Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

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 our 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. Author Summary: With modern genotyping technology, it is now possible to obtain large amounts of genetic data from many populations in a species. An important question that can be addressed with these data is: what is the history of these populations? There is a long history in population genetics of inferring the relationships among populations as a bifurcating tree, analogous to phylogenetic trees for representing the evolution of species. However, it has long been recognized that, since populations from the same species exchange genes, simple bifurcating trees may be an incorrect representation of population histories. We have developed a method to address this issue, using a model which allows for both population splits and gene flow. In application to humans, we show that we are able to identify a number of both previously known and unknown episodes of gene flow in history, including gene flow into Cambodia of a population only distantly related to modern East Asia. In application to dogs, we show that the boxer and basenji breeds have a considerable component of ancestry from grey wolves subsequent to domestication.