INDIVIDUAL IDENTIFICATION: AMPHIBIANS

FROGS AND TOADS

Kenyon N., Phillott A. D., Alford R. A. (2009): Evaluation of the photographic identification method (PIM) as a tool to identify adult Litoria genimaculata (Anura: Hylidae). Herpetological Conservation and Biology 4: 403-410.
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Marking anurans by invasive methods has been strongly debated on the grounds of ethics, public opinion, the potential for infection, and potential impacts on behavior and survival of marked animals. One possible alternative is the use of photographs to enable identification of individuals by their patterns. This requires that individuals have distinguishable markings that remain constant through time. We compared the accuracy of the photographic identification method (PIM) to marked frogs in the field to evaluate whether PIM can be used to identify adult Green-eyed Tree Frogs, Litoria genimaculata. We captured 59 animals on second and subsequent nights of trips. Thirteen were correctly identified as recaptures; 61.5% of them by using the PIM. This was a substantial (39.5%) improvement over chance (expected rate if frogs assigned as recaptures at random was 22%), but was less accurate than the toe-tipping method, with which only one recapture was misidentified (92.3% correct). The majority of frogs, including all of the individuals that were not correctly identified, lacked a distinct dorsal “hourglass” pattern. This may have contributed to the relatively high error rate. We found that the PIM was slower than toe-tipping animals in both time taken for application and identifying individuals. We conclude that the PIM needs to be carefully validated before it is applied to a new species. For L. genimaculata it may be of use in short-term studies when the goal is to reduce the chance of double-sampling individuals. Even then, it will probably only be worth using when a relatively high proportion of the population is being sampled on each occasion, so that a 60 to 70% reduction in double-sampling rates over random is worth achieving.

Werner P., Elle O., Schulte L. M., Lötters S. (2010): Home range behaviour in male and female poison frogs in Amazonian Peru (Dendrobatidae: Ranitomeya reticulata). Journal of Natural History 45: 15-27.
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The poison frog Ranitomeya reticulata was studied for 3 months while mark–recapture surveys were performed. Ranitomeya species deposit terrestrial clutches and carry tadpoles to phytotelmata with few taxa performing biparental brood care including larval feeding. Home range size and spatial affinity to phytotelmata in the genus are linked to mating systems. In R. reticulata, individual home range size and overlap were similar in both sexes, indicating equal levels of site fidelity. Although territory defence was never observed, strong intrasexual intolerance within individuals’ core areas was found. The large intersexual home range overlap for breeding pairs indicated that mate fidelity occurs. Individuals’ home ranges were not overlapping, suggesting that R. reticulata lacks pair-bonding or strongly cooperative behaviour in parental duties. The number of ground bromeliads containing phytotelmata and home range size of males were positively correlated. Our findings suggest that females do not perform egg-feeding and male-only parental care is likely.

Martin L. J., Murray B. R. (2011): A comparison of short-term marking methods for small frogs using a model species, the striped marsh frog (Limnodynastes peronii). The Herpetological Journal 21: 271-273.
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We compared three methods of marking individual small frogs for identification in short-term studies (several days) using a model species, Limnodynastes peronii (the striped marsh frog). We performed a manipulative experiment under laboratory conditions to compare retention times of gentian violet, mercurochrome and powdered fluorescent pigment. Gentian violet produced the most durable marks with retention times between two and four days. Mercurochrome was retained for at least one day by all treated frogs. Fluorescent pigment was either not retained at all or for one day at most, which suggests that this marking method may not be reliable for short-term studies where identification is required. No adverse reactions to any of the marking methods were detected in our study. Our findings indicate that gentian violet represents a promising alternative as a minimally invasive marking technique for studies of small frogs requiring only short-term retention of identification marks.

Ribeiro J., Rebelo R. (2011): Survival of Alytes cisternasii tadpoles in stream pools: a capture-recapture study using photo-identification. Amphibia-Reptilia 32: 365-374.
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For amphibians with complex life cycles, the regulation of populations may occur in each life history stage and although available data stress the importance of studying amphibian population dynamics during the larval stage, most studies so far still focus only on the adult phase, due to the difficulty to estimate larval survival under field conditions. Through a two-months capture-recapture study of 646 photo-identified tadpoles of Alytes cisternasii we aimed to estimate tadpole survival in isolated temporary stream pools – their main habitat – as well as to evaluate how pool characteristics and intraspecific competition (tadpole density) affect this parameter. Photo-identification was performed with the help of the software I3S. We used the POPAN formulation of the Jolly-Seber model to estimate survival rates and population size in 9 stream pools. Tadpole density varied from ∼1 to 40 tadpoles · m–2. Tadpole weekly survival was relatively high, varying from 75 to 99% · week–1. Among-pool differences in survival were best explained by pool depth, and not by tadpole density or other pool characteristics. The lower survival estimates were obtained for the deep pools. The very high survival estimates for some pools are an indication that this type of discrete habitat may play an important role for this species. To our knowledge, this is the first time that photo-identification is used to obtain estimates for survival and density of tadpoles.

Caorsi V. Z., Santos R. R., Grant T. (2012): Clip or snap? An evaluation of toe-clipping and photo-identification methods for identifying individual southern red-bellied toads, Melanophryniscus cambaraensis. South American Journal of Herpetology 7: 79-84.
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The most common method for identifying individual amphibians is toe-clipping (TC), whereby captured individuals are marked by a unique combination of amputated phalanges that corresponds to a unique alphanumeric code. However, ethical and methodological objections to this method have been raised and there is broad interest in developing alternative methods. One alternative is to use photo-identification methods (PIMs) to identify individuals based on their natural markings. We tested the efficacy of TC and two PIMs — visual matching (VM) and computer-assisted matching (CAM) using the software Wild-ID — in identifying individual adults of the endangered southern red-bellied toad, Melanophryniscus cambaraensis. We collected data over 5 mo at Floresta Nacional de São Francisco de Paula, Rio Grande do Sul, Brazil. All specimens were toe-clipped and photographed. The total dataset included 492 captures of 147 individuals. VM was most accurate (99.4%), followed by TC (95.3%) and CAM (90.9%); VM was significantly more accurate than TC and CAM and TC was significantly more accurate than CAM. CAM accuracy diminished as dataset size increased but was considerably faster than VM. All CAM and VM errors were false negatives but involved different images; all TC errors were cross-identifications. Given that misidentifications occurred using both PIMs and TC, our results suggest that studies that require high accuracy should employ at least two methods to allow cross-validation. The performance of each method and the impacts of different kinds and rates of error on inferences depend on the organisms, field conditions, dataset sizes, and study questions. As such, researchers must carefully evaluate the trade-offs of each method before investing significant time and resources in collecting field data.

