Contaminant assessment of stranded and deceased beaked whales (Ziphiidae) on the New South Wales coast of Australia.

Metal and organic pollutants are prominent marine contaminants that disperse widely throughout the environment. Some contaminants biomagnify, leaving long-lived apex predators such as cetaceans at risk of toxicity. Various tissues collected post-mortem from 16 Ziphiidae individuals that stranded on the New South Wales (NSW) coast, Australia, over ∼15 years were investigated for 16 metals/metalloids and 33 organic contaminants. Polychlorinated biphenyls (PCBs) and Dichlorodiphenyltrichloroethanes (DDTs) were commonly detected in blubber and liver tissues. Mercury, cadmium and silver exceeded reported toxicity thresholds in several individuals. The liver tissue of a Mesoplodon layardii specimen had the highest mercury (386 mg/kg dry weight). Liver tissue of a Mesoplodon grayi specimen had the highest silver concentration (19.7 mg/kg dry weight), and the highest cadmium concentration was in Ziphius cavirostris kidney (478 mg/kg dry weight). This study provides important new information for rare Ziphiidae species globally.

Incidence of shark-inflicted bite injuries on Australian snubfin (Orcaella heinsohni) and Australian humpback (Sousa sahulensis) dolphins in coastal waters off east Queensland, Australia.

The ecology and evolution of prey populations are influenced by predation and predation risk. Our understanding of predator-prey relationships between sharks and dolphins is incomplete due to the difficulties in observing predatory events directly. Shark-inflicted wounds are often seen on dolphin bodies, which can provide an indirect measure of predation pressure. We used photographs of Australian humpback and snubfin dolphins from north, central, and south Queensland to assess the incidence of shark-inflicted bite injuries and to examine interspecific differences in bite injuries and their relationship with group sizes, habitat features, and geographical locations characteristic of where these individuals occurred. The incidence of shark-inflicted scarring did not differ between species (χ 2 = 0.133, df = 1, p = .715), with 33.3% of snubfin and 24.1% of humpback dolphins showing evidence of shark bites when data were pooled across all three study sites. Generalized additive models indicated that dolphins closer to the coast, with greater photographic coverage, and in north Queensland were more likely to have a shark-inflicted bite injury. The similar incidence of shark-inflicted wounds found on snubfin and humpback dolphins suggests both are subject to comparable predation pressure from sharks in the study region. Results highlight the importance that habitat features such as distance to the coast and geographical location could have in predation risk of dolphins from sharks, as well as the importance of considering photographic coverage when assessing the incidence of shark-inflicted bites on dolphins or other marine animals. This study serves as a baseline for future studies on shark-dolphin interactions in Queensland and into how predation may influence dolphin habitat usage, group living, and behavior.

Isotopic niche overlap between sympatric Australian snubfin and humpback dolphins.

Ecological niche theory predicts the coexistence of closely related species is promoted by resource partitioning in space and time. Australian snubfin (Orcaella heinsohni) and humpback (Sousa sahulensis) dolphins live in sympatry throughout most of their range in northern Australian waters. We compared stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) in their skin to investigate resource partitioning between these ecologically similar species. Skin samples were collected from live Australian snubfin (n = 31) and humpback dolphins (n = 23) along the east coast of Queensland in 2014-2015. Both species had similar δ13C and δ15N values and high (>50%) isotopic niche space overlap, suggesting that they feed at similar trophic levels, have substantial dietary overlap, and rely on similar basal food resources. Despite similarities, snubfin dolphins were more likely to have a larger δ15N value than humpback dolphins, indicating they may forage on a wider diversity of prey. Humpback dolphins were more likely to have a larger δ13C range suggesting they may forage on a wider range of habitats. Overall, results suggest that subtle differences in habitat use and prey selection are likely the principal resource partitioning mechanisms enabling the coexistence of Australian snubfin and humpback dolphins.

Bioaccumulation of organochlorine compounds in large, threatened elasmobranchs off northern New South Wales, Australia.

