FOXP2, language & Neandertals

The Derived FOXP2 Variant of Modern Humans Was Shared with Neandertals:

...Here, we find that our closest extinct relatives, the Neandertals, share with modern humans two evolutionary changes in FOXP2, a gene that has been implicated in the development of speech and language. We furthermore find that in Neandertals, these changes lie on the common modern human haplotype, which previously was shown to have been subject to a selective sweep. These results suggest that these genetic changes and the selective sweep predate the common ancestor (which existed about 300,000-400,000 years ago) of modern human and Neandertal populations. This is in contrast to more recent age estimates of the selective sweep based on extant human diversity data. Thus, these results illustrate the usefulness of retrieving direct genetic information from ancient remains for understanding recent human evolution.

The discussion unpacks the hypotheses in more detail:

The first scenario is that the positively selected FOXP2 haplotype was transferred into Neandertals from modern humans or vice versa through gene flow. This seems to be an unlikely possibility. Neither mitochondrial nor--as we show here--Y chromosomal gene flow between the two hominid groups can be detected. Furthermore, other tests for admixture that rely on autosomal variation have hitherto failed to detect any gene flow into Neandertals...The second scenario is that the relevant FOXP2 haplotype was present in the ancestral population of modern humans and Neandertals and was later positively selected in humans after their divergence from Neandertals. For this scenario to be likely, the relevant haplotype would have needed to be at a considerable frequency in the ancestral population in order to obtain the relatively high frequencies in Neandertals. However, the higher the frequency of a variant is before it becomes positively selected, the less likely it is to detect a signature of a selective sweep...Hence, this scenario might also be considered relatively unlikely. The third scenario is that the selective sweep started before the divergence of the ancestral populations of Neandertals and modern humans around 300,000- 400,000 years ago....

The elephant in the room is contamination, this has been a major issue of late. With that prior under our belt one has to wonder if that isn't a more parsimonious explanation for their finding? That being said, they do try to address this objection with copious controls, and the other sequences extracted seem to be outgroups to modern humans (e.g., Y & mtDNA, see figure 2 of the paper).

The second major issue is their dismissal of gene flow. In short, introgression. The authors are correct that most data does not imply a great detail of admixture. One major point that needs to be considered is that comparing ancient hominids to modern humans might be a misleading test, since what we are interested is the relationship between the precursors to modern humans and other ancient hominid groups, and the modern lineage itself may have lost many alleles extant in the past (extracting ancient DNA from anatomically modern humans of that period would allow for better calibration in regards to this point). That being said, introgression of one allele would not imply a major perturbation of the rest of the genome, so their rejection of this model is a judgment call. So of course they settle upon an ancient selective sweep across proto-human groups on the order of a few hundred thousand years as the only major alternative (independent sweeps seems unlikely).

Why is this important? Because FOXP2 has been identified as the language gene. The main objection is thought the derived variation may be necessary, it may not be sufficient, for the emergence of modern language faculties. I do have to add that all of these reconstructions use simple models, but I am starting to wonder if we're eliding too much in the way of the complexities of demographic history and evolutionary dynamics.

The Economist has a popular press article on this topic.

Update: Nick Wade has an excellent piece up which surveys all the major issues.