INDIVIDUAL IDENTIFICATION: REPTILES
CROCODILES
Swanepoel D. G. J. (1996): Identification of the Nile crocodile Crocodylus niloticus by the use of natural tail marks. Koedoe 39: 113-115.
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The tail marks of 190 Nile crocodiles Crocodylus niloticus were documented and processed into codes. The size of the crocodiles varied from 45 cm to 4.6 m in total length. Wherever possible, both sides of the tails were observed and the marks documented. In all remaining instances only one side could be identified. A total of 267 sides were identified. The natural marks on nine segments of a specific portion of the tail was recorded and compared as codes. For this comparison two methods were employed. Differences of 95.1 and 100 was found with the respective methods. This is an indication that every crocodile has a unique pattern of natural marks on its tail. The marks can therefore be used to allocate a code to an individual crocodile that partially eliminates the necessity of artificial marking methods.
Bouwman H., Cronje E. (2016): An 11-digit identification system for individual Nile crocodiles using natural markings. Koedoe 58: a1351.
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Research and conservation of wild crocodiles and husbandry of captive crocodiles requires the reliable identification of individuals. We present a method using the individual colour markings on the first 10 single-crest scutes on the tails of Nile crocodiles (Crocodylus niloticus). The scutes are scored by number for colour, with a prefix for left or right providing a binary 11-digit identification number (identification numbers [IDs]; e.g. 12232232242 and 22333233232) per crocodile. A survey of 359 captive Nile crocodiles showed no duplication. However, 42% had asymmetrical scute markings requiring a binary approach. There does not seem to be a change in patterns with age, except that the number of missing scutes increased. A small trial showed that this method can be applied in the field, although more work is needed to determine observer bias and establish parameters for observability in the field. It is unlikely that both left and right IDs would be obtainable for each individual, but other distinctive markings such as scute shape and damage can be used to register the two IDs to one individual. Having two independent IDs for each crocodile provides the possibility of two independent population estimates for equal effort without having to link left and right IDs to individuals. Our proposed method would be useful in conservation, individual tracking and husbandry. Conservation implications : A non-invasive marking and recapture method for Nile crocodile is presented whereby the first 10 single-crest scutes are scored for colour, allowing conservation practitioners to count and monitor crocodile populations and individuals. This method provides two equal-effort estimations of population size, as left and right hand sides are scored independently.
Boucher M., Tellez M., Anderson J. T. (2017): A tail of two crocs: coding tail-spot patterns for individual identification of American (Crocodylus acutus) and Morelet’s (Crocodylus moreletii) crocodiles. Mesoamerican Herpetology 4: 760-772.
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The marking of wildlife is an effective tool for the conservation and management of many species. A range of marking techniques is used in crocodylian management and conservation, and primarily involves the alteration of caudal scutes and the application of tags. Here we present the methods and application for two natural pattern identification techniques, which are used concurrently with research and monitoring of the American Crocodile (Crocodylus acutus) and Morelet’s Crocodile (Crocodylus moreletii) in Belize. We collected and analyzed 547 photographs of observed and captured crocodiles, and identified individuals by coding the spot patterns on the lateral portion of the tail. We investigated the efficacy of an established spot pattern coding protocol for crocodylians, and modified the original coding procedure by integrating vertical caudal scutes and irregular scale groups. We generated a total of 191 tail codes for 105 individual crocodiles (C. moreletii, n = 27; C. acutus, n = 78). The established methodology demonstrated an 84% success rate in differentiating individuals, whereas our new method showed 99% effectiveness in differentiating individuals and species. Using the spot pattern protocols, we identified no individuals with fully repeated codes (both tail sides). This project demonstrates that tail-spot patterns are distinctive, and consequently the coding of spot patterns is an effective way to passively identify individuals across the species. The proposed techniques are a cost-effective and simple tool that can be used by managers and communities to facilitate long-term demographic monitoring, and also can serve to encourage active participation in crocodile conservation via citizen science.
Forero Sr M. G., Lozano J. J., Balaguera-Reina S. A. (2019): Individual identification automation in Crocodylians through imagery processing: American Crocodile as a study case. Applications of Digital Image Processing XLII 11137: 111372A.
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The identification of a crocodile is a complex process. The most used method is invasive and dangerous. Recently, a new method, non-invasive, was introduced, in which the crocodile is identified by its number of post-occipital scales, nuchals, and backs. However, the scale count is done manually. In this work, we present a method based on image processing for the identification and counting of scales improving the above-mentioned method. The results obtained are reproducible and more reliable, facilitating the identification of the crocodiles for their population study.
Velasco Barbieri A. (2020): Individual identification of Crocodylus intermedius (Orinoco crocodile) using tail spot patterns. Cuadernos de Investigación UNED 12: 507-514.
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The Conservation Action Plan of the Orinoco crocodile (Crocodylus intermedius) includes the release of captive-bred specimens back into the wild. By monitoring these specimens in their natural habitat their adaptability is examined. However, an accurate identification system is necessary to recognize the individuals when they are recaptured. Determine if Swanepoel or Boucher, Tellez and Anderson crocodile identification methods are useful for the Orinoco crocodile. A total of 543 Orinoco crocodiles were photographed and each photo was vectorized by drawing dark spots greater than 25% for each scute, in the first 10 lines of double caudal scales of the tail on the right side. Two system codes were evaluated, one is a numeric code described by Swanepoel and the other is an additive code described by Boucher, Tellez and Anderson. A total of 464 Swanepoel codes and 537 Boucher, Tellez and Anderson codes based on the dark spot pattern of the scales on the right side of the tails were generated for the 543 specimens. Both methods yielded high code values, however, the one developed by Boucher, Tellez and Anderson, with a 98.90% differentiation of the analyzed specimens, worked better. The study confirms that using the method of spots in the tail of crocodiles is an effective tool for identifying individual crocodiles.
