A genome from the mid-Holocene of Greenland

I was really busy meeting awesome people and making new friends in Georgia this week. So, although I got to read and think about the Greenland ancient genome paper, I didn’t have a lot of time to sit down and write my thoughts.

If you want a good, non-pay article, I think Alan Boyle has pulled together the essential details as well as some interesting sidelights.

This is really excellent work, in terms of technical achievement and application. Clearly Willerslev and his team was dealing with an exceptional case in terms of preservation, and it won’t be easy to duplicate this kind of sequencing in other ancient sites, certainly not for the next few years.

But…

Somebody ought to take torches and pitchforks over to NIH and find out why we can’t get better coverage of U.S. population diversity. If the Danes can afford to pull a genome out of a 4000-year-old frozen skeleton with 20X coverage, why are we still stuck with a couple of white guys? I mean seriously. There are nine “complete” genomes, and two of them are from ancient skeletons of one kind or another? Awesome for anthropologists. For medicine, not so much.

Yes, yes, I know. Thousand genomes, they’re coming. But they won’t represent the diversity of U.S. resident populations, much less other parts of the world. It’s one thing to say that there’s a region of the world for which our knowledge of ancient genetics may be better than our knowledge of the genetics of living populations. But here, that region is the entire Western Hemisphere.

OK, enough about that. What’s interesting about this paper?

It isn’t the functional SNPs. These are kind of a “show and tell” – like, oooh, if we have the genome, we must know that he had dry earwax. True, but pretty trivial. These are all pretty standard variants common in Asians and New World peoples, and are therefore more a confirmatory negative. If they’d found some recently selected European haplotype, that would be a problem. These data have a lot of promise for studying ancient functional variants, but confirming the presence of high-likelihood known variants is only the first step.

It seems to me there’s something curious about this whole paper. “Ancient human genome sequence of an extinct Palaeo-Eskimo.” Why “extinct”? We don’t usually call ancient peoples extinct, even if they belonged to extinct cultures. In this case, there was a clear culture replacement in Greenland, and previous mtDNA evidence has shown that there was at least a partial biological replacement. The term is used in the text of the paper only in the context of an “extinct culture”, so maybe the title is just extending that use.

Or maybe it’s something in Greenland or Danish politics that I don’t understand. If the same headline were applied to Kennewick, for example, it would be interpreted as a political statement.

I think the most interesting part of the paper is the “Author Information” paragraph at the end:

Sequences have been deposited to the short read archive with accession number SRA010102; summary data are also available via http://www.ancientgenome.dk. Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests. This paper is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share-Alike license, and is freely available to all readers at www.nature.com/nature. Correspondence and requests for materials should be addressed to E.W. (ewillerslev@snm.ku.dk) or J.W. (wangj@genomics.org.cn).

A Nature paper that’s open access. I could kiss them full on the lips for that one. The genome is also available by open access, of course. The equal collaboration between Willerslev’s and Wang’s labs is newsworthy, I’d say. This is all stuff that nobody’s pointed out, at least not that I’ve seen.

What can we learn from this 4000-year-old genome? I have a few ideas. Data are rarely perfect for testing hypotheses. In this case, the fact of population replacement after this ancient culture was already expected based on other ancient DNA work. The individual is not perfectly placed to test hypotheses about the origin of Arctic or New World populations, but yet is clearly relevant – these people might have shared Beringian ancestors, or closely related Asian ones.

There are a few other things that strike me as obvious tests, so I’ll keep quiet about them until we’ve managed to do them. It’s not the iceman I was expecting, but very interesting nonetheless.

References:

Rasmussen M and lots and lots of others. 2010. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463:757-762. doi:10.1038/nature08835