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Monday, December 23, 2013

Ancient human genomes suggest (more than) three ancestral populations for present-day Europeans


This new preprint at bioRxiv is quite the Christmas present for those of us with a passion for European genetics and prehistory. It's the first paper to report on full genomes from Mesolithic and Neolithic Europe.

All of the successfully tested Mesolithic Y-chromosomes, one from Luxembourg and four from Motala, Sweden, belonged to haplogroup I. This probably won't come as a surprise to many people, as this marker was always the main candidate for Europe's indigenous Y-haplogroup. However, three of the results fell into haplogroup I2a1b, and none into I1, which is today the most common Y-haplogroup in most of Scandinavia.

What this suggests is that I1 expanded after the Mesolithic and replaced most of the I2a1b across Northwestern Europe. I'd say these were mostly expansions from North-Central Europe, although recent chatter on the web suggests that two distinct I1 lineages might have arrived in North-Central Europe from Eastern Europe at different times.

All of the Mesolithic mtDNA sequences belonged to haplgroups U2 and U5, which is line with past results. The single Neolithic sample, from a 7500 year-old Linearbandkeramik (LBK) site in Stuttgart, Germany, belonged to mtDNA haplogroup T2. Again, not very surprising considering what we've seen to date.

The genome-wide results, on the other hand, are not as straightforward. The basic upshot is that Northern Europeans are mostly of indigenous European hunter-gatherer origin, while Southern Europeans are largely derived from Neolithic farmers of mixed European and Near Eastern origin. But the authors identify a minimum of three ancestral populations from their stats (WHG, EEF and ANE), and four meta-populations from the available ancient data (WHG, EEF, ANE and SHG). Here are brief summaries of each of these groups:

West European Hunter-Gatherer (WHG): this ancestral component is based on an 8,000 year-old forager from the Loschbour rock shelter in Luxembourg (one of the individuals mentioned above belonging to I2a1b). The WHG meta-population includes the Loschbour sample and two Mesolithic individuals from the La Brana Cave in Spain. However, today the WHG component peaks among Estonians and Lithuanians, in the East Baltic region, at almost 50%.

Early European Farmer (EEF): apparently this is a hybrid component, the result of mixture between "Basal Eurasians" and a WHG-like population possibly from the Balkans. It's based on the aforementioned LBK farmer from Stuttgart, but today peaks at just over 80% among Sardinians. Apart from the Stuttgart sample, the EEF meta-population includes Oetzi the Iceman and a Neolithic Funnelbeaker farmer from Sweden.

Ancient North Eurasian (ANE): this is the twist in the tale, a component based on a previously reported genome of a 24,000 year-old Upper Paleolithic forager from South Central Siberia, belonging to Y-hg R*, and known as Mal'ta boy or MA-1 (see here). This component was very likely present in Southern Scandinavia since at least the Mesolithic (see the summary of SHG below), but only seems to have reached Western Europe after the Neolithic. At some point it also spread into the Americas. In Europe today it peaks among Estonians at just over 18%, and, intriguingly, reaches a similar level among Scots. However, numbers weren't given for Finns, Russians and Mordovians, who, according to one of the maps, also carry very high ANE, but their results are confounded by more recent Siberian admixture (see the discussion on the European outliers below). The ANE meta-population includes Mal'ta boy as well as a late Upper Paleolithic sample from Central Siberia, dubbed Afontova Gora-2 (AG2).

Scandinavian Hunter-Gatherer (SHG): this is a meta-population made up of Swedish Mesolithic and Neolithic forager samples from Motala and Gotland, respectively. It's a more easterly variant of WHG, with probable ANE admixture.

Below are the two most important figures from the paper: a) the three-way mixture model that is a statistical fit to the data, and b) a plot of the proportions of ancestry from each of the three inferred ancestral populations. As per above, East Baltic populations are the most WHG, which is somewhat curious, because they mostly carry Y-DNA R1a and N1c1.




