will be familiar.

Also, my mid-month link round-up is up over at Substack. Please check that out!

I don’t know if I mentioned this elsewhere, but I’m a paying subscriber of FdB. Mostly because I want him to be paid to write stuff like this and this. Most Left-liberals outside of genetics aren’t aware of the decreasing cost of sequencing plot from the NIH, or the existence of companies like Genomic Prediction and Orchid. Freddie is woke to all that. He’s an irascible character; I had my run-ins with him when he decided to send me unsolicited emails telling me what he thinks about me (mixed reviews). But I’ve come to the conclusion only the irascible can really speak the truth at this point. So here we are.

Unless you’ve been asleep, you’ve seen Can Progressives Be Convinced That Genetics Matters?, which is a pretty hagiographic profile of Dr. Kathryn Paige Harden in The New Yorker. This is from the same writer who wrote a hit-piece against David Reich. Is it something in journalism that they can only write hit-pieces or hagiographies? Is this demand side?

Two observations:

– The warm-glow of The New Yorker seems to be allowing the left/mainstream press to approach Harden’s ideas fairly instead of dismissing or demonizing

– A lot of scientists really dislike the profile and there’s been a lot of blowback. This, in contrast to the “circle the wagons” reaction around David Reich more or less. I think this is due to the fact that scientists would prefer more neutrality and a mixed portrait. They thought the profile of Reich was one-sided, and they think the profile of Harden is also one-sided. To be frank, I support both Reich and Harden’s projects.

There are some digs at Reich in Harden’s book, The Genetic Lottery. I actually sent the chapter in question to some human population geneticists to make sure my reaction wasn’t too biased (yes, I’m biased, I admire Reich a lot as a scientist and a human), and they told me I wasn’t crazy. So I have some defense of Reich in my full review of the Harden book (this didn’t make the final cut at UnHerd).

As for Harden’s project, I’m on the more pessimistic side because on social media scientists are connecting it to racism. Whether she’s correct or not if that sticks the project is obviously over. It’s a word of power, and will sink the project before it launches.

The Other Afghan Women. This is basically a story that explains how the rural Afghans viewed the American occupation and intervention, and all the horror we generated. This was published in 2021, but really it could have been published as early as 2001. From what I’ve heard American forces caused a lot of “collateral damage.” In the early years, the press was sympathetic, so they never reported on that. And, the US military has clamped down on leaking too much about the atrocities. When I was in grad school I randomly had beers with some construction workers at UC Davis. One of the guys went into a mental fugue and told us that he shot a dozen Iraqi prisoners in the head after one of his buddies got blown up by an IED. He kind of apologized for freaking us out, and explained: “you all don’t know anything about what’s going on, they cover it up when they can.” Others have told me the same, though they haven’t copped to war crimes.

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Through northern Arabia

Multiple hominin dispersals into Southwest Asia over the past 400,000 years:

We have identified at least five pulses of human dispersal into northern Arabia, each associated with a phase of decreased aridity. The differences in material culture between these phases—with two phases of Acheulean technology and then three distinct forms of Middle Palaeolithic—suggests that diverse hominin populations, and probably even species, were expanding into the region at different times…

From the supplements:

Little is known of the Pleistocene fauna of southern and eastern Arabia, but the repeatedly distinctive, localised, character of material culture suggests that crossing the Red Sea at the Bab al Mandeb was not a primarily dispersal route and that instead populations filtered through northern Arabia. In northern Arabia the growing fossil record suggests repeated connections to Africa across a contiguous grassland zone through the southern Levant which formed during repeated humid episodes (discussed in SI 10). To that we can add significant aspects of material culture which we have reported in this paper. The absence of Acheulo-Yabrudian assemblages in northern Arabia, and the southern Levant, suggests that the Late Acheulean in this area relates more to Africa than to areas to the north. Likewise, with the early Middle Palaeolithic at KAM-4 (Assemblage C of the Northwest Lake) both technological features (such as the methods of Levallois surface preparation, see SI 7) and quantitative characteristics in terms of PCA of Levallois flake shape situate the assemblage between the Levantine Early Middle Palaeolithic the early Middle Stone Age in East Africa (SI 9)…

…The possible MIS 3 presence of Neanderthals in Arabia may suggest that they expanded further south than previously thought, and highlights that there is currently little clarity on where the main pulse of admixture between Homo sapiens and Neanderthals occurred, beyond probably Southwest Asia broadly.

