Pelage Patterns Research Articles

Evaluating the performance of semiautomated photographic identification programs for leopard seals

AbstractThe photographic identification (photo‐ID) of individual animals can be time‐consuming and erroneous. Recent efforts to collect photographs of leopard seals (Hydrurga leptonyx) from across their range have necessitated the technological streamlining of photo‐ID. We constructed a dataset containing 595 photographs of the head and body of individuals recorded in New Zealand between 2008 and 2022 to test the performance of semiautomated 3 photo‐ID programs: HotSpotter, Interactive Individual Identification System's Pattern+ (I3S), and Wild‐ID. We classified attributes of photographs (e.g., quality) and individuals (i.e., pelage patterns) to assess their effect on performance. We compared performance using Top20 and Top1 Accuracy, defined as the proportion of test photographs where the highest ranked correct identity was in the top 20 and top 1, respectively, matched reference photographs. HotSpotter outperformed I3S and Wild‐ID in both Top20 and Top1 Accuracy of most assessed attributes. Maximizing HotSpotter's performance may be achieved through several methods, including increasing the number and variety of photographs of individuals in the dataset. HotSpotter will likely perform better with photographs without obstructions (e.g., debris from beaches), such as on the pack ice of their primary Antarctic range. We highlight the viability of HotSpotter in assisting the photo‐ID of leopard seals, and more broadly, other species with similar markings.

Taxonomic status of Tamarinus imperator subgrisescens (Lönnberg, 1940) (Cebidae, Callitrichinae)

The emperor tamarin, Tamarinus imperator, is composed of two subspecies, the nominal type, T. i. imperator, distributed between the Acre and Purus Rivers, whose range is limited between the Brazilian state of Acre and Peru are unbounded, and T. i. subgrisescens, occurring in Peru, Bolivia, and Brazil, in the Brazilian states of Acre and Amazonas. Morphologically, both taxa are easily identifiable by the pelage pattern (chromogenetic fields), and even being easily distinguishable, both lineages are considered subspecies according to the criterion based on the Biological Concept of Species from the 1970s, even without presenting some necessary criteria, such as the intergradation zone. Here we analyzed pelage traits, cranial morphometry, Cytochrome-b divergence, and distributional pattern data applying the premises of integrative taxonomy to elucidate the taxonomic status of both lineages. We hypothesize that both lineages are considered full species through a series of criteria for species recognition, such as distinguishability, level of phenotypical divergences of several morphological complexes with congruence among them, and some genetic divergence. The hybridization is unknown and the low or the lack of sampling in target areas does not allow us to determine whether a hybridization or even contact zone between the two lineages exists indeed. All character sets analyzed were congruent with each other and reinforced the high level of divergences between the two subspecies including several pelage differences, morphometry (descriptive statistics, PCA, and MANOVA), and mitochondrial DNA Cytochrome-b divergence. Most of the distribution in both lineages are allopatric, and the levels of intra-lineage phenotypical variation are much lower than between the lineages.

The Status of Snow Leopards (Panthera uncia) Conservation in Jigme Khesar Strict Nature Reserve at Haa, Bhutan

Study of Snow Leopard (Panthera uncia, Schreber, 1775) using infrared camera traps along actively used tracks, scent-sprayed rocks, scats and scrape sites was conducted in the mountains of Jigme Khesar Strict Nature Reserve, Haa, Bhutan between October and December 2015 and it is still being continued. A total of 17 grids, each measuring 16km2 were sampled covering a total area of 272 km2 . Thirty-four camera traps were stationed in 17 grids and in a total of 60 trap nights, 215 images of Snow Leopard were captured out of which 163 images were considered for analysis. Using the pelage patterns on the body parts such as forelimbs, face, flanks and dorsum of the tail of the captured individuals, a total of ten different individuals were identified including the one that was recorded during the extended period trapping for a month. Capture history of camera trap station G9 (Kampula) indicated that it had the highest concentration of the species as individuals JKSNR 3, 4, 8 and 9 were all captured at the same station. The capture timing of the species confirms its crepuscular nature as most of them were recorded between dawn and the dusk. Our results suggest that the species can be well monitored and conserved using camera traps. The Reserve can focus on patrolling and monitoring of the species in the identified high-density areas for maintaining the moving population to perpetuity.

