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Thursday, May 5, 2016

On the modern genetic affinities of Ice Age Europeans

Apparently most of them didn't contribute much to our genomes. But for what it's worth, I tested their present-day affinities, and those of several other ancients, with f3 outgroup stats of the form f3(Test,X;Mbuti). For the archaeological contexts and other details about these ancient samples see here.

Not long ago Basques were thought to be by far the best proxies for Upper Paleolithic Europeans; almost a genetic relict from Ice Age Iberia. Clearly, this is not what they are, but they do share relatively high drift with the El Miron lady, which perhaps suggests some genetic continuity in Basque Country for almost 20,000 years. This would still be a remarkable story if confirmed via multiple lines of evidence.

Below are a couple of examples of what can be done with these stats. It's pretty clear that the Vestonice cave men show a preference for Northeast Europeans, in particular Balts, Estonians and Poles. On the other hand, Kostenki14 shares the highest drift with the Dutch, mostly north of the Rhine Dutch. Might that be meaningful in some way?

Are there any other interesting patterns in this data? Please note, however, that it's not possible to compare the stats directly, because they're based on different numbers of markers.

Wednesday, May 4, 2016

Ice Age Europeans in a global PCA

The datasheet can be downloaded here. It might be possible to model many of the populations in the PCA as mixtures of Ice Age Europeans and other ancients using nMonte, but I haven't tried this yet. Most of the samples in this run are from various Reich lab public data releases available here.
See also...

On the modern genetic affinities of Ice Age Europeans

PC/nMonte open thread

For a typical West Eurasian PCA, the Epipaleolithic is the final frontier

Tuesday, May 3, 2016

For a typical West Eurasian PCA, the Epipaleolithic is the final frontier

My dataset now includes the samples from Qiaomei Fu et al. 2016. They're freely available at the Reich lab website here.

Below is a Principal Component Analysis (PCA) featuring 10 of the freshly sequenced genomes from the paper classified as Epigravettian, Epipaleolithic and Mesolithic, as well as the Siberian (late?) Upper Paleolithic forager Afontova Gora 3.

I did try to include all of the new genomes from the paper on the plot, but most were getting results that didn't make any sense. They were simply too old and too far removed in terms of genetic structure from present-day West Eurasians.

But that's OK. I can analyze them with formal statistics, and promise to do so vigorously in the coming weeks.

By the way, Villabruna is the ~14,000 year old genome from Italy belonging to Y-chromosome haplogroup R1b. Gioiello, you still breathing?

See also...

Ice Age Europeans in a global PCA

Monday, May 2, 2016

The genetic history of Ice Age Europe (Qiaomei Fu et al. 2016)

Just in at Nature:

Abstract: Modern humans arrived in Europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. Here we analyse genome-wide data from 51 Eurasians from ~45,000–7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3–6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas there is no evidence of the earliest modern humans in Europe contributing to the genetic composition of present-day Europeans, all individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans. An ~35,000-year-old individual from northwest Europe represents an early branch of this founder population which was then displaced across a broad region, before reappearing in southwest Europe at the height of the last Ice Age ~19,000 years ago. During the major warming period after ~14,000 years ago, a genetic component related to present-day Near Easterners became widespread in Europe. These results document how population turnover and migration have been recurring themes of European prehistory.

Fu et al., The genetic history of Ice Age Europe, Nature 02/05/2016; DOI:10.1038/nature17993

Here are three summaries of the findings from the comments:

Krefter: Europeans dating 36,000-30,000 years old from Russia, Belgium, Czech, and Italy form a clade with 24,000 year old Siberian MA1. But they're more related to each other than to MA1. Also, none of them have an especially close relationship to each other, unless they come from the same archaeological site/region.

DNA from a lady who lived in Spain 19,000 years ago, has a close relationship to people who lived in Belgium 30,000 years ago. She also has a close relationship to "WHGs". So, she looks like a mixture of WHG and those 30,000 year old people from Belgium.

After 14,000 years ago, Europeans from Northern Italy, Germany, France, Luxembourg, Spain, and Hungary all form a tight cluster. They are WHG. They also appear to have minor ancestry related to the 30,000 year old people who lived in Belgium.

Stone age Middle Easterners CHG(Caucasus) and especially EEF(Turkey) have WHG-related ancestry. They're more related to post-14,000 years ago Europeans than to earlier Europeans. There's an unknown link between the Middle East and WHG.


Matt: Trying to interpret this (and probably getting something wrong) the genetic history and cultural of Europe from this so far looks like this

- 42,000-37,580 BP - Oase1 type people (and possibly others) living in Europe (Romania)

- 35,160-34,430 BP - GoyetQ116 type people living in Europe (Belgium) (GoyetQ116 is classified to the Aurignacian culture wave).

