Statistics for all models and all scenarios tested in the study. from Overestimation of the adaptive substitution rate in fluctuating populations.

Estimating the proportion of adaptive substitutions (<i>α</i>) is of primary importance to uncover the determinants of adaptation in comparative genomic studies. Several methods have been proposed to estimate <i>α</i> from patterns polymorphism and divergence in coding sequences. However, estimators of <i>α</i> 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 (<i>N</i>) of the considered species. We show via simulations that ancient demographic fluctuations can generate severe overestimations of <i>α</i>, and this is irrespective of the recent population history.