Photo-identification Of Dolphins Research Articles

ARIANNA: A novel deep learning-based system for fin contours analysis in individual recognition of dolphins

Starting from a digital image that represents the dolphin's body, distinctive features are extracted and used to find the identity of the unknown dolphin in a set of known individuals. This process is called photo identification, used by experts to monitor dolphins, providing relevant data to preserve the environment and its biodiversity. In this work, we show how semantic segmentation can be used to automatically extract a dolphin's fin contour starting from a cropped photo of the fin, and how this contour can be used for individual identification. A novel contour-based system, called ARIANNA, for the automated cetacean photo identification was designed, developed and tested. The novelty of this system is the adoption of two original modules. The first one, which takes as input a new cropped fin image of unknown dolphin, is devoted to the extraction of a mask that depicts the outline of the unknown fin; the core of this module is a trained neural network, specialized in semantic segmentation of images. The second module is designed to compare the outline of the unknown fin with the outlines of all known dolphins, collected in a referring catalogue, returning a ranked list of the best matches where to search the dolphin identity. The experiments were conducted on images collected between 2013 and 2020 in the Northern Ionian Sea (Central-eastern Mediterranean Sea), which presented cropped fins of Risso's dolphin Grampus griseus, one of the least-known cetacean species on a global and Mediterranean scale. The results suggest that ARIANNA provides advances over the state-of-the-art methods, can efficiently assist researchers in the photo identification of dolphins and can be a starting point for further studies on the photo identification of different species based on semantic segmentation.

Foraging preferences of an apex marine predator revealed through stomach content and stable isotope analyses

Insights into the food habits of predators are essential for maintaining healthy predator populations and the functioning of ecosystems. Stomach content and stable isotope analyses were used to investigate the foraging habits of an apex predator, the Indo-Pacific bottlenose dolphin (Tursiops aduncus) in south-western Australia. A total of 2,594 prey items from 26 families were identified from the stomachs of 10 deceased stranded dolphins. Fish otoliths from stomach contents were used to identify fish to family or species level. Ninety-three percent of identified stomach contents were perciforme fishes, however, perciformes comprised only 30% of the catch during prey sampling. Gobiidae species, small fish generally <100 mm in total length, were the most prevalent family identified in dolphin stomachs, accounting for 82% of identified prey, yet Gobiidae accounted for 12.7% of the catch during prey sampling. For stable isotope analyses, tissue samples from 14 free-ranging dolphins were analyzed for nitrogen (δ15N) and carbon (δ13C) ratios. From stable isotope analyses and boat-based dolphin photo-identification surveys (n = 339, 2007–2011), results indicated niche differentiation between coastal and inshore (bay and estuarine habitat) dolphins. Carbon signatures showed that coastal dolphins had a more pelagic diet compared to a benthic diet observed in the inshore dolphins. Whereas, nitrogen signatures of inshore dolphins showed higher nitrogen levels than coastal dolphins, likely attributed to feeding on enriched prey typical of estuarian environments. Overall, these results indicated that bottlenose dolphins in the study area were selective foragers and that their foraging is specialized by the habitats most frequently used.

Indo‐Pacific humpback dolphins (Sousa chinensis) in the Moyang River Estuary: The western part of the world's largest population of humpback dolphins

Abstract Information gaps from uninvestigated habitats can hinder population assessments and the efficacy of conservation actions for marine mammals, particularly for populations of widely distributed species. The full extent of occurrence of the world's largest (putative) population of Indo‐Pacific humpback dolphins (Sousa chinensis) in the Pearl River estuary (PRE) is not known due to a poor understanding of the western boundary of the population's range. This information gap is the basis of the most critical obstacle for assessing the population's status. To determine the distribution and abundance of the PRE humpback dolphins in the far western portion of its range, systematic line‐transect vessel surveys were conducted in the Moyang River estuary (MRE) during 2013–2015. Photo identification of dolphins and cross‐matching of individual dolphins between different regions were also undertaken to examine individual movement patterns. The abundance of humpback dolphins in the MRE was estimated to be 528 individuals (coefficient of variation: 28.7–50.2%). Cross‐matching of individually identified dolphins from the MRE (present survey area) with those from other survey areas of the PRE showed that dolphins moved frequently across different regions of the PRE, indicating dolphins from both PRE and MRE comprise a single population (which is renamed to be the PRE–MRE population). The western boundary of this population appears to be in the waters on the eastern side of Hailing Island, as dolphins were never observed further west. Supporting around one‐fifth of the PRE–MRE population and providing a quarter of the habitat of the entire PRE–MRE population, the MRE clearly also deserves consideration for greater conservation measures. Strengthening the management with stringent controls over fishing activities in the MRE and establishing a marine protected area in the core habitat are recommended to facilitate better conservation for the entire PRE–MRE humpback dolphin population.