So if not for the ANE, we'd simply have a two-way mixture model between indigenous European foragers and migrant Near Eastern farmers, at least for most Europeans anyway. Moreover, the seemingly late and sudden arrival of ANE in much of Europe is important, because it's a smoking gun for a major population upheaval across the continent during the Late Neolithic/Early Bronze Age.

Interestingly, archeological data suggest that this was also the period which saw the introduction of new social organization and perhaps Indo-European languages across most of Europe. None of this was lost on the authors of the paper, but it appears they'd rather be cautious pending more ancient genomic data, because they chose not to explicitly mention the Indo-Europeans.

This study raises two questions that are important to address in future research. A first is where the EEF picked up their WHG ancestry. Southeastern Europe is a candidate as it lies along the geographic path from Anatolia into central Europe, and hence it should be a priority to study ancient samples from this region. A second question is when and where ANE ancestors admixed with the ancestors of most present-day Europeans. Based on discontinuity in mtDNA haplogroup frequencies in Central Europe, this may have occurred during the Late Neolithic or early Bronze Age ~5,500-4,000 years ago35. A central aim for future work should be to collect transects of ancient Europeans through time and space to illuminate the history of these transformations.

...

The absence of Y-haplogroup R1b in our two sample locations is striking given that it is, at present, the major west European lineage. Importantly, however, it has not yet been found in ancient European contexts prior to a Bell Beaker burial from Germany (2,800-2,000BC)12, while the related R1a lineage has a first known occurrence in a Corded Ware burial also from Germany (2,600BC)13. This casts doubt on early suggestions associating these haplogroups with Paleolithic Europeans14, and is more consistent with their Neolithic entry into Europe at least in the case of R1b15, 16. More research is needed to document the time and place of their earliest occurrence in Europe. Interestingly, the Mal’ta boy belonged to haplogroup R* and we tentatively suggest that some haplogroup R bearers may be responsible for the wider dissemination of Ancient North Eurasian ancestry into Europe, as their haplogroup Q relatives may have plausibly done into the Americas17.


No doubt, a lot of people will now be wondering about the main source of the ANE that apparently rushed into Europe at the onset of the metal ages. The Siberian steppe will probably be the favored option for many, since this is where Mal'ta boy and Afontova Gora-2 were dug up. However, I'm pretty sure the source was Eastern Europe.

First of all, as already mentioned, it seems that ANE was present in Sweden during the Mesolithic (Figure S12.7 shows around 19% ANE in the Motala12 sample). Secondly, despite the ANE and WHG being classified as separate ancestral and meta-populations, the differences between them appear to be clinal rather than discrete, which I think can be seen in the PCA and ADMIXTURE results from the study (see here and here). Thus, I'd expect a lot more ANE in Eastern Europe during the Mesolithic than in Scandinavia. Thirdly, it's likely that the ancestors of modern Uralic speakers were in Siberia very early, possibly during the Mesolithic, and they were probably East Eurasians aka. Eastern non-Africans (ENA), which ANE is not.

Indeed, latest linguistics research suggests that the pre-proto-Uralics migrated at some point from Siberia into the southern Urals, in far eastern Europe. The Uralics proper then expanded from the southern Urals, probably during the Bronze Age, both to the east and west, as far as the Baltic. This Uralic expansion is certainly reflected in the Lazaridis et al. data, and it's not the only relatively late migration into Europe that shows up in their stats.

While our three-way mixture model fits the data for most European populations, two sets of populations are poor fits. First, Sicilians, Maltese, and Ashkenazi Jews have EEF estimates beyond the 0-100% interval (SI13) and they cannot be jointly fit with other Europeans (SI12). These populations may have more Near Eastern ancestry than can be explained via EEF admixture (SI13), an inference that is also suggested by the fact that they fall in the gap between European and Near Eastern populations in the PCA of Fig. 1B. Second, we observe that Finns, Mordovians, Russians, Chuvash, and Saami from northeastern Europe do not fit our model (SI12; Extended Data Table 3). To better understand this, for each West Eurasian population in turn we plotted f4(X, Bedouin2; Han, Mbuti) against f4(X, Bedouin2; MA1, Mbuti), using statistics that measure the degree of a European population’s allele sharing with Han Chinese or MA1 (Extended Data Fig. 7). Europeans fall along a line of slope >1 in the plot of these two statistics. However, northeastern Europeans fall away from this line in the direction of Han. This is consistent with Siberian gene flow into some northeastern Europeans after the initial ANE admixture, and may be related to the fact that Y-chromosome haplogroup N 30, 31 is shared between Siberian and northeastern Europeans32, 33 but not with western Europeans. There may in fact be multiple layers of Siberian gene flow into northeastern Europe after the initial ANE gene flow, as our analyses reported in SI 12 show that some Mordovians, Russians and Chuvash have Siberian-related admixture that is significantly more recent than that in Finns (SI12).

