A Spatial Framework for Understanding Population Structure and Admixture

PLoS Genetics
Gideon S BradburdGraham Coop

Abstract

Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build "geogenetic maps," which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sa...Continue Reading

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Citations

Mar 20, 2016·Molecular Biology and Evolution·Irina PugachBrigitte Pakendorf
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Methods Mentioned

BETA
PCA

Software Mentioned

SpaceMix
Prior2
Real
SPA
MixMapper
ms
TreeMix
PCA

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