Use of Photo-Identification and Mark-Recapture Methodology to Assess Basking Shark (Cetorhinus maximus) Populations

The biology and ecology of the basking shark: A review

Here we review the literature on the basking shark (Cetorhinus maximus, Gunnerus, 1765), well known as the second largest extant shark (and fish) species globally. Previous reviews were published by Kunzlik in 1988 and Sims in 2008, but in the last 15 years modern electronic and DNA sequencing technologies have resulted in considerable advances in our knowledge of the species' behaviour and ecology. Basking sharks are planktivores and under appropriate conditions spend prolonged periods at the ocean surface feeding on copepod prey that primarily make up their diet, the behaviour that gave rise to their common name. In general, they are migratory and move into higher latitude waters during the summer months, when loose surface-feeding aggregations may form at favoured sites, the best known of which at present occur at hotspots on the west coasts of Britain and Ireland. The species is found circumglobally in temperate waters, but they are also now known on occasion to migrate at depth between northern and southern hemispheres, as well as across oceans within the northern hemisphere. In the past basking shark were more abundant across much of their range, but, consequent on targeted fisheries and in some places intentional eradication, became everywhere scarce, with recent population recovery in the north-east Atlantic being the result of protective measures initiated in the 1990s. Despite their charismatic nature, some of their most fundamental biological processes including copulation, gestation and birth remain largely unknown, due to their migratory and often deep-water lifestyle. In contrast, the deployment of small-scale archival and satellite tags has revealed the details of both broadscale migratory movements and horizontal and vertical foraging behaviours. Recent genetic studies support evidence suggesting a degree of site fidelity in relation to seasonal feeding grounds, which likely explains why in the past local populations have collapsed following periods of intensive fishing. Other recent research using aerial drones and towed cameras has revealed within loose feeding aggregations elements of social behaviour that may have a courtship function as well as enhance feeding efficiency.

FIN-PRINT a fully-automated multi-stage deep-learning-based framework for the individual recognition of killer whales

Biometric identification techniques such as photo-identification require an array of unique natural markings to identify individuals. From 1975 to present, Bigg's killer whales have been photo-identified along the west coast of North America, resulting in one of the largest and longest-running cetacean photo-identification datasets. However, data maintenance and analysis are extremely time and resource consuming. This study transfers the procedure of killer whale image identification into a fully automated, multi-stage, deep learning framework, entitled FIN-PRINT. It is composed of multiple sequentially ordered sub-components. FIN-PRINT is trained and evaluated on a dataset collected over an 8-year period (2011-2018) in the coastal waters off western North America, including 121,000 human-annotated identification images of Bigg's killer whales. At first, object detection is performed to identify unique killer whale markings, resulting in 94.4% recall, 94.1% precision, and 93.4% mean-average-precision (mAP). Second, all previously identified natural killer whale markings are extracted. The third step introduces a data enhancement mechanism by filtering between valid and invalid markings from previous processing levels, achieving 92.8% recall, 97.5%, precision, and 95.2% accuracy. The fourth and final step involves multi-class individual recognition. When evaluated on the network test set, it achieved an accuracy of 92.5% with 97.2% top-3 unweighted accuracy (TUA) for the 100 most commonly photo-identified killer whales. Additionally, the method achieved an accuracy of 84.5% and a TUA of 92.9% when applied to the entire 2018 image collection of the 100 most common killer whales. The source code of FIN-PRINT can be adapted to other species and will be publicly available.

Killer whale (Orcinus orca) population dynamics in response to a period of rapid ecosystem change in the eastern North Atlantic

This study investigates survival and abundance of killer whales (Orcinus orca) in Norway in 1988-2019 using capture-recapture models of photo-identification data. We merged two datasets collected in a restricted fjord system in 1988-2008 (Period 1) with a third, collected after their preferred herring prey shifted its wintering grounds to more exposed coastal waters in 2012-2019 (Period 2), and investigated any differences between these two periods. The resulting dataset, spanning 32 years, comprised 3284 captures of 1236 whales, including 148 individuals seen in both periods. The best-supported models of survival included the effects of sex and time period, and the presence of transients (whales seen only once). Period 2 had a much larger percentage of transients compared to Period 1 (mean = 30% vs. 5%) and the identification of two groups of whales with different residency patterns revealed heterogeneity in recapture probabilities. This caused estimates of survival rates to be biased downward (females: 0.955 ± 0.027 SE, males: 0.864 ± 0.038 SE) compared to Period 1 (females: 0.998 ± 0.002 SE, males: 0.985 ± 0.009 SE). Accounting for this heterogeneity resulted in estimates of apparent survival close to unity for regularly seen whales in Period 2. A robust design model for Period 2 further supported random temporary emigration at an estimated annual probability of 0.148 (± 0.095 SE). This same model estimated a peak in annual abundance in 2015 at 1061 individuals (95% CI 999-1127), compared to a maximum of 731 (95% CI 505-1059) previously estimated in Period 1, and dropped to 513 (95% CI 488-540) in 2018. Our results indicate variations in the proportion of killer whales present of an undefined population (or populations) in a larger geographical region. Killer whales have adjusted their distribution to shifts in key prey resources, indicating potential to adapt to rapidly changing marine ecosystems.

