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

Joseph K. Pickrell¹ and Jonathan K. Pritchard²

Correspondence: (Login to view email address)

1. Harvard Medical School
2. University of Chicago

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Document Type:

Manuscript

Date:

Received 01 March 2012 22:39 UTC; Posted 02 March 2012

Subjects:

Genetics & Genomics, Bioinformatics, Evolutionary Biology

Tags:

• population genetics
• phylogenetics
• graphical models

Abstract:

Many aspects of the historical relationships between populations in a species are reflected 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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This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Pickrell, Joseph and Pritchard, Jonathan. Inference of population splits and mixtures from genome-wide allele frequency data. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2012.6956.1> (2012)

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