What’s old is new in our genomes

The_10,000_Year_Explosion_(Cover)Over at Nature Ewan Callaway has a piece up, Neanderthals had outsize effect on human biology. The upshot is that the few percent of archaic admixture in modern humans, who descend from a Neo-African group ~50,000 years ago, may have significance functionally, and been driven by adaptation. This is not surprising. Greg Cochran and Henry Harpending discussed this dynamic in their The 10,000 Year Explosion (speaking of Greg, he is having a fund raiser). Though not entirely analogous, the work of plant evolutionary geneticists also indicates that we might expect this sort of phenomenon, whereby adaptive variants are absorbed from substrate as populations expand (for a somewhat different angle, though related, see How species evolve collectively: implications of gene flow and selection for the spread of advantageous alleles; I doubt it’s a coincidence that a lot of the deep understanding of evolutionary genetics I have comes from people working on plants).

A few years back I groused to Nick Patterson that the initial Neandertal genome paper in 2010 was overly skeptical of the possibility of admixture resulting in adaptive variants entering the modern human genome pool from archaics. Nick’s argument was simply that they hadn’t detected any such variants at that time, so it was a straightforward thing to report. If you listen to what Ed Green and company stated in the media they were very careful how they parsed their statement in regards non-neutral variants. My rejoinder was that on prior grounds it is hard to imagine that out of a few percent of the genome there wasn’t at least a few significant adaptive alleles.

As Callaway reports above that turned out to be right. I think the original research was a bit too conservative by relying only on empirical results when the theory here seems quite strong. Additionally, I would actually take some issue with the title in the Nature piece. Some of the same researchers have found reduced Neanderthal admixture proportions on the X chromosome, suggesting selection against Neanderthal variants in the admixed genome (a phenomenon common during hybridization between diverged lineages), which is predominantly Neo-African. In other words, the few percent might actually be less than what one might have concluded based on a census count and the genealogy a few generations out of the initial admixture event. It doesn’t really make sense to say that Neanderthal’s had an outsized effect when it is likely that their distinctive variants were also purified somewhat from the genome initially. Perhaps one might say that they had an outsized effect after you control for the fact that deleterious variants from Neanderthals were removed from the equation early on. As it is, and I think as implied in the article, we don’t know enough about the number of functional archaic alleles to adduce whether they have more impact or not. Rather, Neanderthals gave us all things under the sun.

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