Desai B., Patel A., Patel V., Shah S., Raval M. S., Ghosal R. (2022): Identification of free-ranging mugger crocodiles by applying deep learning methods on UAV imagery. Ecological Informatics 72: 101874.
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Individual identification contributes significantly towards investigating behavioral mechanisms of animals and understanding underlying ecological principles. Most studies employ invasive procedures for individually identifying organisms. In recent times, computer-vision techniques have served as an alternative to invasive methods. However, these studies primarily rely on user input data collected from captivity or from individuals under partially restrained conditions. Challenges in collecting data from free-ranging individuals are higher when compared to captive populations. However, the former is a far more important priority for real-world applications. In this paper, we used Unmanned Aerial Vehicle (UAV) to collect data from free-ranging mugger crocodiles, Crocodylus palustris. We applied convolutional neural networks (CNNs) to individually identify muggers based on their dorsal scute patterns. The CNN model was trained on a data set of 88,000 images focusing on the mugger’s dorsal body. The data was collected from 143 individuals across 19 different locations along the western part of India. We trained two CNN models, one with an annotated bounding box approach, the YOLO-v5l, and another without annotations, the Inception-v3. We used two parameters, True Positive Rate (TPR) and True Negative Rate (TNR), to validate the efficiency of the trained models. Using YOLO-v5l, TPR (re-identification of trained muggers) and TNR (differentiating untrained muggers as ‘unknown’) values at the 0.84 decision threshold were 88.8% and 89.6%, respectively. The trained model showed 100% TNR for the non-mugger species, the Gharial, Gavialis gangeticus, and the Saltwater crocodile, Crocodylus porosus. The performance of the CNN model was reliable and accurate while using only 125 images per individual for training purposes. Inception-v3 underperformed for both the parameters, thus, showing that a bounding box approach (YOLO-v5l model) with background elimination is a promising method to individually identify free-ranging mugger crocodiles. Our manuscript demonstrates that UAV imagery appears to be a promising tool for non-invasive collection of data from free-ranging populations. It can be used to train open-source algorithms for individual identification. Further, the identification method is entirely based upon dorsal scute patterns, which can be applied to different crocodilian species, as well.
LIZARDS
Edwards A., Gardner C. (2010): Individual markings are a reliable non-invasive means of identification over time in blotched blue-tongued lizards, Tiliqua nigrolutea. Herpetofauna 40: 26-29.
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There is currently no information available on pattern stability in the blotched blue tongue lizard (Tiliqua nigrolutea). Markings displayed by blue tongue lizards are a combination of very dark blotches and bands on a paler background, and differences in these patterns between individuals are immediately distinguishable. However, it is not enough simply to state that these patterns appear unchanged over time, they must be quantified and scored in some way to confirm that this is so. This project has investigated whether pattern remains sufficiently constant over time to be used as a reliable method of individual identification in T. nigrolutea.
Pellitteri-Rosa D., Maiocchi V., Scali S., Racina L., Cavigioli L., Sacchi R., Fasola M., Galeotti P., Gentilli A., Tettamanti S., Pupin F. (2010): Photographic identification in reptiles: a matter of scales. Amphibia-Reptilia 31: 489-502.
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Photographic identification is a promising marking technique alternative to the toe-clipping, since it is completely harmless, cheap, and it allows long time identification of individuals. Its application to ecological studies is mainly limited by the time consuming to compare pictures within large datasets and the huge variation of ornamentation patterns among different species, which prevent the possibility that a single algorithm can effectively work for more than few species. Scales of Reptiles offer an effective alternative to ornamentations for computer aided identification procedures, since both shape and size of scales are unique to each individual, thus acting as a fingerprint like ornamentation patterns do. We used the Interactive Individual Identification System (I3S) software to assess whether different individuals of two species of European lizards (Podarcis muralis and Lacerta bilineata) can be reliably photographically identified using the pattern of the intersections among pectoral scales as fingerprints. We found that I3S was able to identify different individuals among two samples of 21 individuals for each species independently from the error associated to the ability of the operators in collecting pictures and in digitizing the pattern of intersections among pectoral scales. In a database of 1043 images of P. muralis collected between 2007 and 2008, the software recognized 98% of recaptures within each year, and 99% of the recaptures between years. In addition, 99% and 96% of matches were ranked among the top five, and no more than 5 minutes were needed for digitizing and processing each image. The lepidosis of reptiles is a reliable alternative to ornamentation patterns in photographic identification of reptiles, which can be effectively analysed using the I3S software. This result represents a significant improvement in photographic identification of reptiles since (i) this procedure can be easily extended to most other species of reptiles, (ii) all kind of individuals within a species can be marked (i.e., young, subadults and adults) despite the differences in ornamentation patterns, and (iii) it is the only technique for species, like the western green lizard, which lack a clear ornamentation pattern.
Knox C. D., Cree A., Seddon P. J. (2013): Accurate identification of individual geckos (Naultinus gemmeus) through dorsal pattern differentiation. New Zealand Journal of Ecology 37: 60-66.
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Mark–recapture methods are frequently used to obtain the data needed to inform conservation management of vulnerable species. This typically involves animals being captured, individually marked, then released and later detected by capture or resighting. This may be stressful for individual animals and can be resource-intensive. Photo-identification has emerged as an effective, and potentially less intrusive, alternative to traditional mark–recapture methods. Photo-identification can be used when animals have stable and individually identifiable natural markings that can be photographed in the field and used for long-term identification. A database of photographs and associated capture-history data can be used for robust estimation of demographic parameters such as population size and survival if an appropriate sampling regime is used. In addition, aspects of behavioural ecology, habitat use, movement patterns and home range can be examined. We outline the creation of a photographic database for jewelled geckos (Naultinus gemmeus) from Otago Peninsula and test the accuracy and speed with which human observers can use this database to differentiate between individual jewelled geckos. Jewelled geckos found during visual searches were captured, photographed and their photographs incorporated into a database. Volunteers then had to match 15 photos of randomly selected geckos to different photographs of the same animals, which were contained within a database of 855 individuals. All users correctly matched all 15 randomly selected geckos. Experience appeared to increase the speed of correct identifications. Our results show that photo-identification can provide an effective alternative to potentially more intrusive techniques such as toe-clipping or pit-tagging for jewelled geckos on the Otago Peninsula.
