A phylogenetic approach disentangles interlocus gene conversion tract length and initiation rate

TL;DR

This study introduces a phylogenetic method to distinguish between the length of gene conversion tracts and their initiation rates, revealing that IGC significantly influences the evolution of duplicated genes across species.

Contribution

A novel composite likelihood approach to separately estimate fixed IGC mutation rates and tract lengths from genomic data.

Findings

Estimated IGC tract lengths vary across data types.

IGC contributes substantially to gene evolution.

Challenges remain in precisely estimating initiation rates.

Abstract

Interlocus gene conversion (IGC) homogenizes paralogs. Little is known regarding the mutation events that cause IGC and even less is known about the IGC mutations that experience fixation. To disentangle the rates of fixed IGC mutations from the tract lengths of these fixed mutations, we employ a composite likelihood procedure. We characterize the procedure with simulations. We apply the procedure to duplicated primate introns and to protein-coding paralogs from both yeast and primates. Our estimates from protein-coding data concerning the mean length of fixed IGC tracts were unexpectedly low and are associated with high degrees of uncertainty. In contrast, our estimates from the primate intron data had lengths in the general range expected from IGC mutation studies. While it is challenging to separate the rate at which fixed IGC mutations initiate from the average number of nucleotide positions that these IGC events affect, all of our analyses indicate that IGC is responsible for a substantial proportion of evolutionary change in duplicated regions. Our results suggest that IGC should be considered whenever the evolution of multigene families is examined.