Ramalho W. P., Jorge R. F., Baiocchi L. B., Peña A. P., Pires R. A. (2013): Study on the population structure of the paradoxical frog, Pseudis bolbodactyla (Amphibia: Anura: Hylidae), using natural markings for individual identification. Zoologia (Curitiba) 30: 623-629.
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The goal of this study was to assess the population structure of Pseudis bolbodactyla Lutz, 1925 using natural markings to identify individuals. Recruitment, survival, and population size estimations were obtained using the Jolly-Seber stochastic method. A total of 166 individuals were captured, and the striped, spotted, and dotted patterns that make their recognition possible were recorded. Of the specimens captured, 27 were recaptured, including some at pre and post-metamorphic stages. The estimate maximum population size was 52. The indices of survival and recruitment varied among samplings. Sexual dimorphism in size and in the operational sex ratio were detected. Despite the limited scope of our characterization of the P. bolbodactyla population, our data might be useful in the interpretation and elaboration of new hypotheses about ecological processes acting on anuran populations.

Morrison T. A., Keinath D., Estes-Zumpf W., Crall J. P., Stewart C. V. (2016): Individual identification of the endangered Wyoming Toad Anaxyrus baxteri and implications for monitoring species recovery. Journal of Herpetology 50: 44-49.
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Monitoring the fates of individuals after release in the wild is essential for building effective species recovery programs. Current conservation efforts for the endangered Wyoming Toad (Anaxyrus baxteri) are limited by the size and number of toads that can be individually marked using invasive tagging techniques. We evaluated the use of natural patterns of wart-like glands on the dorsum of Wyoming Toads as a potential identification technique. We photographed 194 known-identity individuals (822 total images, representing 1,554 true matching-image pairs of the same individuals) from two captive-breeding facilities in 2011 and 2012. Spot patterns provided stable markings from metamorphosis through adult life stages, and naïve observers correctly matched 100% of a subset of photo pairs “by eye.” In contrast, computer-assisted identification performed relatively poorly: the two software platforms tested (Wild-ID and Hotspotter) failed to match 47% and 64% of true matching-image pairs, respectively. The use of higher-quality cameras with faster automatic focusing speeds yielded the largest improvement in matching success of any variable tested when using identification software. Simulated capture–recapture data demonstrated that using software to identify individuals would bias abundance estimates high by up to 920%.

Kim M. Y., Borzée A., Kim J. Y., Jang Y. (2017): Treefrog lateral line as a mean of individual identification through visual and software assisted methodologies. Journal of Ecology and Environment 41: 1-6.
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Ecological research often requires monitoring of a specific individual over an extended period of time. To enable non-invasive re-identification, consistent external marking is required. Treefrogs possess lateral lines for crypticity. While these patterns decrease predator detection, they also are individual specific patterns. In this study, we tested the use of lateral lines in captive and wild populations of Dryophytes japonicus as natural markers for individual identification. For the purpose of the study, the results of visual and software assisted identifications were compared. In normalized laboratory conditions, a visual individual identification method resulted in a 0.00 rate of false-negative identification (RFNI) and a 0.0068 rate of false-positive identification (RFPI), whereas Wild-ID resulted in RFNI = 0.25 and RFNI = 0.00. In the wild, female and male data sets were tested. For both data sets, visual identification resulted in RFNI and RFPI of 0.00, whereas the RFNI was 1.0 and RFPI was 0.00 with Wild-ID. Wild-ID did not perform as well as visual identification methods and had low scores for matching photographs. The matching scores were significantly correlated with the continuity of the type of camera used in the field. We provide clear methodological guidelines for photographic identification of D. japonicus using their lateral lines. We also recommend the use of Wild-ID as a supplemental tool rather the principal identification method when analyzing large datasets.

Smith S., Young T., Skydmore D. (2018): Effectiveness of the field identification of individual natterjack toads (Epidalea calamita) using comparisons of dorsal features through citizen science. Herpetological Journal 28: 31-38.
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Citizen science is now making an important contribution, both in the collection of large amounts of data over wide geographical areas and in promoting environmental awareness and engagement communities. However, as there are many participating observers, the reliability of the data collected needs to be assessed. This study used a citizen science approach to investigate whether dorsal features, when photographed, can be used in the identification of individual natterjack toads (Epidalea calamita). Epidalea calamita individuals from a population located at Prestatyn, North Wales, were captured, photographed and released in a legally compliant manner. Forty human participants each completed a timed exercise to match photographs of individual toads that had been taken from different angles. Sixty-five percent of the participants accurately matched photographs on their first attempt. The effect of training on the accuracy and speed at which participants could identify individuals from photographs was then assessed. Twenty of the participants received basic training on recognising the key features of dorsal patterns before carrying out the exercise again. Following training, average accuracy increased to 90% and participants were 41.5% quicker in completing the exercise than those that were untrained. The study revealed that basic training of participants who are involved in citizen science projects was beneficial by having a significant impact on accuracy and speed. In addition, we demonstrate that the dorsal features of tubercles and scarring are useful in identifying individuals of E. calamita in the field.