As a closing note, we emphasise that as well as our results being consistent with repeated pulses of hominin dispersal out of Africa into Southwest Asia, the possibility of movement in the reverse direction should be kept in mind. Given factors such as current uncertainty on the background to the earliest known Homo sapiens in Africae, and discussions on the possible
involvement of a hominin closely related to Homo antecessor as an ancestor of our species, currently only known from Eurasia, as a precursor to Homo sapiens, building reliable records for the later Quaternary in Southwest Asia is not only important for understanding ‘out of Africa’ dispersals, but also for ‘into Africa’ dispersals.

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Back when there was a hereditarian Left…

Over at my Substack I posted a much longer review of The Genetic Lottery (you can find my shorter review at UnHerd).

That prompted a reader to point me to a piece in The Nation, Sociobiology and You, dated to October 31st, 2002, and penned by Steve Berlin Johnson, reviewing The Blank Slate: The Modern Denial of Human Nature. It begins:

If Steven Pinker’s latest 500-page treatise on the brain, The Blank Slate, serves any wider purpose in the popular discussion of science issues, it will, one hopes, be the final demolition of that battle-worn slur, “biological determinism,” still lugged out by the occasional critic when someone starts talking about genes, evolution and human behavior in the same paragraph. Ever since E.O. Wilson first published the 1975 book Sociobiology–which argued that human behavior, like that of all creatures on the planet, was partially shaped by natural selection–certain factions of the left, sometimes led by creditable scientists like Richard Lewontin and Stephen Jay Gould, have lashed out at any attempt to connect human emotions and aptitudes to Darwinian explanations.

He continues:

Of course, the one place in which the neo-Darwinians have in fact emphasized differences over commonalities is the fraught world of the sexes. Because so much of natural selection is predicated on reproductive success or failure, and because men and women have such differing biological stakes in the act of reproduction, it is inevitable that natural selection would craft slightly different toolboxes for each sex. This is no problem for the many schools of feminism that embrace the “different but equal” assessment of the sexes, but it is a major irritant for those on the left who imagine all gender differences to be the product of cultural biases. I suspect, though, that the sexual blank slate isn’t long for this world, for several reasons.

For one, the science is increasingly making its advocates into Flat Earthers…

It is not entirely surprising Johnson wrote something like this. He’s the kind of “counter-intuitive” and “heterodox” science writer who would praise The Blank Slate. But, it says something that The Nation commissioned and accepted this piece in the early 2000’s. I think if I wanted to be mischievous I could get this piece removed from the internet now with the ideological currents that are dominant in our society by creating an anonymous Twitter account. Perhaps I could even demand a public apology from the editor who accepted Johnson’s final draft and Johnson himself.

Johnson may have recanted his earlier views. I don’t know, and I don’t care. We know what the truth is, and we know that academics and journalists routinely lie to you about it. Sometimes, it doesn’t get better.

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The genetic history of the Serbs (and proto-Serbs)

Cosmopolitanism at the Roman Danubian Frontier, Slavic Migrations, and the Genomic Formation of Modern Balkan Peoples:

The Roman Empire expanded through the Mediterranean shores and brought human mobility and cosmopolitanism across this inland sea to an unprecedented scale. However, if this was also common at the Empire frontiers remains undetermined. The Balkans and Danube River were of strategic importance for the Romans acting as an East-West connection and as a defense line against “barbarian” tribes. We generated genome-wide data from 70 ancient individuals from present-day Serbia dated to the first millennium CE; including Viminacium, capital of Moesia Superior province. Our analyses reveal large scale-movements from Anatolia during Imperial rule, similar to the pattern observed in Rome, and cases of individual mobility from as far as East Africa. Between ca 250-500 CE, we detect gene-flow from Central/Northern Europe harboring admixtures of Iron Age steppe groups. Tenth-century CE individuals harbored North-Eastern European-related ancestry likely associated to Slavic-speakers, which contributed >20% of the ancestry of today’s Balkan people.

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The humans of Wallacea

A new open-access paper, Genome of a middle Holocene hunter-gatherer from Wallacea:

Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA. So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunter-gatherer sites: Pha Faen in Laos, dated to 7939–7751 calibrated years before present (yr cal BP; present taken as AD 1950), and Gua Cha in Malaysia (4.4–4.2 kyr cal BP). Here we report, to our knowledge, the first ancient human genome from Wallacea, the oceanic island zone between the Sunda Shelf (comprising mainland southeast Asia and the continental islands of western Indonesia) and Pleistocene Sahul (Australia–New Guinea). We extracted DNA from the petrous bone of a young female hunter-gatherer buried 7.3–7.2 kyr cal BP at the limestone cave of Leang Panninge in South Sulawesi, Indonesia. Genetic analyses show that this pre-Neolithic forager, who is associated with the ‘Toalean’ technocomplex shares most genetic drift and morphological similarities with present-day Papuan and Indigenous Australian groups, yet represents a previously unknown divergent human lineage that branched off around the time of the split between these populations approximately 37,000 years ago. We also describe Denisovan and deep Asian-related ancestries in the Leang Panninge genome, and infer their large-scale displacement from the region today.

