Category: Historical Population Genetics

Mesolithic and Neolithic, Of Cheddar and Bread

Posted on by Razib Khan


It’s been a big week for “Cheddar Man” and the science around him. I already talked about the issue blog-wise for my day job. Additionally, Spencer and I did a podcast on the topic (if you haven’t, please subscribe and leave positive reviews and ratings on iTunes and Stitcher; next we’ll post our conversation with Chris Stringer, don’t miss it!).

So at this point I’ll put some other thoughts here that are “big picture.”

Cheddar Man may have been black but probably wasn’t

Much of the media is focused on the predicted pigmentation of Cheddar Man. That is, dark. Back when the La Brana Western Hunter-Gatherer results came in with the same finding, several population genomics people pointed out that it might not be valid to predict their phenotype based on modern training sets.

Here are some thoughts:

  • Cheddar Man and the WHG in general were probably darker than modern Northern Europeans. There is detectable selection in modern Europeans for pigmentation alleles down to the present, and Northern Europeans are the palest people in the world. And, pigmentation is polygenic, but it’s not hyperpolygenic. That’s why GWAS and early selection tests picked up pigmentation loci as hits so often.
  • Cheddar Man and the WHG in general were probably not as dark as tropical people. The only people who live(d) at very high latitudes who were very darkly complected were Tasmanian Aboriginals and Australian Aboriginals (Melbourne is at the same latitude south as Lisbon is north). In contrast, we see that Khoisan are brown, sometimes rather lightly so, while the peoples of non-European heritage who live in high latitudes are not dark-skinned, though they are not as light-skinned as Europeans.

We don’t have a time machine, so we won’t know with finality. But, it seems that pigmentation pathways are finite, and eventually we can probably be more confident if Cheddar Man had a genetic architecture that would lead to fewer and smaller melanocytes.

The First Farmers replaced WHG to a great extent in Britain

The preprint that came out with the Cheddar Man documentary really focused mostly on the Neolithic farmers. The data set was large, and it emphasized that the discontinuity between the farmers, who were EEF from Anatolian stock (modern Sardinians are their best proxies), the hunter-gatherers. WHG is genetically homogeneous, so they couldn’t reject the proposition that there was no admixture of British hunter-gatherers into the farmer population Basically, the thesis that Peter Bellwood outlined in First Farmers is well supported by these results. The farmers brought agricullture, and pushed aside or absorbed the hunter-gatherers.

It is notable to me that they found more hunter-gatherer ancestry (possibly) in eastern and northern populations, but not much in farmers from Wales. Additionally, though they couldn’t be definitive about it, the EEF settlers of Britain seem to have more affinities with the Western Mediterranean populations than the Central European ones. This suggests that perhaps the farmers arrived by sea or coast-hugging from the south and west, rather than from the south and east.

The arrival of farming to Britain was different

Farmers came to Britain later than to the continent. The shift from hunter-gatherer to farming was rapid. One model for why there was lack of admixture is that the farming cultural package was fully adapted to Northern Europe by the time they began settling the island. In contrast, on the mainland farmers were changing a Middle Eastern lifestyle into something that could take root in cold northern climes where there were already local residents.

Sometimes cultural and ecological changes drive rapid expansions of human populations

Today Europe, and much of Western Eurasia, is characterized by isolation by distance dynamics between populations. What you see in the transition from the Mesolithic to the Neolithic, and later with the arrival of metal age populations (Bell Beakers), is that populations can turnover fast, and that rapid expansion and growth can result in homogeneity across huge distances and then sharp continuities across cultural divides. The classical example of this is that hunter-gatherers and farmers in Central Europe did not exchange much in the way of genes for centuries, and their between population variance accounted for ~10% of their pooled variance (this is what you see comparing Han and Europeans). Additionally, WHG and EEF are both relatively homogeneous, at least before the latter began to absorb WHG at different fractions across its range. WHG descends from a late Pleistocene expansion, after the Last Glacial Maximum. Similarly, the EEF expanded rapidly from its Anatolian point of origin.

