Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans.

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Serval ID
serval:BIB_E977192342AB
Type
Article: article from journal or magazin.
Collection
Publications
Title
Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans.
Journal
Molecular Biology and Evolution
Author(s)
Daub J.T., Moretti S., Davydov I.I., Excoffier L., Robinson-Rechavi M.
ISSN
1537-1719 (Electronic)
ISSN-L
0737-4038
Publication state
Published
Issued date
2017
Peer-reviewed
Oui
Volume
34
Number
6
Pages
1391-1402
Language
english
Abstract
Gene set enrichment approaches have been increasingly successful in finding signals of recent polygenic selection in the human genome. In this study, we aim at detecting biological pathways affected by positive selection in more ancient human evolutionary history. Focusing on four branches of the primate tree that lead to modern humans, we tested all available protein coding gene trees of the Primates clade for signals of adaptation in these branches, using the likelihood-based branch site test of positive selection. The results of these locus-specific tests were then used as input for a gene set enrichment test, where whole pathways are globally scored for a signal of positive selection, instead of focusing only on outlier "significant" genes. We identified signals of positive selection in several pathways that are mainly involved in immune response, sensory perception, metabolism, and energy production. These pathway-level results are highly significant, even though there is no functional enrichment when only focusing on top scoring genes. Interestingly, several gene sets are found significant at multiple levels in the phylogeny, but different genes are responsible for the selection signal in the different branches. This suggests that the same function has been optimized in different ways at different times in primate evolution.

Pubmed
Web of science
Open Access
Yes
Create date
04/04/2017 19:29
Last modification date
09/05/2019 2:52
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