Population genomics of the killer whale; SNP discovery towards the assessment of population structure at functional genes

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Since a Canadian research project in the 1970s first showed how the regional killer whale population could be tracked over time using photographs to identify and follow the associations and movement of individual whales, it has become increasingly apparent that this species offers great potential for advancing our understanding of key evolutionary and ecological processes. Despite their tremendous potential for long-distance dispersion, with social groups travelling 1000s of km in a season, identified populations of associating individuals (divided into social units of 20-50 individuals) are genetically differentiated at neutral markers over small geographic scales. The apparent mechanism is dependence on local or seasonal habitat resources, and in particular, prey resources. In this way picivorous populations can be separated by the direction of migration in their anadromous salmonid prey (migrating north or south of an estuary), and picivorous populations can be isolated from marine-mammal-eating populations even in sympatry. There is a pattern of differentiation associated with geographic distance (as seen for many species), but only within an ecotype. Differentiation among ecotypes is based on biological factors (especially behaviour associated with foraging and social structure). Although the effective size of regional populations is likely small, there are sometimes physical differences that may be associated with resource exploitation (as seen in various other delphinid species, especially associated with buccal morphology), suggesting local adaptation. In this study we will identify genes that are apparently under selection, and associate them where possible with ecological characteristics, especially known aspect of the life history of the different ecotype populations. A key deliverable will be an extensive set of SNP markers, with some identified as likely under selection, to be applied in a follow-on study to an extensive program of population screening. A preliminary assessment based on these SNP markers will be undertaken in the current study as part of the SNP discovery process. This is made possible by the chosen methodology. The initial step will be the sequencing of the full genome for one sample to a quality level sufficient to use as a reference scaffold (to be done through the commercial provider, Eurofins MWG/ Operon). This will then be used to facilitate the RAD-Tag sequencing work and the associated bio-informatics (to be undertaken under the supervision of partner Neil Hall at CGR Liverpool). The RAD-Tag data will then be analysed by the PI in Durham in collaboration with Prof. Hall and with the assistance of the RA. The RAD-Tag sequences will permit the identification of SNP markers, and the reference genome would permit identification of their location and linkage within the killer whale genome. Analysis of an initial 150 whales from 5 populations will provide the preliminary data on signals for selection and a high-resolution assessment of patterns of differentiation. Bayesian and multiple regression methods will be applied to allow interpretation of genetic variation in the context of environmental variables, and to assess which variables explain the largest proportion of the genetic variance. Taken together these analyses will advance our understanding of the evolutionary processes that generate biodiversity within and among species, facilitate more effective programs of biodiversity conservation, and provide the raw material for future studies that will advance these objectives further.