Britons didin’t become Britons genetically until the Bronze Age

Ten years ago many people thought that Cheddar Man and his people were the ancestors of most of the people who lived in Britain today. At the same time as this preprint came out, the Bell Beaker paper was officially published. We now know that Britain went through two massive demographic transitions in less than 2,000 years, with on the order of a 90% replacement in a few centuries both times.

Why? Was this typical? Those are for a later post….

The “Finns” are probably an Iron Age intrusion into the East Baltic

Posted on by Razib Khan

One of the first things I wrote at length about historical population genetics, in late 2002, happened to be a rumination on the Y chromosomal phylogeography of Finnic peoples. At the time there was debate as to the provenance of the N1c Y chromosomal haplotype (this is the haplotype of the Rurikids by the way). Just as R1b is ubiquitous in Western Europe, and R1a in Eastern Europe (and to some extent in Indo-Iranian lands), N1c has an extensive distribution in the northern zone of Eurasia.

The question at the time was whether N1c was from Europe and in particular the Finnic peoples, or, whether it was from Siberia.

NJ Tree of Pairwise Fst

Today we have many of the questions resolved. At this point, we know that the Finns, Sami, and Estonians, all exhibit evidence of gene flow from a Siberian-like population. This is clear on any genome-wide analyses. Though this is very much a minority component, even among the Sami, because it is genetically very different from the Northern European background, it is clear on any analysis.

Ancient DNA has also established the likelihood that this Siberian-like element is relatively new to the Baltic region. In a recent paper, The genetic prehistory of the Baltic Sea region:

We suggest that the Siberian and East Asian related ancestry in Estonia, and Y-haplogroup N in north-eastern Europe, where it is widespread today, arrived there after the Bronze Age, ca. 500 calBCE, as we detect neither in our Bronze Age samples from Lithuania and Latvia.

This is not the only ancient DNA paper that shows this. Of course, sampling is imperfect, and perhaps they’ve missed pockets of ancient Finnic peoples. But the most thorough analysis of Mesolithic hunter-gatherers in Scandinavian does not pick them up either, Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation. Populations, such as the Comb Ceramic Culture, which have been identified as possible ancestors of the modern Finnic culture and ethnicity, lack the distinctive Siberian-like component.

At the SMBE 2017, I saw a poster which had results that were sampled from Finland proper, and distinctive ancestry of Siberian-like peoples was present in an individual who lived after 500 AD. This means that in all likelihood the circumpolar Siberian population which introduced this new element into the East Baltic arrived in the period between 500 BC and 500 AD.

Someone with more knowledge of paleoclimatology and archaeology needs to comment at this point. Something happened in this period, and it probably left a big ethno-linguistic impact. But I don’t know enough detail to say much (the Wikipedia entries are out of date or don’t illuminate).

I will add when I run Treemix Finns get the Siberian gene flow you’d expect. But the Lithuanians get something from the Finns. Since the Lithuanians have appreciable levels of N1c, that is not entirely surprising to me (the basal flow from the Yakut/European region to Belorussians may be more CHG/ANE).

Additionally, I will note that on a f-3 test Lithuanians have nearly as high a z-score (absolute) as Swedes (i.e., Finn; Swede/Lithuanian, Yakut), indicating that the predominant Northern European ancestry isn’t necessarily Scandinavian, as much as something between Lithuanian-like and Swedish-like (on Admixture tests the Finns do seem to have less EEF than Swedes, and Lithuanians probably the least of all among non-Finn peoples).

Addendum: I should note here that the genetics is getting clearer, but I have no great insight into the ethno-linguistic aspect. Perhaps the Siberian-like people did not introduce Finnic languages into the Baltic. Perhaps that was someone else. But I doubt it. That being said, though the Siberian-like component adds great distinctiveness to the Finns, it is important to add that by and large Finns are actually generic (if highly drifted) Northern Europeans.

 

Function & phylogeny, where the twain shall diverge

Posted on by Razib Khan


Every few years I get asked about Nuristanis and Kalash. The reason is that these people are often white. By white, I mean that some Nuristanis and Kalash are fair-skinned, blonde-haired, and blue-eyed. Entering “Nuristani” into Google images returns some very white faces. And you have weird news stories about ‘white’ Taliban, because non-locals don’t realize that some Nuristanis look like Northern Europeans.

