The Ghosts of the European Pleistocene

2011’s Cave of Forgotten Dreams was a strange film. I went to watch it in the theaters mostly to see the paintings of Pleistocene peoples in an immersive manner, but the director and narrator, Werner Herzog, used the film as an instrument to forward his thesis that humanity as we understand it emerged during this period in the European Ice Age.

Whether he knew it or not Herzog was channeling the “Great Leap Forward” model of the origin of our species. That in an almost punctuated manner the cultural proteanism which we take to be a defining hallmark of our species emerged at some point deep in what we call the Ice Age. In The Dawn of Human Culture Richard Klein localized this burst of humanity ~50,000 years ago in Africa, and hypothesized that it was triggered by a biological change which enabled language fluency. In The Humans Who Went Extinct Clive Finlayson posits that cultural changes associated with the Gravettian people in central Eurasia eventually defined what he meant to be human, and explained the marginalization of Neanderthals.

To a rough approximation I’m skeptical of both these models. I don’t think humanity emerged fully formed like Athena over the last 50,000 years. Rather, humanity we understand humanity is deeply primal, and a feature of the root of our lineage, millions of years in the past. If Homo erectus populations were still around they deserve all the rights of humans, despite their numerous differences.

I suspect that we’ll found out that ‘behavioral modernity’ is a cocktail of soft selection on standing variation and cumulative cultural change. But that doesn’t mean that the Pleistocene history of Europe is not important or interesting. And recently we’ve obtained enough ancient DNA to sketch out a general picture of demographic, if not cultural, change.

Everyone should read The genetic history of Ice Age Europe. But I suspect the impact is going to get deeper when more archaeologists are familiar with the implications. Here is the 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. We analyze 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 the earliest modern humans in Europe did not contribute substantially to 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. A ~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 during the Ice Age ~19,000 years ago. During the major warming period after ~14,000 years ago, a new genetic component related to present-day Near Easterners appears in Europe. These results document how population turnover and migration have been recurring themes of European pre-history.

I modified the model of demographic turnover to the left, adding labels for the primary paleoanthropological cultural groups. Instead of starting with the archaeology the authors let the genetic results guide them. What they discover is that there were roughly four turnovers in population defined by four “clusters”:

– the first Europeans who succeeded the Neanderthals, who seem to have left no descendents

– the Goyet cluster, associated with Aurignacians

– the Vestonice cluster is associated with the Gravettians

– the El Miron cluster with the Gravettians

– the Villabruna cluster with various late Pleistocene cultures, and is the direct ancestor of Mesolithic hunter-gatherers present in Europe when the first farmers arrived

A quick calculation suggests that very little of the ancestry of modern Europeans has deep roots across much of the continent going back to before the Last Glacial Maximum ~20,000 years ago. The “Pleistocene” ancestry of Europeans mostly derives from the last group, the Villabruna cluster. In the paper the authors note that this group is unique for several reasons:

– some individuals in this cluster have an affinity with East Asians (earlier Pleistocene groups do not)

– more universally, individuals in the Villabruna cluster have a notable affinity with Middle Eastern populations which was not evident in earlier Pleistocene clusters

Recall Middle Eastern populations can be modeled as a mix of a West Eurasian group similar to European hunter-gatherers, and, “Basal Eurasians,” who are an outgroup to all non-Africans (European hunter-gatherers to Oceanians to Amerindians!). The authors posit that the gene flow is more likely from the Middle East, because earlier European clusters have affinities with Villabruna, but they share nothing with the Middle East. The Villabruna cluster does not have Basal Eurasian ancestry though. So we might be looking at complex population structure.

Two general issues that crop up in this paper are sampling limitations and population expansions into Europe from the east. The disappearance of Goyet ancestry, only to reappear as part of the El Miron cluster, is curious. Perhaps the post-Goyet people occupied ecologies less likely to be fossilized? It reminds us of the resurgence of hunter-gatherer ancestry in Europe of the Middle Neolithic. As for why there seems to be an eastern bias into intrusive populations into Europe, these groups may simply have had a larger population, and so been more likely to avoid meta-population extinction events?

Finally, the authors point out that Gravettian culture in Siberia and Europe does not seem to be genetically related. This suggests that these people were very modern, because a hallmark of the modernity is that ideas can move between groups without too much genetic exchange.

