Human Genomics “out of the box”

51qciM4cBhL._SX258_BO1,204,203,200_A friend of mine proudly told me recently that she’d purchased an unabridged edition of The History and Geography of Human Genes. Turns out that there are some affordable used copies floating around (under $50, like the Atari 2600!). Flipping through the old unabridged edition I had to admit: a lot of the assertions derived from classical autosomal markers hold true. It might be that all you really need to get “up to speed” is an annotated version. Also, I’d get rid of the synthetic maps, which no one uses anymore (there are some methodological reasons, as well as the fact that they just didn’t turn out to be a very intelligible visualization).

Of course things have changed between then and now. Thanks to open data you can do much more powerful analysis than you find in The History and Geography of Human Genes on your notebook computer in a few hours. So I had the idea for this post a few hours ago…and thought perhaps I’d accompany it with a few TreeMix plots. Below are the 1000 Genomes data, with 250,000 markers (I pruned by intersecting with HGDP markers as well as those with very low missingness):

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