Thursday, 18 February 2010

Three new genomes

There's been some exciting stuff in the last two weeks in terms of human genetics. This week, Nature has published two new complete human genomes, from southern Africa. Right now, sampling has been focused on Europe and Asia, which to be fair represents about half the human race right there. However, in terms of where human diversity is located, Europe, Asia, Australia and the North and South America are relatively homogeneous compared to the centre of human radiation, Africa. You can really see this when you take a glance at the number of unique polymophisms shared by various genomes sampled in these diagrams.
The areas that overlap show similarity, the areas that don't overlap show unique diversity.  Immediately what stands out to me is that the African samples have almost double the unique diversity that the other sampled genomes do. This is expected, but it really drives home how much we've been underestimating divergence. This is because we haven't been looking at that diversity before now - all our DNA diversity sites have been based off of European and Asian genomes. This is great for most of the work that has focused on Europe, Asia, and America, since it targets the applicable diversity. But because we haven't been looking at the African-European and the African-Asian big differences, it's underestimated divergence within Africa, and between Africa and other human populations.

Neat stuff. Very very neat. If I were to pick two places to study human genetics, I'd do it in Africa (super high diversity!) or the South Pacific (Lower diversity lets you study gene by environment effects).

The other thing that came out recently was also from Nature, which was the Genome of ancient remains (hair) from Greenland. This is one of the longest look backs we've had, and really tells us a bit about the last migration wave to North America. People in the Eskimo-Aleut language family are generally thought to be late comers to North America, which shouldn't be a massive shock, since most the areas Eskimo live weren't exactly habitable thirteen thousand years ago (They were covered by massive, mile thick ice sheets).
I've thrown up a figure from the Nature Paper. The paleo-Greenlander is labeled Saqqaq in this diagram. Each vertical bar represents one individual. The colours in that bar represent them being assigned to a population, so all the beige bars are 100%% beige population (Koryak), and the beige and yellow are half Beige population, and half yellow (Nganasan). You can see Saqqaq is closest to the modern Chukchi, though there's considerable noise in all the assignments (real data is messy!). More interestingly, if you look at modern east and west Greenlanders, they don't have some of the diversity he has, and they have a strong blue measure of admixture. That's diversity that it shares with Europe and pre-contact Americans.

This is cool because it really tells a story about how this group represented by Saqqaq made a massive journey in an incredibly short period of time. It also helps scientists pin down when that last migration wave came in, peopling the arctic, with better accuracy. It's also cool because we can tell a man 5.5kya was balding through looking at nothing more than his DNA. And it shows how incredibly fast humans adapted culturally to the arctic. The authors of the paper claim some small number of SNPs show that he had metabolic adaptations to cold climates, but I'm suspicious of the genetic effects they're claiming. Even granting them, Saqqaq's people still had to culturally adapt to a huge amount of environment that they'd never encountered before. It's like the first human to step foot out of Africa, only to discover how cold it can get at night, but a thousand fold more severe.

Culture is a powerful and under appreciated tool. I think this ancient DNA study drives that point home to me.

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