Input determining output in ADMIXTURE

By Razib Khan | March 21, 2011 3:39 pm

One reason I posted about how to run ADMIXTURE was so that the more readers themselves could become familiar with the biases of the program. That way they would get cautious about over-reading one particular set of results (the same goes for using PCA to visualize genetic relationships). Dienekes elaborates in detail on this point, A note of caution on admixture estimates:

Much more can be said on this issue, but let’s summarize a couple of lessons:

– The full extent of an admixture cline can be captured only if unadmixed populations on either side of the cline exist. Use as many populations as possible to capture the full extent of an admixture cline.

– Use of an admixed population in lieu of an unadmixed native one inflates the inferred native component. Use native populations if possible instead of admixed ones .

– Even in the absence of unadmixed native populations, it is sometimes possible to reconstruct the admixture proportions as per Reich et al. (2009).

Capturing the complexities of human prehistory from modern populations is tricky. Nonetheless, with increased coverage of human genetic diversity (there are already ~9k individuals in my database), new analytical techniques, and, hopefully some archaeogenetic calibration genotypic, we are bound to learn much more about the distant human past in the not-so distant future.

9,000 individuals in one random guy’s database. Wow. I know Zack has more than 6,000 now. I’ve got around 4,000 myself without much expenditure of effort.

I think it is important to be very cautious about looking at ADMIXTURE results alone and in isolation. The range of possible models one could generate from a set of ADMIXTURE bar plots is enormous. A synthesis of ethnographic, historical, and paleoanthropological information, is necessary to really squeeze further analytic juice out of these powerful new tools.

CATEGORIZED UNDER: Genetics, Genomics
  • http://washparkprophet.blogspot.com ohwilleke

    It is worth recalling that part of the problem is that there isn’t a consensus definition of an unadmixed population.

    Everybody has common ancestors if you go back far enough. But, how long do populations have to be segregated to constitute a “pure type”?

    At one extreme you have populations like Native Americans and post-Columbian arrivals to the Americas who were separated by 12,000+ years, with the Native American population, in turn, diverged from the European and African arrivals by many tens of thousands of years more.

    But, when you get into Ancestral North Indian and Ancestral South Indian populations, for example, the issue gets much muddier.

    The right definition generally hinges on the question you intend to answer when using that definition. This in turn points the issue right back at the people who are using these programs. What precisely do we wish to know?

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    It is worth recalling that part of the problem is that there isn’t a consensus definition of an unadmixed population.

    yes.

    This in turn points the issue right back at the people who are using these programs. What precisely do we wish to know?

    yes. i’ve been wont to look at the results, and make inferences on-the-spot. i think perhaps we be careful of this, and construct the set of questions which we which to differentiate a priori.

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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