Etheostoma perlongum isolate:YFTC_37806 Genome sequencing

Species are the product of myriad evolutionary forces including genetic drift, natural selection, and gene flow. In many groups of organisms such as darters, a clade of North American freshwater fishes, speciation appears primarily facilitated by geographic isolation. Nearly all darter sister species pairs occur in allopatry separated by millions of years of divergence. One of the only exceptions is the lacustrine Etheostoma perlongum, endemic to Lake Waccamaw, North Carolina, and the presumed closest relative of E. maculaticeps in the Waccamaw River. With no geographic isolation, differential ecological selection in lotic and lentic habitats is hypothesized to have driven speciation between E. perlongum and E. maculaticeps. In this project, we examine morphological and genomic evidence of lacustrine speciation using geometric morphometrics, double digest restriction-site associated DNA (ddRAD) sequencing, and a de novo genome assembly for E. perlongum. Our results demonstrate that although E. perlongum is phylogenetically nested within the widespread E. maculaticeps, there is a sharp genetic and morphological break coinciding with the lake-river boundary. Demographic analyses reveal that E. perlongum and E. maculaticeps diverged 8,000-39,000 years ago, consistent with the young age of Lake Waccamaw. Despite an active hybrid zone and ongoing gene flow, we detect a large 10 Mb genomic region with elevated divergence between E. perlongum and E. maculaticeps that is likely a chromosomal inversion. Our results provide the first glimpse of the genomic architecture of speciation in darters and pave the way for future speciation studies of behavior, ecology, plasticity, and genomics. Etheostoma perlongum illustrates that rapid, ecological speciation with gene flow is possible even in clades where geographic isolation is the dominant mechanism driving diversification.