Data from: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta

Background: Genomic variation is widespread, and both neutral and
selective processes can generate similar patterns in the genome. These
processes are not mutually exclusive, so it is difficult to infer the
evolutionary mechanisms that govern population and species divergence.
Boechera stricta,is a perennial relative of Arabidopsis thaliana native to
largely undisturbed habitats with two geographic and ecologically
divergence subspecies. Here we delineate the evolutionary processes
driving genetic diversity and population differentiation in this species.
Results: Using whole genome re-sequencing data from 517 Boechera stricta
accessions, we identify four genetic groups that diverged around 30 - 180
thousand years ago, with long-term small effective population sizes and
recent population expansion after the Last Glacial Maximum. We find three
genomic regions with elevated nucleotide diversity, totaling about 10% of
the genome. These three regions of elevated nucleotide diversity show
excess of intermediate-frequency alleles, higher absolute divergence (dXY)
and lower relative divergence (FST) than genomic background, and
significant enrichment in immune-related genes, reflecting long-term
balancing selection. Scattered across the genome we also find regions with
both high FST and DXY among groups, termed FST-islands. Population genetic
signatures indicate that FST-islands with elevated divergence, which have
experienced directional selection, are derived from divergent sorting of
ancient polymorphisms. Conclusions: Our results suggest that long-term
balancing selection on disease resistance genes may have maintained
ancestral haplotypes across different geographical lineages, and unequal
sorting of balanced polymorphisms may have generated genomic regions with
elevated divergence. This study highlights the importance of ancestral
balanced polymorphisms as crucial components of genome-wide variation.