Data from: Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift

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
specialisations, 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 SNP 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
specialisations 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.