Ottburg F. G., Van der Grift E. A. (2019): Effectiveness of road mitigation for common toads (Bufo bufo) in the Netherlands. Frontiers in Ecology and Evolution 7: 23.
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Roads and traffic may have major impacts on amphibian populations, primarily as a result of amphibian road mortality. A variety of measures have been developed to prevent road mortality of amphibians, such as the construction of fences to keep the animals off the road and amphibian tunnels to provide them a safe passage. We carried out a capture-mark-recapture study to evaluate the performance of two tunnels and permanent drift fences for common toads at a local road in the Netherlands. We found that of the marked toads only 31% used the tunnels to cross the road. We assessed four possible explanations for the fact that a proportion of the toads did not use the tunnels: for toad groups that used the tunnels, as compared to toad groups that did not use the tunnels, (1) the mean distance between the location of first capture and the nearest tunnel was significantly smaller; (2) the mean movement distance along the fence was significantly larger; (3) the number of toad groups that walked in the wrong direction after encountering the drift fence was lower; (4) the mean number of nights between first and last capture of the toad group was significantly higher. Over all study years 28% of the migrating toads—marked and unmarked—that attempted to cross the road ended up on the road pavement, despite the mitigation. Migrating population numbers decreased with about 75% after the mitigation measures were installed. We emphasize that better baseline studies on where toads cross before mitigation and improved knowledge on effects of tunnel design and the distances the animals move along a drift fence are vital to mitigate road impacts properly and maintain viable toad populations. We recommend to base tunnel densities on the mean movement distance of the toads that move only small distances and spent relatively little time along the drift fence, install drift fences that go well beyond the location where toads cross the road, take appropriate measures at entrance roads and at fence ends and consider alternatives to tunnels and fences, such as the creation of breeding waters on both sides of the road.

Valenzuela-Sánchez A., Schmidt B. R., Pérez C., Altamirano T., Toledo V., Pérez Í., Teillier S., Cunningham A. A., Soto-Azat C. (2019): Assessing habitat quality when forest attributes have opposing effects on abundance and detectability: A case study on Darwin’s frogs. Forest Ecology and Management 432: 942-948.
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Forest management can be used to increase the local abundance of species of conservation concern. To achieve this goal, managers must be sure that the relationships between the targeted forest attributes and the focal species abundance are based on robust data and inference. This is a critical issue as the same forest attributes could have opposing effects on species abundance and the detectability of individuals, impairing our ability to detect useful habitat quality surrogates and to provide correct forest management recommendations. Using spatially stratified capture-recapture models (a.k.a. multinomial N-mixture models), we evaluated the effects of stand-level forest attributes on detection probability and local abundance for the endangered Southern Darwin’s frog (Rhinoderma darwinii), a forest-specialist and fully terrestrial amphibian endemic to the South American temperate forest. Our results show that an increase of stand basal area and a decrease of daily microclimatic fluctuation (i.e. an increase in structural complexity) were positively associated with the local abundance of R. darwinii. These stand-level forest attributes also explained the among-population variation in detection probability, although the relationships were opposite to those for abundance. Consequently, an analysis of raw frog counts (i.e. not adjusted for imperfect detection) did not reveal all the factors associated with local abundance. Our results provide further support to previous claims that raw counts of individuals should not be used, generally, as a proxy of abundance in species inhabiting forest ecosystems and elsewhere. More importantly, the opposite effect of forest attributes on abundance and detectability observed in our study highlights the need to use methods that quantify species-habitat relationships in a robust way and which take habitat-specific imperfect detection into account.

Bardier C., Székely D., Augusto-Alves G., Matínez-Latorraca N., Schmidt B. R., Cruickshank S. S. (2020): Performance of visual vs. software-assisted photo-identification in mark-recapture studies: a case study examining different life stages of the Pacific Horned Frog (Ceratophrys stolzmanni). Amphibia-Reptilia 1: 1-12.
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The use of individual phenotypic features as non-invasive marks through photo-identification (photo-ID) has many advantages for individual-based field studies. However, since error rates vary between species, matching techniques, and image qualities, it is important to assess error rates to evaluate the reliability of photo-ID. We tested the performance of this method in the Pacific Horned Frog, Ceratophrys stolzmanni, a threatened anuran with a variable dorsal coloration. We compared the effectiveness of visual (i.e. human recognition) versus software-assisted recognition techniques (Wild-ID and APHIS), and assessed the potential applicability of these techniques to identify post-metamorphic individuals (froglets). The three techniques differed in their performance. The visual technique was the only one to produce type I errors between pairs of images (i.e. matching images which are not true matching pairs), however it also produced fewer type II errors (i.e. not identifying true matching pairs of images) than the software-assisted techniques. For froglets, we found that similarity scores calculated by photo-ID software did not differ significantly between groups of froglets and older individuals, supporting the idea that colour patterns in this species remain stable after metamorphosis. The lack of type I errors and the substantial reduction in required time achieved through the use of software, make software-assisted techniques (particularly Wild-ID) a valid and convenient matching technique for C. stolzmanni. We propose that photo-ID can also be applied to froglets of this species, since the pattern at this stage appears to be as variable as in adults and maintained through life.

Muscat E., Menegucci R. C., Tanaka R. M., Rotenberg E., de Toledo Moroti M., Pedrozo M., Rodrigues Stuginski D., Sazima I. (2020). Natural history of the marsupial frog Gastrotheca albolineata (Anura: Hemiphractidae) in lowland Brazilian Atlantic Forest. Phyllomedusa: Journal of Herpetology 19: 189-200.
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Natural history of the marsupial frog Gastrotheca albolineata (Anura: Hemiphractidae) in lowland Brazilian Atlantic Forest. Gastrotheca albolineata is a marsupial frog endemic to the Atlantic Forest in southeastern Brazil. It remains poorly studied in nature and is uncommon in herpetological collections. We studied the natural history of G. albolineata during a four-year period (2015 to 2019), in Ubatuba, São Paulo state, Brazil, at its southernmost distribution. Our results show that G. albolineata is arboreal, perches from low to medium heights, and breeds during the dry season without chorus aggregation. Calling activity occurs during the day but is more intense during the first half of the night. We used dorsal body markings to identify individuals. Six individuals were recaptured during the study, indicating site fidelity during the active season. The defensive repertory of G. albolineata contains seven different behaviors, including a high-pitched distress call. Egg development in the female’s dorsal pouch took at least 87 days, and fully formed froglets were born with a snout–vent length of 16 mm. Our data substantially add to the knowledge of the natural history of Brazilian marsupial frogs and can be helpful to delineate conservation strategies for elusive species such as G. albolineata.

