INDIVIDUAL IDENTIFICATION: FISH
Arzoumanian Z., Holmberg J., Norman B. (2005): An astronomical pattern‐matching algorithm for computer‐aided identification of whale sharks Rhincodon typus. Journal of Applied Ecology 42: 999-1011.
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The formulation of conservation policy relies heavily on demographic, biological and ecological knowledge that is often elusive for threatened species. Essential estimates of abundance, survival and life‐history parameters are accessible through mark and recapture studies given a sufficiently large sample. Photographic identification of individuals is an established mark and recapture technique, but its full potential has rarely been exploited because of the unmanageable task of making visual identifications in large data sets. We describe a novel technique for identifying individual whale sharks Rhincodon typus through numerical pattern matching of their natural surface ‘spot’ colourations. Together with scarring and other markers, spot patterns captured in photographs of whale shark flanks have been used, in the past, to make identifications by eye. We have automated this process by adapting a computer algorithm originally developed in astronomy for the comparison of star patterns in images of the night sky. In tests using a set of previously identified shark images, our method correctly matched pairs exhibiting the same pattern in more than 90% of cases. From a larger library of previously unidentified images, it has to date produced more than 100 new matches. Our technique is robust in that the incidence of false positives is low, while failure to match images of the same shark is predominantly attributable to foreshortening in photographs obtained at oblique angles of more than 30°. We describe our implementation of the pattern‐matching algorithm, estimates of its efficacy, its incorporation into the new ECOCEAN Whale Shark Photo‐identification Library, and prospects for its further refinement. We also comment on the biological and conservation implications of the capability of identifying individual sharks across wide geographical and temporal spans. An automated photo‐identification technique has been developed that allows for efficient ‘virtual tagging’ of spotted animals. The pattern‐matching software has been implemented within a Web‐based library created for the management of generic encounter photographs and derived data. The combined capabilities have demonstrated the reliability of whale shark spot patterns for long‐term identifications, and promise new ecological insights. Extension of the technique to other species is anticipated, with attendant benefits to management and conservation through improved understanding of life histories, population trends and migration routes, as well as ecological factors such as exploitation impact and the effectiveness of wildlife reserves.
Meekan M. G., Bradshaw C. J., Press M., McLean C., Richards A., Quasnichka S., Taylor J. G. (2006): Population size and structure of whale sharks Rhincodon typus at Ningaloo Reef, Western Australia. Marine Ecology Progress Series 319: 275-285.
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We used photo-identification to produce estimates of population size and structure of whale sharks Rhincodon typus at Ningaloo Reef, Western Australia. We analysed photographs of whale sharks taken from 1992 to 2004. A combination of spot and stripe patterns behind the last gill slit and forward of the dorsal fin (lateral view), and distinctive scars and marks on the body and fins were useful for identifying individual sharks. These patterns appeared to be unique to individuals and distinctive markings could be recognized on some sharks for more than a decade. From 581 photographs, 159 individuals were identified. Of these, 74% were male, 16% were female and 10% were of indeterminate gender. Photographed sharks ranged in estimated size from 3 to 10 m total length (TL). The size distribution of sharks was bimodal with a large peak at 8 m and a smaller peak at 6 m TL. Sixty individuals were resighted during the study. Of these, 46 were resighted at different times during the same year (sometimes on multiple occasions) up to 4 mo after they were initially photographed, and 33 were resighted (4 on >2 occasions) in different years. The interval between inter-annual resightings was typically 1 to 3 yr; however, 2 sharks were resighted after a period of 12 yr. We estimated the super population of whale sharks that visit Ningaloo Reef to consist of approximately 300 to 500 individuals (95% confidence interval) based on closed population models, or 320 to 440 based on Jolly-Seber open-population models. Our study shows that photo-identification offers a practical, non-invasive and non-destructive means to obtain data on the population size and demography of whale sharks.
Chapple T. K., Jorgensen S. J., Anderson S. D., Kanive P. E., Klimley A. P., Botsford L. W., Block B. A. (2011): A first estimate of white shark, Carcharodon carcharias, abundance off Central California. Biology Letters 7: 581-583.