The best model seems to be the one to the right: the new Wallacean hunter-gatherer has some ancestry deeply related to Australo-Melanesians, and, another proportion of its ancestry is deeply related to East Asians. In particular, the East Asian-related ancestry seems to be basal or deeply diverged from the paleo-Southern East Asian ancestry. There’s a lot in the structure of ancient East Asian populations that I think we’re pretty unclear about, and need more DNA to really understand what’s going on.

But, I do want to mention that in about 24 hours I’ll be posting a discussion I had with Max Larena about the Denisovan admixture in the Phillippines on my Substack. It’ll be ungated in a few weeks.

Max, and this paper, convince me that Peter Bellwood’s simple model of the spread of farming into Southeast Asia ~4,000 years ago is probably wrong on some level. Too bad, it was a nice simple story. Basically, Northeast Asian populations may have had a presence further south far earlier, and they may have been hunter-gatherers initially.

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Funnel Beaker, Corded Ware, Únětice, oh my!

Since David hasn’t mentioned it, I’m going to post some notes on Dynamic changes in genomic and social structures in third millennium BCE central Europe. This is a big deal because there’s a huge data-set spanning the Neolithic (older than 3000 BC) to the Bronze Age in Bohemia, looking at Globular Amphora, Corded Ware, Bell Beaker, and Únětice. Since I’m not too familiar with European archaeology, the most surprising thing that jumped out at me is that there was structure and variability in the nature and origins of the Neolithic societies in the region. The Bohemian Funnel Beaker populations seem to have been migrants from the west, for example.

The two big takeaways:

  1. Confirms serial admixture that tends to be female-mediated from Neolithic (though some “pure” steppe women also migrated)
  2. The Corded Ware and successor cultures in the region seem to have an affinity for an unsampled population to the north of the Yamnaya zone, in the forest-steppe

The first part is highlighted by the fact that several individuals with ~0% steppe ancestry are buried early on as “Corded Ware.” These were clearly individuals who were culturally assimilated, but their ancestry was totally different. Some of these women in particular seem to have been non-local as well, though from Neolithic societies. This suggests, unsurprisingly, that the ethnogenesis of Indo-European cultures was synthetic and complex. The figure to the top/right illustrates the trend whereby the earliest Corded Ware population exhibited far greater genetic distances between individuals than is to be found in modern European pairwise comparisons. This is part of the broader trend that over the recent past there’s been a massive worldwide panmixia.

Second, the Corded Ware has always been an awkward fit with a simple Yamnaya+Neolithic admixture. The stylized model, which I’ve repeated for simplicity, is that the Yamnaya moved west and mixed with the locals. Kristian Kristiansen explicitly refers to the Corded Ware as basically Yamnaya when I pushed him on this, and who am I to disagree with him? I think the key distinction here is that archaeologically the Corded Ware seems so much like European adaptations of the Yamnaya cultural toolkit…but genetically there are subtle indications of difference. Basically, the authors argue, plausibly, that the Corded Ware is not derived from the Yamnaya as such (their Y chromosomes do not match anyway), but a Yamnaya-adjacent population in the forest-steppe. This region seems to have also contributed a second pulse of migration which resulted in increased northeastern affinity, and a higher fraction of R1a lineages.

When it comes to the Y chromosomes, the authors conclude that inter-group competition was intense, and resulted in serial replacements of paternal lineages. The reproductive fitness gain they estimate for the elite lineages is 15% per generation, which is a very large number in evolutionary genetics (2% selection coefficients are large in this field). The Bell Beaker group seems to have been reflux from the west, and it itself was replaced later on by the Únětice.

One of the less supported, though still useful, models for the Corded Ware is a genetic influx from Pitted Ware samples, the mostly “EHG” hunter-gatherer group from Sweden. I think this supports the proportion that a group of early Yamnaya penetrated the forest-steppe, and assimilated hunter-gatherers in the southern portions of the taiga. If my read of the archaeology is correct, the overwhelmingly dominant culture of these synthetic groups was Yamnaya-like.

Finally, I have to wonder about these peoples’ association with and relationship to the Fatyanovo culture of western Russia, right in the forest-steppe. These groups seem to have been proto-Indo-Iranian judging by their R1a1a-Z93. One of the individuals in these data was clearly Z282, which is so common among Slavs (and Europe).