PT  - JOURNAL ARTICLE
AU  - Mathieu Brevet
AU  - Nicolas Lartillot
TI  - Reconstructing the history of variation in effective population size along phylogenies
AID  - 10.1101/793059
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 793059
4099  - http://biorxiv.org/content/early/2021/01/12/793059.short
4100  - http://biorxiv.org/content/early/2021/01/12/793059.full
AB  - The nearly-neutral theory predicts specific relations between effective population size (Ne), and patterns of divergence and polymorphism, which depend on the shape of the distribution of fitness effects (DFE) of new mutations. However, testing these relations is not straightforward since Ne is difficult to estimate in practice. For that reason, indirect proxies for Ne have often been used to test the nearly-neutral theory. Here, we introduce an integrative comparative framework allowing for an explicit reconstruction of the phylogenetic history of Ne and u, thus leading to a quantitative test of the nearly-neutral theory and an estimation of the allometric scaling of πN/πS and dN/dS with respect to Ne. As an illustration, we applied our method to primates, for which the nearly-neutral predictions were mostly verified. The variation of πN/πS and dN/dS as a function of Ne appears to be too strong, however, to be compatible with current estimates of the DFE based on site frequency spectra. The reconstructed history of Ne in primates seems consistent with current knowledge, shows a ten-fold variation across primates and shows a clear phylogenetic structure at the super-family level. Altogether, our integrative framework provides a quantitative assessment of the role of Ne in modulating patterns of genetic variation, while giving a synthetic picture of the long-term trends in Ne variation across a group of species.Competing Interest StatementThe authors have declared no competing interest.