Basking shark sub-surface behaviour revealed by animal-towed cameras

While biologging tags have answered a wealth of ecological questions, the drivers and consequences of movement and activity often remain difficult to ascertain, particularly marine vertebrates which are difficult to observe directly. Basking sharks, the second largest shark species in the world, aggregate in the summer in key foraging sites but despite advances in biologging technologies, little is known about their breeding ecology and sub-surface behaviour. Advances in camera technologies holds potential for filling in these knowledge gaps by providing environmental context and validating behaviours recorded with conventional telemetry. Six basking sharks were tagged at their feeding site in the Sea of Hebrides, Scotland, with towed cameras combined with time-depth recorders and satellite telemetry. Cameras recorded a cumulative 123 hours of video data over an average 64-hour deployment and confirmed the position of the sharks within the water column. Feeding events only occurred within a metre depth and made up ¾ of the time spent swimming near the surface. Sharks maintained similar tail beat frequencies regardless of whether feeding, swimming near the surface or the seabed, where they spent surprisingly up to 88% of daylight hours. This study reported the first complete breaching event and the first sub-surface putative courtship display, with nose-to-tail chasing, parallel swimming as well as the first observation of grouping behaviour near the seabed. Social groups of sharks are thought to be very short term and sporadic, and may play a role in finding breeding partners, particularly in solitary sharks which may use aggregations as an opportunity to breed. In situ observation of basking sharks at their seasonal aggregation site through animal borne cameras revealed unprecedented insight into the social and environmental context of basking shark behaviour which were previously limited to surface observations.

Effective number of white shark (Carcharodon carcharias, Linnaeus) breeders is stable over four successive years in the population adjacent to eastern Australia and New Zealand

Population size is a central parameter for conservation; however, monitoring abundance is often problematic for threatened marine species. Despite substantial investment in research, many marine species remain data-poor presenting barriers to the evaluation of conservation management outcomes and the modeling of future solutions. Such is the case for the white shark (Carcharodon carcharias), a highly mobile apex predator for whom recent and substantial population declines have been recorded in many globally distributed populations. Here, we estimate the effective number of breeders that successfully contribute offspring in one reproductive cycle (Nb) to provide a snapshot of recent reproductive effort in an east Australian-New Zealand population of white shark. Nb was estimated over four consecutive age cohorts (2010, 2011, 2012, and 2013) using two genetic estimators (linkage disequilibrium; LD and sibship assignment; SA) based on genetic data derived from two types of genetic markers (single nucleotide polymorphisms; SNPs and microsatellite loci). While estimates of Nb using different marker types produced comparable estimates, microsatellite loci were the least precise. The LD and SA estimates of Nb within cohorts using SNPs were comparable; for example, the 2013 age cohort Nb(SA) was 289 (95% CI 200-461) and Nb(LD) was 208.5 (95% CI 116.4-712.7). We show that over the time period studied, Nb was stable and ranged between 206.1 (SD ± 45.9) and 252.0 (SD ± 46.7) per year using a combined estimate of Nb(LD+SA) from SNP loci. In addition, a simulation approach showed that in this population the effective population size (Ne) per generation can be expected to be larger than Nb per reproductive cycle. This study demonstrates how breeding population size can be monitored over time to provide insight into the effectiveness of recovery and conservation measures for the white shark, where the methods described here may be applicable to other data-poor species of conservation concern.

Can post-capture photographic identification as a wildlife marking technique be undermined by observer error? A case study using King Cobras in northeast Thailand

Identifying individuals with natural markings is increasing in popularity to non-invasively support population studies. However, applying natural variation among individuals requires careful evaluation among target species, snakes for example have little validation of such methods. Here we introduce a mark-free identification method for King Cobras (Ophiophagus hannah) from the Sakaerat Biosphere Reserve, in northeast Thailand using both subcaudal scale pholidosis (scale arrangement and number) and unique ventral body markings to distinguish individuals. This project aims to evaluate the impact of observer error on individual identification. Observers of varying expertise, will distinguish between King Cobra individuals using identifying photographs from a previous study. We will ask randomly assigned observers to distinguish individuals via: 1) subcaudal pholidosis, 2) ventral body markings, and 3) combination of both measures. Using Bayesian logistic regression, we will assess the probability observers correctly distinguish individuals. Based on exploratory observations, we hypothesise that there will be a high probability of correct identifications using subcaudal pholidosis and ventral body markings. We aim to stimulate other studies implementing identification techniques for scrutinous assessment of such methods, in order to avoid subsequent errors during long-term population studies.

