The effective population size modulates the strength of GC biased gene conversion in two passerines

Abstract

Understanding the determinants of genomic base composition is fundamental to understanding genome evolution. GC biased gene conversion (gBGC) is a key driving force behind genomic GC content, through the preferential incorporation of GC alleles over AT alleles during recombination, driving them towards fixation. The majority of work on gBGC has focussed on its role in coding regions, largely to address how it confounds estimates of selection. Non-coding regions have received less attention, particularly in regard to the interaction of gBGC and the effective population size (Ne) within and between species. To address this, we investigate how the strength of gBGC (B = 4Neb, where b is the conversion bias) varies within the non-coding genome of two wild passerines. We use a dataset of published high coverage genomes (10 great tits and 10 zebra finches) to estimate B, nucleotide diversity, changes in Ne, and crossover rates from linkage maps, in 1Mb homologous windows in each species. We demonstrate remarkable conservation of both B and crossover rate between species. We show that the mean strength of gBGC in the zebra finch is more than double that in the great tit, consistent with its twofold greater effective population size. B also correlates with both crossover rate and nucleotide diversity in each species. Finally, we estimate equilibrium GC content from both divergence and polymorphism data, which indicates that B has been increasing in both species, and provide support for population expansion explaining a large proportion of this increase in the zebra finch.

The evolution of GC-biased gene conversion by means of natural selection

“…In mammals, there is a (weak) correlation between effective population size N e and the population-scaled gBGC coefficient (B = 4N e b) (Lartillot, 2013;Galtier, 2021). This correlation is also observed among human populations (Glémin et al, 2015;Subramanian, 2019), and effective population size seems to explain the difference in B between two passerine species (Barton and Zeng, 2021). However, in Leptidea butterflies there is no relationship between B and genetic diversity, suggesting that the transmission bias b is lower in species/populations of higher effective population size (Boman et al, 2021).…”

Base Composition, Codon Usage, and Patterns of Gene Sequence Evolution in Butterflies

“…The presence of a moderate fixation bias of synonymous substitutions towards an increase in GC-content has been identified in population studies in Lepidoptera ( Galtier et al 2018 ; Boman et al 2021 ). Although the impact of gBGC appears to be lower in Lepidoptera compared to for example birds ( Glémin et al 2015 ; Bolívar et al 2018 ; Barton and Zeng 2021 ), such a fixation bias in combination with codon usage preferences can have considerable effects on evolutionary rate estimates. So far, studies of codon usage preferences have been limited in Lepidoptera, and they have only covered specific genes in Bombyx mori and a single pair of other moth species ( Frohlich and Wells 1994 ; Sharma et al 2012 ).…”