The use and abuse of photographic identification in sharks and rays

Performance of different automatic photographic identification software for larvae and adults of the European fire salamander

For many species, population sizes are unknown despite their importance for conservation. For population size estimation, capture-mark-recapture (CMR) studies are often used, which include the necessity to identify each individual, mostly through individual markings or genetic characters. Invasive marking techniques, however, can negatively affect the individual fitness. Alternatives are low-impact techniques such as the use of photos for individual identification, for species with stable distinctive phenotypic traits. For the individual identification of photos, a variety of different software, with different requirements, is available. The European fire salamander (Salamandra salamandra) is a species in which individuals, both at the larval stage and as adults, have individual specific patterns that allow for individual identification. In this study, we compared the performance of five different software for the use of photographic identification for the European fire salamander: Amphibian & Reptile Wildbook (ARW), AmphIdent, I3S pattern+, ManderMatcher and Wild-ID. While adults can be identified by all five software, European fire salamander larvae can currently only be identified by two of the five (ARW and Wild-ID). We used one dataset of European fire salamander larval pictures taken in the laboratory and tested this dataset in two of the five software (ARW and Wild-ID). We used another dataset of European fire salamander adult pictures taken in the field and tested this using all five software. We compared the requirements of all software on the pictures used and calculated the False Rejection Rate (FRR) and the Recognition Rate (RR). For the larval dataset (421 pictures) we found that the ARW and Wild-ID performed equally well for individual identification (99.6% and 100% Recognition Rate, respectively). For the adult dataset (377 pictures), we found the best False Rejection Rate in ManderMatcher and the highest Recognition Rate in the ARW. Additionally, the ARW is the only program that requires no image pre-processing. In times of amphibian declines, non-invasive photo identification software allowing capture-mark-recapture studies help to gain knowledge on population sizes, distribution, movement and demography of a population and can thus help to support species conservation.

Nesting Ecology of Lepidochelys olivacea in Lobito, Angola

The scarcity on the Atlantic coast of the African sea turtle population and its dynamics data is well known. This article discusses the nesting ecology methods and analysis of a nascent Angolan project aimed at preserving the nesting female population of the Olive Ridley turtle (Lepidochelys olivacea) on the coast of Lobito. This study examines the nesting ecology of this species from 2020 to 2023. Females had an average CCL of 70.2 cm and CCW of 68.5 cm. These females laid 127 eggs in nests that averaged 47.0 cm deep. The ex situ nest incubation period averaged 60 days, and the hatchling success was 82.1%. Some techniques used in this project require modifications and enhancements. The utilization of photo identification did not yield the anticipated outcomes, prompting the adoption of passive integrated transponders (PITs) in the last season. However, due to limited funding, the success of this method is contingent upon an augmented field effort, allowing for the recapture of a larger number of females. The continuity of this project hinges upon collaboration between higher authorities and the local community. Together, it is possible to deepen the understanding of the nesting ecology of this species and address pivotal issues for its conservation, thereby implementing the most effective preservation measures.

Citizen science provides valuable data to evaluate elasmobranch diversity and trends throughout the French Polynesia's shark sanctuary

Observers of the Polynesian Shark Observatory (ORP), a citizen science network organized mainly through the Polynesian dive centers, collected an unprecedented amount of data from more than 13,916 dives spanning 43% of the islands of French Polynesia between July 8, 2011, and April 11, 2018. The objective for this type of data collection, which is not accessible within the standard research context, was to provide a unique dataset, and the opportunity to explore the specific diversity, distribution, seasonality and abundance of many elasmobranch species spread out throughout the territory of French Polynesia. Since the data are based on random citizen observations, the spatial distribution was biased toward the most frequented sites and islands where scuba diving is most developed. Overall, the increase in observed abundance of rays and sharks observed in French Polynesia, and the three most sampled islands as well as the high specific diversity recorded for the region, provide first evidence on the effectiveness of the French Polynesia's Shark Sanctuary, established in 2006. These data, collected randomly by the volunteers, also provide insights into potential movement patterns and site fidelity of some of the more commonly observed species. While no final conclusions can be drawn, it is clear that the network of volunteers that regularly contributes information to the Polynesian Shark Observatory plays a very important role in the delivery of much needed data for conservation and management action, as well as providing perspectives for new directions in research on sharks and rays in French Polynesia.

Evidence of Závora Bay as a critical site for reef manta rays, Mobula alfredi, in southern Mozambique

The largest known reef manta ray (Mobula alfredi) population in Africa has been monitored for more than 20 years at several locations on the coast of the Inhambane Province in southern Mozambique. Nonetheless, before this study, little had been reported on the population dynamics of M. alfredi from Závora, a remote bay in the region. Photographic mark-recapture was used to investigate the size and structure of M. alfredi that aggregate at "Red Sands," a reef cleaning station in Závora Bay. An 11 year photographic data set was used to identify 583 M. alfredi individuals between 2010 and 2021. More than half of M. alfredi individuals were resighted at least once, with most encounters (up to 18 for one individual) occurring during the peak sighting period in July-November each year. An even sex ratio was observed, 44% females and 50% males, with no significant difference in resightings between the sexes. Pollock's robust design population models were used to estimate annual abundance, emigration, annual apparent survival and capture probability at Red Sands from July to November over a 6 year period (2016-2021). Abundance estimates varied year to year, ranging from 35 (95% c.i. [30, 45]) up to 233 (95% c.i. [224, 249]) M. alfredi individuals. Given the seasonal affinity of M. alfredi observed at Red Sands, this study highlights the importance of understanding fine-scale site use within the larger home range of this population to develop local management strategies.

