Demographic history and adaptive evolution of Indo-Pacific bottlenose dolphins (Tursiops aduncus) in Western Australia

Demographic processes can substantially affect a species’ response to
changing ecological conditions, necessitating the combined consideration
of genetic responses to environmental variables and neutral genetic
variation. Using a seascape genomics approach combined with population
demographic modelling, we explored the interplay of demographic and
environmental factors that shaped the current population structure in
Indo-Pacific bottlenose dolphins (Tursiops aduncus) along most of the
Western Australian coastline. We combined large-scale environmental data
gathered via remote sensing with RADseq genomic data from 133 individuals
at 19 sampling sites. Using population genetic and outlier detection
anaylses, we identified three distinct genetic clusters, coinciding with
tropical, subtropical and temperate provincial bioregions. In contrast to
previous studies, our demographic models indicated that populations
occupying the paleo-shoreline split into two demographically independent
lineages before the last glacial maximum (LGM). A subsequent split after
the LGM gave rise to the Shark Bay population, thereby creating the three
currently observed clusters. Although multi-locus heterozygosity declined
from north to south, dolphins from the southernmost cluster inhabiting
temperate waters had higher heterozygosity in potentially adaptive loci,
compared to dolphins from subtropical and tropical waters. These findings
suggest ongoing adaptation to cold temperate waters in the southernmost
cluster, possibly linked to distinct selective pressures between the
different bioregions. Our study demonstrated that in the marine realm,
without apparent physical boundaries, only a combined approach can fully
elucidate the intricate environmental and genetic interactions shaping the
evolutionary trajectory of marine mammals.