Opin vísindi

Identifying loci under positive selection in complex population histories

Identifying loci under positive selection in complex population histories

Title: Identifying loci under positive selection in complex population histories
Author: Refoyo-Martínez, Alba
da Fonseca, Rute R.
Halldórsdóttir, Katrín   orcid.org/0000-0002-9682-0286
Árnason, Einar   orcid.org/0000-0003-3686-6407
Mailund, Thomas
Racimo, Fernando
Date: 2019-07-30
Language: English
Scope: 1506-1520
University/Institute: Háskóli Íslands
University of Iceland
School: Verkfræði- og náttúruvísindasvið (HÍ)
School of Engineering and Natural Sciences (UI)
Department: Líf- og umhverfisvísindadeild (HÍ)
Faculty of Life and Environmental Sciences (UI)
Series: Genome Research;29(9)
ISSN: 1088-9051
1549-5469 (eISSN)
DOI: 10.1101/gr.246777.118
Subject: Genetics; History; Natural selection; Genetic selection; Erfðafræði; Náttúruval; Genamengi
URI: https://hdl.handle.net/20.500.11815/1943

Show full item record


Refoyo-Martínez, A., Da Fonseca, R., Halldórsdóttir, K., Árnason, E., Mailund, T., & Racimo, F. (2019). Identifying loci under positive selection in complex population histories. Genome Research, 29(9), 1506-1520.


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.


Publisher's version (útgefin grein)


This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

Files in this item

This item appears in the following Collection(s)