Data from: Population genomic evidence of selection on structural variants in a natural hybrid zone

Structural variants (SVs) can promote speciation by directly causing
reproductive isolation or by suppressing recombination across large
genomic regions. Whereas examples of each mechanism have been documented,
systematic tests of the role of SVs in speciation are lacking. Here, we
take advantage of long-read (Oxford nanopore) whole-genome sequencing and
a hybrid zone between two Lycaeides butterfly taxa (L. melissa and Jackson
Hole Lycaeides) to comprehensively evaluate genome-wide patterns of
introgression for SVs and relate these patterns to hypotheses about
speciation. We found >100,000 SVs segregating within or between the
two hybridizing species. SVs and SNPs exhibited similar levels of genetic
differentiation between species, with the exception of inversions, which
were more differentiated. We detected credible variation in patterns of
introgression among SV loci in the hybrid zone, with 562 of 1419
ancestry-informative SVs exhibiting genomic clines that deviated from null
expectations based on genome-average ancestry. Overall, hybrids exhibited
a directional shift towards Jackson Hole Lycaeides ancestry at SV loci,
consistent with the hypothesis that these loci experienced more selection
on average than SNP loci. Surprisingly, we found that deletions, rather
than inversions, showed the highest skew towards excess ancestry from
Jackson Hole Lycaeides. Excess Jackson Hole Lycaeides ancestry in hybrids
was also especially pronounced for Z-linked SVs and inversions containing
many genes. In conclusion, our results show that SVs are ubiquitous and
suggest that SVs in general, but especially deletions, might
disproportionately affect hybrid fitness and thus contribute to
reproductive isolation.