Evaluating the prevalence and spatial distribution of giraffes injured by non‐target poaching

AbstractIllegal harvest (poaching) is a geographically widespread threat to animal populations. Wire snares are a common poaching technique used in the Global South and are indiscriminate with respect to species, age, and sex of individual animals that they capture. When caught, relatively large mammals frequently break free from the snares, suffering injuries in the process. The prevalence of snaring injuries as well as the ecological and conservation implications of such patterns have not been widely investigated for many animal populations. We evaluated the prevalence and spatial distribution of giraffes (Giraffa camelopardalis) with snaring injuries in Murchison Falls National Park, Uganda, a system experiencing high rates of wire snare poaching. We conducted photographic spatial encounter surveys along five fixed road transects. We photographed detected giraffes, recorded whether a snaring injury was present, and identified individuals via autonomous image processing of pelage patterns. We fitted a spatial capture‐recapture (SCR) model to the encounter history data to estimate abundance and predict the spatial distribution of injured giraffes. We detected 1306 (sub) adult giraffes from the surveys and predicted 1939 (±80) via the SCR model. We encountered 26 giraffes with snaring injuries, corresponding to a population‐level snaring rate of 1.4%. Individuals with higher movement scales were more at risk of being snared. Though not fatal across the three‐month duration of this study, the injuries likely lead to secondary infections, disability, and potentially death in the long term. We explore the implications of bearing snaring injuries for ecology, behavior, and conservation of affected species.

Biological Correlates with Degree of Introgressive Hybridization between Coyotes Canis latrans and Wolves Canis sp. in Pennsylvania, U.S.A.

Descendants of introgressive hybridization between species may have evolutionary advantages over their parental species. Prior studies have documented evidence of introgressive hybridization between coyotes, dogs, grey wolves and eastern wolves. This study attempts to attribute morphology and pelage patterns of Pennsylvania coyotes to sex, ecoregion, and the degree of coyote-wolf introgressive hybridization. A total of 192 coyotes were genotyped at 63 ancestry informative SNPS to determine the percent of coyote genome attributable to wolf origin (percent wolf). Females had higher percent wolf than males, which could be the result of lower survivorship in hybrid males. Percent wolf, sex, and ecoregion each were found to independently influence size using general linear model analysis, and the effect of sex was most pronounced. Coyotes from Northeastern and northcentral ecoregions of Pennsylvania were larger in size and possessed a higher percent wolf. Moreover, coyotes with higher percent wolf were larger, less red in some parts of their pelage, and had a different pelage patchiness composition. This correlates with previous studies that showed ecoregions with increased deer density correlated to coyotes with higher percent wolf. Size and percent wolf may be adaptively advantageous in Northeastern Pennsylvania where there is a relatively high deer population abundance. Furthermore, the degree of redness within coyotes may be used as an indicator for introgression levels for population managers, aiding in understanding the shifting ecological role of coyotes.

SealID: Saimaa Ringed Seal Re-Identification Dataset.

Wildlife camera traps and crowd-sourced image material provide novel possibilities to monitor endangered animal species. The massive data volumes call for automatic methods to solve various tasks related to population monitoring, such as the re-identification of individual animals. The Saimaa ringed seal (Pusa hispida saimensis) is an endangered subspecies only found in Lake Saimaa, Finland, and is one of the few existing freshwater seal species. Ringed seals have permanent pelage patterns that are unique to each individual and that can be used for the identification of individuals. A large variation in poses, further exacerbated by the deformable nature of seals, together with varying appearance and low contrast between the ring pattern and the rest of the pelage makes the Saimaa ringed seal re-identification task very challenging, providing a good benchmark by which to evaluate state-of-the-art re-identification methods. Therefore, we make our Saimaa ringed seal image (SealID) dataset (N = 57) publicly available for research purposes. In this paper, the dataset is described, the evaluation protocol for re-identification methods is proposed, and the results for two baseline methods—HotSpotter and NORPPA—are provided. The SealID dataset has been made publicly available.

