Tag: Historical Population Genetics

Eurasia became a melting pot during the Holocene

Posted on by Razib Khan


One of the things you notice when you look at genome-wide data are peculiar populations that seem to be shifted on PCA and other metrics in relation to exotic genetic affinities. For example, Sardinians, Japanese, and Taiwanese aborigines exhibit this pattern. When looking at Han Chinese data, many of the southern samples seem a bit further shifted away from West Eurasians than all the northern Chinese. That is, almost all northern Chinese seem to have low levels of West Eurasian affinity. Some of the southern Chinese do not.

When you look at West Eurasian data, you see evidence of East Eurasian gene flow into parts of Eastern Europe. Among Lithuanians, it seems to be there. It’s old and well-mixed, so it doesn’t jump out at you. But it’s there. Even more striking is that many of the Muslim populations in the Near East seem to have some proportion of East Asian ancestry because of the Turkic expansions.

We know the reason for this ancestry in West Asia. The rise of the Turks in the Islamic world is historically attested (thank you al-Mu’tasim!). Similarly, the arrival of Tatars and Magyars in Eastern Europe is also recorded. In China, various Turkic and West Asian populations arrived after the fall of the Han dynasty in the northern half of the country. I’ve documented on this weblog strong evidence of Indian ancestry across Southeast Asia.

As more ancient DNA comes to light I think one phenomenon that will become more clear is that the cultural tookit of humans over the last 10,000 years has allowed for more continuous, constant, and frequent, long-distance gene flow. Pairwise Fst values crashed with the rise of agriculture and larger-scale polities. But the adoption of the horse and the emergence of agro-pastoralism also served as a reciprocal conveyer belt of genes across the two antipodes of Eurasia.

West Eurasians and East Eurasians still remain genetically distinct. But evidence from Japanese and Sardinians gives a clear indication that within the last few thousand years have substantial reciprocal gene flows.*

* I am aware that in some of the work in David Reich’s lab there is evidence of East Eurasian gene flow into Mesolithic hunter-gatherers in Europe.

The Yamnaya origins of the Tocharians?

Posted on by Razib Khan

Eurogenes points me to a new paper in Current Biology, Ancient Genomes Reveal Yamnaya-Related Ancestry and a Potential Source of Indo-European Speakers in Iron Age Tianshan. The conclusion:

Combining both the genetic and archaeological evidence, we here provide the first direct evidence of an early stage of population admixture around 2,100 BP in Xinjiang in Western China. Our study supports the “Steppe hypothesis” over the “Bactrian Oasis hypothesis” for the peopling of the Xinjiang region. The high amount of Yamnaya or Afanasievo-related ancestry in the Iron Age Xinjiang individuals indirectly supports the introduction of Indo-European languages into the region that survived in the form of Tocharian until the late first millennium CE. We note that we need more individuals from different sites and time periods to shed more light on the genetic history of the Tarim basin and the whole Xinjiang region.

The ethnolinguistic pattern of the Tarim Basin in early historic times was complicated. In addition to very distinct “Tocharian” languages, some of the cities were dominated by Iranian peoples. The modern-day Uyghurs are almost certainly descended from some of these populations. Uyghur men carry both R1b and R1a.

These results from ~2,000 years ago of ten individuals (five of them well dated) suggest that the northern Tianshan was populated by peoples that were direct descendants of the post-Yamnaya Afanasievo, who mixed to varying degrees with trans-Siberian populations (the mixture seems to have had a wide range of fractions). Two of the males carried R1b, the haplogroup dominant among the Yamnaya, but not latter cultures of the steppe (Andronovo). These individuals lacked European farmer ancestry, again indicative of their isolation from dynamics on the western forest-steppe that resulted in genetic differences between the successors of the Yamnaya and the Yamnaya proper.

The argument here is somewhat by elimination. Historical records indicate that some of the cities of the Tarim, particular those of the southern fringe of the basin, were Iranian speaking. Additionally, Iranian cultures are associated with haplogroup R1a, and the Sintashta-Andronovo cultures all had European farmer ancestry. In contrast, R1b is rare outside of Europe (though it is found in Kalash and Yaghnobi), but is found among Uyghurs and among these samples. Tocharians are the most likely descendants of these people, who arrived in the region almost 5,000 years ago.