Rocha R., Carrilho T., Rebelo R. (2013): Iris photo-identification: A new methodology for the individual recognition of Tarentola geckos. Amphibia-Reptilia 34: 590-596.
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Gekkonid field studies are hampered by the difficulty to individually recognize individuals. In this study we assess the feasibility of using their variegated iris pattern to photo-identify Tarentola boettgeri bischoffi, a threatened Macaronesian endemic. Using a library of 924 photos taken over a 9-month period we also evaluate the use of the pattern matching software Interactive Individual Identification System (I3S) to match photos of known specimens. Individuals were clearly recognized by their iris pattern with no misidentifications, and using I3S lead to a correct identification of 95% of the recaptures in a shorter time than the same process when conducted visually by an observer. The method’s feasibility was improved by increasing the number of images of each animal in the library and hindered by photos that deviate from a horizontal angle.
Sreekar R., Purushotham C. B., Saini K., Rao S. N., Pelletier S., Chaplod S. (2013): Photographic capture-recapture sampling for assessing populations of the Indian gliding lizard Draco dussumieri. Plos One 8: e55935.
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The usage of invasive tagging methods to assess lizard populations has often been criticised, due to the potential negative effects of marking, which possibly cause increased mortality or altered behaviour. The development of safe, less invasive techniques is essential for improved ecological study and conservation of lizard populations. In this study, we describe a photographic capture-recapture (CR) technique for estimating Draco dussumieri (Agamidae) populations. We used photographs of the ventral surface of the patagium to identify individuals. To establish that the naturally occurring blotches remained constant through time, we compared capture and recapture photographs of 45 pen-marked individuals after a 30 day interval. No changes in blotches were observed and individual lizards could be identified with 100% accuracy. The population density of D. dussumieri in a two hectare areca-nut plantation was estimated using the CR technique with ten sampling occasions over a ten day period. The resulting recapture histories for 24 individuals were analysed using population models in the program CAPTURE. All models indicated that nearly all individuals were captured. The estimated probability for capturing D. dussumieri on at least one occasion was 0.92 and the estimated population density was 13±1.65 lizards/ha. Our results demonstrate the potential for applying CR to population studies in gliding lizards (Draco spp.) and other species with distinctive markings.
Gardiner R. Z., Doran E., Strickland K., Carpenter-Bundhoo L., Frère C. (2014): A face in the crowd: a non-invasive and cost effective photo-identification methodology to understand the fine scale movement of eastern water dragons. Plos One 9: e96992.
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Ectothermic vertebrates face many challenges of thermoregulation. Many species rely on behavioral thermoregulation and move within their landscape to maintain homeostasis. Understanding the fine-scale nature of this regulation through tracking techniques can provide a better understanding of the relationships between such species and their dynamic environments. The use of animal tracking and telemetry technology has allowed the extensive collection of such data which has enabled us to better understand the ways animals move within their landscape. However, such technologies do not come without certain costs: they are generally invasive, relatively expensive, can be too heavy for small sized animals and unreliable in certain habitats. This study provides a cost-effective and non-invasive method through photo-identification, to determine fine scale movements of individuals. With our methodology, we have been able to find that male eastern water dragons (Intellagama leuseurii) have home ranges one and a half times larger than those of females. Furthermore, we found intraspecific differences in the size of home ranges depending on the time of the day. Lastly, we found that location mostly influenced females’ home ranges, but not males and discuss why this may be so. Overall, we provide valuable information regarding the ecology of the eastern water dragon, but most importantly demonstrate that non-invasive photo-identification can be successfully applied to the study of reptiles.
Moro D., MacAulay I. (2014): Computer-aided pattern recognition of large reptiles as a noninvasive application to identify individuals. Journal of Applied Animal Welfare Science 17: 125-135.
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For large species, the capture and handling of individuals in capture–mark–recapture studies introduces nonhuman animal welfare issues associated with handling, physical marking, and possible wounding due to tag loss. The use of photographic identification for these species offers an alternative and less invasive marking technique. This study investigated the opportunity offered by photo identification to individually mark individuals of a large reptile, the perentie (Varanus giganteus), in Australia and therefore avoid the stress of physically capturing and handling. Photographs submitted by a remotely located community were first validated to confirm whether perenties could be individually identified from their spots electronically using a computer program. Computer-aided selection of unique patterns was found to be appropriate for the identification of individuals and confirmed 38 individuals during the sampling period. The value of this approach is 2-fold: There is a benefit to animal welfare in that handling an animal is not required to capture him or her, thus reducing capture-related stress; and confirmation that photo identification of distinctive patterns of the perentie is valid and offers a useful option to identify individuals of this large species.
Treilibs C. E., Pavey C. R., Hutchinson M. N., Bull C. M. (2016): Photographic identification of individuals of a free‐ranging, small terrestrial vertebrate. Ecology and Evolution 6: 800-809.
