Variation of the adaptive substitution rate between species and within genomes

TY - JOUR

T1 - Variation of the adaptive substitution rate between species and within genomes

AU - Moutinho, Ana Filipa

AU - Bataillon, Thomas

AU - Dutheil, Julien Y.

PY - 2020/6

Y1 - 2020/6

N2 - The importance of adaptive mutations in molecular evolution is extensively debated. Recent developments in population genomics allow inferring rates of adaptive mutations by fitting a distribution of fitness effects to the observed patterns of polymorphism and divergence at sites under selection and sites assumed to evolve neutrally. Here, we summarize the current state-of-the-art of these methods and review the factors that affect the molecular rate of adaptation. Several studies have reported extensive cross-species variation in the proportion of adaptive amino-acid substitutions (α) and predicted that species with larger effective population sizes undergo less genetic drift and higher rates of adaptation. Disentangling the rates of positive and negative selection, however, revealed that mutations with deleterious effects are the main driver of this population size effect and that adaptive substitution rates vary comparatively little across species. Conversely, rates of adaptive substitution have been documented to vary substantially within genomes. On a genome-wide scale, gene density, recombination and mutation rate were observed to play a role in shaping molecular rates of adaptation, as predicted under models of linked selection. At the gene level, it has been reported that the gene functional category and the macromolecular structure substantially impact the rate of adaptive mutations. Here, we deliver a comprehensive review of methods used to infer the molecular adaptive rate, the potential drivers of adaptive evolution and how positive selection shapes molecular evolution within genes, across genes within species and between species.

AB - The importance of adaptive mutations in molecular evolution is extensively debated. Recent developments in population genomics allow inferring rates of adaptive mutations by fitting a distribution of fitness effects to the observed patterns of polymorphism and divergence at sites under selection and sites assumed to evolve neutrally. Here, we summarize the current state-of-the-art of these methods and review the factors that affect the molecular rate of adaptation. Several studies have reported extensive cross-species variation in the proportion of adaptive amino-acid substitutions (α) and predicted that species with larger effective population sizes undergo less genetic drift and higher rates of adaptation. Disentangling the rates of positive and negative selection, however, revealed that mutations with deleterious effects are the main driver of this population size effect and that adaptive substitution rates vary comparatively little across species. Conversely, rates of adaptive substitution have been documented to vary substantially within genomes. On a genome-wide scale, gene density, recombination and mutation rate were observed to play a role in shaping molecular rates of adaptation, as predicted under models of linked selection. At the gene level, it has been reported that the gene functional category and the macromolecular structure substantially impact the rate of adaptive mutations. Here, we deliver a comprehensive review of methods used to infer the molecular adaptive rate, the potential drivers of adaptive evolution and how positive selection shapes molecular evolution within genes, across genes within species and between species.

KW - Adaptive evolution

KW - Between-species

KW - Intra-molecular

KW - Molecular evolution

KW - Within-genomes

KW - PROTEIN-CODING GENES

KW - DROSOPHILA-MELANOGASTER

KW - MOLECULAR EVOLUTION

KW - AMINO-ACID SUBSTITUTIONS

KW - EFFECTIVE POPULATION-SIZE

KW - POSITIVE SELECTION

KW - CODON-SUBSTITUTION

KW - NATURAL-SELECTION

KW - NEGATIVE SELECTION

KW - DELETERIOUS MUTATIONS

UR - http://www.scopus.com/inward/record.url?scp=85076827480&partnerID=8YFLogxK

U2 - 10.1007/s10682-019-10026-z

DO - 10.1007/s10682-019-10026-z

M3 - Journal article

AN - SCOPUS:85076827480

SN - 0269-7653

VL - 34

SP - 315

EP - 338

JO - Evolutionary Ecology

JF - Evolutionary Ecology

IS - 3

ER -