Recombination rate variation modulates gene sequence evolution mainly via GC-Biased gene conversion, not Hill-Robertson interference, in an avian system

Abstract

The ratio of nonsynonymous to synonymous substitution rates (o) is often used to measure the strength of natural selection. However, o may be influenced by linkage among different targets of selection, that is, Hill-Robertson interference (HRI), which reduces the efficacy of selection. Recombination modulates the extent of HRI but may also affect o by means of GC-biased gene conversion (gBGC), a process leading to a preferential fixation of G:C ("strong," S) over A:T ("weak," W) alleles. As HRI and gBGC can have opposing effects on o, it is essential to understand their relative impact to make proper inferences of o.We used a model that separately estimated S- To-S, S- To-W, W- To-S, and W- To-W substitution rates in 8,423 avian genes in the Ficedula flycatcher lineage. We found that the W- To-S substitution rate was positively, and the S- To-W rate negatively, correlated with recombination rate, in accordance with gBGC but not predicted by HRI. The W- To-S rate further showed the strongest impact on both dN and dS. However, since the effects were stronger at 4- fold than at 0-fold degenerated sites, likely because the GC content of these sites is farther away from its equilibrium, o slightly decreases with increasing recombination rate, which could falsely be interpreted as a consequence of HRI. We corroborated this hypothesis analytically and demonstrate that under particular conditions, o can decrease with increasing recombination rate. Analyses of the site-frequency spectrumshowed thatW- To-Smutations were skewed toward high, and S- To-Wmutations toward low, frequencies, consistent with a prevalent gBGC-driven fixation bias.