TY - JOUR

T1 - Identifying loci under positive selection in complex population histories

AU - Refoyo-Martínez, Alba

AU - da Fonseca, Rute R

AU - Halldórsdóttir, Katrín

AU - Árnason, Einar

AU - Mailund, Thomas

AU - Racimo, Fernando

N1 - Published by Cold Spring Harbor Laboratory Press.

PY - 2019

Y1 - 2019

N2 - 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.

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.

U2 - 10.1101/gr.246777.118

DO - 10.1101/gr.246777.118

M3 - Journal article

C2 - 31362936

VL - 29

SP - 1506

EP - 1520

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 9

ER -