Persistent organic pollutants (POPs) include polychlorinated biphenyls (PCBs) dichlorodiphenyltrichloroethane (DDT) and hexachlorobenzene (HCB), which are resistant to biodegradation and therefore accumulate in the marine environment. In Australia, POPs occur in high concentrations primarily in costal water near farming regions and urban centres. From contaminated sediments and biota, POPs are transferred and biomagnified in larger marine organisms. We quantified POPs concentrations in 57 individuals from ten species of sharks and rays caught in bather-protection gillnets deployed off northern New South Wales, Australia. Polychlorinated biphenyls, DDTs and HCB were detected in all species. For some individuals, concentrations were at levels known to have deleterious sub-lethal effects. Overall, the POP concentrations analysed in this study were comparable to those in similar species from more polluted regions, and may have negative impacts on longer-term health. Future research is warranted to investigate spatio-temporal patterns of species-specific contaminant loads and their implications.

SONiCS: PCR stutter noise correction in genome-scale microsatellites.

Motivation: Massively parallel capture of short tandem repeats (STRs, or microsatellites) provides a strategy for population genomic and demographic analyses at high resolution with or without a reference genome. However, the high Polymerase Chain Reaction (PCR) cycle numbers needed for target capture experiments create genotyping noise through polymerase slippage known as PCR stutter. Results: We developed SONiCS-Stutter mONte Carlo Simulation-a solution for stutter correction based on dense forward simulations of PCR and capture experimental conditions. To test SONiCS, we genotyped a 2499-marker STR panel in 22 humpback dolphins (Sousa sahulensis) using target capture, and generated capillary-based genotypes to validate five of these markers. In these 110 comparisons, SONiCS showed a 99.1% accuracy rate and a 98.2% genotyping success rate, miscalling a single allele in a marker with low sequence coverage and rejecting another as un-callable. Availability and implementation: Source code and documentation for SONiCS is freely available at https://github.com/kzkedzierska/sonics. Raw read data used in experimental validation of SONiCS have been deposited in the Sequence Read Archive under accession number SRP135756. Supplementary information: Supplementary data are available at Bioinformatics online.

Conservation Status of the Australian Humpback Dolphin (Sousa sahulensis) Using the IUCN Red List Criteria.

Australian humpback dolphins (Sousa sahulensis) were recently described as a new species endemic to northern Australia and potentially southern New Guinea. We assessed the species conservation status against IUCN Red List Criteria using available information on their biology, ecology and threatening processes. Knowledge of population sizes and trends across the species range is lacking. Recent genetic studies indicate Australian humpback dolphins live in small and relatively isolated populations with limited gene flow among them. The available abundance estimates range from 14 to 207 individuals and no population studied to date is estimated to contain more than 104 mature individuals. The Potential Biological Removal method indicates populations are vulnerable to even low rates of anthropogenic mortality. Habitat degradation and loss is ongoing and expected to increase across the species range in Australia, and a continuing decline in the number of mature individuals is anticipated. Considering the available evidence and following a precautionary approach, we considered this species as Vulnerable under IUCN criterion C2a(i) because the total number of mature individuals is plausibly fewer than 10,000, an inferred continuing decline due to cumulative impacts, and each of the populations studied to date is estimated to contain fewer than 1000 mature individuals. Ongoing research efforts and recently developed research strategies and priorities will provide valuable information towards the future conservation and management of Australian humpback dolphins.

Sexual Dimorphism and Geographic Variation in Dorsal Fin Features of Australian Humpback Dolphins, Sousa sahulensis.

Determining the sex of free-ranging cetaceans can be challenging. Sexual dimorphism among external features may allow inferences on sex, but such patterns may be difficult to detect and are often confounded by age and geographic variation. Dorsal fin images of 107 female and 54 male Australian humpback dolphins, Sousa sahulensis, from Western Australia (WA) and Queensland (QLD) were used to investigate sex, age and geographic differences in colouration, height/length quotient and number of notches. Adult males exhibited more dorsal fin notches (p<0.001) and a significantly greater loss of pigmentation on the upper half of their dorsal fins (p<0.001) than did adult females. These differences likely reflect that males experience a higher frequency and/or intensity of intraspecific aggression than females. In QLD, heavily spotted dorsal fins were more frequent among females than males (p<0.001). Logistic regression analyses revealed that dorsal fin spotting and loss of pigmentation on the upper half of the dorsal fin provided the best model parameters for predicting the sex of sampled adults, with 97% accuracy. This technique offers a rapid, non-invasive method for predicting sex in Australian humpback dolphins, which could potentially be applied to populations throughout their range. In contrast to adults, presumed immature animals showed little or no loss of pigmentation or spotting; however, the rate of development of these features remains unknown. There were pronounced differences between QLD and WA in the intensity of spotting on dorsal fins and the extent of pigmentation loss around the posterior insertion and trailing edge of the dorsal fin. While based on a limited sample size, these geographic differences may have conservation implications in terms of population subdivision and should be investigated further.

