@article {Brevet793059, author = {Mathieu Brevet and Nicolas Lartillot}, title = {Reconstructing the history of variation in effective population size along phylogenies}, elocation-id = {793059}, year = {2019}, doi = {10.1101/793059}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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, although with mixed results. Here, we introduce an integrative comparative framework allowing for an explicit reconstruction of the phylogenetic history of Ne, thus leading to a quantitative test of the nearly-neutral theory and an independent estimation of the shape parameter of the DFE. We applied our method to primates, for which the nearly-neutral predictions were mostly verified. Estimates of the shape parameter were compatible with independent measures based on site frequency spectra. The reconstructed history of Ne in primates seems consistent with current knowledge 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.}, URL = {https://www.biorxiv.org/content/early/2019/10/15/793059}, eprint = {https://www.biorxiv.org/content/early/2019/10/15/793059.full.pdf}, journal = {bioRxiv} }