This explains how the Tocharian languages were so distinct, and, their deep separation from other Indo-Europeans. The Tocharians were isolated and diverged very early. Later they were joined by Iranian groups. Eventually both these were absorbed by Turkic populations, first the Uyghurs, and later the Karluk Turks (the modern Uyghurs revived an ancient ethnonym).

The genetic origins of the Philistines

Posted on by Razib Khan

A week ago I connected the origins of Islam to genetics. By coincidence, an ancient DNA paper came out yesterday which speaks to particular historical points in the Hebrew Bible.

Ancient DNA sheds light on the genetic origins of early Iron Age Philistines:

The ancient Mediterranean port city of Ashkelon, identified as “Philistine” during the Iron Age, underwent a marked cultural change between the Late Bronze and the early Iron Age. It has been long debated whether this change was driven by a substantial movement of people, possibly linked to a larger migration of the so-called “Sea Peoples.” Here, we report genome-wide data of 10 Bronze and Iron Age individuals from Ashkelon. We find that the early Iron Age population was genetically distinct due to a European-related admixture. This genetic signal is no longer detectible in the later Iron Age population. Our results support that a migration event occurred during the Bronze to Iron Age transition in Ashkelon but did not leave a long-lasting genetic signature.

The most likely scenario has long been that the Biblical Philistines were a composition population, made of Aegean folk who mixed with the local Canaanite substrate. These results confirm that.

That might seem revolutionary, but anyone who reads about the history of the Bible knows that all likely or plausible points are contested. Establishing that the Philistines were indeed associated with the migration of Aegean “Sea Peoples” though a genetic connection between them and Southern Europeans at least narrows the window of argumentation.

A bigger issue is one mooted by many Biblical scholars: what were the origins of the Israelites? The standard narrative implies they were exogenous, with Abraham being from Ur (southern Mesopotamia), with a sojourn in Egypt. But most non-fundamentalist scholars believe that the Hebrews emerged organically out of the Canaanites. The relevance of genetics is clear then: at some point in the near future the origins of the people of Judaea will become more clear.  My bet is that it does turn out that they’re mostly Canaanite, though I wouldn’t be surprised by some exogenous signal, as one sees with the Philistines, who by the time of genotyping seems to have been heavily Levantine, and eventually were likely absorbed..

The Jomon contributed little to the Japanese

Posted on by Razib Khan

A few months ago there was a preprint with an ancient Japanese genome, Jomon genome sheds light on East Asian population history. I read it but didn’t say anything at the time. I read it again, partly because I’m reading a history of Korea where the Wa, the early Japanese, show up to intervene in mainland affairs. This cameo made me think more deeply about what happened in Japan several thousand years ago.

The above genome comes from Honshu, and dates to 2,500 years before the present. And yet it’s quite different from modern Japanese! Here is the abstract:

Anatomical modern humans reached East Asia by >40,000 years ago (kya). However, key questions still remain elusive with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of East Eurasia may shed light on the detail picture of peopling to East Eurasia. Here, we analyze the whole-genome sequence of a 2.5 kya individual (IK002) characterized with a typical Jomon culture that started in the Japanese archipelago >16 kya. The phylogenetic analyses support multiple waves of migration, with IK002 forming a lineage basal to the rest of the ancient/present-day East Eurasians examined, likely to represent some of the earliest-wave migrants who went north toward East Asia from Southeast Asia. Furthermore, IK002 has the extra genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration from Southeast Asia to the Japanese archipelago. This study highlight the power of ancient genomics with the isolated population to provide new insights into complex history in East Eurasia.

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The population turnover in westernmost Europe over the last 8,000 years

Posted on by Razib Khan


The figure above is from The genomic history of the Iberian Peninsula over the past 8000 years. If you had seen something like this five years ago, you’d be gobsmacked. But today this is not atypical, especially in light of the fact that Spain seems to harbor many good sites in relation to the preservation of ancient DNA. In the figure above you see an excellent representation of the different streams of ancestry and settlement within Spain over the last 8,000 years. You can conclude from it, for example, that only a small proportion of the ancestry of modern Spaniards derives from people who were residents of the peninsula during the Pleistocene. Similarly, you can also conclude that a minority, though non-trivial, proportion of the ancestry of modern-day Spaniards derives from people who arrived during Classical Antiquity and the Moorish period.