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Recognition of individuals within an animal population is central to a range of estimates about population structure and dynamics. However, traditional methods of distinguishing individuals, by some form of physical marking, often rely on capture and handling which may affect aspects of normal behavior. Photographic identification has been used as a less‐invasive alternative, but limitations in both manual and computer‐automated recognition of individuals are particularly problematic for smaller taxa (<500 g). In this study, we explored the use of photographic identification for individuals of a free‐ranging, small terrestrial reptile using (a) independent observers, and (b) automated matching with the Interactive Individual Identification System (I3S Pattern) computer algorithm. We tested the technique on individuals of an Australian skink in the Egernia group, Slater’s skink Liopholis slateri, whose natural history and varied scale markings make it a potentially suitable candidate for photo‐identification. From ‘photographic captures’ of skink head profiles, we designed a multi‐choice key based on alternate character states and tested the abilities of observers — with or without experience in wildlife survey — to identify individuals using categorized test photos. We also used the I3S Pattern algorithm to match the same set of test photos against a database of 30 individuals. Experienced observers identified a significantly higher proportion of photos correctly (74%) than those with no experience (63%) while the I3S software correctly matched 67% as the first ranked match and 83% of images in the top five ranks. This study is one of the first to investigate photo identification with a free‐ranging small vertebrate. The method demonstrated here has the potential to be applied to the developing field of camera‐traps for wildlife survey and thus a wide range of survey and monitoring applications.
Mello R. D. S. R., Jarvie S., Hazley L., Cree A. (2019): Comparison among three body parts and three software packages to optimise photographic identification of a reptile (tuatara, Sphenodon punctatus). Amphibia-Reptilia 40: 233-244.
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Individually identifying animals is key to ecological research. Natural marks and patterns of animals that remain stable through time may be used to identify individuals, either manually or with the aid of software. Here we compare the performance of three body parts (chest, right side and right eye) for individual identification of tuatara (Sphenodon punctatus) using three software packages (Wild-ID, I3S and StripeSpotter). We also explored pattern stability over time for the chest and right side, and whether the identification rate differed between life-history stages (adults and juveniles) for this long-lived reptile. We used photos of 196 tuatara, including captive and free-roaming individuals. In an initial analysis with a subset of individuals, chest and right side gave better identification rates than the eye when analysed using Wild-ID (the best-performing software). In a further analysis using all photos and Wild-ID, the false rejection rate was lower for chest (0.6%) than right side (2.4%). Although the effect of time on matching scores for chest (up to 3.5 y) and right-side (up to 1.8 y) was significant, it was not large enough to reduce the matching rate; furthermore, no difference in identification rate between adults and juveniles was detected. Overall, chest was the best-performing body part and Wild-ID the best-performing software. Thus, appropriate choice of body pattern for analysis may significantly increase the matching rate, and, as previously shown, software packages vary in performance.
Moore H. A., Champney J. L., Dunlop J. A., Valentine L. E., Nimmo D. G. (2020): Spot on: using camera traps to individually monitor one of the world’s largest lizards. Wildlife Research 47: 326-337.
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Estimating animal abundance often relies on being able to identify individuals; however, this can be challenging, especially when applied to large animals that are difficult to trap and handle. Camera traps have provided a non-invasive alternative by using natural markings to individually identify animals within image data. Although camera traps have been used to individually identify mammals, they are yet to be widely applied to other taxa, such as reptiles. We assessed the capacity of camera traps to provide images that allow for individual identification of the world’s fourth-largest lizard species, the perentie (Varanus giganteus), and demonstrate other basic morphological and behavioural data that can be gleaned from camera-trap images. Vertically orientated cameras were deployed at 115 sites across a 10 000 km2 area in north-western Australia for an average of 216 days. We used spot patterning located on the dorsal surface of perenties to identify individuals from camera-trap imagery, with the assistance of freely available spot ID software. We also measured snout-to-vent length (SVL) by using image-analysis software, and collected image time-stamp data to analyse temporal activity patterns. Ninety-two individuals were identified, and individuals were recorded moving distances of up to 1975 m. Confidence in identification accuracy was generally high (91%), and estimated SVL measurements varied by an average of 6.7% (min = 1.8%, max = 21.3%) of individual SVL averages. Larger perenties (SVL of >45 cm) were detected mostly between dawn and noon, and in the late afternoon and early evening, whereas small perenties (SVL of <30 cm) were rarely recorded in the evening. Camera traps can be used to individually identify large reptiles with unique markings, and can also provide data on movement, morphology and temporal activity. Accounting for uneven substrates under cameras could improve the accuracy of morphological estimates. Given that camera traps struggle to detect small, nocturnal reptiles, further research is required to examine whether cameras miss smaller individuals in the late afternoon and evening. Camera traps are increasingly being used to monitor reptile species. The ability to individually identify animals provides another tool for herpetological research worldwide.
Tomke S. A., Kellner C. J. (2020): Genotyping validates the efficacy of photographic identification in a capture‐mark‐recapture study based on the head scale patterns of the prairie lizard (Sceloporus consobrinus). Ecology and Evolution 10: 14309-14319.
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Population studies often incorporate capture-mark-recapture (CMR) techniques to gather information on long-term biological and demographic characteristics. A fundamental requirement for CMR studies is that an individual must be uniquely and permanently marked to ensure reliable reidentification throughout its lifespan. Photographic identification involving automated photographic identification software has become a popular and efficient noninvasive method for identifying individuals based on natural markings. However, few studies have (a) robustly assessed the performance of automated programs by using a double-marking system or (b) determined their efficacy for long-term studies by incorporating multi-year data. Here, we evaluated the performance of the program Interactive Individual Identification System (I3S) by cross-validating photographic identifications based on the head scale pattern of the prairie lizard (Sceloporus consobrinus) with individual microsatellite genotyping (N = 863). Further, we assessed the efficacy of the program to identify individuals over time by comparing error rates between within-year and between-year recaptures. Recaptured lizards were correctly identified by I3S in 94.1% of cases. We estimated a false rejection rate (FRR) of 5.9% and a false acceptance rate (FAR) of 0%. By using I3S, we correctly identified 97.8% of within-year recaptures (FRR = 2.2%; FAR = 0%) and 91.1% of between-year recaptures (FRR = 8.9%; FAR = 0%). Misidentifications were primarily due to poor photograph quality (N = 4). However, two misidentifications were caused by indistinct scale configuration due to scale damage (N = 1) and ontogenetic changes in head scalation between capture events (N = 1). We conclude that automated photographic identification based on head scale patterns is a reliable and accurate method for identifying individuals over time. Because many lizard or reptilian species possess variable head squamation, this method has potential for successful application in many species.
