Mitochondrial structure despite nuclear panmixia: sex-specific dispersal dictates population structure in sperm...

Marine mammals have high potential for dispersal, yet behavioral or environmental constraints can limit gene flow. This is true for the endangered sperm whale, Physeter macrocephalus, which has a global distribution and long-distance migrations. While previous studies revealed mitochondrial population structure with weak nuclear structure globally, genomic approaches examining this pattern have been limited. Understanding connectivity is critical for the management of this species due to population declines relative to pre-whaling numbers and increased recent anthropogenic stressors. We investigated connectivity between two regions, the U.S. Gulf of Mexico and the western North Atlantic Ocean, using reduced representation genomic and mitochondrial control region sequencing of 73 sperm whales. Relatedness decreased with geographic distance, likely due to the presence of social groups and familial structure. Nuclear markers showed no population structure (F_ST = 0.001-0.008), while mitochondrial structure was high (F_ST = 0.36-0.65), consistent with male-biased dispersal and female philopatry. Female-only analyses showed higher differentiation for mitochondrial but not nuclear markers; male-only analyses revealed no structure. Across all samples, genetic diversity (nuclear: 0.0014; mitochondrial: 0.0017) and effective population size (N_e = 460) were low. Given this low diversity and evidence for partitioning of genetic variation, we recommend managers treat these two regions as distinct to preserve existing variation and promote resilience of this species. These results illustrate that despite the increased power of a genomic approach, it is essential to consider the biology of the species at hand and leverage both mitochondrial and nuclear markers to understand the genetic structure of threatened species.