Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale

One of the major challenges in evolutionary biology is to link the mechanisms of adaptation at the population level and the diversity of forms and functions observed in the tree of life. In a recent study published in PNAS, Thibault Latrille, Nicolas Rodrigue and Nicolas Lartillot have finally demonstrated that the methods used by population geneticists to detect adaptation and those used by phylogeneticists have found concordant results in mammals. They explain this reconciliation both by the use of a larger and more complete data set, and by a better modeling of non-adaptive processes.

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Bridging the gap between micro-evolution (what shapes genetic variation within populations and how this contributes to short-term adaptation) and macro-evolution (how species have diversified and adapted to various environments) is still one major challenge of evolutionary sciences. This is particularly apparent in current bioinformatic methods for characterizing genetic adaptation: some of these methods focus on the short time scale (using population genetics, e.g., human populations), other on the long time scale (using phylogenies, e.g., across mammals), yet there is still a complete disconnect between them and thus far, they have not agreed with each other. In our study, we detect genes and sites that show adaptive signatures at the mammalian scale. Then we show that these genes and sites are also under adaptation in different populations (cow, goat, horse, sheep, dog, green monkey and human). While providing a mutual confirmation of the two approaches, our work paves the way for further methodological integration between microevolutionary and macroevolutionary genomics.

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Thibault Latrille and Nicolas Lartillot