Gould J., Beranek C., Madani G. (2023): Dragon detectives: citizen science confirms photo-ID as an effective tool for monitoring an endangered reptile. Wildlife Research.
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Among amphibians and reptiles, traditional methods of capture–mark–recapture (CMR) have relied on artificial marking techniques (in particular, toe clipping), which has raised concerns because it may impact climbing ability, survival, and behaviour. A potential alternative involves the exploitation of natural biometric identifiers that are already present, including scale configuration or colour patterns. These natural markers can be applied in photo-based CMR, which has several advantages over artificial markers, including reduced costs, the reduction of harm or stress, and the potential for public participation in conservation and research. Our aim was to test the feasibility of applying citizen science in the manual visual identification of the endangered Monaro grassland earless dragon (Tympanocryptis osbornei) using dorsal pattern as a natural marker. We collected photographs of dorsal patterns of wild T. osbornei individuals using a smartphone device under field conditions. We subsequently recruited participants anonymously from the public using social media to complete an online survey, in which they were asked to correctly match these field-captured images of individuals from small image pools, mimicking the process of detecting recapture events. Participants were able to successfully detect recapture events from small image pools based solely on a comparison of dorsal patterns. High consensus was reached on all matches included in the online survey, with the majority vote among participants representing the correct matching of individuals on all occasions. Our results indicate that there is sufficient intra-specific variability and temporal stability in dorsal patterning for it to be used as a reliable natural marker for identifying T. osbornei at the individual level. Our findings suggest that photo-CMR could be applied to other agamids with similar dorsal patterns, making it a potentially valuable tool and an alternative to artificial marking for monitoring wild populations of Australian lizards in the future.
SNAKES
Yang D., Chen S., Chen Y., Yan Y. (2013): Using head patch pattern as a reliable biometric character for noninvasive individual recognition of an endangered pitviper Protobothrops mangshanensis. Asian Herpetological Research 4: 134-139.
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Mangshan pitviper, Protobothrops mangshanensis (formerly Zhaoermia mangshanensis) is endemic to China. Unfortunately, due to the decreasing size of its wild populations, this snake has been listed as critically endangered. Research carried out on the Mangshan pitviper’s population ecology and captive reproduction has revealed that the unique head patch patterns of different individuals may potentially be used as a noninvasive recognition biometric character. We collected head patch pattern images of 40 individuals of P. mangshanensis between 1994 and 2011. By comparing each pitviper’s head patch pattern, we found that the head patch pattern of individual snakes was different and unique. Additionally, we observed and recorded the head patch pattern characters of four adults and five juveniles before and after ecdysis. Our findings confirmed that head patch patterns of Mangshan pitvipers are unique and stable, remaining unchanged after ecdysis. Thus, individuals can be quickly identified by examining the head patch pattern within a specific recognition area on the head. This method may be useful for noninvasive individual recognition in many other species that display color patch pattern variations, especially in studies of endangered species where the use of invasive marking techniques is undesirable.
Bauwens D., Claus K., Mergeay J. (2018): Genotyping validates photo‐identification by the head scale pattern in a large population of the European adder (Vipera berus). Ecology and Evolution 8: 2985-2992.
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Capture‐mark‐recapture procedures are a basic tool in population studies and require that individual animals are correctly identified throughout their lifetime. A method that has become more and more popular uses photographic records of natural markings, such as pigmentation pattern and scalation configuration. As with any other marking tool, the validity of the photographic identification technique should be evaluated thoroughly. Here, we report on a large‐scale double‐marking study in which European adders (Vipera berus) were identified by both microsatellite genetic markers and by the pattern of head scalation. Samples that were successfully genotyped for all nine loci yielded 624 unique genotypes, which matched on a one‐to‐one basis with the individual assignments based on the head scalation pattern. Thus, adders considered as different individuals by their genotypes were also identified as different individuals by their head scalation pattern, and vice versa. Overall, variation in the numbers, shape, and arrangement of the head scales enabled us to distinguish among 3200+ photographed individual snakes. Adders that were repeatedly sequenced genetically over intervals of 2–3 years showed no indication whatsoever for a change in the head scale pattern. Photographic records of 900+ adders that were recaptured over periods of up to 12 years showed a very detailed and precise match of the head scale characteristics. These natural marks are thus robust over time and do not change during an individual’s lifetime. With very low frequency (0.3%), we detected small changes in scalation that were readily discernible and could be attributed to physical injury or infection. Our study provides a conclusive validation for the use of photo‐identification by head scale patterns in the European adder.
Rotger A., Colomar V., Moreno J. E., Parpal L. (2019): Photo-identification of horseshoe whip snakes (Hemorrhois hippocrepis, Linnaeus, 1758) by a semi-automatic procedure applied to wildlife management. Herpetological Journal 29: 304-307.
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Photo-identification is an increasingly used method for the study of animal populations. Natural marks such as coloration or scale pattern to identify individuals provide an inexpensive and less invasive alternative to conventional tagging methods. Photo-identification has previously been used to distinguish individual snakes, usually by comparing the pileus region. Nevertheless, this method is seldom used in capture-recapture studies. We show the effectiveness of photo-identification in snakes using specific software for individual recognition applied to a wildlife control study of horseshoe whip snakes. Photos were analysed with Automatic Photo Identification Suite (APHIS), which allowed us to compare the variability of head scale patterns surrounding the parietal shields instead of the traditional method of using large scale groups of the pileus. APHIS correctly identified 100% of recaptures of snakes. Although further studies are needed, the variability of the surrounding scales of the pileus region seems a robust method to identify and differentiate individuals.
