Genetic differentiation and population connectivity of humpback whales migrating through Aotearoa New Zealand waters

Context Historically, humpback whales migrating past Aotearoa New Zealand (NZ) were linked to western South Pacific wintering grounds and Antarctic feeding grounds. As populations have recovered, research has focused on contemporary connectivity patterns throughout the South Pacific. Aims To determine the contemporary connectivity of winter breeding grounds for humpback whales on their northern and southern migrations past NZ, and those at the Kermadec Islands (Rangitāhua) migratory stopover. Methods We generated DNA profiles (mitochondrial DNA (mtDNA) haplotypes, genetic sex and microsatellite genotypes) using skin samples collected from whales between 1998 and 2021. We used comparisons of DNA profiles and a mixed-stock analysis of mtDNA haplotypes to determine the most likely wintering grounds of genetically identified individuals. Key results DNA profiles of 350 individual whales from NZ were compared to profiles from Oceania (n > 2000), Central and South America (n = 452) and East Australia (n = 809). This comparison revealed 35 genotype matches, mainly to New Caledonia and East Australia. The mixed-stock analysis showed that northbound whales (n = 145) had approximately equal assignment proportions to East Australia and New Caledonia whereas southbound whales (n = 74) showed a two-fold higher assignment to East Australia. In contrast, whales passing Rangitāhua (n = 112) assigned to New Caledonia and other Pacific wintering grounds but not to East Australia. Conclusions Humpback whales passing mainland NZ on their north and southbound migrations are strongly associated with East Australia and New Caledonia wintering grounds. Those migrating south past Rangitāhua have a broader range of wintering ground destinations, including a connection to Central America.