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“Out of Africa” in 2019

Posted on by Razib Khan

The figure to the left is from Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry. It is a graph which captures general features of human population historical relationships as we understand them today. Or at least the model fits the data (remember, many models may fit the data!). The graph is complex…but even within the text of the preprint, the author admits that it is characterized by simplifying assumptions, which nevertheless are informative of some general dynamics and processes (e.g., pulse admixtures).

To some extent, the whole last generation or so has been characterized by the victory of a simplifying assumption that captures general truths about the past, with the accumulation of modifications on the margins as more nuanced results enter the picture. The simplifying assumption I am talking about here is the “out of Africa” 50,000 years ago with a total replacement of all other human lineages framework.

By the last quarter of the 20th century, a combination of archaeological and genetic evidence pointed to the likelihood of a massive bottleneck and expansion of humans outside of Africa in the relatively recent past. In the pre-genomic era, the tools were coarse, from uniparental lineages, classical markers, microsatellites, morphometric analyses, as well as archaeological surveys. But, they strongly pointed to massive expansion and population turnover ~50,000 years ago. This, combined with a line of thinking which suggested that Neanderthals were “evolutionary dead-ends” led to the thesis that there was a total replacement.

To a great extent, this model seems to hold up in the broad sketch. But not to an absolute and total degree. Some paleoanthropologists and geneticists were pointing out for decades that the tools we had could not exclude the possibility of admixture at lower fractions with earlier lineages in Eurasia on purely statistical grounds. These scholars were correct, as it turns out. There is now high confidence that in the range of 1-5% of the ancestry of non-Africans derives from highly diverged “archaic” lineages, Neanderthals and Denisovans. The fraction is low enough that more coarse methods did not definitively pick them up, and without ancient genomes, the “game of inference” was not dispositive in either direction. This, despite the fact that these Eurasian hominins’ ancestors seem to have diverged from those of modern humans ~750,000 years ago. Ultimately, scientists needed a physical ancient genome which they could compare to modern populations to come to this conclusion (before the Denisovan result, scientists had been noticing anomalies in Oceanian data for a decade or so but generally ignored it as beneath comment…a presentation was given an anthropology conference on archaic admixture in Oceania right before the Denisova cave paper).

The second major issue is that the massive expansion and bottleneck that occurred ~50,000 years ago may not explain all of the remaining ancestry that is not “archaic.” That is, there were many modern human lineages present 50,000 years ago. The major lacunae in the current model is a huge one: populations within Sub-Saharan Africa maintained larger population sizes throughout this event. And, anatomically modern humans predate this expansion by hundreds of thousands of years. From an archaeological perspective, a lower limit is 200,000 years ago, and an upper limit probably exceeds 300,000 years ago. Additionally, there are “deep lineages” within Africa which clearly predate the expansion 50,000 years ago. There is a strong consensus that the Khoisan people have at least some substantial ancestry that diverged more than 150,000 years ago from other humans, and tentative suggestions from several different research groups suggest that there are even more “basal” (deep divergence) lineages in parts of West Africa that the component within the Khoisan.

This does not even address the likelihood that some “archaic” ancestry persists within Sub-Saharan Africa just as it does outside of Sub-Saharan Africa.

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The ancient DNA oligopoly and the stories people tell about David Reich

Posted on by Razib Khan

There is a very long piece in The New York Times Magazine, Is Ancient DNA Research Revealing New Truths — or Falling Into Old Traps?. It’s the talk of DNA-Twitter for obvious reasons. The very fact that you have a long piece in The New York Times Magazine on this topic means that David Reich is almost certainly going to made into something of a villain. The reason I say this is that these sort of narratives pitched to a general audience have to exhibit novelistic drama and plot, and so there are “spots” preexistent for both antagonists and protagonists. If the writer doesn’t create that narrative, the piece would probably never see the light of day. Who would read it?

So before the first pixel loaded, I knew:

1) David Reich was going to be the antagonist
2) And indigenous people, along with supporting archaeologists were going to be protagonists

This does not speak to whether this is “true” or not. It is simply how it was going to work out if the piece was ever going to be published because those are the elements of a story that would appeal to readers of The New York Times. This is a product strongly shaped by consumer demand.

One thing I want to address is a critique, expressed by some academics in the piece, that researchers in ancient DNA do not have the number of samples to make the generalizations that they make. This seems reasonable on the face of it, but one thing you have to consider is that when you obtain an individual’s DNA you get a window onto their whole pedigree. A single individual is actually a pedigree if you have its genome. A genome provides an enormous amount of data. It is an endpoint of a historical process of sexual reproduction that extends back many generations. This is how you can use a single whole genome to infer whole population histories. One of the consequences of humans being “evolutionarily young” is that we all bear the stamp of some common processes and events.

