Whole‐Genome‐Sequencing Reveals Demographic History and Patterns of Parallel Adaptive Evolution in Indo‐Pacific Bottlenose Dolphins ( Tursiops aduncus ) Across Coastal Australian Seascapes

Understanding how demographic dynamics interact with environmental heterogeneity is central to explaining patterns of genomic variation in the marine realm. Indo-Pacific bottlenose dolphins (Tursiops aduncus) occur along most of the Australian coastline, from tropical to temperate waters, encompassing pronounced differences in temperature, salinity, chlorophyll-a concentration and ocean currents. Using whole-genome sequencing of individuals covering this range, we examined population genetic structure and adaptive divergence at a continental scale. Genome-wide variation mirrored geographic patterns, consistent with a common origin in the north, followed by two independent stepping-stone-like colonization patterns along the eastern and the western coastlines from north to south. In contrast, putatively adaptive loci clustered individuals by tropical waters regardless of geographic distance, indicating strong parallel adaptation in tropical habitats. Candidate loci were enriched for functions related to metabolism and ion transport, with some mapping to genes with regulatory functions. Additional signals potentially suggest involvement of neuronal pathways, consistent with adaptation in a highly social and cognitively advanced marine mammal. Our results highlight the complex interplay between demographic history and selection and suggest tropical-temperate, potentially ecotype-like differentiation across Australian waters. In the face of accelerating climate change, recognizing such adaptive structuring is critical for preserving evolutionary potential. Incorporating adaptive genomic information into conservation planning, alongside neutral genetic data, will be essential for anticipating population responses to future environmental change and for identifying biologically meaningful conservation units.