Molecular re-adaptation: compensatory evolution following deleterious episodes of GC-biased gene conversion in rodents

Abstract

GC-biased gene conversion (gBGC) is a widespread evolutionary force associated with meiotic recombination that favours the accumulation of deleterious AT to GC substitutions in proteins, moving them away from their fitness optimum. In many mammals recombination hotspots have a rapid turnover, leading to episodic gBGC, with the accumulation of deleterious mutations stopping when the recombination hotspot dies. Selection is therefore expected to act to repair the damage caused by gBGC episodes through compensatory evolution. However, this process has never been studied or quantified so far. Here, we analysed the nucleotide substitution pattern in coding sequences of a highly diversified group of Murinae rodents. Using phylogenetic analyses of about 70,000 coding exons, we identified numerous exon-specific, lineage-specific gBGC episodes, characterised by a clustering of synonymous AT to GC substitutions and by an increasing rate of non-synonymous AT to GC substitutions, many of which are potentially deleterious. Analysing the molecular evolution of the affected exons in downstream lineages, we found evidence for pervasive compensatory evolution after deleterious gBGC episodes. Compensation appears to occur rapidly after the end of the episode, and to be driven by the standing genetic variation rather than new mutations. Our results demonstrate the impact of gBGC on the evolution of amino-acid sequences, and underline the key role of epistasis in protein adaptation. This study contributes to a growing body of literature emphasizing that adaptive mutations, which arise in response to environmental changes, are just one subset of beneficial mutations, alongside mutations resulting from oscillations around the fitness optimum.