A post-whaling legacy:Differential post-whaling recovery rates resulting in the genetic extinction of native Cape Verde humpback whales

The management of marine mammal populations is mostly concerned with reversing or preventing anthropogenic depletion. Once population abundance and connectivity is restored, priorities shift toward other endangered populations. However, anthropogenic removals have “hidden” long-term effects, such as the loss of (adaptive) genetic diversity, which may elevate long-term extinction rates. Among the baleen whales, the humpback whale was severely depleted globally, but many populations have since recovered well. However, a few populations remain at very low abundances, such as the Cape Verde humpback breeding population. The Cape Verde population is currently at ~300 individuals, down from a pre-whaling abundance at ~5,000. In contrast, the West Indian breeding population has recovered at a much higher rate and is now at ~12,000, from a pre-whaling abundance estimated at ~25,000. The change in relative population sizes between the two North Atlantic breeding populations implies that the Cape Verde population has become sensitive to low rates of immigration of West Indian humpback whales. We estimated the proportion of West Indian and Cape Verdean ancestry in humpbacks sampled in both locations. All humpbacks sampled in the West Indies were of a “pure” West Indian ancestry. However, among the Cape Verde humpbacks, only ~20% were of “pure” Cape Verdean ancestry. The remaining 80% were either West Indian immigrants (30%) or 1st and 2nd generation offspring, i.e., of mixed ancestry. In conclusion, the higher recovery rate of the West Indian humpback population has led to the introgression of West Indian humpback genomes into the Cape Verde population resulting in an ongoing “genetic” extinction of a once distinctive Cape Verde humpback population and will eventually be replaced entirely with West Indian humpback genomes. This study demonstrates that whaling is still resulting in local extinctions long after the cassation of whaling and loss of unique species components of genetic diversity