An exploration of speciation and genome-wide uncertainty in flatfishes based on exon-capture data

Abstract

The flatfishes (Pleuronectiformes) have undergone numerous taxonomic revisions but many of their interrelationships still lack consensus among the scientific community at both the species-level and deep evolutionary timescales. Phylogenetic uncertainty stems from apparent bursts of evolution in short time periods early in the Pleuronectiformes tree, and this uncertainly is exacerbated by an abundance of studies that incompletely and inconsistently sample taxa and genetic markers. In order to partly address the issue of insufficient phylogenetic information, we inferred phylogenies based on the largest molecular dataset (4434 markers via exon-capture) and densest taxon sampling (86 species spanning 11 of the 15 families) of any flatfish study using next-generation sequencing to date. We compared our results to phylogenetic hypotheses across recent works, report several new hypotheses, and identify regions of the flatfish tree that are unlikely to be further resolved with additional sampling. We also conducted species delimitation analyses on four economically valuable species pairs in the family Pleuronectidae to evaluate their utility in being effectively managed. Species pairs in the genera Lepidopsetta and Limanda were found to be good species for management, while species pairs in Hippoglossoides and Atheresthes require further taxonomic analysis.