Patel N. G., Das A. (2020): Shot the spots: a reliable field method for individual identification of Amolops formosus (Anura, Ranidae). Herpetozoa 33: 7.
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Natural body patterns in amphibians are widely used for individual recognition. In this study, we photographed individuals of Amolops formosus for four days of sampling without handling them. We processed 301 photographs of dorsal blotch pattern in HotSpotter software and verified them visually for confirmation. We identified 160 unique individuals of A. formosus based on the images taken in the field, resulting in an abundance estimate of 180 individuals. The success rate in identifying individuals of A. formosus using the HotSpotter software was 94.3%. We tested the effect of image quality and distance on recognition efficiency. Poor image quality reduced the recognition efficiency of the software but with a careful user review it was possible to identify the individual. The difference between using only the software and software plus human confirmation was very small. This protocol is useful for rapid population estimation of frogs with natural body patterns.

Crawford-Ash J., Rowley J. J. (2021): Photo identification of individual Blue Mountains Tree Frogs (Litoria citropa). Herpetology Notes 14: 803-808.
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We used a Photo Identification Method (PIM) to identify individuals of the Blue Mountains Tree Frog, Litoria citropa. By matching the body markings on photographs taken in the field of the lateral, dorsal and anterior views of the frog, we were able to re-match two individuals; one after 88 days and the other after 45 days. We present the first evidence that photo identification is likely to be a useful tool in individual recognition of L. citropa and is one of a few studies on the use of PIM in Australian frogs.

Lima-Araujo F., Brasileiro A. C., Carvalho E. F. F., Passos D. C. (2021): Efficiency of photo identification of inguinal color patterns of Pithecopus gonzagai (Anura: Phyllomedusidae) from northeastern Brazil. Phyllomedusa: Journal of Herpetology 20: 67-74. 
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Animal monitoring research involving mark-recapture techniques increasingly requires non-invasive methods of individual identification. The photographic identification method (PIM) is an excellent tool for this purpose and has been applied successfully to many taxa. However, the utility of PIM is a function of species-specific features that are judged suitable for a given target-species. Herein, the suitability of inguinal color patterns for photo identification of individuals of Pithecopus gonzagai are evaluated by comparing two widely used computer-assisted photographic matching programs (I³S and Wild.ID). Both programs accurately identified more than 70% of individuals in the top 20 potential matching photographs. Wild.ID was slightly better than I³S in matching efficiency and has a faster processing time. Thus, PIM is useful to identify individual P. gonzagai; however, before implementing the technique in animal-monitoring studies of other taxa, one must evaluate the suitability PIM for the target species and calibrate the relative efficiency of the software programs in identifying individuals.

Reyne M., Helyar S., Aubry A., Emmerson M., Marnell F., Reid N. (2021): Combining spawn egg counts, individual photo‐ID and genetic fingerprinting to estimate the population size and sex ratio of an endangered amphibian. Integrative Zoology 16: 240-254.
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According to the International Union for Conservation of Nature Red List, 41% of the world’s amphibian species are threatened with extinction, making them more threatened than any other vertebrate group nowadays. Given the global amphibian crisis, comprehensive understanding of demographics and population trends of declining and threatened species is essential for effective management and conservation strategies. Counting egg spawns is widely used to assess population abundance in pond breeding anurans. However, it is unknown how such counts translate into robust population size estimations. We monitored the breeding activity of the Natterjack toad (Epidalea calamita), combining egg string counts and individual photo-identification with Capture-Mark-Recapture population size and operational sex ratio estimation. Male Natterjack toads were identified by the pattern of natural markings with repeated ID of the same individual confirmed for 10% of the samples using genetic fingerprinting. We identified 647 unique individuals within a closed study population at Caherdaniel, Co Kerry. Population estimates derived from egg string counts estimated a breeding population of 368 females (95% CI 353–384) and Capture-Mark-Recapture estimated a breeding population of 1698 males (95% CI 1000–2397). The female:male sex ratio was conservatively estimated at 1:5 (95% CI 1:3–1:6) where 62% ± 6% of females were assumed to spawn. These substantially departed from any priori assumption of 1:1 which could have underestimated the breeding population by up to 72%. Where amphibian absolute population size estimation is necessary, methods should include empirical survey data on operational sex ratios and not rely on assumptions or those derived from the literature which may be highly population and/or context-dependent.

Aevarsson U., Graves A., Carter K. C., Doherty-Bone T. M., Kane D., Servini F., Tapley B., Michaels C. J. (2022): Individual identification of the Lake Oku clawed frog (Xenopus longipes) using a photographic identification technique. Herpetological Conservation and Biology 17: 67-75.
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Amphibians are challenging to mark for recapture due to their small size and permeable, sensitive, and often frequently shed skins. Photographic identification and pattern matching techniques are increasingly used as a non-invasive method to identify individual amphibians for the purposes of monitoring individuals over time. The Critically Endangered Lake Oku Clawed Frog (Xenopus longipes) has distinctively patterned ventral patterns as adults. We used Wild-ID to explore the use of photographic identification for the longitudinal identification of both adult and juvenile X. longipes. We photographed juvenile frogs twice over a 180-d period and adult frogs seven times over 624 d. Juvenile belly patterns underwent marked ontogenetic shifts over the 180-d period and Wild-ID was not able to match photographs of the same individuals over the study period. Markings were more stable in adult frogs and Wild-ID was successful in matching photographs of individual adult frogs over 180 d but became less effective at distinguishing between individuals at 624 d (i.e., Wild-ID similarity scores halved and false rejection rates increased substantially). We detected no false acceptances. Our results provide evidence to guide management of this species in captivity and in the field and demonstrate the importance of considering life-stage linked ontogenetic changes when validating a photographic identification method for amphibians.

