dc.contributor |
Háskóli Íslands |
dc.contributor |
University of Iceland |
dc.contributor.author |
Refoyo-Martínez, Alba |
dc.contributor.author |
da Fonseca, Rute R. |
dc.contributor.author |
Halldórsdóttir, Katrín |
dc.contributor.author |
Árnason, Einar |
dc.contributor.author |
Mailund, Thomas |
dc.contributor.author |
Racimo, Fernando |
dc.date.accessioned |
2020-08-10T10:53:08Z |
dc.date.available |
2020-08-10T10:53:08Z |
dc.date.issued |
2019-07-30 |
dc.identifier.citation |
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. |
dc.identifier.issn |
1088-9051 |
dc.identifier.issn |
1549-5469 (eISSN) |
dc.identifier.uri |
https://hdl.handle.net/20.500.11815/1943 |
dc.description |
Publisher's version (útgefin grein) |
dc.description.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. |
dc.description.sponsorship |
We thank Jeremy Berg, Anders Albrechtsen, and Kathleen Lotter-hos for helpful advice and discussions. F.R. thanks the Natural History Museum of Denmark and the Villum Foundation (Young Investigator Award, project no. 000253000) for their support. E.Á. and K.H. were supported by a grant from Svala Árnadóttir’s private funds, by a grant from the University of Iceland Research Fund, by institutional funds from R.C. Lewontin, and by a grant from the Icelandic Research Fund (no. 185151-051). R.R.d.F. thanks the Danish National Research Foundation for its support of the Center for Macroecology, Evolution, and Climate (grant DNRF96). |
dc.format.extent |
1506-1520 |
dc.language.iso |
en |
dc.publisher |
Cold Spring Harbor Laboratory |
dc.relation.ispartofseries |
Genome Research;29(9) |
dc.rights |
info:eu-repo/semantics/openAccess |
dc.subject |
Genetics |
dc.subject |
History |
dc.subject |
Natural selection |
dc.subject |
Genetic selection |
dc.subject |
Erfðafræði |
dc.subject |
Náttúruval |
dc.subject |
Genamengi |
dc.title |
Identifying loci under positive selection in complex population histories |
dc.type |
info:eu-repo/semantics/article |
dcterms.license |
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/. |
dc.description.version |
Peer Reviewed |
dc.identifier.journal |
Genome Research |
dc.identifier.doi |
10.1101/gr.246777.118 |
dc.relation.url |
https://syndication.highwire.org/content/doi/10.1101/gr.246777.118 |
dc.contributor.department |
Líf- og umhverfisvísindadeild (HÍ) |
dc.contributor.department |
Faculty of Life and Environmental Sciences (UI) |
dc.contributor.school |
Verkfræði- og náttúruvísindasvið (HÍ) |
dc.contributor.school |
School of Engineering and Natural Sciences (UI) |