Vernot and colleagues recently mined the genomes of Europeans and East Asians scouting for sequences from Neandertals and Denisovans (two archaic hominin lineages with whom ancient humans interbred) . They found an absence of archaic hominin sequence in some regions of the genome. These 'deserts', as they call them, may reflect loci where Neandertal and Densiovan DNA were deleterious and purged. Remarkably, one of the deserts contains FOXP2, a gene involved in speech and language (I refer readers to Geoffrey Pullum's Language Log write-up for how people have thought about FOXP2 and language , as well as to Steven Pinker's elegant discussion of the topic ).
The suggestion that FOXP2 is not under neutral selection is not new [3,4]. In 2002, Enard and colleagues in Svante Paabo's lab compared FOXP2 in humans and chimps, speculating that the human-specific signatures in FOXP2 occurred relatively recently, about 200,000 years ago, Later, these human-specific variants were thought to have arisen somewhat earlier, around 300,000 to 400,000 years ago, before the most recent common ancestor of humans and Neandertals. Why? Because, while humans and chimps have different FOXP2 sequences, it was discovered that humans and Neandertals share the same evolutionary changes in FOXP2 .
Since humans and Neandertals have comparable FOXP2 sequences, it is interesting that FOXP2 falls in a large desert where no archaic hominin introgression was observed. Why is that? The authors state that their findings are inconsistent with neutral selection (implying some kind of regional target for selection?) but that the mechanism explaining the deserts is uncertain. Structural variation, alteration involving segments longer than 1 kb, are one possibility, as large regions of the genome can be substrates for natural selection .
Update (and parenthetical)
A reader let me know that the above synopsis was too technical. He attributed this to him not having the background to understand. But I believe the issue is mine (not his). At the risk of introducing (or exposing) errors in my own thinking, here's my attempt to say what I wrote above but in plain English.
Ancient humans had sex with their now-extinct cousins (Neandertals and Denisovans). By comparing our DNA with theirs, we can get clues about what makes us unique. There are some long stretches in our DNA that don’t have much of our extinct cousins’ DNA mixed in with them. One of these regions contains a gene called FOXP2, which was the first gene discovered (years ago) to have an influence on speech development. Language is a feature that is unique to humans. So interestingly, humans and Neandertals have the same DNA for FOXP2, which implies that Neandertals may have been equipped, like us, to make fine movements with their mouths. This is in contrast with chimpanzees. Chimps have a different DNA signature at FOXP2 than we do, and they don’t speak. But what’s super interesting about recent research is that these long regions of DNA without Neandertal DNA mixed in may give us clues to our evolution. For some reason, FOXP2 occurs in a region that may have been protective for our ancestors’ survival.
I'm a Public Health Genetics PhD student at the University of Washington and a molecular epidemiology research fellow at the Fred Hutchinson Cancer Research Center. I post (mostly) about topics in epidemiology and genetics.