Several delphinid species have shown genetic population structure, both between and within ocean basins. We investigated genetic differentiation in the rough-toothed dolphin, Steno bredanensis, using mitochondrial control region sequences from several localities worldwide (N = 112). Preliminary analyses indicated high levels of genetic differentiation between the Atlantic and Pacific/Indian Oceans, which were further investigated using complete cytochrome b sequences and mitogenomes. Phylogenetic analyses were inconclusive about the existence of cryptic speciation in the genus Steno. Notwithstanding this result, analysis of molecular variance and Φ-statistics analyses revealed strong population differentiation not only between the Atlantic and Pacific, but also within the Atlantic, where three populations were detected: Caribbean, southeastern Brazil, and southern Brazil. We propose that these populations be considered management units for conservation purposes. Our results provide the first perspective on the worldwide genetic differentiation of S. bredanensis.
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