Population genetic structure of the Burrunan dolphin (Tursiops australis) in coastal waters of south-eastern Australia: conservation implications

Organisation and evolution of the major histocompatibility complex class I genes in cetaceans

A quarter of marine mammals are at risk of extinction, with disease and poor habitat quality contributing to population decline. Investigation of the Major Histocompatibility Complex (MHC) provides insight into species' capacity to respond to immune and environmental challenges. The eighteen available cetacean chromosome level genomes were used to annotate MHC Class I loci, and to reconstruct the phylogenetic relationship of the described loci. The highest number of loci was observed in the striped dolphin (Stenella coeruleoalba), while the least was observed in the pygmy sperm whale (Kogia breviceps) and rough toothed dolphin (Steno bredanensis). Of the species studied, Mysticetes had the most pseudogenes. Evolutionarily, MHC Class I diverged before the speciation of cetaceans. Yet, locus one was genomically and phylogenetically similar in many species, persisting over evolutionary time. This characterisation of MHC Class I in cetaceans lays the groundwork for future population genetics and MHC expression studies.

Hepatic concentrations of per- and polyfluoroalkyl substances (PFAS) in dolphins from south-east Australia: Highest reported globally

Per- and polyfluoroalkyl substances (PFAS) concentrations were investigated in hepatic tissue of four dolphin species stranded along the south-east coast of Australia between 2006 and 2021; Burrunan dolphin (Tursiops australis), common bottlenose dolphin (Tursiops truncatus), Indo-Pacific bottlenose dolphin (Tursiops aduncus), and short-beaked common dolphin (Delphinus delphis). Two Burrunan dolphin populations represented in the dataset have the highest reported global population concentrations of ∑25PFAS (Port Phillip Bay median 9750 ng/g ww, n = 3, and Gippsland Lakes median 3560 ng/g ww, n = 8), which were 50-100 times higher than the other species reported here; common bottlenose dolphin (50 ng/g ww, n = 9), Indo-Pacific bottlenose dolphin (80 ng/g ww, n = 1), and short-beaked common dolphin (61 ng/g ww, n = 12). Also included in the results is the highest reported individual ∑25PFAS (19,500 ng/g ww) and PFOS (18,700 ng/g ww) concentrations, at almost 30 % higher than any other Cetacea reported globally. Perfluorooctane sulfonate (PFOS) was above method reporting limits for all samples (range; 5.3-18,700 ng/g ww), and constituted the highest contribution to overall ∑PFAS burdens with between 47 % and 99 % of the profile across the dataset. The concentrations of PFOS exceed published tentative critical concentrations (677-775 ng/g) in 42 % of all dolphins and 90 % of the critically endangered Burrunan dolphin. This research reports for the first time novel and emerging PFASs such as 6:2 Cl-PFESA, PFMPA, PFEECH and FBSA in marine mammals of the southern hemisphere, with high detection rates across the dataset. It is the first study to show the occurrence of PFAS in the tissues of multiple species of Cetacea from the Australasian region, demonstrating high global concentrations for inshore dolphins. Finally, it provides key baseline knowledge to the potential exposure and bioaccumulation of PFAS compounds within the coastal environment of south-east Australia.

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.

Using ecotourism boats for estimating the abundance of a bottlenose dolphin population in south-eastern Australia

It is challenging to collect robust, long-term datasets to properly monitor the viability and social structure of large, long-lived animals, especially marine mammals. The present study used a unique long-term dataset to investigate the population parameters and social structure of a poorly studied population of bottlenose dolphins (Tursiops sp.) in southern Port Phillip Bay, south-eastern Australia. Photo-identification images have been collected between 2012-2022 both opportunistically and following a protocol by patrons, staff, and volunteers of ecotourism companies using their vessels as platforms. The resulting large dataset was available to be processed through the online platform Flukebook and used in capture recapture models to estimate abundance and demographic parameters. In addition, the social structure of the population and the reproductive parameters were investigated. The marked adult population abundance (45.2 ± 2.7 individuals) was found to be stable over the last decade and the calving rate ranged between 0.06-0.19 new calves per identified individuals per year, while the inter-birth interval was 3.7 ± 0.8 years. Social analysis suggested the population has a fission-fusion structure with no apparent clusters. The stability of the population over the study period suggests no deleterious effect of anthropogenic or environmental factors during the last decade. This study is the outcome of the effort of the ecotourism organisations and the results obtained, along with their similarity to those of other dolphin populations worldwide, highlight the importance of such data sources for long-term information that would otherwise be too expensive or logistically difficult to obtain.

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.

