Data from: Population genomics of divergence within an obligate pollination mutualism: selection maintains differences between Joshua tree species

PREMISE OF THE STUDY: Speciation is a complex process that can be shaped
by many factors, from geographic isolation to interspecific interactions.
In Joshua trees, selection from pollinators on style length has been
hypothesized to contribute to the maintenance of differentiation between
two hybridizing sister species. We used population genomics approaches to
measure the extent of genetic differentiation between these species, test
whether selection maintains differences between them, and determine
whether genetic variants associated with style length show signatures of
selection. METHODS: Using restriction-site-associated DNA
(RAD)-sequencing, we identified 9516 single nucleotide polymorphisms
(SNPs) across the Joshua tree genome. We characterized the genomic
composition of trees in a narrow hybrid zone and used genomic scans to
search for signatures of selection acting on these SNPs. We used a
genome-wide association study to identify SNPs associated with variation
in phenotypic traits, including style length, and asked whether those SNPs
were overrepresented among the group under selection. KEY RESULTS: The two
species were highly genetically differentiated (FST = 0.25), and hybrids
were relatively rare in the hybrid zone. Approximately 20% of SNPs showed
evidence of selection maintaining divergence. While SNPs associated with
style length were overrepresented among those under selection (P
<< 0.0001), the same was true for SNPs associated with
highly differentiated vegetative traits. CONCLUSIONS: The two species of
Joshua tree are clearly genetically distinct, and selection is maintaining
differences between them. We found that loci associated with
differentiated traits were likely to be under selection. However, many
traits other than style length appeared to be under selection. Together
with the dearth of intermediate hybrids, these findings reveal that these
taxa are more strongly diverged than previously suspected and that
selection, likely on many targets, is maintaining separation where the two
species meet and hybridize.