According to a new paper in Nature, Ancient gene flow from early modern humans into Eastern Neanderthals, a basal population of anatomically modern humans mixed with eastern Neanderthal populations on the order of ~100,000 years ago. The figure above is from the paper, and shows (on the left) the proportions and direction of gene flow across the phylogenetic tree, and (on the right) the dates of divergences and effective population sizes of the various groups. In The New York Times Carl Zimmer has a write-up, Ancient Humans May Have Left a Genetic Mark on Neanderthals (also, see Ewen Callaway in Nature, Evidence mounts for interbreeding bonanza in ancient human species). It’s useful to read, because he reports that some of the researchers assumed their results were in error, so they double-checked, and, other prominent researchers believe that the results are broadly credible. This doesn’t mean the results are correct…though the team that came out with this has people I trust to attend to details, and the results are not implausible on a priori grounds.

Where does this lead us? As observed on Twitter there are some curious results in this paper in terms of the phylogenetic relationships and demographic history of human populations. The modern human lineage which contributed to the Altai individual seems to have done so ~100,000 years ago. This is 40,000 to 50,000 years before the “Out of Africa” event which we know of, and which seems to have resulted in the patterns of human genetic variation outside of Africa, excepting archaic admixture, that we see today. As noted in the paper there have been recent finds in locations such as China of very ancient pre-“Out of Africa” modern human remains, and there has always been the Skhul and Qafzeh hominids in the Near East. So that’s not too much of a problem necessarily. But, if you look closely at the phylogenetic tree above San diverge from other modern lineages ~200,000 years ago, well before the admixture event, but the modern human ancestry in the Altai Neanderthal looks equally related to all modern humans. That seems peculiar, since in the 100,000 intervening years there should have been significant structure to sample. There are a variety of ways to “resolve” this…though as one of the authors stated, there are many reasons why the date of the divergence of the various groups and admixture differ so much (e.g., archaic admixture into the San might push back their divergence from other groups). I need to think about this more and read the supplements. The picture in the details is getting cloudier, not clearer….

But the overall result does clarify and highlight some big picture inferences we can make in generating a framework toward understanding new results. Mait Metspalu’s group is going to publish a paper on low levels of pre-“Out of Africa” modern admixture in Sahul populations (that is, a earlier movement of modern people than the canonical one), and I now judge that their result is a true positive to a higher degree than earlier. These Altai Neanderthals likely did not contribute to modern human Neanderthal ancestry, as the Neanderthal ancestry in modern humans is closer to that of European Neanderthals (who did not have modern human ancestry like the Altai individual). Follow that?

The upshot is that these results should change our prior expectations about the nature of ancient human population structure. Yes, it was complicated, but there’s a pattern. The genetic patterns indicate that there was selection in the genome against the introgressed variants, so Neanderthals and modern humans exhibited hybrid breakdown. In light of no such genomic evidence for admixture of Eurasian ancestry into KhoeSan (I’ve asked, people have looked), that suggests we know that for hominins hybrid incompabilities seem to arise on the scale of between 200,000 and 600,000 years. It also seems that due meta-population dynamics lineage extinctions were very common in hominins. The genetic relatedness of Neanderthals across human swaths of territory indicate that they were subject to this dynamic, where there were massive lineage pruning events over the 600,000 years that this group was a distinct population. With modern humans, we now know that first settlers do not always leave a genetic impact later on because of extinction events. With these facts under our belt it is less surprising if there were “false dawns” of the “triumph of humanity.”

What these results do warrant though is the final expiration of a particular narrative of the explosion of humanity ~50,000 years ago due to singular biological changes that cascaded themselves into a cultural explosion, where the hominin-made-man swept all before them. Probably the best illustration of this thesis can be found in Richard Klein’s 2002 book, The Dawn of Human Culture. In it he proposes that 50,000 years ago there was a single mutation which resulted in a pleiotropic cascade, and allowed for the emergence of full elaborated language and ergo the package of features which we associate with behavioral modernity. This model was presaged in the earlier decade with popularizations of “mitochondrial Eve” which implied that all humans were descended from a very small tribe resident in East Africa on the order of ~100,000 years ago. (the date varied as a function of the vicissitudes of mutational rate estimates)

Here’s what we know now that changes this. First, there are populations within Africa, in particular the the San of the far south, who diverged much earlier than 50,000 years ago. The most recent genomic estimates are suggesting divergence dates as early as ~200,000 years before the present. Second, the effective population size of humans outside of Africa is incredibly small, suggesting expansion from a very small founding population, but one should be cautious about generalizing to groups within Africa. That is, the blitzkrieg sweep model of modern human expansion does not hold to within Africa, and there is both archaeological and genomic inference to indicate the persistence of highly diverged hominin lineages in that continent until relatively recently. And, these lineages may have admixed with modern humans just as they have outside of Africa.

Finally, the emergence of H. sapiens sapiens supremacy seems to have been a process, not a singular event which emerged de novo like a supernovae in the hominin firmament. The Omo remains in Ethiopia were anatomically modern humans. The people who gave rise to Omo lived ~200,000 years ago. The encephalization of the human lineage increased gradually up until around ~200,000 years ago, and Neanderthals were famously the most encephalized of all. Therefore, some form of modern humans were present within Africa for 150,000 years while other lineages were dominant elsewhere. Remains from places like China suggest though that offshoots of African humanity did push into the rest of the world…but they may not have left much of a genetic trace. This may have been part of movements due to climate change during the Pleistocene, or one of the natural migrations which a consequence of Malthusian pressures and inter-deme competition which afflicted humans. But they clearly did not conquer all before them. Why? We don’t know. And we don’t know why the situation was different 50,000 years ago. As a null hypothesis one might entertain the possibility that it was random. That periodically turnovers occur, and it just so happened that an African lineage lucked out in a massive extinction event. But that’s hard to credit when you consider that these modern humans crossed into Sahul and Siberia after sweeping aside other groups, and then eventually crossed over into the New World. There was something different about us. Additionally, the modern humans eventually absorbed or extirpated other lineages within Africa too.

A generation ago many people thought they had the answer. That man was born 50,000 years ago on the East African plain, and the gods gave him the world. Only he was endowed with a soul. Today we know that that’s wrong. We just don’t know what’s right.

Addendum: We need to start thinking about Eurasian gene-flow into Africa over the Pleistocene.