Using Drones to Assess Volitional Swimming Kinematics of Manta Ray Behaviors in the Wild

Drones have become increasingly popular tools to study marine megafauna but are underutilized in batoid research. We used drones to collect video data of manta ray (Mobula cf. birostris) swimming and assessed behavior-specific kinematics in Kinovea, a semi-automated point-tracking software. We describe a ‘resting’ behavior of mantas making use of strong currents in man-made inlets in addition to known ‘traveling’ and ‘feeding’ behaviors. No significant differences were found between the swimming speed of traveling and feeding behaviors, although feeding mantas had a significantly higher wingbeat frequency than traveling mantas. Resting mantas swam at a significantly slower speed and wingbeat frequency, suggesting that they were continuously swimming with the minimum effort required to maintain position and buoyancy. Swimming speed and wingbeat frequency of traveling and feeding behaviors overlapped, which could point to other factors such as prey availability and a transitional behavior, influencing how manta rays swim. These baseline swimming kinematic data have valuable applications to other emerging technologies in manta ray research.

How Big Is That Manta Ray? A Novel and Non-Invasive Method for Measuring Reef Manta Rays Using Small Drones

This study explores the application of small, commercially available drones to determine morphometric the measurements and record key demographic parameters of reef manta rays (Mobula alfredi) in Raja Ampat, Indonesia. DJI Mavic 2 Pro drones were used to obtain videos of surface-feeding M. alfredi with a floating, known-length PVC pipe as a reference scale—thus avoiding the need to utilize altitude readings, which are known to be unreliable in small drones, in our photogrammetry approach. Three dimensions (disc length (DL), disc width (DW), and cranial width (CW)) from 86 different individuals were measured. A hierarchical multivariate model was used to estimate the true measurements of these three dimensions and their population-level multivariate distributions. The estimated true measurements of these dimensions were highly accurate and precise, with the measurement of CW more accurate than that of DL and, especially, of DW. Each pairing of these dimensions exhibited strong linear relationships, with estimated correlation coefficients ranging from 0.98–0.99. Given these, our model allows us to accurately calculate DW (as the standard measure of body size for mobulid rays) using the more accurate CW and DL measurements. We estimate that the smallest mature M. alfredi of each sex we measured were 274.8 cm (males, n = 30) and 323.5 cm DW (females, n = 8). We conclude that small drones are useful for providing an accurate “snapshot” of the size distribution of surface-feeding M. alfredi aggregations and for determining the sex and maturity of larger individuals, all with minimal impact on this vulnerable species.

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.

A hitchhiker guide to manta rays: Patterns of association between Mobula alfredi, M. birostris, their symbionts, and other fishes in the Maldives

Despite being among the largest and most charismatic species in the marine environment, considerable gaps remain in our understanding of the behavioural ecology of manta rays (Mobula alfredi, M. birostris). Manta rays are often sighted in association with an array of smaller hitchhiker fish species, which utilise their hosts as a sanctuary for shelter, protection, and the sustenance they provide. Species interactions, rather than the species at the individual level, determine the ecological processes that drive community dynamics, support biodiversity and ecosystem health. Thus, understanding the associations within marine communities is critical to implementing effective conservation and management. However, the underlying patterns between manta rays, their symbionts, and other hitchhiker species remain elusive. Here, we explore the spatial and temporal variation in hitchhiker presence with M. alfredi and M. birostris throughout the Maldives and investigate the factors which may influence association using generalised linear mixed effects models (GLMM). For the first time, associations between M. alfredi and M. birostris with hitchhiker species other than those belonging to the family Echeneidae are described. A variation in the species of hitchhiker associated with M. alfredi and M. birostris was identified, with sharksucker remora (Echeneis naucrates) and giant remora (Remora remora) being the most common, respectively. Spatiotemporal variation in the presence of manta rays was identified as a driver for the occurrence of ephemeral hitchhiker associations. Near-term pregnant female M. alfredi, and M. alfredi at cleaning stations, had the highest likelihood of an association with adult E. naucrates. Juvenile E. naucrates were more likely to be associated with juvenile M. alfredi, and a seasonal trend in E. naucrates host association was identified. Remora were most likely to be present with female M. birostris, and a mean number of 1.5 ± 0.5 R. remora were observed per M. birostris. It is hoped these initial findings will serve as the basis for future work into the complex relationships between manta rays and their hitchhikers.

Fine-scale oceanographic drivers of reef manta ray (Mobula alfredi) visitation patterns at a feeding aggregation site

Globally, reef manta rays (Mobula alfredi) are in decline and are particularly vulnerable to exploitation and disturbance at aggregation sites. Here, passive acoustic telemetry and a suite of advanced oceanographic technologies were used for the first time to investigate the fine-scale (5-min) influence of oceanographic drivers on the visitation patterns of 19 tagged M. alfredi to a feeding aggregation site at Egmont Atoll in the Chagos Archipelago. Boosted regression trees indicate that tag detection probability increased with the intrusion of cold-water bores propagating up the atoll slope through the narrow lagoon inlet during flood tide, potentially transporting zooplankton from the thermocline. Tag detection probability also increased with warmer near-surface temperature close to low tide, with near-surface currents flowing offshore, and with high levels of backscatter (a proxy of zooplankton biomass). These combinations of processes support the proposition that zooplankton carried from the thermocline into the lagoon during the flood may be pumped back out through the narrow inlet during an ebb tide. These conditions provide temporally limited feeding opportunities for M. alfredi, which are tied on the tides. Results also provide some evidence of the presence of Langmuir Circulation, which transports and concentrates zooplankton, and may partly explain why M. alfredi occasionally remained at the feeding location for longer than that two hours. Identification of these correlations provides unique insight into the dynamic synthesis of fine-scale oceanographic processes which are likely to influence the foraging ecology of M. alfredi at Egmont Atoll, and elsewhere throughout their range.