Hoefer S., Rotger A., Mills S., Robinson N. J. (2021): Semi-automated photo-identification of Bahamian Racers (Cubophis vudii vudii). Acta Herpetologica 16: 133-136.
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Photo-identification is a non-invasive option for mark-recapture. Here, we tested the effectiveness of APHIS, a semi-automated photo-identification software, to distinguish between individual Bahamian Racers (Cubophis vudii vudii) on the island of Eleuthera, The Bahamas. Over 10 months, we photographed 50 Bahamian Racers. We first identified individuals by manually comparing colouration and scale patterns in the pileus and labial regions. Next, we used APHIS to identify recaptured individuals after manually identifying the locations of intersections of the scales in the pileus and labial regions. In addition, we assessed whether images taken with a hand-held camera or by a smart phone affected the accuracy of APHIS. All recaptured snakes were correctly identified using APHIS from both camera or phone images as validated by our manually derived results. We conclude that APHIS is an effective tool for photo-identification in snakes.
TURTLES
Dunbar S. G., Ito H. E., Bahjri K., Dehom S., Salinas L. (2014): Recognition of juvenile hawksbills Eretmochelys imbricata through face scale digitization and automated searching. Endangered Species Research 26: 137-146.
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Advancements in digital photography have facilitated the use of photo-ID to track individual animals, making this technique of great value for conservation biology. However, the time required to manually match new photographs to those stored in a database is proportional to the size of the database. Therefore, there is need for investigating the potential to automate the searching processes through computerized means. We encountered hawksbill turtles Eretmochelys imbricata (n = 2) that were members of an ongoing study but had lost flipper tags and shell etchings. To identify individuals, we first manually searched photographs of turtles previously captured and released. Manual visual matching of the 2 turtles encountered was successful for 100% of tested photographs. To investigate automated recognition of turtles in a database, we used the spot recognition program, I3S, to digitize scutes on the dorsal and lateral surfaces of the head and to compare spot patterns through the automated system. I3S successfully identified the 2 return turtles as the same turtles identified by the manual visual matching method. To assess the ability of I3S to identify turtles both present in and absent from the database, we blind-tested a series of photographs of turtle heads and faces using both manual visual methods and I3S. With I3S, 84.6% of the computerized photos were successfully matched with photos in the database, with scores produced ranging from 0.069 to 0.435. This study showed the potential for using a photo-database for long-term identification of individual turtles, but that the usefulness of a photo-database depends on the quality of the photos and the flexibility of the computer program used.
Carpentier A. S., Jean C., Barret M., Chassagneux A., Ciccione S. (2016): Stability of facial scale patterns on green sea turtles Chelonia mydas over time: A validation for the use of a photo-identification method. Journal of Experimental Marine Biology and Ecology 476: 15-21.
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Photographic identification (photo-ID) has been increasingly used as a reliable tool to track individuals over time, which provides essential knowledge on a species’ population dynamics. For photo-ID to work, natural markings must be individual-specific and stable over time. In sea turtle research, the use of facial scale patterns has been proposed and tested as a reliable means for individual recognition. Nevertheless, as sea turtles are migratory and long-lived individuals, the stability of those patterns over long periods of time is yet to be confirmed to validate this method. Stability of facial scale patterns was evaluated on green sea turtles, Chelonia mydas, sighted and photographed in coastal waters of Reunion Island (21°06 S, 55°36 E) or reared in captivity. From 53 free-ranging individuals previously identified, 90 head profiles were selected based on the photographic quality and the distinctiveness of facial scale patterns. The time interval between two sightings of a same individual ranged from 2 (738d) to 11 years (3954d). Additionally, facial scale patterns of captive green turtles from two different age groups were compared: (1) from adult-sized individuals reared in captivity (n = 13) and (2) from hatchlings and then at later developmental stages (until 1800d) to assess the stability of facial scale patterns throughout early juvenile development (n = 16). In both the free-ranging and captive-reared groups, there were no significant changes in facial scale patterns over time. Conversely, changes in pigmentation were observed in free-ranging turtles at successive sightings and in captive-reared turtles at different developmental stages. These results on the stability of facial scale patterns over time, combined with previous findings on the uniqueness of patterns between individual green turtles, validate the method of using facial scale patterns as a long-term identification tool for green turtles. Nonetheless, the variability of pigmentation patterns should be kept in mind when using photo-identification on sea turtle species.
Gatto C. R., Rotger A., Robinson N. J., Tomillo P. S. (2018): A novel method for photo-identification of sea turtles using scale patterns on the front flippers. Journal of Experimental Marine Biology and Ecology 506: 18-24.
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Photo-identification using animals’ natural markings is a cheaper and less impactful alternative to the use of more conventional external or internal tags for identifying individual animals. Photo-ID has already been successfully employed to monitor hard-shelled sea turtles, specifically using facial scales. However, photographing facial features might cause stress on photosensitive sea turtles, especially at night. Considering that there are more scales on the flippers than on the face and flipper photography is likely to be less invasive, we proposed an alternative method for photo-identification using the scale patterns on the front flippers. This method might also be suitable for successful photo-identification of hatchlings – which has been ineffectual using facial scales. To test the suitability of using the front flippers for photo-ID sea turtles, we took photos of the right flippers of adult and hatchling green turtles (Chelonia mydas) and olive ridley turtles (Lepidochelys olivacea) from Cabuyal, Costa Rica. The photos were analysed using APHIS, which delimits an area of interest with three reference points and then uses several additional points within this area to mark the intersections between scales. In both species, hatchlings and adults were correctly identified 92.9% and 81.8% of the time respectively but the capability of APHIS to correctly identify individuals was highly dependent on the quality of the photo. We detected similarities in flipper scale pattern between hatchlings of the same species but not between hatchlings from the same nest, indicating that hatchlings have unique flipper markings. The use of flipper scale patterns to identify individual sea turtles is comparable to the use of facial scales, without the risk of disturbing nesting females. Additionally, we were able to reliably identify individual hatchlings, which has not been possible using facial scales or conventional tagging techniques. Flipper scale patterns may potentially be a new methodology for identifying hatchlings both short- and long-term. We discuss the benefits and limitations of using sea turtle flipper scale patterns for identification as well as the benefits and limitation of APHIS.