Examining the viability of dorsal fin pigmentation for individual identification of poorly-marked delphinids

Dolphin photo-identification has traditionally relied only on distinctive markings on the dorsal fin—this is problematic for delphinids whose populations exhibit a low mark ratio. We used common dolphins (genus Delphinus) as a model species to assess the viability of using pigmentation for photo-identification. Using a photo-identification catalogue of 169 adult individuals collected between 2002 and 2013, we extracted features that quantified pigmentation in a manner that was robust to lighting artefacts and dorsal fin orientation. We determined the proportion of individuals which exhibited pigmentation and examined temporal stability by (i) visually examining individuals and (ii) testing for seriation. We found 88–91% of images could be manually matched to the correct individual in the catalogue based on pigmentation patterns alone. A linear discriminant analysis classifier correctly identified the correct individual 77% of the time. We found 95% common dolphins exhibited distinctive pigmentation—all of which were temporarily stable. Our work challenges the current thinking that pigmentation is an unreliable feature for delphinid photo-identification and suggests that this feature could be applied to common dolphins and other poorly-marked delphinids.

Preliminary estimates of the abundance and fidelity of dolphins associating with a demersal trawl fishery

The incidental capture of wildlife in fishing gear presents a global conservation challenge. As a baseline to inform assessments of the impact of bycatch on bottlenose dolphins (Tursiops truncatus) interacting with an Australian trawl fishery, we conducted an aerial survey to estimate dolphin abundance across the fishery. Concurrently, we carried out boat-based dolphin photo-identification to assess short-term fidelity to foraging around trawlers, and used photographic and genetic data to infer longer-term fidelity to the fishery. We estimated abundance at ≈ 2,300 dolphins (95% CI = 1,247–4,214) over the ≈ 25,880-km2 fishery. Mark-recapture estimates yielded 226 (SE = 38.5) dolphins associating with one trawler and some individuals photographed up to seven times over 12 capture periods. Moreover, photographic and genetic re-sampling over three years confirmed that some individuals show long-term fidelity to trawler-associated foraging. Our study presents the first abundance estimate for any Australian pelagic dolphin community and documents individuals associating with trawlers over days, months and years. Without trend data or correction factors for dolphin availability, the impact of bycatch on this dolphin population’s conservation status remains unknown. These results should be taken into account by management agencies assessing the impact of fisheries-related mortality on this protected species.

A Full-Capture Hierarchical Bayesian Model of Pollock's Closed Robust Design and Application to Dolphins

We present a Hierarchical Bayesian version of Pollock's Closed Robust Design for studying the survival, temporary-migration, and abundance of marked animals. Through simulations and analyses of a bottlenose dolphin photo-identification dataset, we compare several estimation frameworks, including Maximum Likelihood estimation (ML), model-averaging by AICc, as well as Bayesian and Hierarchical Bayesian (HB) procedures. Our results demonstrate a number of advantages of the Bayesian framework over other popular methods. First, for simple fixed-effect models, we show the near-equivalence of Bayesian and ML point-estimates and confidence/credibility intervals. Second, we demonstrate how there is an inherent correlation among temporary-migration and survival parameter estimates in the PCRD, and while this can lead to serious convergence issues and singularities among MLEs, we show that the Bayesian estimates were more reliable. Third, we demonstrate that a Hierarchical Bayesian model with carefully thought-out hyperpriors, can lead to similar parameter estimates and conclusions as multi-model inference by AICc model-averaging. This latter point is especially interesting for mark-recapture practitioners, for whom model-uncertainty and multi-model inference have become a major preoccupation. Lastly, we extend the Hierarchical Bayesian PCRD to include full-capture histories (i.e., by modelling a recruitment process) and individual-level heterogeneity in detection probabilities, which can have important consequences for the range of phenomena studied by the PCRD, as well as lead to large differences in abundance estimates. For example, we estimate 8%-24% more bottlenose dolphins in the western gulf of Shark Bay than previously estimated by ML and AICc-based model-averaging. Other important extensions are discussed. Our Bayesian PCRD models are written in the BUGS-like JAGS language for easy dissemination and customization by the community of capture-mark-recapture practitioners.