Using citizen science in the photo-identification of adult individuals of an amphibian based on two facial skin features

Among amphibians, adults have traditionally been identified in capture-mark-recapture studies using invasive marking techniques with associated ethical, cost and logistical considerations. However, species in this group may be strong candidates for photo-identification based on natural skin features that removes many of these concerns, with this technique opening up opportunities for citizen scientists to be involved in animal monitoring programs. We investigated the feasibility of using citizen science to distinguish between individuals of an Australian anuran (the sandpaper frog, Lechriodus fletcheri) based on a visual analysis of their natural skin features. We collected photographs of marked individuals in the field over three breeding seasons using a smartphone device. This photo-database was used to create an online survey to determine how easily members of the general public could photo-match individuals by a comparison of two facial skin features; black banding that runs horizontally above the tympanum and a background array of tubercles present in this region. Survey participants were provided with 30 closed, multiple choice questions in which they were asked to match separate images of a query frog from small image pools of potential candidate matches. Participants were consistently able to match individuals with a low matching error rate (mean ± SD of 26 ± 5) despite the relatively low quality of photographs taken from a smartphone device in the field, with most query frogs being matched by a majority of participants (mean ± SD of 86.02 ± 9.52%). These features were found to be unique and stable among adult males and females. Thus, photo-identification is likely to be a valid, non-invasive method for capture-mark-recapture for L. fletcheri, and likely many anurans that display similar facial skin features. This may become an important alternative to artificial marking techniques, with the challenges of manual photo-matching reduced by spreading workloads among members of the public that can be recruited online.

Estimating Population Abundance of Burying Beetles Using Photo-Identification and Mark-Recapture Methods

Successful conservation and management of protected wildlife populations require reliable population abundance data. Traditional capture-mark-recapture methods can be costly, time-consuming, and invasive. Photographic mark-recapture (PMR) is a cost-effective, minimally invasive way to study population dynamics in species with distinct markings or color patterns. We tested the feasibility and the application of PMR using the software Hotspotter to identify Nicrophorus spp. from digital images of naturally occurring spot patterns on their elytra. We conducted a laboratory study evaluating the identification success of Hotspotter on Nicrophorus americanus (Olivier, 1790) and Nicrophorus orbicollis (Say, 1825) before implementation of a mark-recapture study in situ. We compared the performance of Hotspotter using both 'high-quality' and 'low-quality' photographs. For high-quality photographs, Hotspotter had a false rejection rate of 2.7-3.0% for laboratory-reared individuals and 3.9% for wild-caught individuals. For low-quality photographs, the false rejection rate was much higher, 48.8-53.3% for laboratory-reared individuals and 28.3% for wild-caught individuals. We subsequently analyzed encounter histories of wild-caught individuals with closed population models in Program MARK to estimate population abundance. In our study, we demonstrated the utility of using PMR in estimating population abundance for Nicrophorus spp. based on elytral spot patterns.

Biomechanics of fish swimming and leaping under waterfalls: a realistic field, image-based biophysical model with bioengineering implications

Worldwide river fragmentation by infrastructures is altering essential ecological processes including fish migrations. Unlike laboratory approaches, field methods and biophysical models have the potential to provide realistic representations of interacting fish-obstacle systems, furthering insights in behavioural and biomechanics science, and allowing better bioinspired engineering. We developed a new field, image-based method that integrates a biophysical mechanistic model to describe the swimming and leaping biomechanics of wild populations of fish in the non-lab ecological context where their reproductive migration takes place. A weir obstacle in natural riverine conditions where fish freely migrate upstream to their breeding grounds was filmed. A biophysical model including the relevant biomechanical and hydraulic forces and their interactions was parametrised and calibrated with the spatial coordinates of fish trajectories. The method was validated with independent empirical data under field conditions. The distribution of fish initial velocities and angle of emergence of the sample of filmed leaps were reliably quantified in field conditions. The distribution of burst swimming velocities underwater was differentiated from that of the initial leaping velocities associated with the thrust of hydraulic forces; fish behaviour while emerging from water was described. Fish approximated the optimum angle to negotiate the waterfall but did not reach the minimum velocity needed to negotiate the obstacle. The method demonstrated the ability to provide realistic, accurate and precise ecological data on field-based fish interactions with challenge zones during upstream reproductive migrations. The method is cost-effective as it is based on general purpose digital cameras, image analysis, and modelling equations in spreadsheets; all inexpensive and readily available. This new approach can be directly applied to solve scientific problems and bioengineering challenges in any freshwater ecosystem that has natural or artificial obstacles and migratory fish with leaping behaviour.

Recognition software successfully aids the identification of individual small-spotted catsharks Scyliorhinus canicula during their first year of life

Eighteen captive small-spotted catsharks Scyliorhinus canicula were successfully identified from hatching to 1 year of age using the free computer recognition software, I³ S classic. The effect of increasing the time interval between recognition attempts on the accuracy of the software was investigated, revealing that recognition fiedelity decreases with increasing time intervals for younger (0 to 15 weeks), but not older (15 weeks onwards) sharks. Identification by I³ S was validated using genetic analyses of seven microsatellite markers, revealing a 100% success rate. Thus, this non-invasive recognition method can be used as an inexpensive and effective alternative to invasive tagging, improving animal welfare and complementing ex-situ conservation methods.