Suriyamongkol T., Mali I. (2018): Feasibility of using computer-assisted software for recognizing individual Rio Grande Cooter (Pseudemys gorzugi). Copeia 106: 646-651.
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Mark-recapture methods used in population demography studies involve marking of animals, such as tagging, notching, and tattooing. These techniques are invasive and potentially harmful to the animals. Photo-identification using natural animal markings is less invasive and has become more widely used for a range of taxa including invertebrates, fishes, reptiles, amphibians, and mammals. During 2016 and 2017, we studied the demographics of the Rio Grande Cooter (Pseudemys gorzugi) using traditional mark-recapture techniques (i.e., shell notching and toe clipping). However, P. gorzugi displays plastral marks that could potentially be used for individual recognition. Because the photo-identification process ‘by-eye’ is time consuming, we tested the efficiency of three pieces of software, I3S Pattern+, Wild.ID, and APHIS, for individual identification of P. gorzugi using plastron pattern. Matching results of each program were generated into ranks with the 1st rank being the most likely match. Within the top 20 ranked images, Wild.ID yielded the highest number of correct matches (83.87%), followed by APHIS (ITM; 69.35%), APHIS (SPM; 67.74%), and I3S Pattern+ (61.29%). We found the quality of photos significantly contributed to the software effectiveness; however, turtle age and plastron wear did not affect the accuracy of the photo-identification software. We concluded that Wild.ID can be used as a non-invasive photo-recognition technique for P. gorzugi in a short-term population study.
Dunbar S. G., Anger E. C., Parham J. R., Kingen C., Wright M. K., Hayes C. T., Safi S., Holmberg J., Salinas L., Baumbach, D. S. (2021): HotSpotter: Using a computer-driven photo-id application to identify sea turtles. Journal of Experimental Marine Biology and Ecology 535: 151490.
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Photo identification (PID) in animal studies has been a widely used method for identifying individuals of many species based on unique natural markings and patterns. The use of PID has facilitated investigations in which residency, home ranges, and growth rates have been assessed. However, many PID studies in the past have relied heavily on manual photo matching. More recently, computer-assisted PID programs have been used to identify individuals of different sea turtle species, and reduced time investment in identifying individuals within specific populations. Still, some computer-based PID programs require significant time investment in ensuring photos are captured at consistent angles and lighting conditions, pre-processing image manipulations, and post-processing manual matching confirmation of potential matches provided by the program. For PID to be an effective time and money saving mechanism for wildlife research and conservation, these common drawbacks need to be addressed with a computer-assisted PID program that reduces manipulation and time investment burden, and consistently provides accurate and reliable results. In this study, we evaluated the accuracy of matching individual face images using the HotSpotter (HS) PID program by building a database of 2136 images of hawksbill (Eretmochelys imbricata) turtles, then querying the database with 158 new images to find matches for individual turtles. Overall, we found that with almost no pre-processing manipulation, and with images from highly variable underwater conditions, qualities, and angles, HS correctly matched individuals in the first choice 80% of the time, increasing to 91% in the first six choices. When assessing in-water images only, accuracy for matching increased from 84% in the first choice, to 94% by the sixth choice. We suggest that the integration of HS technology into a global, web-based PID system will increase the ability to remotely identify individual marine organisms on a global scale, and improve usability for community scientists who may have little to no technical training.
Markle C. E., Law T., Freeman H. C., Caverhill B., Davy C. M., Hathaway J., McNeil J., Moxley K., Richer S., Chow-Fraser P. (2021): Using the Blanding’s turtle (Emydoidea blandingii) plastron as a ‘fingerprint’: Photo identification of an endangered species. Canadian Wildlife Biology and Management 10: 47-61.
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The ability to uniquely identify individuals is critical to estimating and monitoring trends in population sizes, one of the key metrics used to evaluate a species’ conservation status and success of mitigation strategies. For freshwater turtles, shell notching and/or passive integrated transponder (PIT) tags are commonly used to mark individuals. However, because notch codes and PIT tags can be lost over time and require more invasive procedures, we explored if photographs offer an effective method to reliably identify individuals. The Blanding’s turtle (Emydoidea blandingii) is a globally endangered species with distinct black and yellow markings on its plastron. We used the I3S Pattern software with custom parameters to classify patterns on Blanding’s turtle plastrons and to identify individuals. We analyzed 826 plastron images from 707 individual Blanding’s turtles taken between 1998 and 2019 from 12 study areas distributed throughout their Canadian range. When plastron photos were pooled across the sampled range (i.e., all study areas), there was an 84% probability of correctly identifying an individual turtle within the top 3 suggested matches, whereas when identifying Blanding’s turtles within a specific study area, identification accuracy was 82% in Central Ontario and 97% in Nova Scotia. Individual identification from plastron markings did not work well in areas where iron staining obscured the plastron pattern or for hatchlings and juveniles whose patterns changed over time. For example, the only misclassification in the Nova Scotia study area was for a turtle with photos through various life stages. In areas without iron staining, plastron photo identification offers a cost-effective, non-invasive method to identify individual adult Blanding’s turtles to support population monitoring and community science initiatives, and has the potential to assist with range-wide coordination to counteract illegal wildlife trade.
Tabuki K., Nishizawa H., Abe O., Okuyama J., Tanizaki S. (2021): Utility of carapace images for long-term photographic identification of nesting green turtles. Journal of Experimental Marine Biology and Ecology 545: 151632.
