Razib Khan One-stop-shopping for all of my content

August 27, 2017

The Ghosts of the European Pleistocene

Filed under: European genetics,Ice Age — Razib Khan @ 9:19 pm

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.

February 23, 2012

Ending the Ice Ages

Filed under: Ice Age — Razib Khan @ 1:58 am

We Are All Panamanians:

When the Isthmus of Panama rose from the sea, it may have changed the climate of Africa–and encouraged the evolution of humans.

The emergence of the Isthmus of Panama has been credited with many milestones in Earth’s history. When it rose from the sea some 3 million years ago, the isthmus provided a bridge for the migration of animals between North and South America, forever changing the fauna of both continents. It also blocked a current that once flowed west from Africa to Asia, diverting it northward to strengthen the Gulf Stream. Now Steven Stanley, a paleobiologist at Johns Hopkins, says that that change in currents may be behind yet another major event: the evolution of humans. When the isthmus rearranged the ocean, he says, it triggered a series of ice ages that in turn had a crucial impact on the evolution of hominids in Africa.

Question: do we have enough nukes to re-open the isthmus?

March 27, 2010

The science of human history as written by Herodotus

The following passage is from the epilogue of The Real Eve: Modern Man’s Journey Out of Africa by Stephen Oppenheimer:

In this book I have offered a synthesis of genetic and other evidence. Everything points to a single southern exodus from Eritrea to the Yemen, and to all the non-African male and female gene lines having arisen from their respective single out-of-Africa founder lines in South Asian (or at least near the southern exit). I regard the genetic logic for this synthesis as a solid foundation, and I have based the rest of my reconstruction of the human diaspora upon it. Obviously, the ‘choice’ of starting point (mine or theirs) determined all the subsequent routes our ancestors and cousins took. Tracing the onward trails is only possible as a result of marked specificity in regional distribution of the genetic branches The geographic clarity of both male and female gene trees is a big departure from the fuzzy inter-regional picture shown by older genetic studies. The degree of segregation of lines into different countries and continents is in itself good evidence that once they got to their chosen new homes, the pioneers generally stayed put, at least until the Last Glacial maximum forced some of them to move. This conservative aspect of our genetic prehistory also provides a partial explanation for the fact that when we look at a person, we can usually tell, to the continent, where their immediate ancestors came from, and underlies differences that some of us still call ‘race.’

Oppenheimer wrote the above in the early aughts, as his book was published in 2003. Much of this is generally in line with the ‘orthodoxy’ of the day. I believe that Oppenheimer’s assertion that there was one southern migration out of Africa by anatomically modern humans has gained some advantage over the alternative model of two routes, northern and southern, over the past ten years (Spencer Wells’ The Journey of Man sketches out the two wave model). Other assertions and assumptions have not stood the test of time. In particular, I would contend that generally the ‘conservative aspect of our genetic prehistory’ can no longer be taken for granted. Specifically, it seems likely now that much occurred after the Ice Age and during the Neolithic.


420px-AGMA_HérodoteThe false inferences of the early aughts were due to two primary problems. First, they relied heavily on the powerful new techniques of extraction and analysis of uniparental ineages; the male and female direct line of descent. Concretely, mtDNA and the nonrecombintant portion of the Y chromosome. The lack of recombination allows for relatively easy reconstruction of phylogenies assuming a coalescent model. Second, the inferences attempt to make connections between the patterns of variation in modern populations, and what one may infer about the past from those patterns. Obviously constructing a phylogeny, or plotting haplogroup frequencies as a function of geography, is rather straightforward science. But using these results to generate inferences of the past is often more of an art than a science, and implicit assumptions lurk behind the causal chains. Consider for example the utilization of modern Anatolian (i.e., Turkish) genetic variation as a reference for the expansion into Europe of Neolithic farmers from the Near East. This of course presumes that modern Anatolians are a good proxy for ancient Anatolians. There are various suggestive reasons for why this is a plausible assumption, but assemble enough plausible assumptions, and rely on their joint likelihood, and you construct a very rickety machinery of possibility.