Stable isotope analyses reveal unique trophic role of reef manta rays (Mobula alfredi) at a remote coral reef

Stable isotope analyses provide the means to examine the trophic role of animals in complex food webs. Here, we used stable isotope analyses to characterize the feeding ecology of reef manta rays (Mobula alfredi) at a remote coral reef in the Western Indian Ocean. Muscle samples of M. alfredi were collected from D'Arros Island and St. Joseph Atoll, Republic of Seychelles, in November 2016 and 2017. Prior to analysis, lipid and urea extraction procedures were tested on freeze-dried muscle tissue in order to standardize sample treatment protocols for M. alfredi. The lipid extraction procedure was effective at removing both lipids and urea from samples and should be used in future studies of the trophic ecology of this species. The isotopic signatures of nitrogen (δ¹⁵N) and carbon (δ¹³C) for M. alfredi differed by year, but did not vary by sex or life stage, suggesting that all individuals occupy the same trophic niche at this coral reef. Furthermore, the isotopic signatures for M. alfredi differed to those for co-occurring planktivorous fish species also sampled at D'Arros Island and St. Joseph Atoll, suggesting that the ecological niche of M. alfredi is unique. Pelagic zooplankton were the main contributor (45%) to the diet of M. alfredi, combined with emergent zooplankton (38%) and mesopelagic prey items (17%). Given the extent of movement that would be required to undertake this foraging strategy, individual M. alfredi are implicated as important vectors of nutrient supply around and to the coral reefs surrounding D'Arros Island and St. Joseph Atoll, particularly where substantial site fidelity is displayed by these large elasmobranchs.

Spotting the "small eyes": using photo-ID methodology to study a wild population of smalleye stingrays (Megatrygon microps) in southern Mozambique

Background

The smalleye stingray (Megatrygon microps) is a large and rare dasyatid ray, patchily distributed across the Indo-West Pacific. Free-swimming individuals have regularly been recorded in Southern Mozambican coastal waters utilizing different inshore environments. Distinctive features of the species include latitudinal rows of white spots on the dorsal surface of their pectoral disc.

Methods

This study aimed to determine if the natural spot patterns on M. microps are sufficiently unique and stable to use in photo-identification studies of wild populations. Research dive logs were combined with opportunistic photographs from local dive centers and recreational divers to create a photographic database from the Inhambane Province coastline.

Results

Seventy different individuals were identified over a 15-year period, all exhibiting uniquely identifiable patterns. Stingrays were easily identifiable over a period of six years with multiple re-sightings of the same individuals recorded. Analysis of encounters across the Inhambane coastline revealed that individual rays regularly use inshore reefs along a 350 km stretch of coastline. Fifteen stingrays were re-sighted during the study period, including one showing a 400 km return movement between Tofo Beach and the Bazaruto Archipelago, which is the longest distance traveled by a dasyatid ray on record. Several presumably pregnant females have also been recorded in the Bazaruto Archipelago National Park.

The challenges of recognising individuals with few distinguishing features: Identifying red foxes Vulpes vulpes from camera-trap photos

Over the last two decades, camera traps have revolutionised the ability of biologists to undertake faunal surveys and estimate population densities, although identifying individuals of species with subtle markings remains challenging. We conducted a two-year camera-trapping study as part of a long-term study of urban foxes: our objectives were to determine whether red foxes could be identified individually from camera-trap photos, and highlight camera-trapping protocols and techniques to facilitate photo identification of species with few or subtle natural markings. We collected circa 800,000 camera-trap photos over 4945 camera days in suburban gardens in the city of Bristol, UK: 152,134 (19%) included foxes, of which 13,888 (9%) contained more than one fox. These provided 174,063 timestamped capture records of individual foxes; 170,923 were of foxes ≥ 3 months old. Younger foxes were excluded because they have few distinguishing features. We identified the individual (192 different foxes: 110 males, 49 females, 33 of unknown sex) in 168,417 (99%) of these capture records; the remainder could not be identified due to poor image quality or because key identifying feature(s) were not visible. We show that carefully designed survey techniques facilitate individual identification of subtly-marked species. Accuracy is enhanced by camera-trapping techniques that yield large numbers of high resolution, colour images from multiple angles taken under varying environmental conditions. While identifying foxes manually was labour-intensive, currently available automated identification systems are unlikely to achieve the same levels of accuracy, especially since different features were used to identify each fox, the features were often inconspicuous, and their appearance varied with environmental conditions. We discuss how studies based on low numbers of photos, or which fail to identify the individual in a significant proportion of photos, risk losing important biological information, and may come to erroneous conclusions.

Detecting, counting and following the giants of the sea: a review of monitoring methods for aquatic megavertebrates in the Caribbean

Abstract The Caribbean is a mega-diverse and bio-geographically important region that consists of the Caribbean Sea, its islands, and surrounding coastlines. Among the billions of aquatic species inhabiting this region, the mega-vertebrates stand out for their social, economic and ecologic relevance. However, the Caribbean has been threatened by climate change, poverty, pollution, environmental degradation and intense growth of the tourism industry, affecting megafauna species directly and indirectly. Population monitoring plays a critical role in an informed conservation process and helps guide management decisions at several scales. The aim of the present review was to critically examine the methods employed for monitoring marine megafauna in the Caribbean, so as to create a framework for future monitoring efforts. In total, 235 documents describing protocols for the monitoring of sirenians, cetaceans, elasmobranchs, sea turtles and crocodilians in the Caribbean region, were reviewed. The methods included community-based monitoring (interviews, citizen science and fisheries monitoring), aerial surveys (by manned and unmanned aerial vehicles), boat-based surveys (including manta tow, and side-scan sonars), land-based surveys, acoustic monitoring, underwater surveys, baited remote underwater video, mark–recapture, photo-identification and telemetry. Monitoring efforts invested on aquatic megafauna in the Caribbean have been highly different, with some species and/or groups being prioritised over others. The present critical review provides a country-based overview of the current and emerging methods for monitoring marine megafauna and a critical evaluation of their known advantages, disadvantages and biases.