Berokoff J., de la Hera I., Reichert M. S. (2023): Image processing of thigh color pattern is an effective method for identifying individual Cope’s Gray Treefrogs, Hyla chrysoscelis. Ichthyology & Herpetology 111: 612-620.
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Photographic mark–recapture is a recently developed method that uses photographs of naturally occurring body patterns to identify individual animals. This method may be especially appropriate for amphibians because they are difficult to externally mark for individual recognition. However, the reliability of the method depends on whether or not the considered pattern differs consistently among individuals over time. We took pictures of the black and yellow thigh pattern of Cope’s Gray Treefrogs (Hyla chrysoscelis) across two years to test whether this trait was consistent enough that individuals could be recognized from photographs, using automated photo recognition in Wild-ID software. We tested the performance of this program using sample sets of photos taken at three different timescales: photos from the same night, different nights within a year, and two different years. We also tested whether the likelihood of correct identifications decreased with increasing sample size. Overall, photographic mark–recapture produced a very high percentage of correct identifications across all timescales and sample sizes. Thus, we conclude that the use of this inexpensive and non-invasive technique on the thigh color pattern of H. chrysoscelis is a highly effective method for individual recognition.

Gould J., Taylor J., Davies B., Donelly R., Schmahl K., Bugir C. K., Beranek C.T., McGregor J., Mahony S.V., Seeto R., Upton R., Callen A. (2023): Tadpole fingerprinting: Using tail venation patterns to photo‐identify tadpole individuals of a threatened frog. Austral Ecology 48:585-599.
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Traditional methods for identifying individual amphibians in capture–mark–recapture (CMR) studies have been primarily confined to post-metamorphic stages, using artificial markers that come with a variety of limitations. An alternative that may open CMR studies to earlier life stages involves the use of a species’ natural external markers in photo-based identification. In this study, we investigated whether it was possible to distinguish tadpoles of the threatened green and golden bell frog (Litoria aurea) at the individual level based on tail venation patterns. We collected photographs of the tails of captive-raised tadpoles using a smartphone over a 4-week period. This photo-library was used to create an electronic survey where participants were asked to detect matches for query tadpoles from small image pools. We found that most participants agreed on a match for each query, with perfect consensus achieved for most queries (83%). We detected a 14% decline in perfect consensus when participants were asked to match images of tadpoles separated by longer time intervals, suggesting that it is more difficult to visually identify recapture events of L. aurea tadpoles over extended periods due to changes to tail appearance. However, consensus was obtained by participants for all queries, with all matches verified as being correct by the primary researcher. The strength of agreement among participants with no prior experience in matching tadpole tails suggests that there is sufficient inter-individual variation in this feature for individuals to be manually identified. We thus propose that photo-identification is likely to be a valid, non-invasive technique that can be used for short-term studies on tadpole populations that display tail venation. This offers an alternative to artificial markers that may not allow for individual identification, while also opening up tadpole monitoring programmes to citizen scientists who can be recruited online to process image data from home.

Lassnig N., Guasch-Martínez S., Pinya Fernández S. (2023): The individual color pattern on the back of Bufotes viridis balearicus (Boettger, 1880) allows individual photo identification recognition for population studies. Canadian Journal of Zoology.
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This study explores the potential of Photo-Identification Methods (PIM) as a viable, noninvasive, and ethical tool for wildlife studies, with a specific focus on anuran species such as Bufotes viridis balearicus (Boettger, 1880). Although the Automatic Photo Identification Suit (APHIS) software was initially designed for lizard identification, our research shows its adaptability for anuran species, achieving a high detection accuracy rate of 95.28%. Thus, obtaining outstanding and higher values comparing to previous studies on this species. Crucially, our findings indicate that the success of PIM and the efficacy of image identification software like APHIS is dependent on the quality and standardization of the images collected. The study also underscores the importance of practical experience and continuous learning for the optimal utilization of software like APHIS. Despite occasional False Rejected Matches (FRM), the overall strong performance metrics with low False Rejection Rate (FRR) demonstrate that these instances do not significantly impact the reliability of the technique. Thus, this research highlights the importance of careful implementation, continuous learning, and image quality control in leveraging the full potential of image identification software in wildlife studies.

SALAMANDERS AND NEWTS

Gamble L., Ravela S., McGarigal K. (2008): Multi‐scale features for identifying individuals in large biological databases: an application of pattern recognition technology to the marbled salamander Ambystoma opacum. Journal of Applied Ecology 45: 170-180.
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Capture–mark–recapture (CMR) studies provide essential information on demography, movement and other ecological characteristics of rare and endangered species. This information is required by managers to focus conservation strategies on the most relevant threats and life stages, identify critical habitat areas, and develop benchmarks for measuring success in recovery plans. However, CMR studies have been limited by individual identification methods that are not effective or practical for many types of organisms. We develop a pattern recognition algorithm and photo‐identification method that uses photographs taken in the field to identify individual marbled salamanders (Ambystoma opacum), using their dorsal patterns as ‘fingerprints.’ The algorithm ranks all images in a database against each other in order of visual similarity. We couple this technology with a graphic user interface to visually confirm or reject top‐ranked algorithm results. Using this process, we analyse all adult salamander captures from one year of a long‐term study. In a database of 1008 images, the algorithm identified 95% of 101 known matches in the top 10 ranks (i.e. top 1% of all images). Time spent on manual elements of the matching process was estimated at one minute per image, permitting full indexing of all capture records. Capture histories constructed from matched images identified 366 individuals that were captured between 2 and 5 times. Of these, less than 2% were captured at more than one of the 14 pond basins included in the study, suggesting that migrations were strongly directional to and from basins and that ‘pond‐shopping’ among first‐time breeders was infrequent. Females arrived at basins later, remained longer, and experienced more weight‐loss than males during the breeding period. Synthesis and applications. We develop, test, and apply a pattern recognition algorithm that enables efficient identification of individual marbled salamanders in a database exceeding 1000 images. We expect that this algorithm can be modified to facilitate individual identification in many other organisms because it does not rely on manual coding or discrete geometric pattern features. High performance results suggest that it can be scaled to larger databases, allowing biologists to address critical conservation‐based questions regarding demography, reproduction and dispersal of rare and endangered species.