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The accurate identification of wildlife is necessary for biological research and population monitoring. In sea turtles, artificial tags have commonly been used for individual identification, but tagging has low long-term reliability because of inherent problems such as tag loss and the stress caused by invasive tagging. Photographic identification (Photo-ID) has been increasingly used as an alternative to tagging. Mostly, facial scute patterns have been used as Photo-ID means for sea turtles; however, for Photo-ID of turtles on nesting beaches, there is a risk of disturbing individuals when attempting to access the head region and capture the entire face. Thus, here, we focused on the posterior part of the carapace (fifth vertebral scute), which can be photographed more easily and less invasively, as a useful natural marker for the identification of nesting green turtles (Chelonia mydas). To establish the utility of the carapace for individual identification, we used photographs (167 images from 77 individuals) collected in a nesting survey conducted over 28 years at Ishigaki Island, Japan, and verified the long-term identifiability of carapace. We initially matched individual turtle images with the HotSpotter program to assess the automated recognition of images, and then conducted a blind test to visually validate the results of automated recognition. High matching accuracy was achieved, especially within the same nesting season (98.1%; 52 out of 53 queries), and logistic regression indicated that the matching accuracy was over 70% when the photographing interval was ≤4 years, which is longer than the mean remigration interval for nesting green turtles on Ishigaki Island. In the blind test of visual identification, 95.4% of the image pairs were correctly judged (as those of the same individual or different individuals). These results show that a query image can be successfully identified in the database even if automated matching to the same individual fails or if the query is taken from a newly recruited individual. This study shows the long-term identifiability of nesting green turtles using carapace photographs and proposes a practical Photo-ID method that is conducive to citizen science.
Buteler C., Bardier C., Cabrera M. R., Gonzalez Y., Vélez-Rubio G. M. (2022): To tag or not to tag: comparative performance of tagging and photo-identification in a long-term mark-recapture of Juvenile Green Turtles (Chelonia mydas). Amphibia-Reptilia 44: 45-58.
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Capture-mark-recapture (CMR) methods are widely used to estimate population parameters and to collect data on animal demography, migration, and life history. Sea turtle research programs generally use artificial tags, an invasive method. Photo-identification (PID) methods have become an important tool for animal identification. Herein, we assessed the effectiveness of a PID method for marking green turtles (Chelonia mydas) compared to traditional methods (artificial tags). As a part of a long-term CMR study, green turtles have been tagged and photographed since 2001. We analyzed 1917 captures with left and right side photographs of tagged turtles using Wild-ID software, these results were compared with tag-recapture data to assess error rates (false positives and negatives), and different effectiveness metrics. A combination of PID and tags (a match from either method was considered a recapture) was the most error-free and efficient criterion for identification of recaptures; however, it was the most time consuming and invasive criterion as well. We also assessed the effect of image quality indicators on the error rates of PID. We found that turtle cleanliness increases the similarity of images (indirectly related to false negatives), but we found no effect of sharpness, angle, light condition, or width and height in pixels of images on error rates. We could conclude that if image quality is improved, tags could be substituted by PID. However, we strongly recommend researchers to consider local situations (occurrence of by-catch or stranded dead turtles, for which tags are still necessary) before deciding to apply only PID.
Papafitsoros K., Dimitriadis C., Mazaris A. D., Schofield G. (2022): Photo‐identification confirms polyandry in loggerhead sea turtles. Marine Ecology: e12696.
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While polyandry in sea turtles is indicated through multiple-paternity analyses of offspring, confirmed observations of the same female mating with multiple males are extremely challenging to obtain. To contribute to this discussion, we analysed a long-term photo-identification database (>20 years) of adult male and female loggerhead sea turtles frequenting the breeding area of Zakynthos, Greece, Mediterranean. A total of 38 records of mating individuals within and across seasons were assimilated via field surveys and citizen science records between 2003 and 2020. For one female, we recorded it mating with two different males within a 5.5-h interval on the same day in 2015. This observation constitutes the first direct evidence of polyandry in sea turtles, in addition to highlighting the potential for photo-identification to contribute information on less well-known aspects of sea turtle biology, such as validating outputs of genetic studies.
Neves-Ferreira, I., Mello-Fonseca, J., & Ferreira, C. E. (2023). Photo-identification shows the spatio-temporal distribution of two sea turtle species in a Brazilian developmental foraging ground. Marine Biology 170: 83.
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Sea turtles spend most of their life cycle in foraging grounds. Research in developmental habitats is crucial to understanding individual dynamics and to support conservation strategies. One approach to gather information in foraging grounds is the use of cost-effective and non-invasive techniques that allow public participation. The present study aimed to use photographic-identification (photo-ID) to investigate the spatio-temporal distribution of Chelonia mydas and Eretmochelys imbricata. Furthermore, we describe fibropapillomatosis occurrence. This work was carried out at subtropical rocky reefs of the Brazilian coast in Arraial do Cabo (22°57ʹS, 42°01ʹW), within a sustainable conservation unit. A total of 641 images were obtained through social media screening (n = 447), citizen science (n = 168), or intentional capture (n = 26) dated between 2006 and 2021. Additionally, 19 diving forms (between 2019 and 2021) were received from citizen scientists. All diving forms presented at least one turtle. Photo-ID identified 174 individuals of C. mydas, with 45 being resighted, while E. imbricata had 32 individuals, with 7 individuals resighted. The median interval between the first and last individual sighting was 1.7 years for C. mydas and 2.4 years for E. imbricata. Fibropapillomatosis was only observed in C. mydas, with a prevalence of 13.99% (20 of 143 individuals) and regression in 2 individuals (10.00%). Our results indicated that Arraial do Cabo is an important development area with individuals residing for at least 6 years. This study demonstrated that social media, along with photo-ID, can be useful to provide sea turtle estimates in a foraging ground using a non-invasive, low-cost method.