Thursday, March 8, 2012

Inference of population splits and mixtures from genome-wide allele frequency data

In this paper, Joe Pickrell and Jonathan Pritchard announce a cool software package that plots genetic population relationships.   They use the software to analyze populations of humans and dogs.  For humans, it shows the continuous, linear process of genetic drift between populations, and also estimates the statistical likelihood of admixture between populations.  Their plot demonstrates the effect of geography, with clear jump discontinuites between African, European, Central Asian, East Asian and Indigenous American populations. The authors also plot dogs, who, like humans, exhibit a pattern of genetic drift from wolf to German Shepherd.  From that point onward, the dog pattern is very different from the human one, probably because at this point, humans started to take command of dog reproduction.  It's interesting to consider that in the period before dog breeding, the wolf-Akita-Husky-Saluki-German Shepherd axis geographically tracks the human Mongolian-Burusho-European axis. It would be interesting to see some samples of indigenous South American dogs, if there were such a thing.

Using the software, the authors identify SNPs that diverge from the overall genome wide patterns. (See comments on Genomes Unzipped.)  For humans, SNPs related to skin pigmentation and hair morphology diverge from the genetic drift patterns, indicating that those features are likely to be under selective pressure.

One further point of interest of this paper is that Palestinians, the Bedouin and Mozabites are indicated to be an offshoot of the Druze, a Northern Levant population.   Publications, described in the posts The Origin of Y-chromozome Haplogroup J1 and The Bedouin, have previously suggested these relationships.  The branching of Western European populations from the Near East has been suggested by Haak, et al and others.


Joseph K. Pickrell and Jonathan K. Pritchard

paper (Link)
further comments on the Genomes Unzipped Blog (Link)

Abstract:

" Many aspects of the historical relationships between populations in a species are reected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In this model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication, and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and ancient Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.com/."

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