The authors are actually referring to the Kargopol Russians from the HGDP in that quote. But from my own analyses with a wide variety of samples from Russia, I know that other Russians show similar levels of Siberian admixture to Belorussians, Ukrainians and Estonians.

In any case, this of course means that there are more than three ancestral populations for present-day Europeans, albeit not all of them influenced all Europeans. Also, it's very clear that to learn all the details about the peopling of Europe, these sorts of studies really need to start focusing on the large swath of land that stretches from present-day Poland to the Urals. In other words, Eastern Europe.

I was also going to discuss the genetically inferred pigmentation of the ancient individuals, but, because of the small sample size, there's not much to discuss at this stage. The Loschbour forager possibly had blue eyes (50% chance), but dark hair and skin. On the other hand, the Stuttgart farmer definitely had dark eyes and hair, but relatively light skin. I wonder if this swarthy hunter-gatherer skin complexion has anything to do with the fact that today lots of people from around the Baltic tan really well?

Citation...

Iosif Lazaridis, Nick Patterson, Alissa Mittnik, et al., Ancient human genomes suggest three ancestral populations for present-day Europeans, bioRxiv, Posted December 23, 2013, doi: 10.1101/001552

See also...

Another look at the Lazaridis et al. ancient genomes preprint

The really old Europe is mostly in Eastern Europe

EEF-WHG-ANE test for Europeans

Scratch the North Caucasus

First genome of an Upper Paleolithic human

ADMIXTURE analysis of Allentoft et al. and Haak et al. ancient genomes

Monday, December 16, 2013

Cluster analysis of West Eurasia: 13 clusters from 18 dimensions


I ran a quick Mclust analysis to get a better idea of the substructures in my recently updated dataset of West Eurasian samples. Mclust found that the optimal outcome was produced with 18 dimensions of genetic variation and 13 clusters, the latter of which are superimposed on a two dimensional MDS plot below. I chose the labels for the clusters myself and flipped the canvass to fit geography.


Here you can see the 13 clusters superimposed on all possible combinations of the 18 dimensions. Clicking on the image will take you to a 10.3MB PDF file.



It's interesting to note the presence of the very tight Jewish cluster, which includes Ashkenazi, Sephardic and Moroccan Jews. The Basques and Sardinians also cluster together, despite being clearly distinct from each other in the fist two dimensions. This is fascinating because these two groups have been mentioned a few times now in various studies and presentations as being the best modern proxies for Europe's Neolithic farmers.

The widespread Central and Eastern European cluster mostly includes individuals from populations that aren't easily characterized in these sorts of tests, and that's basically because they're of mixed origin. Indeed, I suspect things would look somewhat different in that part of the plot if I had more sizable samples from Germany, Scandinavia, Poland and nearby areas.

Mclust can produce many more clusters than just 13 from the same data, but as per above, I wanted to see what would happen if it was asked to come up with the optimal solution. For more on this type of analysis check out the articles here, here and here.


Update 17/12/2013: On a related note, here's an Mclust analysis of West, Central and South Asia. The optimal result was obtained with 10 dimensions and 14 clusters. Please note that although some of the clusters have the same names as in the analysis above, they aren't the same clusters.




See also...

Principal component analysis (PCA) of West Eurasia

Multidimensional views of South Asia, West Asia and Eastern Europe

Eurogenes' North Euro clusters - phase 2, final results