Using citizen science data to assess the difference in marine debris loads on reefs in Queensland, Australia

The prevalence of marine debris in global oceans is negatively impacting the marine environment. In Australia, marine debris has been an increasing concern for sensitive marine environments, such as coral reefs. Citizen science can contribute data to explore patterns of subtidal marine debris loads. This study uses data from Reef Check Australia to describe patterns of debris abundance on reef tourism sites in two Queensland regions, the Great Barrier Reef (GBR) and Southeast Queensland (SEQ). Debris was categorized into three groups, fishing line, fishing net, and general rubbish. Overall, debris abundance across reefs was relatively low (average 0.5-3.3 items per survey (400 m²)), but not absent on remote reefs surveyed in the GBR region. Highest debris loads were recorded in SEQ near cities and high use areas. These results indicate the presence of marine debris on remote and urban reefs, and the applicability of using citizen science to monitor debris abundance.

Courtship and mating behaviour of manta rays Mobula alfredi and M. birostris in the Maldives

The aim of this 14 year study was to elucidate the entire courtship and mating behaviour of manta rays Mobula alfredi and M. birostris using behavioural observations, video and photographic records. From 2003 to 2016, over 11,000 surveys were undertaken at known manta ray aggregation sites in the Maldives to record any observed manta rays reproductive activity. From 47,591 photo-ID sightings, 4,247 individual M. alfredi were identified and 226 individual M. birostris from 229 photo-ID sightings, all recorded at 22 atolls across 265 different sites. Courtship activity was observed on 206 surveys at 30 different sites. A total of 229 courtship events were recorded, with 90% (n = 205) of them occurring at cleaning sites. The observed courtship activity was categorised into seven distinct stages which are described in detail: initiation, endurance, evasion, pre-copulatory positioning, copulation, post-copulatory holding and separation. Photographs provide the first scientific record of the entirety of manta rays courtship and mating. Both M. alfredi and M. birostris appear to engage in the same elaborate courtship rituals, exhibiting the same behaviours during all stages of the courtship and mating process.

Site affinity of whitespotted eagle rays Aetobatus narinari assessed using photographic identification

Photographic identification was used to track the movements of the whitespotted eagle ray Aetobatus narinari around South Caicos, Turks and Caicos Islands. A total of 165 individuals were identified, aided by the computer program I³ S Spot. The sex ratio across all study sites in 2015 was not significantly different from 1:1 (χ²  = 2·8, P > 0·05). 33·9% of all individual rays were resighted at least once and the maximum number of days between the first and last sighting was 1640 (median 165, interquartile range, IQR = 698). Sightings of individuals occurred at locations differing from the original sighting location 24·6% of the time (0·7-20 km away). The entire population around South Caicos has yet to be sampled and these rays exhibited site affinity during the study period; they are either resident to South Caicos or are using the area for parts of the year before making movements elsewhere and then returning. Given these results, A. narinari is suited to local-scale management and conservation efforts.

Oceanic adults, coastal juveniles: tracking the habitat use of whale sharks off the Pacific coast of Mexico

Eight whale sharks tagged with pop-up satellite archival tags off the Gulf of California, Mexico, were tracked for periods of 14–134 days. Five of these sharks were adults, with four females visually assessed to be pregnant. At least for the periods they were tracked, juveniles remained in the Gulf of California while adults moved offshore into the eastern Pacific Ocean. We propose that parturition occurs in these offshore waters. Excluding two juveniles that remained in the shallow tagging area for the duration of tracking, all sharks spent 65 ± 20.7% (SD) of their time near the surface, even over deep water, often in association with frontal zones characterized by cool-water upwelling. While these six sharks all made dives into the meso- or bathypelagic zones, with two sharks reaching the maximum depth recordable by the tags (1285.8 m), time spent at these depths represented a small proportion of the overall tracks. Most deep dives (72.7%) took place during the day, particularly during the early morning and late afternoon. Pronounced habitat differences by ontogenetic stage suggest that adult whale sharks are less likely to frequent coastal waters after the onset of maturity.

Validation of photo-identification as a mark-recapture method in the spotted eagle ray Aetobatus narinari

The spotted eagle ray Aetobatus narinari is characterized by pigmentation patterns that are retained for up to 3·5 years. These pigmentations can be used to identify individuals through photo-identification. Only one study has validated this technique, but no study has estimated the percentage of correct identification of the rays using this technique. In order to carry out demographic research, a reliable photographic identification technique is needed. To achieve this validation for A. narinari, a double-mark system was established over 11 months and photographs of the dorsal surface of 191 rays were taken. Three body parts with distinctive natural patterns were analysed (dorsal surface of the cephalic region, dorsal surface of the pectoral fins and dorsal surface of the pelvic fins) in order to determine the body part that could be used to give the highest percentage of correct identification. The dorsal surface of the pectoral fins of A. narinari provides the most accurate photo-identification to distinguish individuals (88·2%).

Error rates and variation between observers are reduced with the use of photographic matching software for capture-recapture studies

Photographic capture-mark-recapture (CMR) permits individual recognition whilst avoiding many of the concerns involved with marking animals. However, the construction of capture histories from photographs is a time-consuming process. Furthermore, matching accuracy is determined based on subjective judgements of the person carrying out the matching, which can lead to errors in the resulting datasets – particularly in long-term projects where multiple observers match images. We asked 63 volunteers to carry out two photographic-matching exercises using a database of known individuals of the yellow-bellied toad (Bombina variegata). From these exercises, we quantified the matching accuracy of volunteers in terms of false-acceptance and false-rejection rates. Not only were error rates greatly reduced with the use of photographic-matching software, but variation in error rates among volunteers was also lowered. Furthermore, the use of matching software led to substantial increases in matching speeds and an 87% reduction in the false-rejection rate. As even small error rates have the potential to bias CMR analyses, these results suggest that computer software could substantially reduce errors in CMR datasets. The time-savings and reduction in variance among observers suggest that such methods could be particularly beneficial in long-term CMR projects where a large number of images may be matched by multiple observers.

