Abstract
Rough‐toothed dolphins (Steno bredanensis) have a global tropical and subtropical distribution with oceanic, neritic, and island‐associated populations. To inform conservation and management for this species, we used sequences from the mtDNA control region (n = 360), mitogenomes (n = 19), and six nuclear introns (n = 35) to provide multiple lines of evidence to critically evaluate the potential taxonomic status of rough‐toothed dolphins. Using samples from the Pacific, Indian, and Atlantic Oceans, we examined the null hypothesis that rough‐toothed dolphins are one panmictic species and the alternate hypothesis of oceanic subspecies. Phylogenetic analyses of mitogenomes revealed a private Atlantic clade sister to a larger cosmopolitan clade including individuals from all tropical and subtropical oceans. We dated the split between the Atlantic clade and the cosmopolitan clade to 890,000 years ago. We determined that Atlantic rough‐toothed dolphins could be correctly diagnosed with 98% accuracy with the mtDNA control region and calculated the net nucleotide divergence as 0.02. Population level analyses revealed significant genetic differentiation using mtDNA among most regions, while significant differentiation using nuclear markers occurred only between the Atlantic and the Indian/Pacific regions. Therefore, the oceanic divergence and diagnosability of rough‐toothed dolphins in the Atlantic and the Indian/Pacific Oceans meet proposed criteria for recognition as two subspecies.