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VCF-file for: The effects of GC-biased gene conversion on patterns of genetic diversity among and across butterfly genomes

Citation

Backström, Niclas (2021), VCF-file for: The effects of GC-biased gene conversion on patterns of genetic diversity among and across butterfly genomes, Dryad, Dataset, https://doi.org/10.5061/dryad.fj6q573tr

Abstract

Recombination reshuffles the alleles of a population through crossover and gene conversion. These mechanisms have considerable consequences on the evolution and maintenance of genetic diversity. Crossover, for example, can increase genetic diversity by breaking the linkage between selected and nearby neutral variants. Bias in favor of G or C alleles during gene conversion may instead promote the fixation of one allele over the other, thus decreasing diversity. Mutation bias from G or C to A and T opposes GC-biased gene conversion (gBGC). Less recognized is that these two processes may when balanced promote genetic diversity. Here we investigate how gBGC and mutation bias shape genetic diversity patterns in wood white butterflies (Leptidea sp.). This constitutes the first in-depth investigation of gBGC in butterflies. Using 60 re-sequenced genomes from six populations of three species, we find substantial variation in the strength of gBGC across lineages. When modeling the balance of gBGC and mutation bias and comparing analytical results with empirical data, we reject gBGC as the main determinant of genetic diversity in these butterfly species. As alternatives, we consider linked selection and GC content. We find evidence that high values of both reduce diversity. We also show that the joint effects of gBGC and mutation bias can give rise to a diversity pattern which resembles the signature of linked selection. Consequently, gBGC should be considered when interpreting the effects of linked selection on levels of genetic diversity.

Methods

The data set consists of SNPs from 10 whole-genome re-sequenced males from each of six different populations representing three species of wood white butterflies (L. sinapis, L. reali, L. juvernica). The SNPs have been filtered for genotype quality and all SNPs located in repetitive sequences have been removed.

Usage Notes

The SNPs have been filtered for genotype quality and all SNPs located in repetitive sequences have been removed.

Funding

Swedish Research Council (VR), Award: 2013-4508

Swedish Research Council (VR), Award: 2019-04791

Swedish Research Council (VR), Award: 2013-4508