Further questions on the meaning of effective population size

Abstract

Genetic drift is an important evolutionary force of strength inversely proportional to *Ne*, the effective population size. The impact of drift on genome diversity and evolution is known to vary among species, but quantifying this effect is a difficult task. Here we assess the magnitude of variation in drift power among species of animals via its effect on the mutation load - which implies also inferring the distribution of fitness effects of deleterious mutations (DFE). To this aim, we analyze the non-synonymous (amino-acid changing) and synonymous (amino-acid conservative) allele frequency spectra in a large sample of metazoan species, with a focus on the primates vs. fruit flies contrast. We show that a Gamma model of the DFE is not suitable due to strong differences in estimated shape parameters among taxa, while adding a class of lethal mutations essentially solves the problem. Using the Gamma + lethal model and assuming that the mean deleterious effects of non-synonymous mutations is shared among species, we estimate that the power of drift varies by a factor of at least 500 between large-*Ne* and small-*Ne* species of animals, *i.e.*, an order of magnitude more than the among-species variation in genetic diversity. Our results are relevant to Lewontin's paradox while further questioning the meaning of the Ne parameter in population genomics.