Europe has the best coverage of ancient DNA. What we find here are repeated population turnovers and a lot of complexity and contingency. Is Europe peculiar? There is circumstantial evidence from modern DNA that Australians are descendants of first settlers. And to some extent this is also true in the case of East Asians if the work reported out of the Fu lab holds up. South Asians though are more likely to be like Europeans, and Middle Easterners show some of the same dynamics during the Holocene.

3 thoughts on “The Ghosts of the European Pleistocene

  1. Razib: There is circumstantial evidence from modern DNA that Australians are descendants of first settlers. And to some extent this is also true in the case of East Asians if the work reported out of the Fu lab holds up.

    We will kind of need a lot of samples to understand this stuff in detail. For West Eurasia we know that Europeans are the descendants, largely, of some of the first settlers in the general West Eurasian region (e.g. people like the Kostenki14 sample), and we know that they share the most drift with the paleolithic Europeans out of all present day people.

    However we also know from extended sampling through time that we can pretty much model present day Europeans as linear combinations of groups related to UP Europeans who lived within West Eurasia but outside Europe itself around 16,000 BC (Anatolians, EHG, CHG, Villabruna), with no real need for earlier groups.

    From what we know Fu’s sampling of Tianyuan so far (and you may have more of a hookup on the data), we know that the sample shares more drift with East Asians than other ancient samples (at least from outside the Americas and at the same time depth), and we know that he shares the most drift with present day East Asians.

    However, what we don’t know is whether Han Chinese can best wholly be explained by descendants and relatives of Tianyuan Man, living within China, or whether it’ll end up being the case that various East Eurasian related groups living outside of China around 16,000 BC will actually be what we need for working models. (Or if living within China, whether there was strong population structure and lots of replacement there, as the state that is China today is a huge place). Other groups in East Asia seem obviously to descend largely from pretty large migrations out of China (e.g. Japanese, Korean, Tibetans, etc.), so we kind of already know the answer there, with regard to recent continuity.

  2. Also regarding turnovers –

    http://www.eshe.eu/static/eshe/files/PESHE/PESHE_2017_FINAL.pdf (page 83):
    “We identified five Neandertal specimens from the sites of the Troisième caverne of Goyet (Belgium), Spy (Belgium), Les Cottés (France), Vindija Cave (Croatia), and Mezmaiskaya Cave (Russia) (individual ‘Mezmaiskaya 2’) with sufficient amounts of endogenous DNA to enable the sequencing of their nuclear genomes to an average coverage of between 1- and 2.7-fold. The specimens were radiocarbon dated either directly or by dating of associated finds to between 39,000 and 47,000 years calBP.

    We find that all late Neandertals were genetically more similar to each other than to the Altai Neandertal, regardless of their geographical origin…. The Neandertals from Vindija Cave were more similar to each other than to any other Neandertal; as was the case for the three Neandertals from Belgium and France, supporting the presence of geographical substructure in Neandertal populations. All these individuals in turn were more closely related to each other than to the younger Neandertal individual from Mezmaiskaya Cave (Mezmaiskaya 2). Nonetheless, the latter individual is more closely related to the other late Neandertals than to the older Neandertal individual from the same site (Mezmaiskaya 1)” at 60-70,000 years BP.

    “This may point to a genetic population turnover towards the end of Neandertal history.”

  3. My bet for now is that Villabruna is the result of an in-situ expansion from the Balkans, both into the rest of Europe and the Near East.

    The reason I say this is because R1b, and indeed R1, look like they’re native to the Balkans rather than the Near East. Also, as per Matt’s comment, Kostenki14 from near there looks like part of a very early proto-European clade, even if not directly ancestral to modern Europeans.

    One of the weak points of the Fu paper was their scant sampling from the Balkans and Eastern Europe, especially from the key period prior to the formation of the Villabruna cluster. That’s when there’s a shift in Mammoth mtDNA in much of Europe, so something was going on.

    http://eurogenes.blogspot.com.au/2016/05/following-mammoth-herds.html

    Although to be fair, there’s not much in terms of human remains to sample in Eastern Europe from this period.

    Interestingly, and no one’s talking about this much yet, but based on some of the Mesolithic samples from the Balkans it looks like R1b-V88 might be from there too. If this pans out, it’ll be a remarkable story, because I don’t think anyone expected African R1b to derive from Balkan Mesolithic foragers. How’d it get there? I reckon via Iberia (one Iberian Neolithic farmer belongs to R1b-V88).

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