Résumé
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 irrespective of the recent population
history.