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The decline of sharks in the global oceans underscores the need for careful assessment and monitoring of remaining populations. The northeastern Pacific is the home range for a genetically distinct clade of white sharks (Carcharodon carcharias). Little is known about the conservation status of this demographically isolated population, concentrated seasonally at two discrete aggregation sites: Central California (CCA) and Guadalupe Island, Mexico. We used photo-identification of dorsal fins in a sequential Bayesian mark–recapture algorithm to estimate white shark abundance off CCA. We collected 321 photographs identifying 130 unique individuals, and estimated the abundance off CCA to be 219 mature and sub-adult individuals ((130, 275) 95% credible intervals), substantially smaller than populations of other large marine predators. Our methods can be readily expanded to estimate shark population abundance at other locations, and over time, to monitor the status, population trends and protection needs of these globally distributed predators.
Martin‐Smith K. M. (2011): Photo‐identification of individual weedy seadragons Phyllopteryx taeniolatus and its application in estimating population dynamics. Journal of Fish Biology 78: 1757-1768.
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Forty‐three individual adult weedy seadragons Phyllopteryx taeniolatus were identified from underwater images using patterns of spots and blotches on the lateral surface of the abdomen. These patterns were unique and did not change over the 18 month course of the study and could therefore be used to identify individuals when estimating population variables using non‐invasive capture–mark–recapture and accumulation curve methods. Two similar neighbouring sites in southern Tasmania showed considerable differences in their estimated populations of P. taeniolatus. Estimated annual survival was >80% at one site suggesting that P. taeniolatus may be considerably longer lived than other syngnathids with a maximum life span in excess of 10 years. Males incubating embryos were observed from October to March and at least two clutches could be borne during this period. This technique of photo‐identification could provide a cheap and effective way to monitor populations of this iconic species across its range, particularly in conjunction with optimized pattern‐recognition software.
Merz J. E., Skvorc P., Sogard S. M., Watry C., Blankenship S. M., Van Nieuwenhuyse E. E. (2012): Onset of melanophore patterns in the head region of Chinook Salmon: a natural marker for the reidentification of individual fish. North American Journal of Fisheries Management 32: 806-816.
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We used pattern recognition algorithms and image processing to identify individual Chinook salmon Oncorhynchus tshawytscha. Using melanophore spot patterns located on the dorsal head region, algorithms ranked all database images against each other. We coupled this technology with a graphical user interface to visually confirm or reject top-ranked algorithm results and tested this process on 295 juvenile Chinook salmon in seven photo sessions over a 251-d period. Juveniles began developing spots, identifiable in photo images, between 167 and 197 d after conception (52.7-mm fork length [FL]). Unique spot patterns appeared 197–232 d from conception, beginning at approximately 104-mm FL. Of 254 fish surviving the experimental period, 106 (42%) demonstrated identifiable patterns, 102 (40%) developed spots but patterns were insufficient for identification, and 46 (18%) exhibited a complete lack of spots. Spot patterns continued developing on individual fish by study end. On average, fish that developed recognizable spot patterns did so at approximately 140-mm FL. Once they did, reidentification was 100% correct in up to four subsequent trials. Patterns remained identifiable even after a 25–32% size increase over a 55-d period and as juveniles went through smoltification. Although patterns occurred at sizes typically larger than salmon observed at some California Central Valley monitoring locations, this technique provides a potentially valuable, noninvasive method of identifying individual salmon during emigration. Improved image collection techniques and use of body areas exhibiting identifiable patterns at earlier developmental stages may increase fish available for pattern identification. These results demonstrate the indexing of a large database using pattern recognition algorithms for Chinook salmon. The utility of such an approach may be valuable for addressing specific biological questions associated with mass-produced (wild and hatchery), migratory salmonids, especially as individuals develop, grow, and move through the various habitats available to them.
Huntingford F. A., Borçato F. L., Mesquita F. O. (2013): Identifying individual common carp Cyprinus carpio using scale pattern. Journal of Fish Biology 83: 1453-1458.
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Volunteers were able to match photographs of the same common carp Cyprinus carpio taken on two occasions. Images were identified correctly on 95.76% of occasions. Thus, scale patterns can be used for non‐invasive identification of C. carpio over a period of time.
Town C., Marshall A., Sethasathien N. (2013): Manta Matcher: automated photographic identification of manta rays using keypoint features. Ecology and Evolution 3: 1902-1914.
