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

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

Conservation status of Australian snubfin dolphin, \u3cem\u3eOrcaella heinsohni\u3c/em\u3e, and Indo-Pacific humpback dolphin, \u3cem\u3eSousa chinensis\u3c/em\u3e, in the Capricorn Coast, Central Queensland, Australia

This study examined populations of Australian snubfin dolphins (Orcaella heinsohni) and Indo-Pacific humpback dolphins (Sousa chinensis) inhabiting the coastal waters of the Capricorn Section of the Great Barrier Reef Marine Park, Queensland, Australia. A total of 189 humpback dolphins and 54 snubfin dolphins were identified during 1,760 hours and 20,248 kms of transect surveys completed between 2006 and 2008 in the Capricorn Coast region. Humpback dolphins were found in three different sites: Port Curtis, Keppel Bay and the Northern Region of the study area. In contrast, snubfin dolphins were found only in the Keppel Bay study area. Both humpback and snubfin dolphins were found year round with no significant variation among sampling periods and between seasons. Similarly, no substantial variation was found in pod size and composition among sampling periods and seasons. Based on the distribution of resighted individuals and the pattern of associations, it was established that humpback dolphins in the Capricorn Coast were grouped into three largely geographically distinct communities, referred to as the Port Curtis, Keppel Bay and the Northern Region communities. The interaction recorded among communities was lower than the level of association within communities. However, interaction among some members of different communities and movement of individuals between sites was recorded. Analysis of molecular variance showed high gene flow among Port Curtis and Keppel Bay study sites, which corroborates results from photo-identification data and social structure analysis. Very low gene flow was found between humpback dolphin populations from the Capricorn Coast and the Great Sandy Strait, which suggests that humpback dolphins from the Capricorn Coast form a separate management unit, which is geographically and mostly genetically isolated from populations elsewhere. Interestingly, migration rates for humpback dolphins between the Northern and Southern Great Sandy Strait was low, and significant differences in microsatellite loci frequency were evident between these communities. Abundance of humpback dolphins was estimated for the entire population and by geographical area using open population models. Estimates for Port Curtis, Keppel Bay and the Northern Region indicate that about 85 (PC = 85.1, SE = 4.36, 95% CI: 76.64–93.68), 107 (KB = 107.08, SE = 4.87, 95% CI: 97.53–116.5) and 64 (NR = 64.1, SE = 4.82, 95% CI: 54.66–73.46) humpback dolphins used those areas respectively during the study. The total humpback dolphin population size in the Capricorn Coast region was estimated to be 256 (Ntot= 75.80, SE = 8.12, 95% CI = 240.4–271.9), of which 178 (Nma= 178.1, SE = 4.14, 95% CI: 169.9–186.1) were adults. In contrast, snubfin dolphins were found only in Keppel Bay, and social structure analysis did not provide any evidence of structure in the population. This population appears to be geographically and demographically isolated. Genetic evidence based on a small sample size suggests that this population is genetically isolated from populations in North Queensland. A review of sighting information indicates that the Keppel Bay snubfin dolphin population is the southernmost population of snubfin dolphins along the Queensland coast. Population estimates indicate that about 74 snubfin dolphins (SD = 74.03, SE = 4.14, 95% CI: 65.91–82.09) live year round in Keppel Bay

Chapter seven – 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

Feasibility of Using Small UAVs to Derive Morphometric Measurements of Australian Snubfin (Orcaella heinsohni) and Humpback (Sousa sahulensis) Dolphins

Analysis of animal morphometrics can provide vital information regarding population dynamics, structure, and body condition of cetaceans. Unmanned aerial vehicles (UAVs) have become the primary tool to collect morphometric measurements on whales, whereas on free ranging small dolphins, have not yet been applied. This study assesses the feasibility of obtaining reliable body morphometrics from Australian snubfin (Orcaella heinsohni) and humpback dolphins (Sousa sahulensis) using images collected from UAVs. Specifically, using a dolphin replica of known size, we tested the effect of the altitude of the UAV and the position of the animal within the image frame on the accuracy of length estimates. Using linear mixed models, we further assessed the precision of the total length estimates of humpback and snubfin dolphins. The precision of length estimates on the replica increased by ~2% when images were sampled at 45–60 m compared with 15–30 m. However, the precision of total length estimates on dolphins was significantly influenced only by the degree of arch and edge certainty. Overall, we obtained total length estimates with a precision of ~3% and consistent with published data. This study demonstrates the reliability of using UAV based images to obtain morphometrics of small dolphin species, such as snubfin and humpback dolphins

Feasibility of Using Small UAVs to Derive Morphometric Measurements of Australian Snubfin (<i>Orcaella heinsohni</i>) and Humpback (<i>Sousa sahulensis</i>) Dolphins

