At the recent SMBE meeting in Dublin, there was an interesting talk (judging from the abstract) about archaic genes in modern humans. The authors were Sriram Sankararaman, Nick Patterson, Swapan Mallick,, Svante Paabo, and David Reich. They believe that they can identify regions of the genome that are of Neanderthal origin and are at high frequency today, enough so that they were almost certainly favored by natural selection. They say that they have found over 100 such regions. They mention one in particular – a Neanderthal-derived segment that overlaps CLOCK, a key gene in regulating circadian rhythms. That segment has a frequency of 85% in Europeans.
This was predictable, in that Henry and I (and John Hawks) predicted it. To be exact, in our book, Henry and I predicted that at least some people today would turn out to have Neanderthal admixture, that some Neanderthal alleles would be favored by selection and be common, and that genes in involved in circadian rhythm would be particularly likely to experience such selection, since the Neanderthals had spent hundred of thousands of years in Europe, where the length of day varies a lot, while anatomically modern humans (AMH) had spent that time much closer to the equator, where the length of day varies little.
It should be interesting to see what the function of those other selected, Neanderthal-derived alleles will be. So far, the only other published discussion of this topic has concerned Neanderthal-derived HLA alleles – involved in disease defense, which we also thought a likely category . A couple of (probably) Denisovan-derived HLA alleles have also been found, as well as Denisovan versions of a couple of genes in the innate immune system.