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For species which bear unique markings, such as natural spot patterning, field work has become increasingly more reliant on visual identification to recognize and catalog particular specimens or to monitor individuals within populations. While many species of interest exhibit characteristic markings that in principle allow individuals to be identified from photographs, scientists are often faced with the task of matching observations against databases of hundreds or thousands of images. We present a novel technique for automated identification of manta rays (Manta alfredi and Manta birostris) by means of a pattern‐matching algorithm applied to images of their ventral surface area. Automated visual identification has recently been developed for several species. However, such methods are typically limited to animals that can be photographed above water, or whose markings exhibit high contrast and appear in regular constellations. While manta rays bear natural patterning across their ventral surface, these patterns vary greatly in their size, shape, contrast, and spatial distribution. Our method is the first to have proven successful at achieving high matching accuracies on a large corpus of manta ray images taken under challenging underwater conditions. Our method is based on automated extraction and matching of keypoint features using the Scale‐Invariant Feature Transform (SIFT) algorithm. In order to cope with the considerable variation in quality of underwater photographs, we also incorporate preprocessing and image enhancement steps. Furthermore, we use a novel pattern‐matching approach that results in better accuracy than the standard SIFT approach and other alternative methods. We present quantitative evaluation results on a data set of 720 images of manta rays taken under widely different conditions. We describe a novel automated pattern representation and matching method that can be used to identify individual manta rays from photographs. The method has been incorporated into a website (mantamatcher.org) which will serve as a global resource for ecological and conservation research. It will allow researchers to manage and track sightings data to establish important life‐history parameters as well as determine other ecological data such as abundance, range, movement patterns, and structure of manta ray populations across the world.
Towner A. V., Wcisel M. A., Reisinger R. R., Edwards D., Jewell O. J. (2013): Gauging the threat: the first population estimate for white sharks in South Africa using photo identification and automated software. Plos One 8: e66035.
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South Africa is reputed to host the world’s largest remaining population of white sharks, yet no studies have accurately determined a population estimate based on mark-recapture of live individuals. We used dorsal fin photographs (fin IDs) to identify white sharks in Gansbaai, South Africa, from January 2007 – December 2011. We used the computer programme DARWIN to catalogue and match fin IDs of individuals; this is the first study to successfully use the software for white shark identification. The programme performed well despite a number of individual fins showing drastic changes in dorsal fin shape over time. Of 1682 fin IDs used, 532 unique individuals were identified. We estimated population size using the open-population POPAN parameterisation in Program MARK, which estimated the superpopulation size at 908 (95% confidence interval 808–1008). This estimated population size is considerably larger than those described at other aggregation areas of the species and is comparable to a previous South African population estimate conducted 16 years prior. Our assessment suggests the species has not made a marked recovery since being nationally protected in 1991. As such, additional international protection may prove vital for the long-term conservation of this threatened species.
Correia M., Palma J., Koldewey H., Andrade J. P. (2014): The use of a non‐invasive tool for capture–recapture studies on a seahorse Hippocampus guttulatus population. Journal of Fish Biology 84: 872-884.
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In this study, the spot pattern in Hippocampus guttulatus was analysed using a computer programme algorithm that allowed individual comparison. This methodology was first tested in a controlled environment using 51 adult and 55 juvenile H. guttulatus. Positive matches were obtained in 86.3 and 83.6% of the adults and juveniles, respectively. In a second experiment, monthly surveys were carried out in five selected locations in the Ria Formosa Lagoon, south Portugal, over the course of a year and a total of 980 photographs were analysed. Photographed H. guttulatus were re‐sighted one to nine times during the course of the survey period with an overall re‐sight record of over 30%. Photo‐identification was therefore shown to be a useful tool for non‐invasive mark–recapture studies that can be successfully used to survey the population abundance of H. guttulatus aged 6 months or older in consecutive years. This could be of great value when considering the assessment of H. guttulatus populations and understanding changes over time.
Monteiro N. M., Silva R. M., Cunha M., Antunes A., Jones A. G., Vieira M. N. (2014): Validating the use of colouration patterns for individual recognition in the worm pipefish using a novel set of microsatellite markers. Molecular Ecology Resources 14: 150-156.
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In studies of behaviour, ecology and evolution, identification of individual organisms can be an invaluable tool, capable of unravelling otherwise cryptic information regarding group structure, movement patterns, population size and mating strategies. The use of natural markings is arguably the least invasive method for identification. However, to be truly useful natural markings must be sufficiently variable to allow for unique identification, while being stable enough to permit long‐term studies. Non‐invasive marking techniques are especially important in fishes of the Family Syngnathidae (pipefishes, seahorses and seadragons), as many of these taxa are of conservation concern or used extensively in studies of sexual selection. Here, we assessed the reliability of natural markings as a character for individual identification in a wild population of Nerophis lumbriciformis by comparing results from natural markings to individual genetic assignments based on eight novel microsatellite loci. We also established a minimally invasive method based on epithelial cell swabbing to sample DNA. All pipefish used in the validation of natural markings, independently of sex or time between recaptures, were individually recognized through facial colouration patterns. Their identities were verified by the observation of the same multilocus genotype at every sampling event for each individual that was identified on the basis of natural markings. Successful recaptures of previously swabbed pipefish indicated that this process probably did not induce an elevated rate of mortality. Also, the recapture of newly pregnant males showed that swabbing did not affect reproductive behaviour.