Assessment on the effectiveness of vessel-approach regulations to protect cetaceans in Australia: A review on behavioral impacts with case study on the threatened Burrunan dolphin (Tursiops australis)

Vessels cause considerable disturbance to cetaceans world-wide, with potential long-term impacts to population viability. Here we present a comprehensive review of vessel impacts to cetacean behavior in Australian waters (2003–2015), finding inadequate protections to be in place. The majority of these studies found trends of decreased animal travel and resting behavioral states as well as low compliance to regulations, and they recommended further regulatory action such as greater enforcement or monitoring, or passive management strategies. As a case study, we conducted the first field assessment of vessel compliance with the Wildlife (Marine Mammal) Regulations 2009 in Gippsland Lakes, Australia, and provide the first assessment of the endangered Gippsland Lakes Burrunan dolphin (Tursiops australis) population’s behavioral ecology. Dolphin behavior and vessel regulation compliance data were collected during boat-based surveys of Gippsland Lakes from July 2017 to January 2018, with a total of 22 dolphin group sightings resulting in 477 five-minute point samples. 77% of dolphin sightings involved vessel interactions (within 400 m), and 56 regulation breaches were observed. These breaches were most severe in summer (mean = 4.54 breaches/hour). Vessels were found to alter dolphin behavior before, during, and after interactions and regulation breaches, including increased mating (mate guarding) and milling behavioral states, and increased ‘fish catch’, ‘high leap’ and ‘tail slap’ behavioral events. These behavioral changes may indicate masking of the dolphins' acoustic communication, disturbance of prey, increased dolphin transition behaviors, and/or induced stress and changes to group structure (including increased mate guarding). While our results provide evidence of short-term altered behavior, the potential for long-term effects on population dynamics for this threatened species is high. In the context of reported inadequate cetacean protection Australia-wide, our management recommendations include greater monitoring and enforcement, and the utilisation of adaptive management.

Fresh water skin disease in dolphins: a case definition based on pathology and environmental factors in Australia

A distinct ulcerative dermatitis known as “freshwater skin disease” is an emerging clinical and pathological presentation in coastal cetaceans worldwide. In Australia, two remarkably similar mortality events enabled the creation of a case definition based on pathology and environmental factors. The first affected a community of endemic Tursiops australis in the Gippsland Lakes, Victoria, while the second occurred among T. aduncus resident in the Swan-Canning River system, Western Australia. The common features of both events were (1) an abrupt and marked decrease in salinity (from > 30ppt to < 5ppt) due to rainfall in the catchments, with hypo-salinity persisting weeks to months, and (2) dermatitis characterized grossly by patchy skin pallor that progressed to variable circular or targetoid, often raised, and centrally ulcerated lesions covering up to 70% of the body surface. The affected skin was often colonized by a variety of fungal, bacterial and algal species that imparted variable yellow, green or orange discoloration. Histologic lesions consisted of epidermal hydropic change leading to vesiculation and erosion; alternately, or in addition, the formation of intra-epithelial pustules resulting in ulceration and hypodermal necrosis. Thus, the environmental factors and characteristic pathologic lesions, are necessary components of the case definition for freshwater skin disease.

Cetacean biodiversity, spatial and temporal trends based on stranding records (1920-2016), Victoria, Australia

Cetacean stranding records can provide vital information on species richness and diversity through space and time. Here we collate stranding records from Victoria, Australia and assess them for temporal, spatial and demographic trends. Between 1920 and 2016, 424 stranding events involving 907 individuals were recorded across 31 Cetacea species from seven families, including five new species records for the state. Seven of these events were mass strandings, and six mother and calf strandings were recorded. Importantly, 48% of the species recorded are recognised as data deficient on the IUCN Red List. The most commonly recorded taxa were Tursiops spp. (n = 146) and Delphinus delphis (common dolphins, n = 81), with the greatest taxonomic richness (n = 24) and highest incidence of stranding events documented within the Otways mesoscale bioregion. We found no seasonal stranding patterns anywhere in the state. While our findings improve understanding of the spatial and temporal patterns of cetacean diversity within Victoria, we suggest greater effort to collect demographic data at stranding events in order to better study state-wide patterns through time. We conclude with guidelines for minimum data collection standards for future strandings to maximise information capture from each event.