Like mother like daughter: quantifying the relationship between relatedness and phenotypic similarity in leopard pelage patterns

Like mother like daughter: quantifying the relationship between relatedness and phenotypic similarity in leopard pelage patterns

Density estimates reveal that fragmented landscapes provide important habitat for conserving an endangered mesopredator, the spotted-tailed quoll

Native predators are increasingly exposed to habitat loss and fragmentation globally. When developing conservation and management strategies, it is important to determine whether fragmented landscapes can still support similar predator densities to intact areas, and thereby constitute important habitat for these species. The spotted-tailed quoll (Dasyurus maculatus) is an endangered Australian mesopredator that is often considered to be forest-dependent. While quolls are known to occur in some fragmented forest landscapes, it is unclear whether these areas represent sub-optimal habitat where quolls merely persist, or whether quolls can still occur at densities similar to those observed in intact forest landscapes. We used camera traps to detect quolls in both a fragmented and intact forested site, over three years. We used each quoll’s unique pelage pattern to identify individual quolls and estimate population density at each site. We were able to assign more than 94% of quoll image sequences across both sites to identify 173 individuals during the study. Density estimates of 0.13–0.66 quolls per km2 at the fragmented site were comparable to estimates of 0.28–0.48 quolls per km2 at the intact site. Our results highlight the importance of retaining and protecting forest fragments for the conservation of endangered quoll populations.

Matching individual Ladoga ringed seals across short-term image sequences

Automated wildlife reidentification has attracted increasing attention in recent years as it provides a non-invasive tool to identify and to track individual wild animals over time. In this paper, the first steps are taken towards the automatic photo-identification of the Ladoga ringed seals (Pusa hispida ladogensis). A method is proposed that takes a sequence of images, each containing multiple individuals as the input, and produces cropped images of seals grouped based on one certain individual per group. The method starts by detecting each seal from the images and proceeds to matching the individual seals between the images. It is shown that high grouping accuracy can be obtained with a general-purpose image retrieval method on an image sequence taken from the same location within a relatively short period of time. Each resulting group contains multiple images of one individual with slightly different variations, for example, in pose and illumination. Utilizing these images simultaneously provides more information for the individual re-identification compared to the traditional approach, i.e., which utilizes just one image at a time. It is further demonstrated that a convolutional neural network based method can be used to extract the unique pelage patterns of the seals despite the low contrast. Finally, a method is proposed and experiments with the novel Ladoga ringed seals data are carried out to provide a proof-of-concept for the individual re-identification.

Camera trapping and spatially explicit capture–recapture for the monitoring and conservation management of lions: Insights from a globally important population in Tanzania

Abstract Accurate and precise estimates of population status are required to inform and evaluate conservation management and policy interventions. Although the lion (Panthera leo) is a charismatic species receiving increased conservation attention, robust status estimates are lacking for most populations. While for many large carnivores population density is often estimated through spatially explicit capture–recapture (SECR) applied to camera trap data, the lack of pelage patterns in lions has limited the application of this technique to the species. Here, we present one of the first applications of this methodology to lion, in Tanzania's Ruaha‐Rungwa landscape, a stronghold for the species for which no empirical estimates of status are available. We deployed four camera trap grids across habitat and land management types, and we identified individual lions through whisker spots, scars and marks, and multiple additional features. Double‐blind identification revealed low inter‐observer variation in photo identification (92% agreement), due to the use of xenon‐flash cameras and consistent framing and angles of photographs. Lion occurred at highest densities in a prey‐rich area of Ruaha National Park (6.12 ± SE 0.94 per 100 km2), and at relatively high densities (4.06 ± SE 1.03 per 100 km2) in a community‐managed area of similar riparian‐grassland habitat. Miombo woodland in both photographic and trophy hunting areas sustained intermediate lion densities (1.75 ± SE 0.62 and 2.25 ± SE 0.52 per 100 km2, respectively). These are the first spatially explicit density estimates for lion in Tanzania, including the first for a trophy hunting and a community‐managed area, and also provide some of the first insights into lion status in understudied miombo habitats. We discuss in detail the methodology employed, the potential for scaling‐up over larger areas, and its limitations. We suggest that the method can be an important tool for lion monitoring and explore the implications of our findings for lion management.

A novel camera trapping method for individually identifying pumas by facial features.

