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

Daub, Joséphine; Moretti, S.; Davydov, I.I.; Excoffier, Laurent; Robinson-Rechavi, M. (2017). Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans. Molecular Biology and Evolution, 34(6), pp. 1391-1402. Oxford University Press 10.1093/molbev/msx083

msx083.pdf - Published Version
Available under License Creative Commons: Attribution (CC-BY).

Download (384kB) | Preview

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 likelihoodbased 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.

Item Type:

Journal Article (Original Article)


08 Faculty of Science > Department of Biology > Institute of Ecology and Evolution (IEE)

UniBE Contributor:

Daub, Joséphine and Excoffier, Laurent


500 Science > 570 Life sciences; biology




Oxford University Press




Susanne Holenstein

Date Deposited:

24 Jul 2018 07:59

Last Modified:

24 Oct 2019 06:59

Publisher DOI:





Actions (login required)

Edit item Edit item
Provide Feedback