Photo-identification of bottlenose dolphins in the far south of New Zealand indicates a ‘new’, previously unstudied population

Declines in the abundance of bottlenose dolphins in the Bay of Islands and in Doubtful Sound have contributed to the species being classified as Nationally Endangered in New Zealand waters. Updated information on distribution and abundance nationwide is therefore a high priority. This study presents data from the first photo-identification surveys of Paterson Inlet, Stewart Island, conducted to document bottlenose dolphin presence, abundance and residency. Open-population mark-recapture models indicate that 18 (95%CI = 15–20) dolphins regularly use Paterson Inlet. Photo-identification of dolphins from unknown populations during two chance encounters in Otago Harbour and Dusky Sound included 11 individuals previously identified at Stewart Island. These results indicate that dolphins found regularly at Stewart Island are part of a larger, wide ranging southern population with a minimum population abundance of 92 (95%CI = 80–111) individuals.

Long-term trends in the use of a protected area by small cetaceans in relation to changes in population status

The requirement to monitor listed species in European designated sites is challenging for long-lived mobile species that only temporarily occupy protected areas. We use a 21 year time series of bottlenose dolphin photo-identification data to assess trends in abundance and conservation status within a Special Area of Conservation (SAC) in Scotland. Mark–recapture methods were used to estimate annual abundance within the SAC from 1990 to 2010. A Bayesian mark–recapture model with a state-space approach was used to estimate overall population trends using data collected across the populations’ range. Despite inter-annual variability in the number of dolphins within the SAC, there was a >99% probability that the wider population was stable or increasing. Results indicate that use of the SAC by the wider population has declined. This is the first evidence of long-term trends in the use of an EU protected area by small cetaceans in relation to changes in overall population status. Our results highlight the importance of adapting the survey protocols used in long-term photo-identification studies to maintain high capture probabilities and minimise sampling heterogeneity. Crucially, these data demonstrate the value of collecting data from the wider population to assess the success of protected areas designated for mobile predators.

A Long-Term Opportunistic Photo-Identification Study of Bottlenose Dolphins (&lt;I&gt;Tursiops truncatus&lt;/I&gt;) off Aberdeen, United Kingdom: Conservation Value and Limitations

The waters of the Inner Moray Firth were designated a Special Area of Conservation (SAC) in 2005 for the conservation of the bottlenose dolphin (Tursiops truncatus) in northeast Scotland. However, the long-term conservation of this population requires monitoring throughout its entire known range. Opportunistic photo-identification of bottlenose dolphins occurred during 65 cetacean surveys conducted between 1999 and 2008 in the coastal waters of Aberdeenshire. A total of 88 bottlenose dolphin photo-identification encounters resulted in one to 45 animals identified per survey. The minimum annual total population size based on marked animals alone was 62 individuals, and the discovery curve indicated that the population has not yet been adequately sampled. Of 40 highly distinctive adult animals, the annual sighting rate ranged from 0.167 (seen in one year only) to 1.000 (seen every year). The cumulative monthly sighting rate varied from 0.091 (photographed in one month only) to 0.636 (photographed during seven of the 11 combined survey months in the 2001 to 2008 study period). The overall seasonal occurrence of dolphins off Aberdeenshire peaked during May and June, when 65% of distinctively marked animals were recorded per month (combined data for 2001 to 2008). Eighty-four percent of distinctively marked dolphins were matched with those photographed in the Inner Moray Firth, while 93% were matched with those photographed in the southern Outer Moray Firth. Despite its opportunistic nature, the photo-identification study provided valuable information on a population of bottlenose dolphins in a poorly studied part of their range. The high percentage of matches with dolphins from the Moray Firth SAC indicates that over half of the known northeast Scotland population uses the Aberdeenshire region, and some individuals do so regularly. The frequent occurrence off Aberdeen of bottlenose dolphins from a protected SAC has repercussions for the conservation and management of the population and for the effectiveness of the SAC for their longterm protection.