Camera traps (CTs), used in conjunction with capture–mark–recapture analyses (CMR; photo‐CMR), are a valuable tool for estimating abundances of rare and elusive wildlife. However, a critical requirement of photo‐CMR is that individuals are identifiable in CT images (photo‐ID). Thus, photo‐CMR is generally limited to species with conspicuous pelage patterns (e.g., stripes or spots) using lateral‐view images from CTs stationed along travel paths. Pumas (Puma concolor) are an elusive species for which CTs are highly effective at collecting image data, but their suitability to photo‐ID is controversial due to their lack of pelage markings. For a wide range of taxa, facial features are useful for photo‐ID, but this method has generally been limited to images collected with traditional handheld cameras. Here, we evaluate the feasibility of using puma facial features for photo‐ID in a CT framework. We consider two issues: (1) the ability to capture puma facial images using CTs, and (2) whether facial images improve human ability to photo‐ID pumas. We tested a novel CT accessory that used light and sound to attract the attention of pumas, thereby collecting face images for use in photo‐ID. Face captures rates increased at CTs that included the accessory (n = 208, χ 2 = 43.23, p ≤ .001). To evaluate if puma faces improve photo‐ID, we measured the inter‐rater agreement of 5 independent assessments of photo‐ID for 16 of our puma face capture events. Agreement was moderate to good (Fleiss’ kappa = 0.54, 95% CI = 0.48–0.60), and was 92.90% greater than a previously published kappa using conventional CT methods. This study is the first time that such a technique has been used for photo‐ID, and we believe a promising demonstration of how photo‐ID may be feasible for an elusive but unmarked species.

Genetic analysis of hybridization between white-handed (Hylobates lar) and pileated (Hylobates pileatus) gibbons in a contact zone in Khao Yai National Park, Thailand.

Natural hybridization has played various roles in the evolutionary history of primates. Its consequences range from genetic introgression between taxa, formation of hybrid zones, and formation of new lineages. Hylobates lar, the white-handed gibbon, and Hylobates pileatus, the pileated gibbon, are largely allopatric species in Southeast Asia with a narrow contact zone in Khao Yai National Park, Thailand, which contains both parental types and hybrids. Hybrid individuals in the zone are recognizable by their intermediate pelage and vocal patterns, but have not been analyzed genetically. We analyzed mitochondrial and microsatellite DNA of 52 individuals to estimate the relative genetic contributions of the parental species to each individual, and the amount of introgression into the parental species. We obtained fecal samples from 33 H. lar, 15 H. pileatus and four phenotypically intermediate individuals in the contact zone. Both mitochondrial and microsatellite markers confirmed distinct differences between these taxa. Both H. lar and H. pileatus contributed to the maternal lineages of the hybrids based on mitochondrial analysis; hybrids were viable and present in socially normal reproductive pairs. The microsatellite analysis identified ten admixed individuals, four F1 hybrids, which corresponded to phenotypic hybrids, and six H. lar-like backcrosses. All 15 H. pileatus samples were identified as originating from genetically H. pileatus individuals with no H. lar admixture; hence, backcrossing is biased toward H. lar. A relatively low number of phenotypic hybrids and backcrossed individuals along with a high number of parental types indicates a bimodal hybrid zone, which suggests relatively strong bias in mate selection between the species.

Social Sensors for Wildlife: Ecological Opportunities in the Era of Camera Ubiquity

Expansive study areas, such as those used by highly-mobile species, provide numerous logistical challenges for researchers. Community science initiatives have been proposed as a means of overcoming some of these challenges but often suffer from low uptake or limited long-term participation rates. Nevertheless, there are many places where the public has a much higher visitation rate than do field researchers. Here we demonstrate a passive means of collecting community science data by sourcing ecological image data from the digital public, who act as “eco-social sensors,” via a public photo-sharing platform—Flickr. To achieve this, we use freely-available Python packages and simple applications of convolutional neural networks. Using the Weddell seal (Leptonychotes weddellii) on the Antarctic Peninsula as an example, we use these data with field survey data to demonstrate the viability of photo-identification for this species, supplement traditional field studies to better understand patterns of habitat use, describe spatial and sex-specific signals in molt phenology, and examine behavioral differences between the Antarctic Peninsula’s Weddell seal population and better-studied populations in the species’ more southerly fast-ice habitat. While our analyses are unavoidably limited by the relatively small volume of imagery currently available, this pilot study demonstrates the utility an eco-social sensors approach, the value of ad hoc wildlife photography, the role of geographic metadata for the incorporation of such imagery into ecological analyses, the remaining challenges of computer vision for ecological applications, and the viability of pelage patterns for use in individual recognition for this species.

