For many highly mobile species, the marine environment presents few obvious barriers to
gene flow. Even so, there is considerable diversity within and among species, referred to by
some as the ‘marine speciation paradox’. The recent and diverse radiation of delphinid
cetaceans (dolphins) represents a good example of this. Delphinids are capable of extensive
dispersion and yet many show fine-scale genetic differentiation among populations.
Proposed mechanisms include the division and isolation of populations based on habitat
dependence and resource specializations, and habitat release or changing dispersal
corridors during glacial cycles. Here we use a phylogenomic approach to investigate the
origin of differentiated sympatric populations of killer whales (Orcinus orca). Killer whales
show strong specialization on prey choice in populations of stable matrifocal social groups
(ecotypes), associated with genetic and phenotypic differentiation. Our data suggest
evolution in sympatry among populations of resource specialists.