In early 2007 I began to have serious doubts about the orthodoxy of genetic conservatism. The primary trigger was the story of the Etruscans. Here is the crux of the issue: there are two models for the origins of the Etruscans, first, that they were the pre-Indo-European autochthons of Italy, or, that they were the migrants from the eastern Mediterranean, in particular Anatolia. The second may seem an outlandish hypothesis, but there were several tendrils of evidence to support it. But perhaps the ’support’ which weighed most against it is that the fact that the Anatolian model has an ancient source, the Greek historian Herodotus. I should perhaps put historian in quotes as well, because Herodotus is often viewed more as a repeater of myths, and derided by some as the ‘father of lies’ (in this he stands in sharp contrast to contemporary perceptions of the ‘modern’ Thucydides, though revisionists have begun to challenge this narrative). In contrast, the model that Etruscans are indigenous to Italy, and that their ‘exotic’ foreign traits were simply acquired through trade and cultural diffusion, dovetailed well with the post-World War II ‘pots not peoples’ paradigm. That cultural change was ubiquitous, while at the same time populations were immobile. It was boring, prosaic, and conservative, and so an ideal null hypothesis.

But here it turns out that Herodotus was right, and archaeologists were wrong. Genetic analysis of modern Tuscans from isolated villages shows that some are surprisingly closely related to extant eastern Mediterranean lineages. Genetic analysis of Tuscan cattle showed that they were surprisingly closely related to extant eastern Mediterranean lineages of cattle. Finally, extraction of ancient Etruscan DNA showed that they were closely related to extant eastern Mediterranean lineages. The overlap was often with Anatolia, and combined with fragmentary linguistic and archaeological data, the evidence clearly points to an exogenous origin for the Etruscans. The boring null hypothesis was wrong. After these genetic stories gained prominence I went and reread recent archaeological texts on the Etruscans, and there were many models which showed exactly how Etruscan cultural uniqueness derived back to prehistoric Italy. It seems in hindsight that the prior assumption served as an interpretative filter, and people saw patterns that they were primed to see based on what they ‘knew’ to be the history of prehistoric and early Iron Age Tuscany.

Of course to refute the primacy of Oppenheimer’s conservative model of genetics one has to offer more examples than that of the Etruscans, and in particular, examples which are of greater scope and weight. I believe those examples exist. In the early aughts based on the mtDNA evidence the likelihood was that South Asian genetic variation is by and large a product of changes wrought upon the basic elements extant in the region around the end of the last Ice Age. The Y chromosomal data was more confused, though it did imply a closer relationship to groups in western Eurasia. But based on the mtDNA Oppenheimer posited a model whereby India was the mother of all non-Africans, that is, all non-African lineages derived from roots within the Indian subcontinent before the Last Glacial Maximum. This is at sharp variance with colonialist narratives of an Aryan invasion of the subcontinent, and the subjugation of the natives by quasi-European overlords, who are the ancestors of the moder upper castes. The charged ideological import of this model is transparently obvious.

Unfortunately the reality is likely more complex. I suspect that some form of Oppenheimer’s model is correct, insofar as South Asia was likely an important way station for modern humans as they left Africa, and pushed into other regions of Eurasia, on to Australasia and the New World. This interpretation does gain support from mtDNA, the direct maternal lineage. But a new analysis of South Asian genetic variation using a substantial proportion of the autosomal genome implies in fact that South Asians are possibly descendants of an ancient hybridization event between a native population with deep roots in the subcontinent, and a quasi-European population which was exogenous to the subcontinent.* Genetically the quasi-European population is quite close to northern Europeans, similar to the genetic distance between modern Finns and Italians, not trivial, but far closer than that between modern South Asians and Europeans. Was this the ancient Aryan invasion? I remain skeptical of this particular detail for various reasons, as I suspect that the history of the Indian subcontinent is in fact even more complex than has been assumed before (I think it is more likely that the quasi-Europeans came before the Indo-Aryans, who arrived late, and had a stronger cultural than genetic influence).

