Genetic and Ecological Divergence Between Northwest Atlantic Killer Whale Populations

Killer whales (Orcinus orca) exhibit substantial genetic and ecological variation across their global distribution. Differentiation between neighboring or sympatric populations is thought to be driven by foraging specialization and social organization, which can lead to reproductive isolation and facilitate the emergence of distinct ecotypes or morphotypes. Here, we use whole-genome resequencing and compound-specific stable isotope analysis of amino acids to investigate links between genetic and ecological differentiation in two genetically distinct killer whale populations in the northwest Atlantic, specifically in the eastern Canadian Arctic and Greenland (ECAG1 and ECAG2). Essential amino acid stable carbon isotope ratios (δ¹³C) suggest that the populations maintain largely distinct distributions or habitat use patterns. Amino acid-specific stable nitrogen isotope ratios (δ¹⁵N) indicate ECAG1 has a higher trophic level diet than ECAG2. Previously undetected genetic substructure within the ECAG1 population revealed finer-scale genetic differentiation between individuals sampled in the eastern Canadian Arctic and those sampled in more temperate northwest Atlantic waters. However, small sample sizes prevented exploration of isotopic differentiation among them. Within ECAG1, considerable interannual variation in δ¹³C and δ¹⁵N amino acid values of seven individuals sampled across different years suggests some degree of ecological plasticity. Concurrent genetic and ecological differentiation suggests that northwest Atlantic killer whales have diverged ecologically, possibly in allopatry, and are now reproductively isolated under secondary contact, comparable to population-level differences observed in other regions. However, their degree of ecological plasticity and secondary contact within expanding Arctic ranges raises questions about whether current levels of divergence will be maintained or eroded with ongoing Arctic warming.