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

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.