Mitogenomic differentiation in spinner (Stenella longirostris) and pantropical spotted dolphins (S. attenuata) from the eastern tropical Pacific Ocean

Abstract Spinner dolphins ( Stenella longirostris ) and pantropical spotted dolphins ( S. attenuata ) show high intraspecific morphological diversity and endemic subspecies in the eastern tropical Pacific Ocean (ETP). Previous studies of mitochondrial DNA have found low genetic differentiation among most of these groups, possibly due to demographic factors, ongoing gene flow, and/or recent divergence. These species were heavily depleted due to bycatch in the ETP yellowfin tuna fishery. Because understanding population structure is important for accurate management of the recovery of these species, we collected whole mitochondrial genome sequences from 104 spinner and 76 spotted dolphins to test structure hypotheses at multiple hierarchical taxonomic levels. Results show differences between subspecies of spinner and spotted dolphins, but no support for the division of existing offshore stocks of spotted dolphins. We compare these results to previous results of genome‐wide nuclear SNP data and suggest high haplotype diversity, female dispersal, and/or relative power of the two data sets explains the differences observed. Interestingly, increasing the amount of mitochondrial data (base pairs and genes) did not increase ability to delimit population units. This study supports a genetic basis for management units at the subspecies level, and provides critical information for mitigating historical and continued fisheries impacts.