A natural history of Chlorocebus dryas from camera traps in Lomami National Park and its buffer zone, Democratic Republic of the Congo, with notes on the species status of Cercopithecus salongo

The natural history and taxonomic status of two central African primates, Cercopithecus dryas and Cercopithecus salongo have long been in question. Recent studies confirmed that C. dryas is a basal member of the savanna monkey clade, and that it prefers dense undergrowth in lowland rainforest. While these studies advanced our knowledge of this enigmatic species, key aspects of its natural history remain poorly documented. Furthermore, the lack of a field study that documents pelage patterns of both sexes and different age classes of C. dryas has led to a disagreement over the validity of C. salongo as a sister taxon to C. dryas. Using the results of two multi-strata camera trap surveys in Lomami National Park (Democratic Republic of the Congo) and its buffer zone, we conducted a third survey in the understory of degraded forest to accumulate videos of C. dryas/salongo. We used these videos to test the hypothesis that C. dryas and C. salongo are synonymous, and to assess the species' group composition, density, behavior and vocalizations. Camera traps revealed an ontogenetic change in pelage pattern that supports the view that C. salongo is the adult of C. dryas. Videos revealed that adult males develop a blue perineum and scrotum, and a red subcaudal patch, similar to other savanna monkeys. We provide a preliminary assessment of C. dryas' group composition, density, behavior, and vocalizations. This long-overlooked monkey is an exceptional member of the Chlorocebus clade, and all aspects of its biology require further investigation.

Taxonomic diversity of Cebuella in the western Amazon: Molecular, morphological and pelage diversity of museum and free-ranging specimens.

We investigated the diversity of the pygmy marmoset, Cebuella pygmaea, by comparing genetic, morphological and pelage traits of animals from Peru and Ecuador. We extracted DNA from museum specimen osteocrusts and from fecal samples collected from free-ranging individuals. We sequenced the mtDNA cytochrome b gene and the control region from samples collected at 13 different sites and used Bayesian inference and Maximum Likelihood to identify distinct clades. We took measurements of the crania of a subset of these specimens (n = 26) and ran a logistic regression to determine if any of the cranial measurements (n = 22) could predict a specimen's clade. In addition, we examined the pelage patterns of the museum specimens and photographs taken of free-ranging individuals and divided them into pelage types based on coloration of the underbelly. We identified two divergent clades, and two distinct groups with clear geographic boundaries within one of those clades. Two measurements of the zygomatic bone perfectly predicted a given individual's mtDNA clade. We found four distinct pelage patterns in our samples, but these patterns are variable within clades and among individuals within the same population. These analyses indicate that the two recognized subspecies of pygmy marmoset should be elevated to the species level (C. pygmaea and C. niveiventris) based on molecular and cranial differences but not on pelage patterns. We provide evidence on the geographic limits of the two clades and identify regions where additional sampling is required to better define the geographic distribution of the two clades.

How can spatio-temporal overlap in mammals assist in maximizing biodiversity conservation? A case study of Periyar Tiger Reserve

While global mammalian diversity is collapsing due to increased poaching and habitat loss, evidence-based conservation in protected areas is often regarded as a panacea. Tiger reserves in India set an example, where annual camera trap monitoring is conducted for understanding the trends in the tiger population. However, less is known about other co-predators and their prey species that occur in the same area. The fundamental hindrance being the absence of individual pelage pattern within these species (i.e. unique pattern on the body), as well as the absence of species-specific monitoring. As a result, there is a demand in techniques that can avail maximum biodiversity information from the existing monitoring protocols. Here, we conducted camera trapping in Periyar Tiger Reserve to evaluate spatiotemporal overlaps within different carnivores, and between prey-predators. Camera trapping was conducted at high resolution (2 km2) for 30 days at 253 locations that yielded 6092 photographs of 18 mammals. Their temporal overlap was estimated using ‘overlap’ R package, while the spatial association was estimated using ‘co-occur’ package. Three large-ranging top predators (tiger, leopard and dhole) were found to have activity peaks segregated temporally. Relationship of these predators with their prey species highlighted the role of body sizes, where largest predator (tiger) had higher overlap with large-bodied prey (gaur and sambar), while small-bodied predator (leopard and dhole) overlapped small-bodied prey (barking deer and wild pig). Results highlight the importance of large-sized prey in conserving the tiger densities of this region. However, selectively conserving only large-bodied prey can have repercussions on other sympatric carnivores, who require different body-sized prey species. Our results have implications for all protected areas in the tropical developing countries, which are mostly smaller in area with species-centered conservation agenda. We highlight the importance of considering species-specific carrying capacity of all co-predators in the region, to optimally conserve the prey-base through habitat restoration, so as to maximize biodiversity conservation within a limited area.

