Another look at the Lazaridis et al. ancient genomes preprint

I've now had a chance to look over the Lazaridis et al. preprint a few times, and also take part in several online discussions about the results, at these blogs and elsewhere. So I thought it might be useful to put together another post on the paper to report what I've learned and reiterate a few points. First of all, to understand the results, it's really important to known what the four main ancestral components in this study represent:

- West European Hunter-Gatherer (WHG), based on an 8,000 year-old genome from Loschbour, Luxembourg

- Ancient North Eurasian (ANE), based on a 24,000 year-old genome from South Siberia (dubbed Mal'ta boy or MA-1)

- Early European Farmer (EEF), based on a 7,500 year-old genome from Stuttgart, Germany, belonging to the Neolithic Linearbandkeramik (LBK) culture

- Eastern non-African (ENA), this basically means East Eurasian, and is based on samples of present-day Onge, Han Chinese and Atayal from Taiwan

Now, from what I've seen online, many people seem to think that ANE is more East Asian than European, and can be considered a signal of pretty much any population expansion from the east into Europe. This is not true. ANE is Amerindian-like, but actually also very similar to WHG. In fact, they're equidistant from ENA:

The results of Table S12.1 provide suggestive evidence that Onge share more common ancestry with hunter-gatherers than with Stuttgart. All statistics involving two hunter-gatherer populations have |Z|<0.9, so ancient Eurasian hunter-gatherers are approximately symmetrically related to Onge, and they are all more closely related to them than is Stuttgart.

We next consider the relationship of ancient samples to East Asia using the set (Ami, Atayal, Han, Naxi, She). East Asians are more closely related to all hunter-gatherers than to Stuttgart, but there are no significant differences between hunter-gatherers (all such statistics have |Z|<1.1) (Table S12.2).

...

We have conveniently labeled MA1-related ancestry “Ancient North Eurasian” because of the provenance of MA1 in Siberia, but at present we cannot be sure whether this type of ancestry originated there or was a recent migrant from some western region.

The various Uralic, Turkic and Mongolian groups expanding into Europe, usually after the Bronze Age, no doubt carried significant ENA, so these groups can't be the source of the fairly high levels of ANE across Europe today, because most Europeans lack ENA. Below is a graph based on two f4 tests, comparing ANE and ENA ancestry among Europeans, this time with the Han Chinese as ENA proxies. Note that most of the samples fall within a cline that runs from the Stuttgart sample to Estonians. The only outliers in the direction of the Han are groups from current or former Uralic and Turkic speaking areas of Europe.

ANE was actually present in Scandinavia during the Mesolithic, because Motala12, the 8,000 year-old hunter-gatherer genome from Sweden, has an ANE ratio of 19%. But this isn't enough to explain the ANE levels carried by most present-day Europeans, so it's very likely there were at least two expansions of ANE into Europe.

Considering that Loschbour and Stuttgart totally lack ANE, it's plausible that a major wave of ANE moved across much of Europe sometime after the early Neolithic, but obviously before the Uralic and Turkic expansions, which, as per above, were rich in ENA. Based on recently published ancient mtDNA evidence from Central Europe (see here), Lazaridis et al. propose that this timeframe was the Copper and/or Bronze Age.

This of course is the generally accepted Proto-Indo-European timeframe. Indeed, the theory I put forward in the previous blog entry (see here) that most of the ANE in Europe today was the result of the Proto-Indo-European expansion, probably from Eastern Europe, looks even better on closer inspection.

Note the elongated cline formed by the European samples running from WHG to EEF on Fig 2B, shown below. It correlates well with latitude, and very likely reflects northward migrations of Neolithic farmers into Europe from the Mediterranean Basin, followed by isolation-by-distance. In other words, this cline probably took thousands of years to form.

On the other hand, there is no cline running from WHG/EEF to ANE, but all of the Indo-European and/or Eastern European samples are fairly evenly lifted up towards ANE relative to a few outliers. These outliers are all southwestern Europeans: Basques, Pais Vasco (Basque Country) Spaniards, southern French and Sardinians.

Of course, southwestern Europe is the most distant part of the continent from the generally accepted Indo-European homeland near the middle Volga. Moreover, Basques don't speak an Indo-European language, while Sardinians were only Indo-Europeanized during historic times.

Indeed, even though a couple of tables in the study report considerable ANE ancestry among Basques and Pais Vasco Spaniards, the authors admit that this need not be the case. For instance:

We next attempted to fit individual West Eurasian populations as a mixture of Loschbour and Stuttgart, as representatives of Early European farmers and West European Hunter Gatherers.

Fig. 1B suggests that this is not possible, as most Europeans form a cline that cannot be reconciled with such a mixture [Davidski's note: I think they actually mean Fig. 2B]. Nonetheless, for Sardinians (Extended Data Table 1), the most negative f3-statistic is of the form f3(Test; Loschbour, Stuttgart), which suggests that at least some Europeans may be consistent with having been formed by such a mixture. We thus fit each European population into the topology of Fig. S12.6. Only Basques, Pais_Vasco, and Sardinians, can be fit successfully with this model. Fig. S12.8 shows a successful fit.

Most European populations cannot be fit as this type of 2-way mixture and, intuitively, this is due to their tendency (Fig. 1B) towards Ancient North Eurasians that is not modeled by such a mixture.

Another intriguing thing about the results shown in Fig 2B is that the expansions of ANE across Europe appear not to have disturbed the presumably Neolithic WHG/EEF cline to any great extent. What this suggests is that ANE was spread largely independently of EEF and even WHG. In other words, the groups that pushed ANE deep into Europe probably had very high ratios of this component. This also seems to be true for the groups that brought ANE to the Near East:

A geographically parsimonious hypothesis would be that a major component of present-day European ancestry was formed in eastern Europe or western Siberia where western and eastern hunter-gatherer groups could plausibly have intermixed. Motala12 has an estimated WHG/(WHG+ANE) ratio of 81% (S12.7), higher than that estimated for the population contributing to modern Europeans (Fig. S12.14). Motala and Mal’ta are separated by 5,000km in space and about 17 thousand years in time, leaving ample room for a genetically intermediate population. The lack of WHG ancestry in the Near East (Extended Data Fig. 6, Fig. 1B) together with the presence of ANE ancestry there (Table S12.12) suggests that the population who contributed ANE ancestry there may have lacked substantial amounts of WHG ancestry, and thus have a much lower (or even zero) WHG/(WHG+ANE) ratio.

So perhaps the 17,000 year-old Afontova Gora 2 (AG2) genome from Central Siberia, classified as part of the ANE meta-population by Lazaridis et al., is genetically the closest sample we have to the Proto-Indo-Europeans? Based on a couple of the PCA from Lazaridis et al. (below) and Raghavan et al. (see here), this genome doesn't appear to be 100% ANE. My very rough estimate is 85/15 ANE/WHG.

If my assumptions are correct here, then it's no wonder that this Bronze Age Danish sample (M4) from the recent Carpenter et al. paper (see here) shows a clear shift towards the Americans on the global PCA. M4 is better known as "the old man" from the giant Borum Eshøj barrow (see here), presumably built by some of the earliest Indo-Europeans in Scandinavia. We can probably expect such Afontova Gora 2-like results from many European samples archeologically linked to the early Indo-Europeans.