The ecological connectivity of whale shark aggregations in the Indian Ocean: a photo-identification approach

Genetic and modelling studies suggest that seasonal aggregations of whale sharks (Rhincodon typus) at coastal sites in the tropics may be linked by migration. Here, we used photo-identification (photo-ID) data collected by both citizen scientists and researchers to assess the connectedness of five whale shark aggregation sites across the entire Indian Ocean at timescales of up to a decade. We used the semi-automated program I³S (Individual Interactive Identification System) to compare photographs of the unique natural marking patterns of individual whale sharks collected from aggregations at Mozambique, the Seychelles, the Maldives, Christmas Island (Australia) and Ningaloo Reef (Australia). From a total of 6519 photos, we found no evidence of connectivity of whale shark aggregations at ocean-basin scales within the time frame of the study and evidence for only limited connectivity at regional (hundreds to thousands of kilometres) scales. A male whale shark photographed in January 2010 at Mozambique was resighted eight months later in the Seychelles and was the only one of 1724 individuals in the database to be photographed at more than one site. On average, 35% of individuals were resighted at the same site in more than one year. A Monte Carlo simulation study showed that the power of this photo-ID approach to document patterns of emigration and immigration was strongly dependent on both the number of individuals identified in aggregations and the size of resident populations.

Automated Visual Fin Identification of Individual Great White Sharks

This paper discusses the automated visual identification of individual great white sharks from dorsal fin imagery. We propose a computer vision photo ID system and report recognition results over a database of thousands of unconstrained fin images. To the best of our knowledge this line of work establishes the first fully automated contour-based visual ID system in the field of animal biometrics. The approach put forward appreciates shark fins as textureless, flexible and partially occluded objects with an individually characteristic shape. In order to recover animal identities from an image we first introduce an open contour stroke model, which extends multi-scale region segmentation to achieve robust fin detection. Secondly, we show that combinatorial, scale-space selective fingerprinting can successfully encode fin individuality. We then measure the species-specific distribution of visual individuality along the fin contour via an embedding into a global 'fin space'. Exploiting this domain, we finally propose a non-linear model for individual animal recognition and combine all approaches into a fine-grained multi-instance framework. We provide a system evaluation, compare results to prior work, and report performance and properties in detail.

Population Structure, Abundance and Movement of Whale Sharks in the Arabian Gulf and the Gulf of Oman

Data on the occurrence of whale sharks, Rhincodon typus, in the Arabian Gulf and Gulf of Oman were collected by dedicated boat surveys and via a public-sightings scheme during the period from 2011 to 2014. A total of 422 individual whale sharks were photo-identified from the Arabian Gulf and the northern Gulf of Oman during that period. The majority of sharks (81%, n = 341) were encountered at the Al Shaheen area of Qatar, 90 km off the coast, with the Musandam region of Oman a secondary area of interest. At Al Shaheen, there were significantly more male sharks (n = 171) than females (n = 78; X2 = 17.52, P < 0.05). Mean estimated total length (TL) for sharks was 6.90 m ± 1.24 (median = 7 m; n = 296). Males (7.25 m ± 1.34; median = 8 m, n = 171) were larger than females (6.44 m ±1.09; median = 7 m, n = 78; Mann-Whitney U test, p < 0.01). Of the male sharks assessed for maturity 63% were mature (n = 81), with 50% attaining maturity by 7.29 m and 100% by 9.00 m. Two female sharks of >9 m individuals were visually assessed as pregnant. Connectivity among sharks sighted in Qatari, Omani and UAE waters was confirmed by individual spot pattern matches. A total of 13 identified sharks were re-sighted at locations other than that at which they were first sighted, including movements into and out of the Arabian Gulf through the Strait of Hormuz. Maximum likelihood techniques were used to model an estimated combined population for the Arabian Gulf and Gulf of Oman of 2837 sharks ± 1243.91 S.E. (95% C.I. 1720-6295). The Al Shaheen aggregation is thus the first site described as being dominated by mature males while the free-swimming pregnant females are the first reported from the Indian Ocean.

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

Following centuries of exploitation, basking sharks (Cetorhinus maximus) are considered by IUCN as Endangered in the Northeast Atlantic, where they have now been substantially protected for over two decades. However, the present size of this population remains unknown. We investigated the use of photo-identification of individuals' dorsal fins, combined with mark-recapture methodology, to investigate the size of populations of basking shark within the west coast of Scotland. From a total of 921 encounters photographed between 2004 and 2011, 710 sharks were found to be individually identifiable based on dorsal fin damage and natural features. Of these, only 41 individuals were re-sighted, most commonly both within days of, and close to the site of, the initial encounter. A smaller number were re-sighted after longer periods of up to two years. A comparison of the distinguishing features of individuals on first recording and subsequent re-sighting showed that in almost all cases these features remained little changed, suggesting the low re-sighting rate was not due to a loss of distinguishing features. Because of the low number of re-sighting we were not able to produce reliable estimates for the long-term regional population. However, for one 50 km diameter study area between the islands of Mull, Coll and Tiree, we were able to generate closed-population estimates for 6-9 day periods in 2010 of 985 (95% CI = 494-1683), and in 2011 of 201 (95% CI = 143-340). For the same 2011 period an open-population model generated a similar estimate of 213 (95% CI = 111-317). Otherwise the low rate and temporal patterning of re-sightings support the view that such local basking shark populations are temporary, dynamic groupings of individuals drawn from a much larger regional population than previously supposed. The study demonstrated the feasibility and limitations of photo-identification as a non-invasive technique for identifying individual basking sharks.

