Data from: Genomic atolls of differentiation in coral reef fishes (Hypoplectrus spp, Serranidae)

Because the vast majority of species are well-diverged, relatively little
is known about the genomic architecture of speciation during the early
stages of divergence. Species within recent evolutionary radiations are
often minimally diverged from a genomic perspective, and therefore provide
rare opportunities to address this question. Here, we leverage the hamlet
radiation (Hypoplectrus spp, brightly colored reef fishes from the
tropical western Atlantic) to characterize genomic divergence during the
early stages of speciation. Transect surveys and spawning observations in
Belize, Honduras, and Panama confirm that sympatric barred (H. puella),
black (H. nigricans) and butter (H. unicolor) hamlets are phenotypically
distinct and reproductively isolated, although hybrid spawnings and
individuals with intermediate phenotypes are seen on rare occasions. A
survey of approximately 100,000 restriction-site associated SNPs in 126
samples from the three species across the three replicate populations
reveals extremely slight genome-wide divergence among species
(Fst=0.0038), indicating that ecomorphological differences and functional
reproductive isolation are maintained in sympatry in a backdrop of
extraordinary genomic similarity. Nonetheless, a very small proportion of
SNPs (0.05% on average) are identified as Fst outliers among sympatric
species. Remarkably, a single SNP is identified as an outlier in repeated
populations for the same species pair. A mini-contig assembled de novo
around this SNP falls into the genomic region containing the HoxCa10 and
HoxCa11 genes in 10 teleost species, suggesting an important role for Hox
gene evolution in this radiation. This finding, if confirmed, would
provide a better understanding of the links between micro- and
macroevolutionary processes.