Hirsch P. E., Eckmann R. (2015): Individual identification of Eurasian perch Perca fluviatilis by means of their stripe patterns. Limnologica 54: 1-4.
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In this study we show that the number, position and shape of stripes were sufficiently unique to demonstrate that juvenile Eurasian perch Perca fluviatilis can be individually identified based on their stripe patterns. The stripe patterns in perch and also other species may thus be used in experiments as an alternative to conventional marking techniques that frequently cause stress to the fish.
Dala-Corte R. B., Moschetta J. B., Becker F. G. (2016): Photo-identification as a technique for recognition of individual fish: a test with the freshwater armored catfish Rineloricaria aequalicuspis Reis & Cardoso, 2001 (Siluriformes: Loricariidae). Neotropical Ichthyology 14: e150074.
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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.
González‐Ramos M. S., Santos‐Moreno A., Rosas‐Alquicira E. F., Fuentes‐Mascorro G. (2017): Validation of photo‐identification as a mark–recapture method in the spotted eagle ray Aetobatus narinari. Journal of Fish Biology 90: 1021-1030.
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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%).
Cerutti-Pereyra F., Bassos-Hull K., Arvizu-Torres X., Wilkinson K. A., García-Carrillo I., Perez-Jimenez J. C., Hueter R. E. (2018): Observations of spotted eagle rays (Aetobatus narinari) in the Mexican Caribbean using photo-ID. Environmental Biology of Fishes 101: 237-244.
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The spotted eagle ray is an iconic species for the recreational diving and snorkeling industry in the Mexican Caribbean although it is heavily fished in nearby waters of the southern Gulf of Mexico and in Cuba. This species is listed on the IUCN Red List of Threatened Species as ‘Near Threatened’ with a decreasing population trend. Few studies have reported on the populations and migrations of spotted eagle rays in the Atlantic Ocean, Gulf of Mexico and Caribbean Sea, and no regulations currently exist for the fishery or tourism industries in Mexico. Photographic identification techniques were used to produce the first photo-ID catalog of spotted eagle rays in the Mexican Caribbean using 1096 photographs submitted by researchers and divers between 2003 and 2016. In total, 282 individual spotted eagle rays were identified through photographs at nine sites across the Mexican Caribbean. Of these individuals, 14.9% were resighted at least once at the same site. The longest period between re-sighting events was 342 days. This is the first study evaluating free-swimming spotted eagle rays in the Mexican Caribbean and highlights the value of using photo-ID for monitoring populations of this ray. Because a targeted subsistence fishery for spotted eagle rays exists in nearby waters, management efforts to monitor and prevent overexploitation at key diving locations should be a priority for local government agencies.
Navarro J., Perezgrueso A., Barría C., Coll M. (2018): Photo‐identification as a tool to study small‐spotted catshark Scyliorhinus canicula. Journal of Fish Biology 92: 1657-1662.
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Photo-identification (photo-ID) was tested as a means to identify individual small-spotted catsharks Scyliorhinus canicula. The spotting pattern of the caudal region of S. canicula was used for the tests and revealed that photo-ID is an efficient method to identify individuals. Photo-ID is logistically simple, making it a potential alternative to traditional tagging to provide information on the distribution patterns and population dynamics of S. canicula and related species.
Hook S. A., McMurray C., Ripley D. M., Allen N., Moritz T., Grunow B., Shiels H. A. (2019): Recognition software successfully aids the identification of individual small‐spotted catsharks Scyliorhinus canicula during their first year of life. Journal of Fish Biology 95: 1465-1470.
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Eighteen captive small‐spotted catsharks Scyliorhinus canicula were successfully identified from hatching to 1 year of age using the free computer recognition software, I3S 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 I3S 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.
Foldvik A., Jakobsen F., Ulvan E. M. (2020): Individual recognition of Atlantic Salmon using iris biometry. Copeia 108: 767-771.