Estimating population parameters of broadnose sevengill sharks (Notorynchus cepedianus) using photo identification capture-recapture

The broadnose sevengill shark (Notorynchus cepedianus) is a common high trophic-level predator around coastal New Zealand. Data on the ecology of the species in New Zealand are severely lacking, and anthropogenic impacts are unquantified. To partially address this, the authors undertook a study of the demographics of a population at Stewart Island. Sampling trips were carried out seasonally from winter 2016 to spring 2017. A baited underwater video system (BUV) was deployed on 133 occasions (mean = 22.2 deployments per season) in a shallow coastal embayment to capture underwater video of N. cepedianus for photo identification of individuals. N. cepedianus was detected on all but one deployment. Images extracted from video recorded the presence of 149 different individuals. Capture-recapture analysis of these data using robust design methods indicated a seasonal trend in abundance of the population using the study area, ranging from 34 (95% C.I. = 21-55) during winter 2016, to 94 (95% C.I. = 44-199) during spring 2017. This study presents the first data on demographic parameters of N. cepedianus in New Zealand.

Spatio-temporal genetic tagging of a cosmopolitan planktivorous shark provides insight to gene flow, temporal variation and site-specific re-encounters

Migratory movements in response to seasonal resources often influence population structure and dynamics. Yet in mobile marine predators, population genetic consequences of such repetitious behaviour remain inaccessible without comprehensive sampling strategies. Temporal genetic sampling of seasonally recurring aggregations of planktivorous basking sharks, Cetorhinus maximus, in the Northeast Atlantic (NEA) affords an opportunity to resolve individual re-encounters at key sites with population connectivity and patterns of relatedness. Genetic tagging (19 microsatellites) revealed 18% of re-sampled individuals in the NEA demonstrated inter/multi-annual site-specific re-encounters. High genetic connectivity and migration between aggregation sites indicate the Irish Sea as an important movement corridor, with a contemporary effective population estimate (Ne) of 382 (CI = 241-830). We contrast the prevailing view of high gene flow across oceanic regions with evidence of population structure within the NEA, with early-season sharks off southwest Ireland possibly representing genetically distinct migrants. Finally, we found basking sharks surfacing together in the NEA are on average more related than expected by chance, suggesting a genetic consequence of, or a potential mechanism maintaining, site-specific re-encounters. Long-term temporal genetic monitoring is paramount in determining future viability of cosmopolitan marine species, identifying genetic units for conservation management, and for understanding aggregation structure and dynamics.

Serendipitous re-sighting of a basking shark Cetorhinus maximus reveals inter-annual connectivity between American and European coastal hotspots

Transatlantic stock mixing in basking sharks Cetorhinus maximus is supported by low genetic diversity in populations throughout the Atlantic Ocean. However, despite significant focus on the species' movements; >1500 individual sharks marked for recapture and >150 individuals equipped with remote tracking tags, only a single record of transatlantic movment has been previously recorded. Within this context, the seredipitous re-sighting of a female basking shark fitted with a satellite transmitter at Malin Head, Ireland 993 days later at Cape Cod, USA is noteworthy.

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.

Comparison of photo-matching algorithms commonly used for photographic capture-recapture studies

Photographic capture–recapture is a valuable tool for obtaining demographic information on wildlife populations due to its noninvasive nature and cost‐effectiveness. Recently, several computer‐aided photo‐matching algorithms have been developed to more efficiently match images of unique individuals in databases with thousands of images. However, the identification accuracy of these algorithms can severely bias estimates of vital rates and population size. Therefore, it is important to understand the performance and limitations of state‐of‐the‐art photo‐matching algorithms prior to implementation in capture–recapture studies involving possibly thousands of images. Here, we compared the performance of four photo‐matching algorithms; Wild‐ID, I3S Pattern+, APHIS, and AmphIdent using multiple amphibian databases of varying image quality. We measured the performance of each algorithm and evaluated the performance in relation to database size and the number of matching images in the database. We found that algorithm performance differed greatly by algorithm and image database, with recognition rates ranging from 100% to 22.6% when limiting the review to the 10 highest ranking images. We found that recognition rate degraded marginally with increased database size and could be improved considerably with a higher number of matching images in the database. In our study, the pixel‐based algorithm of AmphIdent exhibited superior recognition rates compared to the other approaches. We recommend carefully evaluating algorithm performance prior to using it to match a complete database. By choosing a suitable matching algorithm, databases of sizes that are unfeasible to match “by eye” can be easily translated to accurate individual capture histories necessary for robust demographic estimates.

Long-term satellite tracking reveals variable seasonal migration strategies of basking sharks in the north-east Atlantic

Animal migration is ubiquitous in nature with individuals within a population often exhibiting varying movement strategies. The basking shark (Cetorhinus maximus) is the world's second largest fish species, however, a comprehensive understanding of their long-term wider-ranging movements in the north-east Atlantic is currently lacking. Seventy satellite tags were deployed on basking sharks over four years (2012-2015) off the west coast of Scotland and the Isle of Man. Data from 28 satellite tags with attachment durations of over 165 days reveal post-summer ranging behaviours. Tagged sharks moved a median minimum straight-line distance of 3,633 km; achieving median displacement of 1,057 km from tagging locations. Tagged individuals exhibited one of three migration behaviours: remaining in waters of UK, Ireland and the Faroe Islands; migrating south to the Bay of Biscay or moving further south to waters off the Iberian Peninsula, and North Africa. Sharks used both continental shelf areas and oceanic habitats, primarily in the upper 50-200 m of the water column, spanning nine geo-political zones and the High Seas, demonstrating the need for multi-national cooperation in the management of this species across its range.