Genomic Divergence and the Evolution of Ecotypes in Bottlenose Dolphins (Genus Tursiops)

Climatic changes have caused major environmental restructuring throughout the world's oceans. Marine organisms have responded to novel conditions through various biological systems, including genomic adaptation. Growing accessibility of next-generation DNA sequencing methods to study nonmodel species has recently allowed genomic changes underlying environmental adaptations to be investigated. This study used double-digest restriction-site associated DNA (ddRAD) sequence data to investigate the genomic basis of ecotype formation across currently recognized species and subspecies of bottlenose dolphins (genus Tursiops) in the Southern Hemisphere. Subspecies-level genomic divergence was confirmed between the offshore common bottlenose dolphin (T. truncatus truncatus) and the inshore Lahille's bottlenose dolphin (T. t. gephyreus) from the southwestern Atlantic Ocean (SWAO). Similarly, subspecies-level divergence is suggested between inshore (eastern Australia) Indo-Pacific bottlenose dolphin (T. aduncus) and the proposed Burrunan dolphin (T. australis) from southern Australia. Inshore bottlenose dolphin lineages generally had lower genomic diversity than offshore lineages, a pattern particularly evident for T. t. gephyreus, which showed exceptionally low diversity. Genomic regions associated with cardiovascular, musculoskeletal, and energy production systems appear to have undergone repeated adaptive evolution in inshore lineages across the Southern Hemisphere. We hypothesize that comparable selective pressures in the inshore environment drove similar adaptive responses in each lineage, supporting parallel evolution of inshore bottlenose dolphins. With climate change altering marine ecosystems worldwide, it is crucial to gain an understanding of the adaptive capacity of local species and populations. Our study provides insights into key adaptive pathways that may be important for the long-term survival of cetaceans and other organisms in a changing marine environment.

Seascape genomics of coastal bottlenose dolphins along strong gradients of temperature and salinity

Heterogeneous seascapes and strong environmental gradients in coastal waters are expected to influence adaptive divergence, particularly in species with large population sizes where selection is expected to be highly efficient. However, these influences might also extend to species characterized by strong social structure, natal philopatry and small home ranges. We implemented a seascape genomic study to test this hypothesis in Indo-Pacific bottlenose dolphins (Tursiops aduncus) distributed along the environmentally heterogeneous coast of southern Australia. The datasets included oceanographic and environmental variables thought to be good predictors of local adaptation in dolphins and 8,081 filtered single nucleotide polymorphisms (SNPs) genotyped for individuals sampled from seven different bioregions. From a neutral perspective, population structure and connectivity of the dolphins were generally influenced by habitat type and social structuring. Genotype-environment association analysis identified 241 candidate adaptive loci and revealed that sea surface temperature and salinity gradients influenced adaptive divergence in these animals at both large- (1,000s km) and fine-scales (<100 km). Enrichment analysis and annotation of candidate genes revealed functions related to sodium-activated ion transport, kidney development, adipogenesis and thermogenesis. The findings of spatial adaptive divergence and inferences of putative physiological adaptations challenge previous suggestions that marine megafauna is most likely to be affected by environmental and climatic changes via indirect, trophic effects. Our work contributes to conservation management of coastal bottlenose dolphins subjected to anthropogenic disturbance and to efforts of clarifying how seascape heterogeneity influences adaptive diversity and evolution in small cetaceans.

Genetic relatedness delineates the social structure of southern Australian bottlenose dolphins

Social relationships represent an adaptive behavioral strategy that can provide fitness benefits to individuals. Within mammalian societies, delphinids are known to form diverse grouping patterns and show a variety of social systems. However, how ecological and intrinsic factors have shaped the evolution of such diverse societies is still not well understood. In this study, we used photo-identification data and biopsy samples collected between March 2013 and October 2015 in Coffin Bay, a heterogeneous environment in South Australia, to investigate the social structure of southern Australian bottlenose dolphins (Tursiops cf. australis). Based on the data from 657 groups of dolphins, we used generalized affiliation indices, and applied social network and modularity methods to study affiliation patterns among individuals and investigate the potential presence of social communities within the population. In addition, we investigated genetic relatedness and kinship relationships within and between the communities identified. Modularity analysis revealed that the Coffin Bay population is structured into 2 similar sized, mixed-sex communities which differed in ranging patterns, affiliation levels and network metrics. Lagged association rates also indicated that nonrandom affiliations persisted over the study period. The genetic analyses suggested that there was higher relatedness, and a higher proportion of inferred full-sibs and half-sibs, within than between communities. We propose that differences in environmental conditions between the bays and kinship relationships are important factors contributing to the delineation and maintenance of this social structure.

Modelling Dolphin Distribution to Inform Future Spatial Conservation Decisions in a Marine Protected Area

As marine predators experience increasing anthropogenic pressures, there is an urgent need to understand their distribution and their drivers to inform spatial conservation planning. We used an ensemble modelling approach to investigate the spatio-temporal distribution of southern Australian bottlenose dolphins (Tursiops cf. australis) in relation to a variety of ecogeographical and anthropogenic variables in Coffin Bay, Thorny Passage Marine Park, South Australia. Further, we evaluated the overlap between current spatial management measures and important dolphin habitat. Dolphins showed no distinct seasonal shifts in distribution patterns. Models of the entire study area indicate that zones of high probability of dolphin occurrence were located mainly within the inner area of Coffin Bay. In the inner area, zones with high probability of dolphin occurrence were associated with shallow waters (2-4 m and 7-10 m) and located within 1,000 m from land and 2,500 m from oyster farms. The multi-modal response curve of depth in the models likely shows how the different dolphin communities in Coffin Bay occupy different embayments characterized by distinct depth patterns. The majority of areas of high (>0.6) probability of dolphin occurrence are outside sanctuary zones where multiple human activities are allowed. The inner area of Coffin Bay is an important area of year-round habitat suitability for dolphins. Our results can inform future spatial conservation decisions and improve protection of important dolphin habitat.

High site fidelity and restricted ranging patterns in southern Australian bottlenose dolphins

Information on site fidelity and ranging patterns of wild animals is critical to understand how they use their environment and guide conservation and management strategies. Delphinids show a wide variety of site fidelity and ranging patterns. Between September 2013 and October 2015, we used boat‐based surveys, photographic identification, biopsy sampling, clustering analysis, and geographic information systems to determine the site‐fidelity patterns and representative ranges of southern Australian bottlenose dolphins (Tursiops cf. australis) inhabiting the inner area of Coffin Bay, a highly productive inverse estuary located within Thorny Passage Marine Park, South Australia. Agglomerative hierarchical clustering (AHC) of individuals’ site‐fidelity index and sighting rates indicated that the majority of dolphins within the inner area of Coffin Bay are “regular residents” (n = 125), followed by “occasional residents” (n = 28), and “occasional visitors” (n = 26). The low standard distance deviation indicated that resident dolphins remained close to their main center of use (range = 0.7–4.7 km, X ± SD = 2.3 ± 0.9 km). Representative ranges of resident dolphins were small (range = 3.9–33.5 km², X ± SD = 15.2 ± 6.8 km²), with no significant differences between males and females (Kruskal–Wallis, χ² = 0.426, p = .808). The representative range of 56% of the resident dolphins was restricted to a particular bay within the study area. The strong site fidelity and restricted ranging patterns among individuals could be linked to the high population density of this species in the inner area of Coffin Bay, coupled with differences in social structure and feeding habits. Our results emphasize the importance of productive habitats as a major factor driving site fidelity and restricted movement patterns in highly mobile marine mammals and the high conservation value of the inner area of Coffin Bay for southern Australian bottlenose dolphins.