PT  - JOURNAL ARTICLE
AU  - Alba Refoyo-Martínez
AU  - Rute R. da Fonseca
AU  - Katrín Halldórsdóttir
AU  - Einar Árnason
AU  - Thomas Mailund
AU  - Fernando Racimo
TI  - Identifying loci under positive selection in complex population histories
AID  - 10.1101/453092
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 453092
4099  - http://biorxiv.org/content/early/2018/10/25/453092.short
4100  - http://biorxiv.org/content/early/2018/10/25/453092.full
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 particular bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation due to inversions in the history of Atlantic codfish.