RT Journal Article
SR Electronic
T1 Identifying loci under positive selection in complex population histories
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 453092
DO 10.1101/453092
A1 Alba Refoyo-Martínez
A1 Rute R. da Fonseca
A1 Katrín Halldórsdóttir
A1 Einar Árnason
A1 Thomas Mailund
A1 Fernando Racimo
YR 2018
UL http://biorxiv.org/content/early/2018/11/16/453092.abstract
AB Detailed modeling of a species’ history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method—called Graph-aware Retrieval of Selective Sweeps (GRoSS)—has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish and human population genomic data containing multiple population panels related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in under-studied human populations, as well as muscle mass, milk production and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation due to inversions in the history of Atlantic codfish.