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Cetacean Assessment & Ecology Program

Killer Whale Genetics: Insight into Population Structure

transient killer whales
Figure 4.  Identification photograph of transient killer whales in the Aleutian Islands and a biopsy dart rebounding from the animal's dorsal surface.  Photo by S. Ingram.

The Cetacean Assessment and Ecology Program (CAEP) has been conducting annual vessel surveys for killer whales (Orcinus orca) throughout the Aleutian Islands and western Gulf of Alaska since 2001. These surveys comprise part of CAEP's ongoing research to determine the distribution, abundance, stock structure, and diet of killer whales off western Alaska. Two of the primary objectives of the vessel surveys are to collect identification photographs and tissue biopsy samples of individual killer whales throughout the surveyed region.

To maximize the geographic extent of our survey coverage and include killer whales from neighboring regions, samples collected by CAEP surveys are supplemented by biopsies collected by several other research groups within both Russian and Alaska waters. The scope of this large, collaborative project provides us with the opportunity to explore patterns of genetic subdivision among killer whales sampled across the northern North Pacific Ocean.

Untethered, lightweight darts are used to collect tissue biopsies from photographically identified killer whales (Fig. 4). These small biopsy darts collect samples of both skin and blubber for the purposes of ecotoxicology, dietary, and genetic analyses. Biopsies are subsampled according to tissue type, preserved according to protocols established for each of the target analyses, and later shared among the participating research groups for a battery of analyses including stable isotope, persistent organic pollutants, and genetic assays.

The whole genomic DNA extracted from a skin subsample yields ample template DNA for both mitochondrial control region (CR) sequencing and nuclear microsatellite genotyping. This suite of genetic markers will allow us to confirm field identifications of the three ecologically distinct killer whale types ("residents," "transients," and "offshores"), often referred to as "ecotypes"; test for significant subdivisions among the sampled individuals within each type; and potentially identify significant geographic or ecological boundaries that define killer whale stocks.

To date, our samples represent killer whales from the Gulf of Alaska across to the Sea of Okhotsk (Fig. 5). We have amassed a collection of 449 samples, of which 249 were collected by NMML scientists. The dataset comprises 6 offshores, 248 fish-eating residents, 134 mammal-eating transients, and 61 samples of unknown ecotype.

figure 5 map, see caption
Figure 5.  Map of killer whale biopsy sample locations in the northern North Pacific Ocean.  Symbols indicate > 1 individual sample.

Mitochondrial CR sequencing has been performed for 97% of all samples (provided by the NMFS Southwest Fisheries Science Center and L. Barrett-Lennard at the Vancouver Aquarium/University of British Columbia), and alignment of the 980 base-pair (bp) fragment revealed 16 unique haplotypes, several of which are "rare" within our sampled dataset and previously unreported. All CR haplotypes are exclusive to one of the three ecotypes, supporting the genetic discreteness of the three killer whale types.

Currently, analyses are under way to test hypotheses based on CR phylogeny and photographic resighting data and to assess the existence of significant genetic subdivisions within the northern North Pacific using nuclear genetic markers. CAEP scientists are genotyping all killer whale samples using a suite of 27 polymorphic microsatellite markers. Individual samples are assigned to putative populations based on type and geographic sampling location.

So far, multilocus genotypes have been generated for 385 samples, of which 369 represent unique individual whales. Preliminary analyses support the subdivisions according to type, with significant genetic differences among the three North Pacific types, and suggest that there may be significant differences between Gulf of Alaska and Aleutian Islands killer whales.

The final round of microsatellite genotyping, commencing in fall 2009, will include biopsies collected during the 2009 CAEP killer whale survey and additional samples collected in Russian waters. The resulting dataset will represent one of the largest genotyping studies of killer whales in North Pacific waters and will provide valuable insight into the structuring of killer whales throughout the region.

By Kim Parsons

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