Data from: Nuclear and mitochondrial patterns of population structure in North Pacific false killer whales (Pseudorca crassidens)

False killer whales (Pseudorca crassidens) are large Delphinids typically found in deep water far offshore. However, in the Hawaiian Archipelago there are two resident island-associated populations of false killer whales, one in the waters around the main Hawaiian Islands (MHI) and one in the waters around the Northwestern Hawaiian Islands (NWHI). We use mitochondrial DNA (mtDNA) control region sequences and genotypes from 16 nuclear (nucDNA) microsatellite loci from 206 individuals to examine levels of differentiation among the two island-associated populations and offshore animals from the central and eastern North Pacific. Both mtDNA and nucDNA exhibit highly significant differentiation between populations, confirming limited gene flow in both sexes. The mtDNA haplotypes exhibit a strong pattern of phylogeographic concordance, with island-associated populations sharing three closely related haplotypes not found elsewhere in the Pacific. However, nucDNA data suggests that NWHI animals are at least as differentiated from MHI animals as they are from offshore animals. The patterns of differentiation revealed by the two marker types suggest that the island-associated false killer whale populations likely share a common colonization history, but have limited contemporary gene flow.