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Biol Lett. 2018 May;14(5). pii: 20180055. doi: 10.1098/rsbl.2018.0055.

Overestimation of the adaptive substitution rate in fluctuating populations.

Author information

1
UMR-5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France marjolaine.rousselle@umontpellier.fr.
2
BiRC-Bioinformatics Research Center, Aarhus University, Aarhus, Denmark.
3
UMR-5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France.

Abstract

Estimating the proportion of adaptive substitutions (α) is of primary importance to uncover the determinants of adaptation in comparative genomic studies. Several methods have been proposed to estimate α from patterns polymorphism and divergence in coding sequences. However, estimators of α can be biased when the underlying assumptions are not met. Here we focus on a potential source of bias, i.e. variation through time in the long-term population size (N) of the considered species. We show via simulations that ancient demographic fluctuations can generate severe overestimations of α, and this is irrespective of the recent population history.

KEYWORDS:

coding sequence evolution; effective population size; fitness effect of mutations; molecular adaptation; simulations

PMID:
29743267
PMCID:
PMC6012701
[Available on 2019-05-01]
DOI:
10.1098/rsbl.2018.0055

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