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Personal genomics & rare populations notes

Gene Expression
By Razib Khan
Sep 14, 2011 9:32 PMNov 20, 2019 12:59 AM


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I'm going to address two points in this post. The next possible target for getting an undersampled population, and the Malagasy results. First, lots of great submissions in regards to populations which are undersampled. Some of them are actually already in the data sets. For example, the Burusho and Kalash are in the HGDP. There has been a major dump of data from the Americans recently as well. Zack Ajmal at HAP has the most systematic description online about where to find these that I know of. Additionally, I'm looking for stuff which is interesting where N = 1 would make a difference. I think that was the case for the Tutsi sample, as well as the Malagasy. When you have no prior information, adding one data point is notable. Obviously I can't afford the money, time, and energy, required to get a good representative sample from a given region. Though I hope researchers who have a gusher of grant money might look at the above thread for ideas. I think the next population to look for is someone with Ainu ancestry. This is easier said that done, so I need to think about it (both because of dilution and the language barrier). But then again, the Tutsi and Malagasy requests had a much more positive and faster turnaround than I had expected. So I'm not going to get all down about the likelihood. Second, we've got the issue of the Malagasy results. As with the Tutsi genotype there are lots of impassioned responses, some of which I don't post. After reading through the Malagasy related comments I'm starting to wonder if people have a natural cognitive bias to over-complicate their ancestral narrative because it makes it more memorable and salient. I think I didn't appreciate this because in the New World in admixed populations there is often a tendency to obscure mixed origins of groups due to social norms (e.g., black ancestry among Mexicans). But this may be atypical. People are very worried about issues of representativeness in regards to the Merina I analyzed, and that's a legitimate issue. That being said, the previous run of someone who was 33% Sakalava seemed to give the same qualitative results (though this is complicated by that individual's extreme admixture). I'm pretty sure that the Betsileo sample which I'll get in ~1 month is going to be similar to the Merina one. If not, all the more exciting! We might not be able to answer questions with novel and unexpected results, but we'll proliferate the questions. The major aspect which I'm now confident of in regard to the Malagasy is that it seems unlikely that they have exotic African ancestry, whether it be Pygmy, Khoisan, or something else. An N = 2 is a lot to base this on, but there are plenty of other circumstantial elements which confirm the likely Bantu origin of the African component of Malagasy ancestry. One question though would be whether this element arrived in successive waves due to slave trading, or whether the Malagasy ethnogenesis occurred on the mainland, and they arrived a hybrid population. In any case, please don't leave impassioned comments about Madagascar's ethnic politics anymore. I understand this is serious stuff for some people, but not for me. I don't care about that much, though I know the broad outlines.

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