First Direct Evidence for Natal Wintering Ground Fidelity and Estimate of Juvenile Survival in the New Zealand Southern Right Whale Eubalaena australis

Juvenile survival and recruitment can be more sensitive to environmental, ecological and anthropogenic factors than adult survival, influencing population-level processes like recruitment and growth rate in long-lived, iteroparous species such as southern right whales. Conventionally, Southern right whales are individually identified using callosity patterns, which do not stabilise until 6–12 months, by which time the whale has left its natal wintering grounds. Here we use DNA profiling of skin biopsy samples to identify individual Southern right whales from year of birth and document their return to the species’ primary wintering ground in New Zealand waters, the Subantarctic Auckland Islands. We find evidence of natal fidelity to the New Zealand wintering ground by the recapture of 15 of 57 whales, first sampled in year of birth and available for subsequent recapture, during winter surveys to the Auckland Islands in 1995–1998 and 2006–2009. Four individuals were recaptured at the ages of 9 to 11, including two females first sampled as calves in 1998 and subsequently resampled as cows with calves in 2007. Using these capture-recapture records of known-age individuals, we estimate changes in survival with age using Cormack-Jolly-Seber models. Survival is modelled using discrete age classes and as a continuous function of age. Using a bootstrap method to account for uncertainty in model selection and fitting, we provide the first direct estimate of juvenile survival for this population. Our analyses indicate a high annual apparent survival for juveniles at between 0.87 (standard error (SE) 0.17, to age 1) and 0.95 (SE 0.05: ages 2–8). Individual identification by DNA profiling is an effective method for long-term demographic and genetic monitoring, particularly in animals that change identifiable features as they develop or experience tag loss over time.

Photo-identification as a technique for recognition of individual fish: a test with the freshwater armored catfish Rineloricaria aequalicuspis Reis & Cardoso, 2001 (Siluriformes: Loricariidae)

Abstract Photo-identification allows individual recognition of animal species based on natural marks, being an alternative to other more stressful artificial tagging/marking techniques. An increasing number of studies with different animal groups has shown that photo-identification can successfully be used in several situations, but its feasibility to study freshwater fishes is yet to be explored. We demonstrate the potential use of photo-identification for intraspecific recognition of individuals in the stream-dwelling loricariid Rineloricaria aequalicuspis . We tested photo-identification in laboratory and field conditions based on the interindividual variability in abdominal bony plates. Our test yielded high correct matches in both laboratory (100%) and field conditions (> 97%), comparable to other reliable techniques and to studies that successfully used photo-identification in other animals. In field conditions, the number of correct matches did not differ statistically between computer-assisted and naked-eye identification. However, the average time expended to conclude computer-assisted photo evaluations was about half of the time expended to conclude naked-eye evaluations. This result may be exacerbated when using database with large number of images. Our results indicate that photo-identification can be a feasible alternative technique to study freshwater fish species, allowing for a wider use of mark-recapture in ecological and behavioral studies.

Manta ray tourism management, precautionary strategies for a growing industry: a case study from the Ningaloo Marine Park, Western Australia

Localised population declines and increased pressure from fisheries have prompted the promotion of manta ray interaction tourism as a non-consumptive, yet economically attractive, alternative to the unsustainable harvesting of these animals. Unfortunately, however, wildlife tourism activities have the potential to adversely impact focal species. In order to be sustainable, operations must be managed to mitigate negative impacts. A preliminary assessment of reef manta ray, Manta alfredi, behaviour identified short-term behavioural responses during a third of tourism interactions in the Ningaloo Marine Park, Western Australia. Although it remains unknown whether these responses translate to biologically significant impacts on the population as a whole, it is proposed that the precautionary principle be used to guide management intervention in the absence of conclusive evidence of the magnitude of tourism impacts. The principle supports the implementation of precautionary strategies to protect species and their environment from harm, even when the extent of the harm is yet to be confirmed. An increase in the level of industry management is recommended, including the implementation of a licensing system and adherence of all operators to a mandatory code of conduct during manta ray interactions. Considering the well designed and precautionary-driven management program of the Ningaloo whale shark tourism industry operating within the same marine park, a management program with the same underlying principles and objectives is deemed to be an ideal framework to build a comprehensive management plan for the manta ray interaction industry.

Multi-Year Impacts of Ecotourism on Whale Shark (Rhincodon typus) Visitation at Ningaloo Reef, Western Australia

In-water viewing of sharks by tourists has become a popular and lucrative industry. There is some concern that interactions with tourists with ecotourism operations might harm sharks through disruption of behaviours. Here, we analysed five years of whale shark (Rhincodon typus) encounter data by an ecotourism industry at Ningaloo Reef, Western Australia, to assess the impact of ecotourism interactions on shark visitation, within the context of the biological and physical oceanography of the region. Our data base consisted of 2823 encounter records for 951 individual whale sharks collected by ecotourism operators between 2007 and 2011. We found that total encounters per whale shark and encounters per boat trip increased through time. On average, whale sharks re-encountered in subsequent years were encountered earlier, stayed longer and tended to be encountered more often within a season than sharks that were only encountered in a single year. Sequential comparisons between years did not show any patterns consistent with disturbance and the rate of departure of whale sharks from the aggregation was negatively correlated to the number of operator trips. Overall, our analysis of this multi-year data base found no evidence that interactions with tourists affected the likelihood of whale shark re-encounters and that instead, physical and biological environmental factors had a far greater influence on whale shark visitation rates. Our approach provides a template for assessing the effects of ecotourism interactions and environmental factors on the visitation patterns of marine megafauna over multiple years.

There and back again: a review of residency and return migrations in sharks, with implications for population structure and management

The overexploitation of sharks has become a global environmental issue in need of a comprehensive and multifaceted management response. Tracking studies are beginning to elucidate how shark movements shape the internal dynamics and structure of populations, which determine the most appropriate scale of these management efforts. Tracked sharks frequently either remain in a restricted geographic area for an extended period of time (residency) or return to a previously resided-in area after making long-distance movements (site fidelity). Genetic studies have shown that some individuals of certain species preferentially return to their exact birthplaces (natal philopatry) or birth regions (regional philopatry) for either parturition or mating, even though they make long-distance movements that would allow them to breed elsewhere. More than 80 peer-reviewed articles, constituting the majority of published shark tracking and population genetic studies, provide evidence of at least one of these behaviors in a combined 31 shark species from six of the eight extant orders. Residency, site fidelity, and philopatry can alone or in combination structure many coastal shark populations on finer geographic scales than expected based on their potential for dispersal. This information should therefore be used to scale and inform assessment, management, and conservation activities intended to restore depleted shark populations.

