1. gnxp
  2. Signals of recent positive selection, words vs. figures

Signals of recent positive selection, words vs. figures

By razib on March 25, 2009.

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
Tags
genetics
iHS
selection

More like this

Genetic signatures of recent human evolution, continued
Pickrell, J., Coop, G., Novembre, J., Kudaravalli, S., Li, J., Absher, D., Srinivasan, B., Barsh, G., Myers, R., Feldman, M., & Pritchard, J. (2009). Signals of recent positive selection in a worldwide sample of human populations Genome Research DOI: 10.1101/gr.087577.108 I pointed yesterday to…
Signals of recent positive selection in a worldwide sample of human populations...maybe
John Hawks & Daniel MacArthur have already pointed to a new paper in Genome Research, Signals of recent positive selection in a worldwide sample of human populations. As Dan notes, it's Open Access, so you can read the PDF yourself. That being said, "Just read it!" might be somewhat a tall…
Do It Yourself: searching for evolution's signature in 53 human populations
Note: I'm introducing Do It Yourself as a new and hopefully semi-regular section on Genetic Future. The aim is to provide readers with instructions on how to access online resources for sequence analysis - an activity traditionally restricted to researchers, but one that will no doubt become more…
Natural selection of a human gene: FUT2
A few months ago I reviewed a paper which examined the various complexities of interpreting signals of natural selection from recently developed genomic tests in response to the avalanche of human sequence data. In the paper, Signals of recent positive selection in a worldwide sample of human…

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...

What does this mean?

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.

By Graham Coop (not verified) on 26 Mar 2009 #permalink

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?