- 34,580-31,210 BP - Vestonice cluster types seem to replace the GoyetQ116 type

(Except the GoyetQ116 type, Aurignancians(?) are likely to still be living in Iberia, as they're ancestral to the El Miron cluster, from later in history)

Vestonice types seem to all be classified as Gravettian.

- Glaciation then wipes out the Vestonice / Gravettian types around 24,000 BP.

- 18,830-18,610 BP - El Miron is an admixture of a GoyetQ116 and the Villabruna branch (the latter thought to be Near Eastern in origin due to greater sharing with present day Near Eastern people)

All samples from then on in Europe, are identified with the Magdalenian culture and with the same cluster membership as El Miron, as these guys expand across Europe after the retreat of the ice.

- 14,180-13,780 BP - Villabruna branch ancestry in samples increases a lot, and material culture transitions to other industries - Epigravettian, Azilian, Epipaleolithic and Mesolithic. Looks like another great migration to Europe (out of the East via Italy?).


Colin: There was no Basal Eurasian admixture in pre Neolithic Europe. The reasoning was that Ust Ishim (45kya Eurasian) does not contain Basal Eurasian and Ust Ishim is equally related to East Asians and pre Neolithic Europeans.

There was no ANE, Mal'ta cluster, admixture in pre Neolithic Europe (presumably they are talking about the portion of Europe that is West of Russia and Ukraine). The reasoning here is that the mal'ta cluster is equally related to all pre Neolithic "Europeans" starting with Kostenki (37kya).

-Consequently, ANE only entered "Europe" during the Neolithic and Bronze Age, probably from the Eurasian Steppe.

So far, GoyetQ (35kya Belgium) and Kosteni (37kya Russia) are the first ancient Europeans to exhibit closer relations to modern Europeans over East Asians. The older Eurasian samples of Ust Ishim and Oaste do not show higher affinity to modern Europeans over East Asians.

European samples from about 37kya to 14kya tend to be equally unrelated to non-European Eurasians. However, there are 14kyo samples, representing the Villabruna cluster, that show a higher affinity to the modern Near Easterners. The 13kyo to 10kyo samples from the Caucasus, representing the Satsurblia cluster, show more affinity to the Villabruna cluster than to the earlier Europeans. The Villabruna cluster can not be the result of admixture with the Satsurblia cluster since the former does not contain Basal Eurasian while the later does. GoyetQ (35kya Belgium) type ancestry shows a resurgence in the Miron Cluster of 19kya centered in Iberia. About half of the ancestry in the Miron Cluster derives from GoyetQ types.

Because of the large number of individuals in the Villabruna cluster, the researchers were able to identify structure within the cluster. One interesting tid bit is that certain individuals in the Villabruna Cluster showed extra affinity towards East Asians. The oldest of which is the 13kyo sample from Switzerland. Two other Villabruna individuals, Loschbour and La Brana, for example, show extra affinity to Han Chinese over Kostenki. Because all three individuals are equally related to Ust Ishim, hypothetical differences in levels of Basal Eurasian cannot explain the greater affinity Loschbour and La Brana have to the Han.

See also...

On the modern genetic affinities of Ice Age Europeans

For a typical West Eurasian PCA, the Epipaleolithic is the final frontier

Sunday, May 1, 2016

ESHG 2016 abstracts

See the Programme Planner here. Below is an abstract on the population history of the Caucasus. The emphasis is mine. Who actually believes the 20,000 year estimate? It sounds far fetched to me; probably blown out by minor East and/or South Asian admixture not accounted for by the authors.

Abstract: Archaeological findings suggest that modern humans have inhabited the Caucasus since Paleolithic times but little is known about their origin and how they have interacted with neighboring populations. Previous genetic studies of present-day populations from the Steppe suggested the Caucasus acted as a barrier, leading to genetic discontinuity between the Caucasus and the East European Plain. Furthermore, geography, ethnicity, and language are also expected to influence the mating patterns of the populations inhabiting the Caucasus and thus create genetic structure within this region.

Here we use whole-genome genotyping and sequencing data to fully understand the genetic diversity of the Caucasus and its role in the demographic process that shaped modern Eurasian genomes.

Combining data from 12 high-coverage whole-genome sequences, four each from Georgia, Armenia, and Azerbaijan with SNP-genotype data from more than 250 individuals from the same populations, we present one of the most comprehensive datasets for this region. Principal component analyses, followed by model-based clustering, reveal previously unreported structure among the Caucasus populations. In particular, we discovered three different clusters among Georgians and two in Azerbaijan, in addition to different ancestral proportions in these clusters. MSMC analysis of the whole genomes shows Caucasus populations have diverged in the last 20,000 years from other Eurasians and have experienced different demographic changes in recent times.

