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Power and limits of selection genome scans on temporal data from a selfing population

de Navascués, Miguel1, 2, 3  ; Becheler, Arnaud1, 4 ; Gay, Laurène5; Ronfort, Joëlle5; Loridon, Karine5; Vitalis, Renaud1, 3 
1 CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
2 Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
3 Institut de Biologie Computationnelle, Montpellier, France
4 Current affiliation: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
5 AGAP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France

10.24072/pcjournal.47 - Peer Community Journal, Volume 1 (2021), article no. e37.

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Tracking genetic changes of populations through time allows a more direct study of the evolutionary processes acting on the population than a single contemporary sample. Several statistical methods have been developed to characterize the demography and selection from temporal population genetic data. However, these methods are usually developed under the assumption of outcrossing reproduction and might not be applicable when there is substantial selfing in the population. Here, we focus on a method to detect loci under selection based on a genome scan of temporal differentiation, adapting it to the particularities of selfing populations. Selfing reduces the effective recombination rate and can extend hitch-hiking effects to the whole genome, erasing any local signal of selection on a genome scan. Therefore, selfing is expected to reduce the power of the test. By means of simulations, we evaluate the performance of the method under scenarios of adaptation from new mutations or standing variation at different rates of selfing. We find that the detection of loci under selection in predominantly selfing populations remains challenging even with the adapted method. Still, selective sweeps from standing variation on predominantly selfing populations can leave some signal of selection around the selected site thanks to historical recombination before the sweep. Under this scenario, ancestral advantageous alleles at low frequency leave the strongest local signal, while new advantageous mutations leave no local footprint of the sweep.
Published online:
DOI: 10.24072/pcjournal.47
de Navascués, Miguel 1, 2, 3; Becheler, Arnaud 1, 4; Gay, Laurène 5; Ronfort, Joëlle 5; Loridon, Karine 5; Vitalis, Renaud 1, 3

1 CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
2 Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
3 Institut de Biologie Computationnelle, Montpellier, France
4 Current affiliation: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
5 AGAP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
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de Navascués, Miguel; Becheler, Arnaud; Gay, Laurène; Ronfort, Joëlle; Loridon, Karine; Vitalis, Renaud. Power and limits of selection genome scans on temporal data from a selfing population. Peer Community Journal, Volume 1 (2021), article  no. e37. doi : 10.24072/pcjournal.47. https://peercommunityjournal.org/articles/10.24072/pcjournal.47/

Peer reviewed and recommended by PCI : 10.24072/pci.evolbiol.100110

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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