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Traditional tagging methods for fishes can have issues relating to both animal welfare and economic costs. Biometric data such as iris patterns can be captured via digital cameras, which allows for non-invasive tagging and inexpensive and rapid analysis. The purpose of this study was to investigate if the iris of Atlantic Salmon (Salmo salar) is a suitable biometric template for long-term identification of individuals. Atlantic Salmon were individually tagged in the body cavity using PIT tags at the juvenile pre-smolt stage, and the left eye was photographed six times over a 533-day period. Changes in iris stability were assessed both qualitatively and using iris-recognition software. Identification of individual Atlantic Salmon using the iris was not successful over the entire period, as the iris pattern changed significantly with time. Over a shorter time period (four months) with frequent samplings, iris software was able to correctly identify individual fish. The results show that iris identification has potential to replace other methods for Atlantic Salmon over short timeframes.
Kristensen E., Sand-Jensen K., Martinsen K. T., Madsen-Østerbye M., Kragh T. (2020): Fingerprinting pike: The use of image recognition to identify individual pikes. Fisheries Research 229: 105622.
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It is difficult to determine the individual behaviour, growth, and survival of large predatory freshwater fish without stressing or even killing them. In this study, we tested the ability of an image recognition program to identify individual recaptured pike (Esox lucius) based on skin pattern. We and local anglers caught 209 pike individuals, including 45 recaptures, over the course of 1.5 years. The software correctly identified the image of all recaptured fish as already present in the database. Based on recaptures, we predicted a population of 560 pike in the lake and showed a much more comprehensive size structure than seen using standardized gillnet sampling which only yielded four pike. Angling and photographic identification involving reporting by citizen-scientists provided valuable temporal data in a non-invasive manner compared to traditional sampling. This methodology is based on freeware software and removes the need for any tagging equipment. It can potentially be used on other freshwater fish species and larger populations if the skin pattern is distinctive. However, it relies on the willingness of anglers to report their catches.
Cisar P., Bekkozhayeva D., Movchan O., Saberioon M., Schraml R. (2021): Computer vision based individual fish identification using skin dot pattern. Scientific Reports 11: 16904.
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Precision fish farming is an emerging concept in aquaculture research and industry, which combines new technologies and data processing methods to enable data-based decision making in fish farming. The concept is based on the automated monitoring of fish, infrastructure, and the environment ideally by contactless methods. The identification of individual fish of the same species within the cultivated group is critical for individualized treatment, biomass estimation and fish state determination. A few studies have shown that fish body patterns can be used for individual identification, but no system for the automation of this exists. We introduced a methodology for fully automatic Atlantic salmon (Salmo salar) individual identification according to the dot patterns on the skin. The method was tested for 328 individuals, with identification accuracy of 100%. We also studied the long-term stability of the patterns (aging) for individual identification over a period of 6 months. The identification accuracy was 100% for 30 fish (out of water images). The methodology can be adapted to any fish species with dot skin patterns. We proved that the methodology can be used as a non-invasive substitute for invasive fish tagging. The non-invasive fish identification opens new possibilities to maintain the fish individually and not as a fish school which is impossible with current invasive fish tagging.
Correia M., Antunes D., Andrade J. P., Palma J. (2021): A crown for each monarch: a distinguishable pattern using photo‐identification. Environmental Biology of Fishes 104: 195-201.
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Photo-identification has been proven to be a successful individual recognition tool in seahorse species (e.g., long-snout seahorse Hippocampus reidi (Ginsburg, 1933) and long-snouted seahorse Hippocampus guttulatus (Cuvier, 1829)). Its use was deemed valuable for the assessment of wild populations and to understand variations in abundance over time when capture-recapture methods are needed. In this study, a computer software with a pattern recognition algorithm (I3S® Contour 3.0) was used for individual identification of short-snouted seahorses Hippocampus hippocampus (Linnaeus 1758) in the laboratory. Using this methodology, differences in the shape of each individual’s coronet were tested as a unique and distinguishable characteristic. Two different contours were used as reference and tested to assess the effectiveness of this method in individual identification. A total of 94 captive-bred H. hippocampus, 45 adults (> 1 year old) and 49 young adults (4 months old), were tested. Positive matches were obtained in 55.1 % of the young adults and 84.4 % of the adults using contour 1; and in 77.6 % and 97.8 % for young adults and adults, respectively, using contour 2. All un-matched photos were later successfully matched by visual comparison, using additional traits (e.g., spot patterns) and gender. This methodology yielded very promising results and could be further used in wild individuals to allow population size estimates.
Haxton T. (2021): Use of unique brook trout spot patterns over a short duration for a mark-recapture study. Environmental Biology of Fishes 104: 1391-1399.
