Data from: Demography or selection on linked cultural traits or genes? Investigating the driver of low mtDNA diversity in the sperm whale using complementary mitochondrial and nuclear genome analyses

Mitochondrial DNA has been heavily utilized in phylogeography studies for
several decades. However, underlying patterns of demography and
phylogeography may be misrepresented due to coalescence stochasticity,
selection, variation in mutation rates, and cultural hitchhiking (linkage
of genetic variation to culturally transmitted traits affecting fitness).
Cultural hitchhiking has been suggested as an explanation for low genetic
diversity in species with strong social structures, counteracting even
high mobility, abundance and limited barriers to dispersal. One such
species is the sperm whale, which shows very limited phylogeographic
structure and low mtDNA diversity despite a worldwide distribution and
large population. Here, we use analyses of 175 globally distributed
mitogenomes and three nuclear genomes to evaluate hypotheses of a
population bottleneck/expansion versus a selective sweep due to
cultural-hitchhiking or selection on mtDNA as the mechanism contributing
to low worldwide mitochondrial diversity in sperm whales. In contrast to
mtDNA control region (CR) data, mitogenome haplotypes are largely
ocean-specific, with only one of 80 shared between the Atlantic and
Pacific. Demographic analyses of nuclear genomes suggest low mtDNA
diversity is consistent with a global reduction in population size that
ended approximately 125,000 years ago, correlated with the Eemian
interglacial. Phylogeographic analysis suggests that extant sperm whales
descend from maternal lineages endemic to the Pacific during the period of
reduced abundance, and have subsequently colonized the Atlantic several
times. Results highlight the apparent impact of past climate change, and
suggest selection and hitchhiking are not the sole processes responsible
for low mtDNA diversity in this highly social species.