Analysis of animal morphometrics can provide vital information regarding population dynamics, structure, and body condition of cetaceans. Unmanned aerial vehicles (UAVs) have become the primary tool to collect morphometric measurements on whales, whereas on free ranging small dolphins, have not yet been applied. This study assesses the feasibility of obtaining reliable body morphometrics from Australian snubfin (Orcaella heinsohni) and humpback dolphins (Sousa sahulensis) using images collected from UAVs. Specifically, using a dolphin replica of known size, we tested the effect of the altitude of the UAV and the position of the animal within the image frame on the accuracy of length estimates. Using linear mixed models, we further assessed the precision of the total length estimates of humpback and snubfin dolphins. The precision of length estimates on the replica increased by ~2% when images were sampled at 45–60 m compared with 15–30 m. However, the precision of total length estimates on dolphins was significantly influenced only by the degree of arch and edge certainty. Overall, we obtained total length estimates with a precision of ~3% and consistent with published data. This study demonstrates the reliability of using UAV based images to obtain morphometrics of small dolphin species, such as snubfin and humpback dolphins

Metal contamination among endangered, threatened and protected marine vertebrates off south-eastern Australia

Ambient concentrations of many essential and non-essential trace elements in coastal waters off New South Wales (NSW), Australia are among the lowest reported anywhere in the Southern Hemisphere. Nevertheless, concentrations of various contaminants in regional and migratory marine biota have been recorded above existing, established thresholds, and with possible implications for various negative biological effects. We quantified the concentrations of 24 trace elements in 57 individuals from 13 species (dolphins, sharks, rays and teleosts) caught in bather-protection gillnets deployed off northern NSW at 29°S. While muscle concentrations of most elements were below detection limits, >50% of specimens (mostly larger sharks) had Hg at concentrations exceeding thresholds that might damage biomechanical processes, while several others had As and Cd concentrations elevated to within the ranges of values previously demonstrated to cause negative effects among other species, including deformities among eggs, embryos or larvae. Future research is warranted to quantify the broader extent of the observed contaminant loads and any physiological impacts on wild populations

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

Abundance and site fidelity of Indo-Pacific Humpback dolphins in the Great Sandy Strait, Queensland, Australia

This study examined the population of Indo-Pacific humpback dolphins, Sousa chinensis, inhabiting the Great Sandy Strait Marine Park, Queensland, Australia. A total of 106 dolphins were identified during 228 boat-based surveys, completed between April 2004 and April 2007. Based on the distribution of resighted individuals and the pattern of associations, it was established that this population consists of two largely geographically distinct communities, referred to as the Northern Community (NC) and the Southern Community (SC). The only recorded interaction between the two groups was a single pod composed of one member of the NC and 11 dolphins from the SC. Abundance was estimated for the entire population and by geographical area using open population models. Estimates for the Great Sandy Strait indicate that about 150 dolphins (NGSS= 148.4, SE = 8.3, 95% CI: 132.5–165.2) used this area during the study. The NC and SC total population sizes was estimated to be 76 (NNGSS= 75.80, SE = 3.88, 95% CI = 71–86) and 75 (NSGSS= 74.98, SE = 4.43, 95% CI: 66–83), respectively. Analysis of residence patterns indicates that a majority of the identified dolphins are long-term residents

Top predators marini ed accumulo di organoclorurati: il Mar Mediterraneo a confronto con altre aree del mondo

Sommario: I top predators sono rappresentati da varie specie di animali che occupano i vertici della rete trofica. Per la loro posizione e per il lungo ciclo vitale sono sottoposti a numerose minacce tra le quali l'accumulo di contaminanti organoclorurati. Sono stati presi in considerazione i top predators marini di diverse specie di Mammiferi odontoceti e Condroitti elasmobranchi (Tursiops truncatus, Tursiops aduncus, Stenella coeruleoalba, Delphinus delphis, Orcaella heinsohni, Sousa sahulensis, Sphyrna mokarran, Carcarhinus limbatus, Carcharodon carcharias, Heptranchias perlo, Squalus Blainvillei, Isurus oxyrinchus e Prionace glauca) campionati in 3 aree del mondo (Mediterraneo, Australia e Sud Africa). I campioni dei cetacei e di C. carcharias (Sud Africa) sono stati prelevati tramite il metodo non distruttivo della biopsia cutanea su esemplari "free-ranging", mentre i campioni degli elasmobranchi campionati nel Mediterraneo ed in Australia sono stati ottenuti da esemplari rimasti intrappolati accidentalmente nelle reti dei pescatori o nelle reti anti-squalo. In questi ultimi individui, quindi, si suppone un buono stato di salute per cui è possibile paragonare i valori ottenuti a quelli degli esemplari campionati tramite biopsia cutanea. Con questo studio abbiamo cercato di colmare alcune di queste lacune relativamente ad alcune aree del mondo e ad alcuni xenobiotici clorurati che, anche se “dinosauri” della contaminazione ambientale, rimangono prioritari nel rischio chimico di questi animali. Inoltre, abbiamo cercato di valutare quanto realmente le specie che vivono nel Mar Mediterraneo siano più impattate dalla contaminazione di quelle che si trovano in altre acque del mondo