We thus provide a detailed analysis of the past and present demography of the Caucasus which will be useful for understanding the genetic diversity of this region and the relationship with European populations.

Mezzavilla et al., Genetic structure and demographic history of the Caucasus: insights from whole-genome sequences, ESHG EMPAG 2016 Presentation Abstract, P18.020D

See also...

Ancient Polish admixture in Denmark

Saturday, April 30, 2016

Y-hg J2 cannot be a Proto-Indo-European marker

The claim that the Proto-Indo-Europeans came from West Asia and largely belonged to Y-haplogroup J2 seems to be popular online nowadays. I won't discuss here in detail the reasons why, but suffice to say it has a lot do with aggressive lobbying on several online forums and blogs by a few people of Southern European extraction, like Dienekes Pontikos.

It was always a shaky proposition, but difficult to debunk thoroughly. Until now.

Thanks to recent advances in both modern and ancient DNA research, we can now safely say that Y-haplogroup J2 was not involved in any rapid, large scale population expansions during the Late Neolithic/Early Bronze Age (LN/EBA), the generally accepted Proto-Indo-European time frame.

It thus fails to meet even the most basic criteria of a Proto-Indo-European diagnostic marker. The Proto-Indo-Europeans, after all, were surely highly patriarchal and patrilineal, and therefore expected to have left a clear signal of their migrations in the Y-chromosomes of many present-day Indo-European speakers.

For instance, an analysis of data from the deep sequencing of human Y-chromosomes as part of the 1000 Genomes Project suggests that not a single major subclade of J2 began expanding even roughly close to the LN/EBA. See here.

In the plot above three lineages jump out at you. E1b, R1a, and R1b. The first is associated with the Bantu expansion, that occurred over the last 4,000 years. The second two are likely associated with Indo-Europeans in both Asia and Europe, respectively. The timescale is on the order of 4 to 5,000 years in the past. The association between culture and genes, or the genetic lineages of males, is rather clear, in these cases. In other instances the growth was more gradual. For example, the lineages likely associated with the first Neolithic pulses, J and G.

Moreover, not a single instance of J2 has been reported from remains classified as belonging to the Andronovo, Battle-Axe, Corded Ware, Khvalynsk, Poltavka, Potapovka, Sintashta, Srubnaya and Yamnaya archaeological cultures. In other words, Kurgan and Kurgan-derived groups generally accepted to be early Indo-European, whch is a view that now has very strong support from ancient genomics. See here and here.

To date, most of these samples have probably come from elite burials. So at some point, when many more non-elite samples are sequenced, we are likely to see J2 among a few supposedly early Indo-European individuals. But so what?

There might be a couple of ways to salvage the Proto-Indo-Europeans = J2 theory. We'd have to argue that...

- the Proto-Indo-European time frame was actually the early Neolithic


- the Proto-Indo-Europeans were a small group that Indo-Europeanized the steppe Kurgan people, perhaps mainly via female migrations, and then did not partake in the main early Indo-European expansions

But the former is not particularly clever when viewed in the context of historical linguistics data. See here.

For instance, almost all IE language branches testify to a word designating ‘wool’. Since archaeological evidence suggests that wool sheep did not exist until the beginning of the fourth millennium BCE, the existence of the word in PIE would indicate that the disintegration of the proto-language could not have taken place before this date. Similarly, words for concepts such as ‘wheel’, ‘yoke’, ‘honey bee’ and ‘horse’ may be correlated directly with concrete, datable archaeological evidence.

And the latter isn't very parsimonious, and to me looks like special pleading. Why even bother?

Monday, April 25, 2016

Signals of ancient population explosions in our Y-chromosomes

Nature Genetics has a massive new paper on human Y-chromosomes based on the latest 1000 Genomes data. I'm still getting my head around the details, but at first glance it looks like a very capable effort. This part basically reads like some of my blog entries in recent years. The emphasis is mine.

In South Asia, we detected eight lineage expansions dating to ~4.0–7.3 kya and involving haplogroups H1-M52, L-M11, and R1a-Z93 (Supplementary Fig. 14b,d,e). The most striking were expansions within R1a-Z93, occurring 4.0–4.5 kya. This time predates by a few centuries the collapse of the Indus Valley Civilization, associated by some with the historical migration of Indo-European speakers from the Western Steppe into the Indian subcontinent 27. There is a notable parallel with events in Europe, and future aDNA evidence may prove to be as informative as it has been in Europe.

Poznik et al., Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences, Nature Genetics, Published online 25 April 2016; doi:10.1038/ng.3559

See also...

The Poltavka outlier