Running the gauntlet: regional movement patterns of Manta alfredi through a complex of parks and fisheries

Manta rays (Genus Manta) are economically important for fisheries and tourism in Indonesia. These species have been listed by the International Union for the Conservation of Nature Red List as Vulnerable to extinction; therefore, human exploitation of manta rays must be regulated. A better understanding of the habitat use and movement patterns of manta rays in Indonesia is needed in order to employ effective conservation measures. To gain better insight into the movements of Manta alfredi we used ‘Manta Matcher’, an online database with an integrated automated matching algorithm, to compare photographs from 2,604 encounters of M. alfredi collected by recreational divers and dive operators throughout Indonesia over a nine-year period. This photographic comparison revealed that manta rays migrated between regional sanctuaries such as Nusa Penida, the Gili Islands, and the Komodo National Park (up to 450 km straight-line distance). The areas between these sanctuaries are heavily fished and trafficked by ships, and when manta rays travel through these regions they risk being fished and injured by ship strikes. These long-range manta ray movements suggest connectivity between M. alfredi populations in neighboring islands and raise concerns about the future management of regional populations. It is recommended that a national conservation strategy be developed to protect the remaining populations in the country.

Monitoring the effects of tourism on whale shark Rhincodon typus behaviour in Mozambique

The whale shark Rhincodon typus is a popular focal species in the marine tourism industry. We analysed 689 encounters with at least 142 individual sharks during 2008–2010 to assess their behaviour in the presence of swimmers at Tofo Beach, Mozambique. Sharks varied in size (estimated 3.0–9.5 m total length) and the majority (74%) were males. The sharks displayed avoidance behaviours during 64.7% of encounters. Encounter duration decreased significantly, from 12 minutes 37 s with undisturbed sharks to 8 minutes 25 s when sharks expressed avoidance behaviours, indicating that interactions with tourists affected the sharks’ short-term behaviour. However, during the 2.5-year study period we found no trend in the mean encounter duration, the overall expression of avoidance behaviour or the likelihood of an individual shark exhibiting avoidance behaviours. Potential effects of tourism may be mitigated by the non-breeding status and transient behaviour of sharks at this aggregation site.

Population structure and residency patterns of whale sharks, Rhincodon typus, at a provisioning site in Cebu, Philippines

This study represents the first description of whale sharks, Rhincodon typus, occurring at a provisioning site in Oslob, Cebu, Philippines. Frequent observations of sharks are often difficult, even at tourism sites, giving rise to provisioning activities to attract them. The present study provides repeated longitudinal data at a site where daily provisioning activities took place, and whale sharks were present every day. A total of 158 individual whale sharks were photographically identified between Mar 2012 and Dec 2013, with 129 males (82%), 19 females (12%) and 10 (6%) of undetermined sex. Mean estimated total length was 5.5 m (±1.3 m S.D.). Twenty individuals were measured with laser photogrammetry to validate researchers’ estimated sizes, yielding a good correlation (r² = 0.83). Fifty-four (34%) individuals were observed being hand-fed by local fishermen (provisioned), through in-water behavioural observations. Maximum likelihood methods were used to model mean residency time of 44.9 days (±20.6 days S.E.) for provisioned R. typus contrasting with 22.4 days (±8.9 days S.E.) for non-provisioned individuals. Propeller scars were observed in 47% of the animals. A mean of 12.7 (±4.3 S.D.) R. typus were present in the survey area daily, with a maximum of 26 individuals (Aug 10 2013) and a minimum of 2 (Dec 6 2012). Twelve (8%) individuals were seen on at least 50% of survey days (n = 621), with a maximum residency of 572 days for one individual (P-396). Twenty four individuals were photographically identified across regional hotsposts, highlighting the species’ migratory nature and distribution. Extended residency and differences in lagged identification rates suggest behavioural modification on provisioned individuals, underlying the necessity for proper management of this tourism activity.

A re-evaluation of the size of the white shark (Carcharodon carcharias) population off California, USA

White sharks are highly migratory and segregate by sex, age and size. Unlike marine mammals, they neither surface to breathe nor frequent haul-out sites, hindering generation of abundance data required to estimate population size. A recent tag-recapture study used photographic identifications of white sharks at two aggregation sites to estimate abundance in “central California” at 219 mature and sub-adult individuals. They concluded this represented approximately one-half of the total abundance of mature and sub-adult sharks in the entire eastern North Pacific Ocean (ENP). This low estimate generated great concern within the conservation community, prompting petitions for governmental endangered species designations. We critically examine that study and find violations of model assumptions that, when considered in total, lead to population underestimates. We also use a Bayesian mixture model to demonstrate that the inclusion of transient sharks, characteristic of white shark aggregation sites, would substantially increase abundance estimates for the adults and sub-adults in the surveyed sub-population. Using a dataset obtained from the same sampling locations and widely accepted demographic methodology, our analysis indicates a minimum all-life stages population size of >2000 individuals in the California subpopulation is required to account for the number and size range of individual sharks observed at the two sampled sites. Even accounting for methodological and conceptual biases, an extrapolation of these data to estimate the white shark population size throughout the ENP is inappropriate. The true ENP white shark population size is likely several-fold greater as both our study and the original published estimate exclude non-aggregating sharks and those that independently aggregate at other important ENP sites. Accurately estimating the central California and ENP white shark population size requires methodologies that account for biases introduced by sampling a limited number of sites and that account for all life history stages across the species' range of habitats.