Bendik N. F., Morrison T. A., Gluesenkamp A. G., Sanders M. S., O’Donnell L. J. (2013): Computer-assisted photo identification outperforms visible implant elastomers in an endangered salamander, Eurycea tonkawae. Plos One 8: 59424.
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Despite recognition that nearly one-third of the 6300 amphibian species are threatened with extinction, our understanding of the general ecology and population status of many amphibians is relatively poor. A widely-used method for monitoring amphibians involves injecting captured individuals with unique combinations of colored visible implant elastomer (VIE). We compared VIE identification to a less-invasive method – computer-assisted photographic identification (photoID) – in endangered Jollyville Plateau salamanders (Eurycea tonkawae), a species with a known range limited to eight stream drainages in central Texas. We based photoID on the unique pigmentation patterns on the dorsal head region of 1215 individual salamanders using identification software Wild-ID. We compared the performance of photoID methods to VIEs using both ‘high-quality’ and ‘low-quality’ images, which were taken using two different camera types and technologies. For high-quality images, the photoID method had a false rejection rate of 0.76% compared to 1.90% for VIEs. Using a comparable dataset of lower-quality images, the false rejection rate was much higher (15.9%). Photo matching scores were negatively correlated with time between captures, suggesting that evolving natural marks could increase misidentification rates in longer term capture-recapture studies. Our study demonstrates the utility of large-scale capture-recapture using photo identification methods for Eurycea and other species with stable natural marks that can be reliably photographed.

Šukalo G., Đorđević S., Golub D., Dmitrović D., Tomović L. (2013): Novel, non-invasive method for distinguishing the individuals of the fire salamander (Salamandra salamandra) in capture-mark-recapture studies. Acta Herpetologica 8: 41-45.
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Recently we started implementing a highly efficient, non-invasive method of direct individual marking (i.e., typifying) in a population study of the fire salamander, Salamandra salamandra. Our technique is based on the unique alphanumeric code for every individual, generated upon the numbers of openings of repellent/toxic skin glands in the yellow areas of the selected regions of the body. This code was proved reliable in the sample of 159 individuals from two separate populations and enabled easy and quick recognition of recaptured animals. The proposed method is inexpensive, easily applicable in the field, involves minimum stress for the animals and does not affect their behaviour and the possibility of repeated captures of “marked” (i.e., coded) individuals. It is particularly suitable for dense populations.

Drechsler A., Helling T., Steinfartz S. (2015): Genetic fingerprinting proves cross‐correlated automatic photo‐identification of individuals as highly efficient in large capture–mark–recapture studies. Ecology and Evolution 5: 141-151.
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Capture–mark–recapture (CMR) approaches are the backbone of many studies in population ecology to gain insight on the life cycle, migration, habitat use, and demography of target species. The reliable and repeatable recognition of an individual throughout its lifetime is the basic requirement of a CMR study. Although invasive techniques are available to mark individuals permanently, noninvasive methods for individual recognition mainly rest on photographic identification of external body markings, which are unique at the individual level. The re‐identification of an individual based on comparing shape patterns of photographs by eye is commonly used. Automated processes for photographic re‐identification have been recently established, but their performance in large datasets (i.e., > 1000 individuals) has rarely been tested thoroughly. Here, we evaluated the performance of the program AMPHIDENT, an automatic algorithm to identify individuals on the basis of ventral spot patterns in the great crested newt (Triturus cristatus) versus the genotypic fingerprint of individuals based on highly polymorphic microsatellite loci using GENECAP. Between 2008 and 2010, we captured, sampled and photographed adult newts and calculated for 1648 samples/photographs recapture rates for both approaches. Recapture rates differed slightly with 8.34% for GENECAP and 9.83% for AMPHIDENT. With an estimated rate of 2% false rejections (FRR) and 0.00% false acceptances (FAR), AMPHIDENT proved to be a highly reliable algorithm for CMR studies of large datasets. We conclude that the application of automatic recognition software of individual photographs can be a rather powerful and reliable tool in noninvasive CMR studies for a large number of individuals. Because the cross‐correlation of standardized shape patterns is generally applicable to any pattern that provides enough information, this algorithm is capable of becoming a single application with broad use in CMR studies for many species.

Mettouris O., Megremis G., Giokas S. (2016): A newt does not change its spots: using pattern mapping for the identification of individuals in large populations of newt species. Ecological Research 31: 483-489.
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The correct identification of individuals is a requirement of capture-mark-recapture (CMR) methods, and it is commonly achieved by applying artificial marks or by mutilation of study-animals. An alternative, non-invasive method to identify individuals is to utilize the patterns of their natural body markings. However, the use of pattern mapping is not yet widespread, mainly because it is considered time consuming, particularly in large populations and/or long-term CMR studies. Here we explore the use of pattern mapping for the identification of adult individuals in the alpine (Ichthyosaura alpestris) and smooth (Lissotriton vulgaris) newts (Amphibia, Salamandridae), using the freely available, open-source software Wild-ID. Our photographic datasets comprised nearly 4000 captured animals’ images, taken during a 3-year period. The spot patterns of individual newts of both species did not change through time, and were sufficiently varied to allow their individual identification, even in the larger datasets. The pattern-recognition algorithm of Wild-ID was highly successful in identifying individual newts in both species. Our findings indicate that pattern mapping can be successfully employed for the identification of individuals in large populations of a broad range of animals that exhibit natural markings. The significance of pattern-mapping is accentuated in CMR studies that aim in obtaining long-term information on the demography and population dynamics of species of conservation interest, such as many amphibians facing population declines.