Abundance estimates and habitat preferences of bottlenose dolphins reveal the importance of two gulfs in South Australia

Informed conservation management of marine mammals requires an understanding of population size and habitat preferences. In Australia, such data are needed for the assessment and mitigation of anthropogenic impacts, including fisheries interactions, coastal zone developments, oil and gas exploration and mining activities. Here, we present large-scale estimates of abundance, density and habitat preferences of southern Australian bottlenose dolphins (Tursiops sp.) over an area of 42,438km² within two gulfs of South Australia. Using double-observer platform aerial surveys over four strata and mark-recapture distance sampling analyses, we estimated 3,493 (CV = 0.21; 95%CI = 2,327-5,244) dolphins in summer/autumn, and 3,213 (CV = 0.20; 95%CI = 2,151-4,801) in winter/spring of 2011. Bottlenose dolphin abundance and density was higher in gulf waters across both seasons (0.09-0.24 dolphins/km²) compared to adjacent shelf waters (0.004-0.04 dolphins/km²). The high densities of bottlenose dolphins in the two gulfs highlight the importance of these gulfs as a habitat for the species. Habitat modelling associated bottlenose dolphins with shallow waters, flat seafloor topography, and higher sea surface temperatures (SSTs) in summer/autumn and lower SSTs in winter/spring. Spatial predictions showed high dolphin densities in northern and coastal gulf sections. Distributional data should inform management strategies, marine park planning and environmental assessments of potential anthropogenic threats to this protected species.

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.

Eco-Evolutionary Processes Generating Diversity Among Bottlenose Dolphin, Tursiops truncatus, Populations off Baja California, Mexico

For highly mobile species that nevertheless show fine-scale patterns of population genetic structure, the relevant evolutionary mechanisms determining structure remain poorly understood. The bottlenose dolphin (Tursiops truncatus) is one such species, exhibiting complex patterns of genetic structure associated with local habitat dependence in various geographic regions. Here we studied bottlenose dolphin populations in the Gulf of California and Pacific Ocean off Baja California where habitat is highly structured to test associations between ecology, habitat dependence and genetic differentiation. We investigated population structure at a fine geographic scale using both stable isotope analysis (to assess feeding ecology) and molecular genetic markers (to assess population structure). Our results show that there are at least two factors affecting population structure for both genetics and feeding ecology (as indicated by stable isotope profiles). On the one hand there is a signal for the differentiation of individuals by ecotype, one foraging more offshore than the other. At the same time, there is differentiation between the Gulf of California and the west coast of Baja California, meaning that for example, nearshore ecotypes were both genetically and isotopically differentiated either side of the peninsula. We discuss these data in the context of similar studies showing fine-scale population structure for delphinid species in coastal waters, and consider possible evolutionary mechanisms.

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.

Genetic diversity of bottlenose dolphin (Tursiops sp.) populations in the western North Pacific and the conservation implications

The evolutionary processes that shape patterns of diversity in highly mobile marine species are poorly understood, but important towards transferable inference on their effective conservation. In this study, bottlenose dolphins (Tursiops sp.) are studied to address this broader question. They exhibit remarkable geographical variation for morphology, life history, and genetic diversity, and this high level of variation has made the taxonomy of the genus controversial. A significant population structure has been reported for the most widely distributed species, the common bottlenose dolphin (T. truncatus), in almost all ocean basins, though no data have been available for the western North Pacific Ocean (WNP). The genetic diversity of bottlenose dolphins in the WNP was investigated based on 20 microsatellite and one mitochondrial DNA markers for samples collected from Taiwanese, Japanese, and Philippine waters (9°-39°N, 120°-140°E) during 1986-2012. The results indicated that there are at least four genetically differentiated populations of common bottlenose dolphins in the western and central North Pacific Ocean. The pattern of differentiation appears to correspond to habitat types, resembling results seen in other populations of the same species. Our analyses also showed that there was no evident gene flow between the two "sister species", the common bottlenose dolphins, and the Indo-Pacific bottlenose dolphins (T. aduncus) occurring sympatrically in our study region.

The First Isolation and Characterisation of the Protist Labyrinthula sp. in Southeastern Australia

As a result of anthropogenic influences and global climate change, emerging infectious marine diseases are thought to be increasingly more common and more severe than in the past. The aim of our investigation was to confirm the presence of Labyrinthula, the aetiological agent of the seagrass wasting disease, in Southeastern Australia and provide the first isolation and characterisation of this protist, in Australia. Colonies and individual cells were positively identified as Labyrinthula using published descriptions, diagrams, and photographs. Their identity was then confirmed using DNA barcoding of a region of the 18S rRNA gene. Species level identification of isolates was not possible as the taxonomy of the Labyrinthula is still poorly resolved. Still, a diversity of Labyrinthula was isolated from small sections of the southeast coast of Australia. The isolates were grouped into three haplotypes that are biogeographically restricted. These haplotypes are closely related to previously identified saprotrophic clades. The study highlights the need for further investigation into the global distribution of Labyrinthula, including phylogenetic pathogenicity and analysis of host-parasite interactions in response to stressors. Given the results of our analyses, it is prudent to continue research into disease and epidemic agents to better prepare researchers for potential future outbreaks.