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. Recent evolutionary radiations provide rare opportunities to address this question, because species within such radiations are often minimally diverged from a genomic perspective. 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). Thus, 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.