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Identifying individuals by their natural body markings is an excellent surrogate for artificial tags. Photo identification has been primarily tested in oceanic species but has not been extensively used on freshwater fish. Brook trout are renowned for their lateral spot patterns. In this study, Interactive Individual Identification System was used to digitize and assess spot pattern uniqueness for identifying individual brook trout within a population for a short-term mark-recapture study. Brook trout were sampled over multiple days in Harper Creek and captured 315 specimens. Photo images were collected of their left lateral side and digitized. Based on photo identification, 263 unique brook trout were sampled. Additionally, there were 36 recaptures: 29 sampled twice, six sampled three times, and one sampled four times enabling a population estimate to be derived. In 2019, Harper Creek supported a spawning population of 514.4 (408–659; 95% CIs) brook trout. Ninety-four unique brook trout were sampled from a geographically distinct population of which none of the spot patterns matched the Harper Creek population. Spot patterns were distinct between lateral sides of an individual fish. Spot patterns on brook trout are unique and can be used to as a non-invasive means to identify individual at least in short-term projects.
Pedersen M., Mohammed A. (2021): Photo identification of individual Salmo trutta based on deep learning. Applied Sciences 11: 9039.
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Individual fish identification and recognition is an important step in the conservation and management of fisheries. One of most frequently used methods involves capturing and tagging fish. However, these processes have been reported to cause tissue damage, premature tag loss, and decreased swimming capacity. More recently, marine video recordings have been extensively used for monitoring fish populations. However, these require visual inspection to identify individual fish. In this work, we proposed an automatic method for the identification of individual brown trouts, Salmo trutta. We developed a deep convolutional architecture for this purpose. Specifically, given two fish images, multi-scale convolutional features were extracted to capture low-level features and high-level semantic components for embedding space representation. The extracted features were compared at each scale for capturing representation for individual fish identification. The method was evaluated on a dataset called NINA204 based on 204 videos of brown trout and on a dataset TROUT39 containing 39 brown trouts in 288 frames. The identification method distinguished individual fish with 94.6% precision and 74.3% recall on a NINA204 video sequence with significant appearance and shape variation. The identification method takes individual fish and is able to distinguish them with precision and recall percentages of 94.6% and 74.3% on NINA204 for a video sequence with significant appearance and shape variation.
Bekkozhayeva D., Cisar P. (2022): Image-based automatic individual identification of fish without obvious patterns on the body (scale pattern). Applied Sciences 12: 5401.
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The precision fish farming concept has been widely investigated in research and is highly desirable in aquaculture as it creates opportunities for precisely controlling and monitoring fish cultivation processes and increasing fish welfare. The automatic identification of individual fish could be one of the keys to enabling individual fish treatment. In a previous study, we already demonstrated that the visible patterns on a fish’s body can be used for the non-invasive individual identification of fishes from the same species (with obvious skin patterns, such as salmonids) over long-term periods. The aim of this study was to verify the possibility of using fully-automatic non-invasive photo-identification of individual fish based on natural marks on the fish’s body without any obvious skin patterns. This approach is an alternative to stressful invasive tagging and marking techniques. Scale patterns on the body and operculum, as well as lateral line shapes, were used as discriminative features for the identification of individuals in a closed group of fish. We used two fish species: the European seabass Dicentrarchus labrax and the common carp Cyprinus carpio. The identification method was tested on four experimental data sets for each fish species: two separate short-term data sets (pattern variability test) and two long-term data sets (pattern stability test) for European seabass (300 individual fish) and common carp (32 individual fish). The accuracy of classification was 100% for both fish species in both the short-term and long-term experiments. According to these results, the methods used for automatic non-invasive image-based individual-fish identification can also be used for fish species without obvious skin patterns.
Germanov E. S., Pierce S. J., Marshall A. D., Hendrawan I. G., Kefi A., Bejder L., Loneragan N. (2022): Residency, movement patterns, behavior and demographics of reef manta rays in Komodo National Park. PeerJ 10: e13302.
