Interaction between selection and biased gene conversion in mammalian protein-coding sequence evolution revealed by a phylogenetic covariance analysis

Molecular Biology and Evolution
Nicolas Lartillot

Abstract

According to the nearly-neutral model, variation in long-term effective population size among species should result in correlated variation in the ratio of nonsynonymous over synonymous substitution rates (dN/dS). Previous empirical investigations in mammals have been consistent with this prediction, suggesting an important role for nearly-neutral effects on protein-coding sequence evolution. GC-biased gene conversion (gBGC), on the other hand, is increasingly recognized as a major evolutionary force shaping genome nucleotide composition. When sufficiently strong compared with random drift, gBGC may significantly interfere with a nearly-neutral regime and impact dN/dS in a complex manner. Here, we investigate the phylogenetic correlations between dN/dS, the equilibrium GC composition (GC*), and several life-history and karyotypic traits in placental mammals. We show that the equilibrium GC composition decreases with body mass and increases with the number of chromosomes, suggesting a modulation of the strength of biased gene conversion due to changes in effective population size and genome-wide recombination rate. The variation in dN/dS is complex and only partially fits the prediction of the nearly-neutral theory. However, spe...Continue Reading

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Citations

Jun 21, 2013·BMC Evolutionary Biology·Lindell BromhamRobert Lanfear
Mar 7, 2014·Molecular Biology and Evolution·Alex Wong
Jul 24, 2014·Bioinformatics·Benjamin Horvilleur, Nicolas Lartillot
Mar 6, 2016·Molecular Biology and Evolution·Emeric FiguetNicolas Galtier
Sep 2, 2015·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Nicolas Lartillot
Dec 21, 2014·Genome Biology and Evolution·Emeric FiguetNicolas Galtier
Sep 30, 2017·Molecular Biology and Evolution·Fidel Botero-CastroNicolas Galtier
Feb 10, 2018·BMC Evolutionary Biology·Alexander PlattDavid A Liberles
May 23, 2015·Genome Research·Sylvain GléminLaurent Duret
Mar 7, 2017·Frontiers in Genetics·Jonathan Romiguier, Camille Roux
Feb 23, 2017·Frontiers in Genetics·Xia Hua, Lindell Bromham
Apr 2, 2021·Frontiers in Molecular Biosciences·Mathieu MortzPierre U Blier
Jul 1, 2021·Genome Biology and Evolution·Mathieu Brevet, Nicolas Lartillot

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