Population Structure and Genetic Variability in Northeastern Pacific Killer Whales: Towards an Assessment of Population Viability

Long term studies of killer whales (Orcinus orca) in the coastal waters of British Columbia have identified two sympatric non-associating populations: fish-eating residents and mammal-eating transients. A third group, the offshores, frequents the outer continental shelf. The resident population contains two regional subpopulations in British Columbia and is currently listed as threatened by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). In Alaska one additional putative subpopulation of residents and two of transients have been reported. This complex of populations and subpopulations persisting in the absence of obvious dispersal barriers presents a problem to conservation managers who must decide whether subpopulations should be assessed separately or in combination. Clearly, the decisions should rest on an understanding of the discreteness of the subpopulations. Here, we report a molecular study designed to contribute to such an understanding. This study a) characterized each known subpopulation of killer whales genetically, b) compared genetic variability between the subpopulations and c) analysed mating patterns within the resident subpopulations to determine inbreeding levels. Lightweight pneumatic darts were used to take biopsy samples from 269 individuallyidentified killer whales off British Columbia and Alaska. Nuclear DNA from the samples was typed at 11 polymorphic microsatellite loci, and the entire mitochondrial D-loop was sequenced. The results were used to construct population phylogenies, assess genetic diversity, calculate fixation indices (F-statistics), and conduct paternity analyses. The following findings were key: 1) resident and transient killer whales are reproductively isolated, 2) the division of each into three regional subpopulations is supported genetically, 3) offshores are genetically differentiated from all known resident and transient subpopulations, 4) residents have lower levels of genetic variation than transients, 5) the observation from field studies that residents remain in their natal groups for life is typical of the recent history of the population, 6) despite their lack of permanent dispersal, residents mate outside their natal groups. One transient subpopulation (the critically endangered AT1 population of the northern Gulf of Alaska) appears to be genetically isolated from all other subpopulations. Permanent dispersal between the remaining two transient subpopulations is very rare or non-existent, but gene flow mediated by occasional intermatings could not be ruled out. In the resident population, occasional intermatings may occur between the northern resident subpopulation (which inhabits central and northern British Columbian waters) and the Alaska resident subpopulation (found off the panhandle region of southern Alaska and the Gulf of Alaska coast). Our findings are consistent with the complete genetic isolation of the southern resident subpopulation of southern British Columbia and northern Washington. The southern resident subpopulation is of conservation concern because of its small size (less than 85 individuals), a recent decline, and high contaminant loads. Paternity analysis showed that resident killer whales have strong (presumably behavioural) inbreeding avoidance mechanisms. In all but one instance, pod members