Oceanographic barriers, divergence, and admixture : phylogeography and taxonomy of two putative subspecies of short-finned pilot whale

Funding:Commander, U.S. Pacific Fleet Environmental Readiness Division and NMFS Pacific Islands Fisheries Science Center; NMFS West Coast Region; Scripps Institution of Oceanography Edna Bailey Sussman Research Fellowship; and Woods Hole Oceanographic Institution.Genomic phylogeography plays an important role in describing evolutionary processes and their geographic, ecological, or cultural drivers. These drivers are often poorly understood in marine environments, which have fewer obvious barriers to mixing than terrestrial environments. Taxonomic uncertainty of some taxa (e.g., cetaceans), due to the difficulty in obtaining morphological data, can hamper our understanding of these processes. One such taxon, the short‐finned pilot whale, is recognized as a single global species but includes at least two distinct morphological forms described from stranding and drive hunting in Japan, the “Naisa” and “Shiho” forms. Using samples (n = 735) collected throughout their global range, we examine phylogeographic patterns of divergence by comparing mitogenomes and nuclear SNP loci. Our results suggest three types within the species: an Atlantic Ocean type, a western/central Pacific and Indian Ocean (Naisa) type, and an eastern Pacific Ocean and northern Japan (Shiho) type. mtDNA control region differentiation indicates these three types form two subspecies, separated by the East Pacific Barrier: Shiho short‐finned pilot whale, in the eastern Pacific Ocean and northern Japan, and Naisa short‐finned pilot whale, throughout the remainder of the species' distribution. Our data further indicate two diverging populations within the Naisa subspecies, in the Atlantic Ocean and western/central Pacific and Indian Oceans, separated by the Benguela Barrier off South Africa. This study reveals a process of divergence and speciation within a globally‐distributed, mobile marine predator, and indicates the importance of the East Pacific Barrier to this evolutionary process.PostprintPeer reviewe

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

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

FKW genotypes for Dryad

Nuclear genotype data for false killer whales. Genotypes are from 16 nuclear microsatellite loci. AnimalID is the identifier from the SWFSC Tissue Archive. The column Stratum specifies the way in which samples were stratified in Martien et al., 2014, Journal of Heredity. Abbreviations are CNP=Central North Pacific, ETP=Eastern Tropical Pacific, MHI=Main Hawaiian Islands, NWHI=Northwest Hawaiian Island

Data from: Mitogenomic phylogenetics of fin whales (Balaenoptera physalus spp.): genetic evidence for revision of subspecies

There are three described subspecies of fin whales (Balaenoptera physalus): B. p. physalus Linnaeus, 1758 in the Northern Hemisphere, B. p. quoyi Fischer, 1829 in the Southern Hemisphere, and a recently described pygmy form, B. p. patachonica Burmeister, 1865. The discrete distribution in the North Pacific and North Atlantic raises the question of whether a single Northern Hemisphere subspecies is valid. We assess phylogenetic patterns using ~16 K base pairs of the complete mitogenome for 154 fin whales from the North Pacific, North Atlantic - including the Mediterranean Sea - and Southern Hemisphere. A Bayesian tree of the resulting 136 haplotypes revealed several well-supported clades representing each ocean basin, with no haplotypes shared among ocean basins. The North Atlantic haplotypes (n = 12) form a sister clade to those from the Southern Hemisphere (n = 42). The estimated time to most recent common ancestor (TMRCA) for this Atlantic/Southern Hemisphere clade and 81 of the 97 samples from the North Pacific was approximately 2 Ma. 14 of the remaining North Pacific samples formed a well-supported clade within the Southern Hemisphere. The TMRCA for this node suggests that at least one female from the Southern Hemisphere immigrated to the North Pacific approximately 0.37 Ma. These results provide strong evidence that North Pacific and North Atlantic fin whales should not be considered the same subspecies, and suggest the need for revision of the global taxonomy of the species. There were a total of 103 CR haplotypes in the Sanger-sequenced data set (Table 1). Haplotypic diversity was high both within ocean basins as well as across all samples. The minimum diversity within an ocean basin was 0.828 for the North Atlantic, which also had the fewest samples. There were no shared haplotypes among ocean basins. There were two fixed differences between the North Atlantic and North Pacific (sites 181 and 198), and one between the North Atlantic and Southern Hemisphere sequences (site 198)