Identifying loci under positive selection in complex population histories

Alba Refoyo-Martínez; Rute R da Fonseca; Katrín Halldórsdóttir; Einar Árnason; Thomas Mailund; Fernando Racimo

doi:10.1101/gr.246777.118

Identifying loci under positive selection in complex population histories

Alba Refoyo-Martínez, Rute R da Fonseca, Katrín Halldórsdóttir, Einar Árnason, Thomas Mailund, Fernando Racimo

11 Citations (Scopus)

Abstract

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 panels of multiple populations related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in understudied 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 owing to inversions in the history of Atlantic codfish.

Original language	English
Journal	Genome Research
Volume	29
Issue number	9
Pages (from-to)	1506-1520
ISSN	1088-9051
DOIs	https://doi.org/10.1101/gr.246777.118
Publication status	Published - 2019

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title = "Identifying loci under positive selection in complex population histories",

abstract = "Detailed modeling of a species{\textquoteright} 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 panels of multiple populations related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in understudied 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 owing to inversions in the history of Atlantic codfish.",

author = "Alba Refoyo-Mart{\'i}nez and {da Fonseca}, {Rute R} and Katr{\'i}n Halld{\'o}rsd{\'o}ttir and Einar {\'A}rnason and Thomas Mailund and Fernando Racimo",

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year = "2019",

doi = "10.1101/gr.246777.118",

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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 panels of multiple populations related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in understudied 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 owing 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 panels of multiple populations related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in understudied 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 owing to inversions in the history of Atlantic codfish.

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DO - 10.1101/gr.246777.118

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SN - 1088-9051

VL - 29

SP - 1506

EP - 1520

JO - Genome Research

JF - Genome Research

IS - 9

ER -

Identifying loci under positive selection in complex population histories

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