Gene Expression

Dan MacArthur already posted some of the supplementary figures from Signals of recent positive selection in a worldwide sample of human populations, but he didn’t put up one that I thought was really striking. The text:

First, there is extensive sharing of extreme iHS and XP-EHH signals between Europe, the Middle East, and Central Asia, while overlap between other regions is much more limited. In fact, 44% of the genomic segments in the 1% tail of iHS in Europe fall in the 5% tail for both the Middle East and Central Asia (89% are shared between Europe and at least one of these two), while only 12% of European signals are present in East Asia by the same criterion. Second, XP-EHH signals seemto be shared on a larger geographic scale than iHS signals.

Below the fold the figures. Rather stark.


iHS

i-2492b15b91af5c66aebce935eaabf105-fig4ihs.png


XP-EHH

i-b746b2b030115b99b902f7edb01854d9-fig5xpehh.png

Comments

  1. #1 Daniel MacArthur
    March 26, 2009

    Nice pics – yep, I should have posted ‘em. :-)

    It’s worth spelling out, though, that the stark contrast between African and non-African populations in the second graph is partly an artifact of the XP-EHH algorithm. The algorithm requires the use of an outgroup reference population, and the authors used Bantu as the reference for all non-African pops and Europe as a reference for both African. The authors thus say in the supp methods that “the non-overlap between African and non-African populations by XP-EHH is not meaningful.”

    That’s not to say that there aren’t striking differences in selective signatures between Africans and non-Africans, of course (you can still see that in the iHS test, which doesn’t use a reference population) – I just wanted to be sure no-one over-interpreted the second graph…

  2. #2 Kosmo
    March 26, 2009

    What does this mean?

  3. #3 Graham Coop
    March 26, 2009

    Thanks for clarifying that point Dan. As we say in the paper, the need for a ref. population in the XP-EHH test means that such a strong divide between Af.-non Af. is indeed an artifact. Though as you say the iHS result backs up the idea that there are few obvious shared sweeps.

  4. #4 razib
    March 26, 2009

    right. i was going to say, “but i assume everyone read the paper!” but then why would i spotlight the sups :-) east vs. west eurasia is still interesting though.

    What does this mean?

    the description to the figures seems pretty clear, no?