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The reef manta ray (Mobula alfredi) is a globally threatened species and an iconic tourist attraction for visitors to Indonesia’s Komodo National Park (NP). In 2013, manta ray fishing was banned in Komodo NP and its surroundings, preceding the nationwide manta ray protection in 2014. Over a decade ago, a previous acoustic telemetry study demonstrated that reef manta rays had high fidelity to sites within the park, while more recent photo-identification data indicated that some individuals move up to 450 km elsewhere. Characterization of manta ray demographics, behavior, and a focused assessment on site use of popular tourism locations within the park is vital to assist the Komodo NP Management Authority formulate appropriate manta ray conservation and management policies. This study uses a long-term library (MantaMatcher.org) of photo-identification data collected by researchers and citizen scientists to investigate manta ray demographics and habitat use within the park at four sites frequented by tour operators: Cauldron, Karang Makassar, Mawan, and Manta Alley. Residency and movements of manta rays were investigated with maximum likelihood analyses and Markov movement models. A total of 1,085 individual manta rays were identified from photographs dating from 2013 to 2018. In general, individual manta rays displayed a higher affinity to specific sites than others. The highest re-sighting probabilities came from the remote southern site, Manta Alley. Karang Makassar and Mawan are only ~5 km apart; however, manta rays displayed distinct site affinities. Exchange of individuals between Manta Alley and the two central sites (~35.5 km apart) occurred, particularly seasonally. More manta rays were recorded traveling from the south to the central area than vice versa. Female manta rays were more mobile than males. Similar demographic groups used Karang Makassar, Mawan, and Manta Alley for foraging, cleaning, cruising, or courtship activities. Conversely, a higher proportion of immature manta rays used the northern site, Cauldron, where foraging was commonly observed. Fishing gear-related injuries were noted on 56 individuals (~5%), and predatory injuries were present on 32 individuals (~3%). Tourism within the park increased from 2014 to 2017, with 34% more dive boats per survey at Karang Makassar and Mawan. The Komodo NP contains several distinct critical habitats for manta rays that encompass all demographics and accommodate seasonal manta ray movements. While the present study has not examined population trends, it does provide foundational data for such work. Continued research into manta ray abundance, long-range movements, and identifying and protecting other critical aggregation areas within the region is integral to securing the species’ recovery. We provide management recommendations to limit undue pressure on manta rays and their critical habitats from tourism.
Harty K., Guerrero M., Knochel A. M., Stevens G. M., Marshall A., Burgess K., Stewart J. D. (2022): Demographics and dynamics of the world’s largest known population of oceanic manta rays Mobula birostris in coastal Ecuador. Marine Ecology Progress Series 700: 145-159.
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Information on the life history and demographics of oceanic manta rays Mobula birostris remains scarce. Using photo-ID data, we describe the demographic structure, population size, and possible environmental drivers of the seasonal occurrence of M. birostris at Isla de la Plata and Bajo Copé, Ecuador. We identified a total of 2803 individuals from 3322 encounters over a period of 14 yr (2005-2018). The population sampled at these sites was significantly biased towards males (sex ratio 1F:1.67M) and only 12.9% of individuals were resighted. We used mark-resight models to estimate demographic parameters of the population, including superpopulation size, survival probability, entry/recruitment probability, and detection probability. We also evaluated how these parameters were related to environmental predictors, such as El Niño-Southern Oscillation (ENSO), sea surface temperature (SST), and chlorophyll a (chl a). Mark-resight analyses indicated that SST, chl a, time, and sex, but not ENSO, were important predictors of estimated population parameters. Entry probability peaked in 2012, which coincided with the lowest SST and highest chl a concentrations. The best-fit mark-resight model estimated a superpopulation size of 22316 individuals, with annual estimated abundances of 949-7650 females and 5226-9340 males. Localised sampling of this highly mobile species limits the interpretations of mark-resight analyses, but provides lower bounds for total abundance that indicate the population of M. birostris in coastal Ecuador and Peru is likely the largest in the world.
Setyawan E., Stevenson B. C., Erdmann M. V., Hasan A. W., Sianipar A. B., Mofu I., Putra M. I., Izuan M., Ambafen O., Fewster R. M., Aldridge-Sutton R., Mambrasar R., Constantine R. (2022): Population estimates of photo-identified individuals using a modified POPAN model reveal that Raja Ampat’s reef manta rays are thriving. Frontiers in Marine Science 9: 1014791.
