The evolution of diversity in the marine ecosystem is poorly understood, given the relatively
high potential for connectivity, especially for highly mobile species such as
whales and dolphins. The killer whale (Orcinus orca) has a worldwide distribution,
and individual social groups travel over a wide geographic range. Even so, regional
populations have been shown to be genetically differentiated, including among different
foraging specialists (ecotypes) in sympatry. Given the strong matrifocal social
structure of this species together with strong resource specializations, understanding
the process of differentiation will require an understanding of the relative importance
of both genetic drift and local adaptation. Here we provide a high-resolution analysis
based on nuclear single-nucleotide polymorphic markers and inference about differentiation
at both neutral loci and those potentially under selection. We find that all population
comparisons, within or among foraging ecotypes, show significant
differentiation, including populations in parapatry and sympatry. Loci putatively
under selection show a different pattern of structure compared to neutral loci and are
associated with gene ontology terms reflecting physiologically relevant functions (e.g.
related to digestion). The pattern of differentiation for one ecotype in the North Pacific
suggests local adaptation and shows some fixed differences among sympatric ecotypes.
We suggest that differential habitat use and resource specializations have promoted
sufficient isolation to allow differential evolution at neutral and functional loci, but
that the process is recent and dependent on both selection and drift.