Data from: Repeatability of adaptation in sunflowers reveals that genomic regions harbouring inversions also drive adaptation in species lacking an inversion

Local adaptation commonly involves alleles of large effect, which
experience fitness advantages when in positive linkage disequilibrium
(LD). Because segregating inversions suppress recombination and facilitate
the maintenance of LD between locally adapted loci, they are also commonly
found to be associated with adaptive divergence. However, it is unclear
what fraction of an adaptive response can be attributed to inversions and
alleles of large effect, and whether the loci within an inversion could
still drive adaptation in the absence of its recombination-suppressing
effect. Here, we use genome-wide association studies to explore patterns
of local adaptation in three species of sunflower: Helianthus annuus, H.
argophyllus, and H. petiolaris, which each harbour a large number of
species-specific inversions. We find evidence of significant genome-wide
repeatability in signatures of association to phenotypes and environments,
which are particularly enriched within regions of the genome harbouring an
inversion in one species. This shows that while inversions may facilitate
local adaptation, at least some of the loci can still harbour mutations
that make substantial contributions without the benefit of recombination
suppression in species lacking a segregating inversion. While a large
number of genomic regions show evidence of repeated adaptation, most of
the strongest signatures of association still tend to be species-specific,
indicating substantial genotypic redundancy for local adaptation in these
species.