Data from: Natural selection and genetic diversity in the butterfly Heliconius melpomene

A combination of selective and neutral evolutionary forces shape patterns
of genetic diversity in nature. Among the insects, most previous analyses
of the roles of drift and selection in shaping variation across the genome
have focused on the genus Drosophila. A more complete understanding of
these forces will come from analysing other taxa that differ in population
demography and other aspects of biology. We have analysed diversity and
signatures of selection in the neotropical Heliconius butterflies using
resequenced genomes from 58 wild-caught individuals of H. Melpomene, and
another 21 resequenced genomes representing 11 related species. By
comparing intra-specific diversity and inter-specific divergence, we
estimate that 31% of amino acid substitutions between Heliconius species
are adaptive. Diversity at putatively neutral sites is negatively
correlated with the local density of coding sites as well as
non-synonymous substitutions, and positively correlated with recombination
rate, indicating widespread linked selection. This process also manifests
in significantly reduced diversity on longer chromosomes, consistent with
lower recombination rates. Although hitchhiking around beneficial
non-synonymous mutations has significantly shaped genetic variation in H.
Melpomene, evidence for strong selective sweeps is limited overall. We did
however identify two regions where distinct haplotypes have swept in
different populations, leading to increased population differentiation. On
the whole, our study suggests that positive selection is less pervasive in
these butterflies as compared to fruit flies; a fact that curiously
results in very similar levels of neutral diversity in these very
different insects.