Population differentiation and hybridisation of Australian snubfin (Orcaella heinsohni) and Indo-Pacific humpback (Sousa chinensis) dolphins in north-western Australia.

Little is known about the Australian snubfin (Orcaella heinsohni) and Indo-Pacific humpback (Sousa chinensis) dolphins ('snubfin' and 'humpback dolphins', hereafter) of north-western Australia. While both species are listed as 'near threatened' by the IUCN, data deficiencies are impeding rigorous assessment of their conservation status across Australia. Understanding the genetic structure of populations, including levels of gene flow among populations, is important for the assessment of conservation status and the effective management of a species. Using nuclear and mitochondrial DNA markers, we assessed population genetic diversity and differentiation between snubfin dolphins from Cygnet (n = 32) and Roebuck Bays (n = 25), and humpback dolphins from the Dampier Archipelago (n = 19) and the North West Cape (n = 18). All sampling locations were separated by geographic distances >200 km. For each species, we found significant genetic differentiation between sampling locations based on 12 (for snubfin dolphins) and 13 (for humpback dolphins) microsatellite loci (FST = 0.05-0.09; P<0.001) and a 422 bp sequence of the mitochondrial control region (FST = 0.50-0.70; P<0.001). The estimated proportion of migrants in a population ranged from 0.01 (95% CI 0.00-0.06) to 0.13 (0.03-0.24). These are the first estimates of genetic diversity and differentiation for snubfin and humpback dolphins in Western Australia, providing valuable information towards the assessment of their conservation status in this rapidly developing region. Our results suggest that north-western Australian snubfin and humpback dolphins may exist as metapopulations of small, largely isolated population fragments, and should be managed accordingly. Management plans should seek to maintain effective population size and gene flow. Additionally, while interactions of a socio-sexual nature between these two species have been observed previously, here we provide strong evidence for the first documented case of hybridisation between a female snubfin dolphin and a male humpback dolphin.

Anthropogenic contaminants in Indo-Pacific humpback and Australian snubfin dolphins from the central and southern Great Barrier Reef.

We present the first evidence of accumulation of organochlorine compounds (DDTs, PCBs, HCB) and polycyclic aromatic hydrocarbons (PAHs) in Indo-Pacific humpback and Australian snubfin dolphins from the central and southern Great Barrier Reef. These dolphins are considered by the Great Barrier Marine Park Authority to be high priority species for management. Analyses of biopsy samples, collected from free ranging individuals, showed PAHs levels comparable to those reported from highly industrialized countries. DDTs and HCB were found at low levels, while in some individuals, PCBs were above thresholds over which immunosuppression and reproductive anomalies occur. These results highlight the need for ongoing monitoring of these and other contaminants, and their potential adverse effects on dolphins and other marine fauna. This is particularly important given the current strategic assessment of the Great Barrier Reef World Heritage Area being undertaken by the Australian Government and the Queensland Government.

At the heart of the industrial boom: Australian snubfin dolphins in the Capricorn Coast, Queensland, need urgent conservation action.

The recent industrial boom along the Australian coastline has increased concerns about the long term conservation of snubfin dolphins along the Queensland coast. National assessment of the conservation status and management of the Australian snubfin dolphin is currently hindered by the lack of adequate biological and ecological information throughout most of its range. In response to the issue of determining the conservation status of species with broad ranges, the IUCN has provided a framework for assessing the threatened status of regional populations. In this study we assessed the conservation status of a small geographically isolated population of snubfin dolphins living in the Fitzroy River region, Queensland, Australia, against the IUCN criteria for regional populations. A review of all available sightings data and stranding information indicates that this is the southernmost resident population of snubfin dolphins in Australian waters. The Fitzroy River snubfin dolphin population is composed of less than 100 individuals, with a representative range and core area of less than 400 and 300 km(2) respectively. The area most often used by snubfin dolphins within the representative range and core area was estimated to be about 292 and 191 km(2), respectively. A decrease in representative range, core area and preferred habitat between 14 and 25% is projected to occur if a planned industrial port development were to occur. These results are robust to uncertainty and considering the low level of formal protection and future threats, a classification of this subpopulation under the IUCN Red List as "Endangered" is appropriate.