Multiple chromosomal inversions contribute to adaptive divergence of a dune sunflower ecotype

We detected seven large genomic regions that exhibit a different population structure than the rest of the genome and that vary in frequency between dune and non-dune populations. These regions also show high linkage disequilibrium and high heterozygosity between, but not within arrangements, consistent with the behavior of large inversions, an inference subsequently validated in part by comparative genetic mapping. Genome-environment association analyses show that key environmental variables, including vegetation cover and soil nitrogen, are significantly associated with inversions.

The inversions co-locate with previously described “islands of differentiation,” and appear to play an important role in adaptive divergence and incipient speciation within H. petiolaris.

Usage notes

N.full.st.table: non-dune family SNP set called on the HA412 reference genome and filtered with Genome Analysis Tool Kit for linkage mapping D.full.st.table: dune family SNP set called on the HA412 reference genome and filtered with Genome Analysis Tool Kit for linkage mapping