Lau A., Karraker N. E., Dudgeon D. (2017): Does forest extent affect salamander survival? Evidence from a long‐term demographic study of a tropical newt. Ecology and Evolution 7: 10963-10973.
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Forest loss has been associated with reduced survival in many vertebrates, and previous research on amphibians has mostly focused on effects at early life stages. Paramesotriton hongkongensis is a tropical newt that breeds in streams but spends up to 10 months per year in terrestrial habitats. Populations are threatened by habitat degradation and collection for the pet trade, but the cryptic terrestrial lifestyle of this newt has limited our understanding of its population ecology, which inhibits development of a species-specific conservation plan. We conducted an eight-year (2007–2014) mark–recapture study on four P. hongkongensis populations in Hong Kong and used these data to evaluate relationships between forest cover, body size, and rainfall on survival and to estimate population sizes. Hong Kong has been subjected to repeated historic territory-wide deforestation, and thus, we wanted to determine whether there was a link between forest extent as a proxy of habitat quality and newt demography. Annual survival was positively associated with forest cover within core habitat of all populations and negatively related to body size. Mean annual survival (~60%) was similar to that of other stream-dwelling amphibians, but varied among years and declined substantially in 2012–2013, perhaps due to illegal collection. Despite the link between forest extent and survival, population sizes declined at the most forested site by 40% and increased by 104% and 134% at two others. Forest protection and consequential secondary succession during recent decades in Hong Kong may have been responsible for persistence of P. hongkongensis populations.

Speybroeck J., Steenhoudt K. (2017): A pattern-based tool for long-term, large-sample capture-mark-recapture studies of fire salamanders Salamandra species (Amphibia: Urodela: Salamandridae). Acta Herpetologica 12: 55-63.
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Solid population studies depend on reliable capture-mark-recapture (CMR) methodology. The available methods for such studies on amphibians are often invasive, unsuitable for long-term studies, time-consuming and/or expensive. We present a new software tool, connected to a MS Access database, ManderMatcher, for CMR study of fire salamanders (Salamandra salamandra and related species) by means of a robust matching algorithm using 44 pattern characteristics. Metadata related to standardised counts (e.g. weather and lunar variables) as well as a myriad of individual sighting variables can be entered and saved as well. Application of the presented method to a database of 9,397 sighting records gathered over a period of eight years, as well as a random sample validation, demonstrate the accuracy of the applied matching algorithm. Differences with other methods are discussed. The program is made freely available for download and widespread application is encouraged, especially given the contemporary context of a fungal disease threatening survival of fire salamander populations.

Gutierrez A. M., Guess S. T., Pierce B. A. (2018): Within-spring movement of the Georgetown salamander (Eurycea naufragia). Herpetological Conservation and Biology 13: 383-390.
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Movement is a critical ecological and evolutionary factor for many species, and understanding patterns of movement is important in conservation planning and management. Faced with increasing urbanization, aquifer depletion, and pollution, spring- and cave-dwelling salamanders of the genus Eurycea on the Edwards Plateau of Texas are of conservation concern, yet relatively little is known about their patterns of movements within and between habitats. We studied movement of the Georgetown Salamander (Eurycea naufragia) within two spring sites in central Texas over 32 mo. Using capture-recapture methods, we tracked the movement of individual salamanders and found limited movement at both sites: only 23% of recaptured salamanders at Swinbank Spring and only 17% of recaptured salamanders at Twin Springs moved beyond their 5 m section of original capture. A higher proportion of gravid salamanders than nongravid salamanders moved, and gravid salamanders exhibited a higher rate of movement. Salamanders that moved had larger body size, and there was a positive correlation between rate of movement and body size. Body condition, as measured by initial relative tail width, was not significantly different between salamanders that moved and those that did not move, and was not correlated with rate of movement. We found no differences in body condition or body size between salamanders that moved upstream and those that moved downstream. These findings are consistent with other studies of headwater and spring salamanders that found limited dispersal. Our findings suggest that Eurycea naufragia exhibits limited movement within surface springs.

Romano A., Basile M., Costa A. (2018): Skewed sex ratio in a forest salamander: artefact of the different capture probabilities between sexes or actual ecological trait?. Amphibia-Reptilia 39: 79-86.
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Sex ratio is an essential demographic parameter and distortions from a balanced sex ratio may have contrasting effects on the population dynamics. However, observation of distorted sex ratio using counts or captures may reflect an actual ecological trait of the studied population but may also be an artefact due to different capture probabilities of males and females. We compared results obtained from Counts and Capture-Marking-Recapture (CMR) on both sexes in a population of a forest dwelling salamander, Salamandrina perspicillata, and we investigated if males and females had different capture probabilities. We surveyed available literature to compare information on sex ratio from other populations of S. perspicillata. The sex ratio from our counts was 0.65 and was significantly male-biased as reported in other studies. The estimated sex ratio from CMR data was 0.57. Although males showed higher recapture rates than females in every capture session, these differences were not statistically significant. Therefore, the skewed sex ratio towards males is not only an artefact due to different capture probabilities between males and females but reflects an actual demographic trait, although the magnitude of the skeweness was overestimated by counts.

Romano A., Costa A., Salvidio S., Menegon M., Garollo E., de Fatis K.T., Miserocchi D., Matteucci G., Pedrini P. (2018): Forest management and conservation of an elusive amphibian in the Alps: Habitat selection by the Golden Alpine Salamander reveals the importance of fine woody debris. Forest Ecology and Management 424: 338-344.
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Amphibians are declining worldwide and one of the major causes of such decline is habitat loss. Forestry practices have a primary role in causing habitat loss and fragmentation, detrimental to amphibians. We studied the ecological requirements of a fully terrestrial and threatened amphibian, the Golden Alpine Salamander Salamandra atra aurorae, which is endemic to a small portion of the Italian Alps. This rare and elusive salamander lives exclusively in forest environments and forestry practices are considered among its major threats. We employed both a capture-mark-recapture (CMR) and an occupancy approach in fifty 400 m2 plots, within a managed mixed forest dominated by Norway spruce and to a lesser extent beech, and silver fir. Modelling salamander occupancy as a function of site-specific habitat features allowed us to understand the ecological requirements of this salamander and provide precise guidelines for forest management. The application of hierarchical models (occupancy) for evaluating forest management plans is highly effective, requires less effort and is a less impacting methodology than CMR performed by searching for salamanders under shelters also in non-optimal weather conditions. Distance from open pasture edges significantly affects the distribution of salamanders while, at a smaller scale, brushwood piles, classified as fine woody debris (FWD, diameter from 1 to 10 cm), play a key role in providing suitable habitat for this endangered amphibian. The importance of FWD in the conservation of small vertebrates is generally poorly studied and probably underestimated. However, our results show that FWD should be considered as an additional element that has to be managed to enhance habitat suitability for this and, intuitively, for other small forest vertebrates.