Apparent piebald variants in quolls (Dasyurus): examples of three recent cases in the spotted-tailed quoll Dasyurus maculatus

Pelage patterning plays an important role in animal behaviour. Variation in pelage patterns can change with pigment distribution and quantity in individuals. We present three cases of apparent piebaldism – a condition where the body is patchily unpigmented – in the spotted-tailed quoll Dasyurus maculatus. Using a comprehensive dataset of historical descriptions (from Dunlop et al. 2020), we conclude that these cases represent the first description of this phenotype in the genus Dasyurus, but acknowledge capture and testing of these individuals is required to be certain of the cause. Little is known about the implications of pelage patterning in quoll species and further investigation is required to understand the evolutionary and functional role of unaffected and unpigmented variants.

Giant otter Pteronura brasiliensis density and abundance in Llanos Orientales de Colombia in the Orinoco basin

AbstractThe giant otter Pteronura brasiliensis, categorized as Endangered on the IUCN Red List, was once widely distributed throughout South America. By the middle of the 20th century the giant otter had become locally extinct along the main rivers of the Orinoco basin. Although some populations seem to have recovered, the paucity of information available does not permit a full evaluation of the species' conservation status. The objective of this study was to estimate the abundance and density of the giant otter population along the Orinoco river in the municipality of Puerto Carreño, Vichada, Colombia, where there is important commercial and recreational fishing. Thirty-nine linear km were surveyed, repeatedly, with a total of 315 km of surveys. Population size was estimated by direct counts of individuals. All individuals detected were photographed and identified individually from their throat pelage patterns. In total, 30 otters were identified, giving a minimum density of 0.77 individuals per km, one of the highest reported for the species in Colombia. Given the high density in this well-developed area, our results highlight the importance of this population for the conservation of the species.

Spatial partial identity model reveals low densities of leopard and spotted hyaena in a miombo woodland

AbstractDecline in global carnivore populations has led to increased demand for assessment of carnivore densities in understudied habitats. Spatial capture–recapture (SCR) is used increasingly to estimate species densities, where individuals are often identified from their unique pelage patterns. However, uncertainty in bilateral individual identification can lead to the omission of capture data and reduce the precision of results. The recent development of the two‐flank spatial partial identity model (SPIM) offers a cost‐effective approach, which can reduce uncertainty in individual identity assignment and provide robust density estimates. We conducted camera trap surveys annually between 2016 and 2018 in Kasungu National Park, Malawi, a primary miombo woodland and a habitat lacking baseline data on carnivore densities. We used SPIM to estimate density for leopard (Panthera pardus) and spotted hyaena (Crocuta crocuta) and compared estimates with conventional SCR methods. Density estimates were low across survey years, when compared to estimates from sub‐Saharan Africa, for both leopard (1.9 ± 0.19 sd adults/100 km2) and spotted hyaena (1.15 ± 0.42 sd adults/100 km2). Estimates from SPIM improved precision compared with analytical alternatives. Lion (Panthera leo) and wild dog (Lycaon pictus) were absent from the 2016 survey, but lone dispersers were recorded in 2017 and 2018, and both species appear limited to transient individuals from within the wider transfrontier conservation area. Low densities may reflect low carrying capacity in miombo woodlands or be a result of reduced prey availability from intensive poaching. We provide the first leopard density estimates from Malawi and a miombo woodland habitat, whilst demonstrating that SPIM is beneficial for density estimation in surveys where only one camera trap per location is deployed. The low density of large carnivores requires urgent management to reduce the loss of the carnivore guild in Kasungu National Park and across the wider transfrontier landscape.

Giraffe taxonomy, geographic distribution and conservation

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