Ancient genomes giving up their secrets

Last week, Nature ran a story by Ewen Callaway [1] that hits the highlights of research on ancient genomes this year: "Ancient DNA reveals secrets of human history". The news hook is a bevy of studies trying to estimate the time that Neandertals contributed their genes to recent human populations.

By comparing individual DNA letters in multiple modern human genomes with those in the Neanderthal genome, the date of that interbreeding has now been pinned down to 65,000–90,000 years ago. Montgomery Slatkin and Anna-Sapfo Malaspinas, theoretical geneticists from the University of California, Berkeley, presented the finding at the Society for Molecular Biology and Evolution meeting in Kyoto, Japan, held on 26–30 July.

It will be great to dig into the details of these comparisons, which Callaway reports have also been carried out by some other groups. The basic idea is that over time, recombination would have broken up chunks of chromosome inherited from Neandertals. If we know the intensity of recombination across the genome, we should be able to use the lengths of Neandertal-derived blocks to estimate the time that their population contributed to ours. But much depends on the details of the population model. The simplest model supposes that all the gene flow from Neandertals happened at a single moment in time. If we doubt that assumption (as I do) then the estimate will not represent reality. But until we see papers reporting these results, it's hard to know how much they may be affected by different assumptions.

The article turns toward functional insights from the ancient genomes, and my lab puts in an appearance:

Unlike most scientists mining the ancient genomes, Hawks has reported some of his more prosaic findings — Denisovans didn't have red hair, for example — on his blog (see go.nature.com/irclra). "These genomes are publicly available. There's nothing stopping high-school students from doing this, and the kind of stuff that I'm putting out on my blog is the stuff that a smart high-school student could do."

I was really pleased that the article featured some of the research from my graduate student, Aaron Sams, who has been investigating the evolution of celiac disease. What does celiac disease have to do with Neandertals? Short answer: We're feeling our way though the study of gene networks that connect genetic evolution with phenotypes. We can use our knowledge of human evolution during the last 100,000 years to figure out how genes work. And we can use knowledge from living humans about how genes work to investigate their evolution in archaic people. Ancient genomes give us that potential, because genes that work together have evolved in ways that reflect selection on the system as a whole.

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