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The 6.7-million-hectare Raja Ampat archipelago is home to Indonesia’s largest reef manta ray (Mobula alfredi) population and a representative network of nine marine protected areas (MPAs). However, the population dynamics of M. alfredi in the region are still largely unknown. Using our photo-identification database, we fitted modified POPAN mark-recapture models with transience and per capita recruitment parameters to estimate key demographic characteristics of M. alfredi from two of Raja Ampat’s largest MPAs: Dampier Strait and South East (SE) Misool. A total of 1,041 unique individuals were photo-identified over an 11-year period (2009–2019) from Dampier Strait (n = 515) and SE Misool (n = 536). In our models, apparent survival probabilities and per capita recruitment rates were strongly linked with El Niño–Southern Oscillation (ENSO) events. Our models also estimated high apparent survival probabilities and significant increases in (sub)population sizes in both MPAs over a decade. In Dampier Strait, the estimated population size increased significantly (p = 0.018) from 226 (95% CI: 161, 283) to 317 (280, 355) individuals. Likewise, the estimated population size in SE Misool increased significantly (p = 0.008) from 210 (137, 308) to 511 (393, 618) individuals. Regardless of variation in the percentage change in population size between years throughout the study, the estimated overall population change shows a compound growth of 3.9% (0.7, 8.6) per annum in Dampier Strait and 10.7% (4.3, 16.1) per annum in SE Misool. Despite the global decline in oceanic sharks and rays due to fishing pressure in the last five decades, our study demonstrates the positive impact of a suite of long-term conservation efforts, coupled with the influence of ENSO events, on increasing M. alfredi abundance in Raja Ampat MPAs. Our study also underscores the importance of long-term monitoring to evaluate the effectiveness of conservation management measures on manta ray populations. Our modification of the standard POPAN model by incorporating per capita recruitment and transience parameters represents an important advance in mark-recapture modelling that should prove useful when examining other manta ray populations and other highly migratory species that are likely to have a substantial percentage of transient individuals.
Conan A., Dennis M. M., Gilbert K., Lenain E., Bruns S., Henderson A. C. (2023): Occurrence of the endangered whitespotted eagle ray Aetobatus narinari around the Lesser Antilles island of Saint Kitts: a photo-identification study. Environmental Biology of Fishes 106: 1529-1538.
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The extinction risk of the whitespotted eagle ray Aetobatus narinari was recently elevated from near-threatened to endangered by the International Union for the Conservation of Nature. However, many aspects of its basic ecology remain poorly understood, hampering efforts to develop meaningful conservation strategies. In this photo-identification study, the spatial and temporal occurrence of A. narinari around the island of St. Kitts was assessed across multiple years, with a view to informing marine conservation efforts in St. Kitts and Nevis. Seventy-four individual rays were identified during the study, of which 46 were encountered on more than one occasion. The median time at liberty for re-encountered animals was 225 days, with some animals encountered across years. These re-encounters confirmed that the animals utilise multiple sites and are capable of extensive local movements. Taken together, the results of this study suggest that A. narinari in the waters around St. Kitts and Nevis would benefit from local-scale management and conservation measures.
Nyegaard, M., Karmy, J., McBride, L., Thys, T. M., Welly, M., & Djohani, R. (2023). Rapid physiological colouration change is a challenge-but not a hindrance-to successful photo identification of giant sunfish (Mola alexandrini, Molidae). Frontiers in Marine Science 10: 1179467.
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Photo ID is a common tool in ecology, but has not previously been attempted for the ocean sunfishes (Mola spp., Molidae; ‘molids’). The technique, based on body patterns, could potentially be informative for studying the seasonal occurrence of giant sunfish (Mola alexandrini) on the Bali reefs (Indonesia), where this species is an important drawcard for the local SCUBA diving tourism. However, molids are capable of rapid physiological colouration change, which may complicate the application of the method. Our study aimed to determine if photo ID is nevertheless achievable and informative. To test this, we created the citizen-science platform ‘Match My Mola’ for crowd-sourcing imagery (photos and video) of M. alexandrini in Bali, and undertook trial matching (n=1,098 submissions). The submitted imagery revealed a wide range of pattern clarity, from fish with no pattern to bold displays. Video confirmed physiological colouration change can occur in seconds in this species from low to high contrast, and cause individuals to look very different between moments. However, individual patterns appear to be stable although at least some parts can become inconspicuous during low contrast displays. Despite of this, photo ID is possible, including in some instances, where only partial patterns are visible on one image compared with another. However, true negatives (confirming two fish are not the same) can be challenging. Most identified matches were of fish photographed by different divers on the same day. Only a small number (n=9) were found with resighting durations ≥1 day (1 – 2,652 days). These matches demonstrate that at least some individuals return to the same reefs both within and between seasons, with the resighting duration of 7.2 years constituting the longest known example of molid site fidelity. Comparing body morphology between resightings of > 1 year (n=6) revealed limited indications of growth, contradicting the current understanding of rapid growth in captive molids (Mola mola), and highlighting the knowledge gap regarding growth in the wild. Continued photo ID in the Bali area could provide valuable complementary information to future growth studies using other methods as well as provide further insights into molid site fidelity.