From a naive perspective, you can say things like “how do you know this person is related to other people in the area?” And taken in the aggregate there are cases where unrepresentative individuals will yield results that mislead researchers. But on the whole over the last decade or so these groups have developed certain intuitions and guidelines, and have been rather good at making inferences based on a few data rich individuals. They make mistakes. But most objections about the nature of the data are really unfounded (albeit, widespread).

Many of the aspects of the piece do ring true. There are only a few huge laboratories in the ancient DNA space which tend to hoover up samples and collaborators. I have a suspicion I know who this is: ‘One geneticist compared competing with the big labs to battling an entire navy ‘with a little dinghy, armed with a small knife.”‘ For Holocene period analysis, the two big players are the Reich group and that of Eske Willerslev (Johannes Krause is going to make a splash with Late Antiquity). Though Eske’s group is mentioned offhand, it is curious that he himself is not mentioned at all.

Young Eske

In many ways, Eske is a much more colorful figure than Reich, and many of the issues applicable to the work of the latter and his relationships with indigenous peoples and archaeologists apply to the former. But in the United States David Reich is a brand name to the general public that Eske is not, and there can be only one devil in the underworld. But from a narrative perspective, Reich presents less raw material. He is a soft-spoken and delicately built vegetarian computational biologist. Eske Willerslev is the scion of Vikings whose background is in fieldwork as an anthropologist. His autobiography, written in Danish, is apparently very colorful!

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Are Turks Armenians under the hood?

Posted on by Razib Khan

Benedict Anderson’s Imagined Communities: Reflections on the Origin and Spread of Nationalism is one of those books I haven’t read, but should. In contrast, I have read Azar Gat’s Nations, which is a book-length counterpoint to Imagined Communities. To take a stylized and extreme caricature, Imagined Communities posits nations to be recent social and historical constructions, while Nations sees them as primordial, and at least originally founded on on ties of kinships and blood.

The above doesn’t capture the subtlety of  Gat’s book, and I’m pretty sure it doesn’t capture that of Anderson’s either. But, those are the caricatures that people take away and project in public, especially Anderson’s (since Gat’s is not as famous).

When it comes to “imagined communities” I recently have been thinking how much that of modern Turks fits into the framework well. Though forms of pan-Turkic nationalism can be found as earlier as 9th-century Baghdad, the ideology truly emerges in force in the late 19th century, concomitantly with the development of a Turkish identity in Anatolia which is distinct from the Ottoman one.

The curious thing is that though Turkic and Turkish identity is fundamentally one of language and secondarily of religion (the vast majority of Turkic peoples are Muslim, and there are periods, such as the 17th century when the vast majority of Muslims lived in polities ruled by people of Turkic origin*), there are some attempts to engage in biologism. This despite the fact that the physical dissimilarity of Turks from Turkey and groups like the Kirghiz and Yakut is manifestly clear.

Several years ago this was made manifestly clear in the paper The Genetic Legacy of the Expansion of Turkic-Speaking Nomads across Eurasia. This paper clearly shows that Turkic peoples across Eurasia have been impacted by the local genetic substrate. In plainer language, the people of modern-day Turkey mostly resemble the people who lived in Turkey before the battle of Manzikert and the migration of Turkic nomads into the interior of the peninsula in the 11th century A.D. Of course, there is some genetic element which shows that there was a migration of an East Asian people into modern day Anatolia, but this component in the minority one.**

Sometimes the Turkish fascination with the biological comes out in strange ways, Turkish genealogy database fascinates, frightens Turks. Much of the discussion has to do with prejudice against Armenians and Jews. But the reality is that most Turks at some level do understand that they are descended from Greeks, Armenians, Georgians, etc.

To interrogate this further I decided to look at a data set of Greeks, Turks, Armenians, Georgians, and a few other groups, including Yakuts, who are the most northeastern of Turkic peoples. The SNP panel was >200,000, and I did some outlier pruning. Additionally, I didn’t have provenance on a lot of the Greeks, except some labeled as from Thessaly. I therefore just split those up with “1” being closest to the Thessaly sample and “3” the farthest.

First, let’s look at the PCA.

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