New evidence for archaic admixture in African hunter gatherers (Lachance et al. 2012)

At the end of last year I predicted that full genome sequencing would begin turning up evidence for more archaic admixture in Africa. Halfway into the year, it appears that my prediction has proven to be correct: a new study in Cell by Lachance et al. documents the existence of such admixture between an archaic hominin and Pygmies from Cameroon, and the East African Hadza and Sandawe.

Archaic admixture in Biaka and San was previously detected by Hammer et al. Hence, we now have evidence for archaic admixture from several regions that encompass all major regions within sub-Saharan Africa. It seems that my old idea about layers of Palaeoafricans being absorbed by early modern humans in Africa was basically correct, and that some of these layers correspond to archaic African populations.

But not all agree. The New York Times coverage of the paper suggests that there is a controversy surrounding the new study:

All human fossil remains in Africa for the last 100,000 years, and probably the last 200,000 years, are of modern humans, providing no support for a coexistent archaic species. 

... 

Paleoanthropologists like Dr. Klein consider it “irresponsible” of the geneticists to publish genetic findings about human origins without even trying to show how they may fit in with the existing fossil and archaeological evidence. Dr. Akey said he agreed that genetics can provide only part of the story. “But hopefully this is just a period when new discoveries are being made and there hasn’t been enough incubation time to synthesize all the disparities,” he said.

This is of course completely wrong; as Chris Stringer mentions in the NY Times piece, there is ample evidence for archaic Africans down to quite recent times in the form of Iwo Eleru and Ishango, and there is more evidence besides. Indeed, it does not appear at all that there was a punctuational event that replaced archaic hominins with a new Homo sapiens species. If anyone wants to criticize the new study, complaining about it being in disharmony with physical anthropology is not a good way to go about it. Nor is it, of course, "irresponsible" to report the new findings.  And, apparently, there is more on the way:

In a report still under review, a third group of geneticists says there are signs of Neanderthals having interbred with Asians and East Africans. But Neanderthals were a cold-adapted species that never reached East Africa.

Things are bound to become quite interesting.

From the paper:

A striking finding in our data set is that compelling evidence exists that extant hunter-gatherer genomes contain introgressed archaic sequence, consistent with previous studies (Hammer et al., 2011; Plagnol and Wall, 2006; Reich et al., 2010; Shimada et al., 2007; Wall et al., 2009). We note that unambiguous evidence of introgression is difficult to obtain in the absence of an archaic reference sequence, which currently does not exist and may never be feasible given the rapid decay of fossils in Africa. Although we carefully filtered our data set in an attempt to analyze only high-quality sequences (Supplementary Information), it is possible that unrecognized structural variants or other alignment errors could generate a spurious signature similar to introgression. Encouragingly, we did not see an enrichment of structural variation calls in our candidate introgression regions. Additionally, through extensive simulations and analysis of European whole-genome sequences (Supplementary Information), we have demonstrated that the signatures of introgression that we observed are unlikely to be entirely accounted for due to other aspects of population demographic history, natural selection, or sequencing errors. Moreover, we did not find strong evidence that introgressed regions were clustered in the genome more often than expected by chance (p > 0.05; Supplemental Information). Nor did we find significant evidence that introgressed regions were enriched in genic regions (p > 0.05); rather, genic regions were significantly depleted for introgression in several populations (Supplemental Information). Therefore, the simplest interpretation of these data is that introgressed regions in extant human populations represent neutrally evolving vestiges of archaic sequences. In short, we find that low levels of introgression from an unknown archaic population or populations occurred in the three African hunter-gatherer samples examined, consistent with findings of archaic admixture in non-Africans (Reich et al., 2010). 

What are the implications of the new research? Where did modern humans actually originate and how can their archaic admixture be explained?

One possible explanation, consistent with multi-regional evolution (MRE) theory, is that modern humans didn't originate anywhere in particular; they emerged out of Homo populations that lived everywhere. And, certainly, the discovery of archaic admixture of a local origin is quickly reducing the number of places where the common ancestors of modern humans could have begun their expansion. Western Eurasia is out due to Neandertals; East Eurasia and Oceania is out due to Denisovans; the entirety of Sub-Saharan Africa seems to also be out. North Africa and Southwest Asia appear to be the only remaining candidates.

I don't particularly agree with MRE; one of its predictions (about the relevance of archaic hominins to the human story) has proven to be correct: it increasingly seems that there never was a new Homo sapiens species that was in reproductive isolation from the rest of the Homo genus. On the other hand, the existence of local admixture with different sets of archaic hominins, together with the relative homogeneity of our species is indicative of a range expansion that largely replaced archaic humans -- but not completely.

There does seem to have been a Big Bang of modern humans which caused the demographical explosion of a particular subset of genetic variation. This Big Bang is often associated with Out-of-Africa, but there are good reasons to doubt the traditional 60,000-year old Out-of-Africa theory, according to which humans from South or East Africa crossed into Arabia and followed the coast to populate the world. We now have more reasons to doubt this: evidence of archaic admixture in both the postulated homelands: South Africa, often cited as the region where the first signs of behavioral modernity appear, and East Africa, where the earliest anatomically modern human fossils appear.

My money continues to be on the "two deserts" theory I have proposed some time ago:

• A green Sahara pumping the ancestors of modern humans pre-100 thousand years ago, and 
• a deteriorating green Arabia pumping them post-70 thousand years ago, with some back-migration into Africa.

This would relate the two regions where no evidence (yet?) for archaic humans exist (North Africa and South West Asia), explain the causes of their dispersal (climate change), and harmonize with the evidence for archaic admixture, since the expanding wave of modern humans would partially absorb pre-existing hominins in both Sub-Saharan Africa and across Eurasia.


It must be noted that scientists have been rather conservative in their estimates of archaic admixture in the absence of ancient DNA sequence. Recombination obliterates traces of really old admixture, because introgressed segments become ever smaller, resulting in a pastiche of modern and archaic sequence that no longer looks statistically archaic. But, hopefully, the ever-solidifying case for archaic admixture in our species will finally deal the death blow to tree models, and reveal a much more interesting story of our origins.


Other coverage of the new paper: Nature, Science, ScienceDaily, EurekAlert, Washington Post, SciAm.


Cell doi:10.1016/j.cell.2012.07.009

Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers

Joseph Lachance et al.


To reconstruct modern human evolutionary history and identify loci that have shaped hunter-gatherer adaptation, we sequenced the whole genomes of five individuals in each of three different hunter-gatherer populations at >60x coverage: Pygmies from Cameroon and Khoesan-speaking Hadza and Sandawe from Tanzania. We identify 13.4 million variants, substantially increasing the set of known human variation. We found evidence of archaic introgression in all three populations, and the distribution of time to most recent common ancestors from these regions is similar to that observed for introgressed regions in Europeans. Additionally, we identify numerous loci that harbor signatures of local adaptation, including genes involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing. Within the Pygmy population, we identify multiple highly differentiated loci that play a role in growth and anterior pituitary function and are associated with height.


Link