Data from: First circumglobal assessment of Southern Hemisphere humpback whale mitochondrial genetic variation and implications for management

The description of genetic population structure over a species’ geographic
range can provide insights into its evolutionary history and also support
effective management efforts. Assessments for globally distributed species
are rare, however, requiring significant international coordination and
collaboration. The global distribution of demographically discrete
populations for the humpback whale Megaptera novaeangliae is not fully
known, hampering the definition of appropriate management units. Here, we
present the first circumglobal assessment of mitochondrial genetic
population structure across the species’ range in the Southern Hemisphere
and Arabian Sea. We combine new and existing data from the mitochondrial
(mt)DNA control region that resulted in a 311 bp consensus sequence of the
mtDNA control region for 3009 individuals sampled across 14 breeding
stocks and subpopulations currently recognized by the International
Whaling Commission. We assess genetic diversity and test for genetic
differentiation and also estimate the magnitude and directionality of
historic matrilineal gene flow between putative populations. Our results
indicate that maternally directed site fidelity drives significant genetic
population structure between breeding stocks within ocean basins. However,
patterns of connectivity differ across the circumpolar range, possibly as
a result of differences in the extent of longitudinal movements on feeding
areas. The number of population comparisons observed to be significantly
differentiated were found to diminish at the subpopulation scale when
nucleotide differences were examined, indicating that more complex
processes underlie genetic structure at this scale. It is crucial that
these complexities and uncertainties are afforded greater consideration in
management and regulatory efforts.