Renet J., Leprêtre L., Champagnon J., Lambret P. (2019): Monitoring amphibian species with complex chromatophore patterns: a non-invasive approach with an evaluation of software effectiveness and reliability. Herpetological Journal 29: 13-22.
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The estimation of demographic parameters in wild populations is strengthened by individual identification. For amphibians, various techniques are used to either temporarily or permanently mark individuals for identification. Photo-identification of body patterns offers a non-invasive technique. However, the reliability of photo-recognition software is key to the reliable estimation of the true demographic parameters. In the current study, we assessed the effectiveness of fully-automated and semi-automated software: Wild-ID and APHIS. We used the cryptic salamander Hydromantes strinatii as our study species. We used the False Rejection Rate (FRR) of Top 1, Top 5 and Top 10 matches of chest and cloaca pictures. Finally, we assessed the bias induced by our FRR for the estimation of population size through simulation. Wild-ID FRRs ranged from 0.042 to 0.093 while APHIS’ ranged from 0.227 to 0.547. Wild-ID was equally efficient with pictures from the chest and from the cloaca, while APHIS was significantly more efficient with chest pictures than cloaca pictures. Cropping pictures did not significantly improve Wild-ID effectiveness. Our Wild-ID FRRs are among the lowest ever obtained from pictures of an amphibian with a complex chromatophore pattern. Simulation showed that the Top 10 FRR from selected software Wild-ID induced a low bias 2.7% on the estimation of population size. The effectiveness and plasticity of Wild-ID provides opportunities for reliably monitoring amphibian species with complex colour patterns.

Dalibard M., Buisson L., Calvez O., Nguyen-Hong M., Trochet A., Laffaille P. (2021): Can ventral pattern be used for individual recognition of the vulnerable Pyrenean brook newt (Calotriton asper)?. Herpetological Journal 31: 99-110.
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Individual recognition of animal species is a prerequisite for capture-mark-recapture (CMR) studies. For amphibians, photoidentification of body pattern is a non-invasive and less expensive alternative than classical marking methods (e.g. passive integrated transponder). However, photo-identification is effective only if the patterns are (i) sufficiently variable between individuals, and (ii) stable over time. This method also depends on the observer’s judgment. In the present study, we assessed the effectiveness of an automatic algorithm (AmphIdent) to recognise ventral colour patterns of the Pyrenean brook newt (Calotrion asper), endemic to the Pyrenees Mountains of France. To assess the performance of the tested method, 113 individuals from two different streams were marked with passive integrated transponders (PIT-tags). We used false rejection rate (FRR), false acceptance rate (FAR) and true acceptance rate (TAR) as metrics to evaluate performances of photoidentification. Mean FRR was 7.3 %, FAR was 5.2 %, and TAR was 92 % across both streams, both sexes and all the observers. FAR was significantly different between sexes, while FRR and TAR were significantly influenced by the interaction between the sex and the stream. Despite these differences, our error rates are among the lowest values found in the literature for both amphibian and non-amphibian computer-assisted photo-identification. We found that poor-quality reference pictures could lead to an increasing difficulty to achieve a correct match when time since first capture rose. Consequently, individual photo-identification using AmphIdent software is a reliable tool to aid in the monitoring the Pyrenean brook newts, provided that pictures are taken with care, reference images are regularly updated and observers are properly trained to use the software and interpret images.

Romano A., Roner L., Costa A., Salvidio S., Trenti M., Pedrini P. (2021): When no color pattern is available: application of double observer methods to estimate population size of the Alpine salamander. Arctic, Antarctic, and Alpine Research 53: 300-308.
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Monitoring wild populations is an essential tool to assess the conservation status and the ecological requirements of a species. Capture–mark–recapture (CMR), based on individual recognition, is the most commonly used and most effective technique. However, in cases of species with no individual color pattern, tracing the encounter history of individuals without invasive marking methods is impossible. In this study we aimed to (1) estimate population abundance and density using a less effort-intensive and nonstressful technique, (2) test a long-term monitoring protocol, and (3) assess the fine-scale ecological requirements of a black-colored amphibian, Salamandra atra, in the Italian Alps. For three populations we applied an N-mixture model on data collected using a dependent double-observer approach. To understand ecological requirements, we assessed the relative importance of a set of environmental and topographical variables. The double-observer approach was a cost-effective technique that provided reliable demographic estimates of population density. Our results suggest that the most important fine-scale ecological variables positively associated with salamander abundance were canopy cover and terrain ruggedness, which are strictly related to shelter availability and soil moisture.

Faul C., Wagner N., Veith M. (2022): Successful automated photographic identification of larvae of the European Fire Salamander, Salamandra salamandra. Salamandra 58: 52-63.
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Computer-aided individual recognition of animals based on their natural markings has become an indispensable tool in ecology research. However, this is problematic in species with faint patterns. Here we test whether individually reared larvae of the European Fire Salamander (Salamandra salamandra) can be reliably recognized from images of their lateral tail patterns. We used Wild-ID software to (1) estimate the recognition uncertainty resulting from pre-processing the images, (2) quantify how pre-contrasting improves recognition, (3) assess the effect of ontogenetic pattern change on recognition until metamorphosis, and (4) test how recognition performs with larger image libraries. Our results show that discrimination of larvae is highly successful. Pre-processing did not lead to a relevant change in the recognition probability, while pre-contrasting even reduced the recognition probability. The shorter the time interval between two photos, the more readily an individual will be recognized. The overall recognition rate was 99.81%, with false rejection rates (FRR, calculated as the number of falsely rejected images divided by the number of matching attempts) amounting to 4.66, 0.77 and 0.20% for FRR1 (first image provided by Wild-ID does not match), FRR10 (none of the first ten images provided by Wild-ID match- es) and FRR21 (none of the first 20 images provided by Wild-ID matches), respectively. These rates are among the lowest ever reported. The inclusion of images of 130 wild-caught larvae did not negatively affect successful individual recognition. Automated photo-identification may therefore be considered a reliable tool for fieldwork on European Fire Salamander larvae.