Finally, there is another region of the world where it seems likely that the old orthodoxies of genetic conservatism will be overthrown. That region is Europe. The scientific orthodoxy of deep time continuity is strong enough that it has percolated into the public consciousness, the leader of the British National Party even referred to the deep roots of white British in demarcating who he believed ‘indigenous people’ of the Isles were. But newer data is more supportive of the hypothesis that in fact Neolithic farmers who arrived from elsewhere are the likely ancestors of most Europeans, not the hunter-gatherers who remained after the Ice Age. Extraction of ancient DNA has yielded a set of results which simply are not explicable assuming the older models of genetic continuity, which were based on inferences made from modern population variation. If I had to hazard a guess, I would have some, though not high, confidence in the following story. First, the indigenous hunter-gatherers are assimilated or marginalized by waves of Neolithic farmers pushing out from the eastern Mediterranean. The demographic expansion does not necessarily sweep outward along a southeast-northwest axis, rather, it follows the Mediterranean and Atlantic fringes, as well as along river systems in the interior. Its impact is weakest in the northeast of Europe, where Middle Eastern crops are least suitable, and the natives have the most time to absorb the cultural toolkit of the newcomers so as to resist their advance. Second, and far later, there was another wave pushing out from the region of the Ukraine to the Volga, likely the ancestors of the Indo-Europeans. Tentatively I would contend that these were the carriers of the Kurgan culture, and also brought the allele for lactase persistence. Again, for ecological reasons the populations of the northeast Baltic and into the forests of northern Russia were most insulated from this push (and non-Indo-European languages persisted in Iberia down to Roman times, and specifically in the Basque-country down to modern times, though I suspect this is a function of distance). So modern European populations may be assumed to be tri-hybrid, first a synthesis of Middle Eastern farmers overlain upon the Paleolithic substrate, and second a synthesis of Indo-Europeans from the east overlain upon pre-Indo-European substrate. Unlike the case of India I suspect teasing out these patterns in modern populations is more difficult because the genetic distance between the three ancestral populations is far smaller than between the indigenous peoples of India before the quasi-Europeans arrived.

This leaves much of the world untouched by my speculations, but I believe showing that the genetically conservative null hypothesis is now in serious doubt in South Asia and Europe is sufficient to knock it from being a necessarily default assumption through which we must filter our interpretations. I do not believe that the reordering of human variation and the welter of population movement after the Ice Age was equivalent in effect to the Out of Africa migration, but I do believe that it was important enough to make the world of 2000 BCE very different from that of 15000 BCE in regards to genetic variation. In some cases, such as Central Asia from the Caspian to the Taklamakan the world of 2000 CE is fundamentally different from the world of 0 CE.

I will then end with a prediction, one in which I do not have much confidence, but which may no longer be wrong on the face of it with these new data in mind. Here is a passage from page 7 of Jared Diamond’s Guns, Germs, and Steel:

Initially, archaeologists considered the possibility that the colonization of Australia/New Guinea was achieved accidentally by just a few people swept to sea while fishing on a raft near an Indonesian island. In an extreme scenario the first settlers are pictured as having consisted of a single pregnant young woman carrying a male fetus…..

Let me stipulate that Diamond seems skeptical of the extreme model, but it illustrates the consensus that Australian Aboriginal populations are descended from the first settlers. That is, the modern populations of indigenous Australians are the direct descendants of those who swept Out of Africa along the fringe of the Indian ocean, through Southeast Asia, and arrived in Australia (more specifically, Sahul), on the order of 40 to 60 thousand years ago. From what genetic data I have seen this may be true. But I do not know of any extractions of ancient DNA, and it seems to me that the analysis of the phylogenetics of Australian Aboriginals is relatively sketchy. Therefore, I will suggest that within the last 10,000 years there has been a major new migration of people into Australia, and the modern range of genetic variation of Australian Aboriginals is significantly different from that of the populations of the Ice Age. I suggest this primarily because the dingo arrived within the last 10,000 years, more likely as recently as 4,000 years ago. With the expansion of the utility of ancient DNA extraction and analysis this question may be answered in the near future. I would still bet I’m wrong with the hypothesis I just offered, but I’m far less sure than I would have been 2 years ago.

Note: This post emerged from a conversation I had with Kevin Zelnio and Dave Munger.

* I say ‘quasi-European’ because the population may have origins outside of the boundaries of modern Europe at the Urals. Perhaps in western Siberia. Additionally, the idea of ‘Europe’ is relatively new, and exhibits little ancient cultural coherency.

Image source: Wikipedia

Powered by WordPress