Since the vast majority of people who look like white Northern Europeans are white Northern Europeans, many people assume that the Nuristanis and Kalash must have some kinship to white Northern Europeans. More precisely, many have spread the legend that these people have some relationship to the soldiers of Alexander the Great (even though Macedonians are Southern European…details).

As it turns out, they do have some kinship to Europeans…but not inordinately more than any of the other peoples of the region. The TreeMix plot at the top of this post shows that Greeks are far closer to Iranian Jews than they are to Kalash. In fact, the Kalash clearly have a non-trivial proportion of “Ancestral South Indian” South Asian ancestry.

Because of their high genetic drift (they’re endogamous and kind of inbred) a lot of population genetic analyses are a bit more difficult with the Kalash samples that are out there. But their genetic affinities are clear:

Table S4 show highly significant evidence (p value < 10−10) in the Kalash when using Armenia and Chamar as surrogates. Eight other pairings of surrogates give p values < 10−5. In all cases, the surrogate pairs include one group from South Asia (Chamar, Kol) and the other from West Eurasia (Armenia, Adygei, Brahui, Hungarians, Palestinians, Tuscans), consistent with admixture from a West Eurasian source.

Chamar are a Dalit caste of Northern India if you don’t know.

So what’s going on with the Kalash and Nuristanis? Appreciable frequencies of alleles which are correlated with traits like blue-eyes are found amongst them. Though the frequencies are much lower than in Northern Europeans. Very white looking Nuristanis and Kalash may be highly salient to photographers and the Western media, but it turns out most Nuristanis and Kalash look West Asian, with a minority who are dark-skinned enough that their South Asian ancestry is also quite clear.

This disjunction between appearance and ancestry should not surprise us. There has been a lot of recent change in physical appearance across populations over the last 10,000 years. Europeans themselves have changed in appearance. Similarly, other populations have as well. Some of them look similar to Europeans due to happenstance or convergence.

Another case are the Ainu of Japan. Though as an unadmixed group they no longer exist, old photos show some of them exhibiting an appearance not typical of East Asians. This led early anthropologists to posit that the Ainu were a “lost white race.” And yet to my knowledge, no European ancestry is found in Hokkaido, or in the Tohoku region, where Ainu-like people lived down to the early medieval period.

The moral of the story: don’t judge the contents of the book by its cover.

From the eastern edge of the sea of grass

Posted on by Razib Khan

A new preprint, Mitogenomic data indicate admixture components of Asian Hun and Srubnaya origin in the Hungarian Conquerors, throws a rather large sample of medieval mtDNA samples at the question of the ethnogenesis of the Magyar people. The context here is that Maygars speak a non-Indo-European language, with a distant relationship to the Finnic ones, but genetically are not much distinguished from their neighbors.

But the differences are not non-zero, ‘best of breed’ methods can pick up a small fraction of exotic ancestry.

The results above are based on samples from cemeteries of the Magyar elite. These are people who identified with a steppe confederacy which coalesced in the 9th century in the Volga region, and in 895 conquered the region of Central Europe which we now term Hungary. In the 10th century, the Magyar tribes were an alien and predatory force within Europe, pagan and exotic. They were, in fact, the latest in a long time of mobile Central Asian horsemen, going back to the Scythian, Sarmatians, Huns, and Avars.

What the data from these results confirm is that a substantial proportion of the maternal lineages of the Hungarian nobility were East Eurasian. Their genetic profiles, in fact, resembled Scythians who had mixed with Altaic peoples, even if they were not descended from those people. What this suggests is that the Magyar conquest elite was part of a broader landscape of ethnolinguistically distinct, but interconnected, steppe confederations. The preprint gives great space to the likelihood that a substantial proportion of the Magyar elite was in fact Turkic in origin.

This leads to one of the major assertions of the paper: the distinctive linguistic identity of modern Hungarians is a legacy of the Hunnic period, and not the Magyar conquest. From what I can tell they didn’t have older DNA, so I don’t know how they came to this conclusion, except that the conquest Magyars were small in number, and seem to have been decimated over time (Mongol invasion, the battle of Mohacs).