A Multi-Point Identification Approach for the Recognition of Individual Leopards (Panthera pardus kotiya)

Simple Summary

All of the previous research on photography-based leopard identification was conducted based on the assumption that leopard spots and rosette formations do not change in shape or form. We observed 29 instances of changes to spot and rosette formations in continuously observed leopards at Yala National Park, Block 1. Since the previous approaches have flaws and errors, the same leopard may be misdiagnosed and counted numerous times, overestimating leopard populations if the spot and rosette formation of a leopard has changed. To address this issue, we developed the multi-point leopard identification method, which is a novel process for identifying Sri Lankan leopards. The minimum leopard population of Yala National Park, Block 1, on 31 March 2021, was established during the study.

Abstract

Visual leopard identifications performed with camera traps using the capture–recapture method only consider areas of the skin that are visible to the equipment. The method presented here considered the spot or rosette formations of either the two flanks or the face, and the captured images were then compared and matched with available photographs. Leopards were classified as new individuals if no matches were found in the existing set of photos. It was previously assumed that an individual leopard’s spot or rosette pattern would not change. We established that the spot and rosette patterns change over time and that these changes are the result of injuries in certain cases. When compared to the original patterns, the number of spots may be lost or reduced, and some spots or patterns may change in terms of their prominence, shape, and size. We called these changes “obliterate changes” and “rejig changes”, respectively. The implementation of an earlier method resulted in a duplication of leopard counts, achieving an error rate of more than 15% in the population at Yala National Park. The same leopard could be misidentified and counted multiple times, causing overestimated populations. To address this issue, we created a new two-step methodology for identifying Sri Lankan leopards. The multi-point identification method requires the evaluation of at least 9–10 spot areas before a leopard can be identified. Moreover, the minimum leopard population at the YNP 1 comprises at least 77 leopards and has a density of 0.5461 leopards per km².

Genetics and Evolution of Mammalian Coat Pigmentation

The diversity of mammalian coat colors, and their potential adaptive significance, have long fascinated scientists as well as the general public. The recent decades have seen substantial improvement in our understanding of their genetic bases and evolutionary relevance, revealing novel insights into the complex interplay of forces that influence these phenotypes. At the same time, many aspects remain poorly known, hampering a comprehensive understanding of these phenomena. Here we review the current state of this field and indicate topics that should be the focus of additional research. We devote particular attention to two aspects of mammalian pigmentation, melanism and pattern formation, highlighting recent advances and outstanding challenges, and proposing novel syntheses of available information. For both specific areas, and for pigmentation in general, we attempt to lay out recommendations for establishing novel model systems and integrated research programs that target the genetics and evolution of these phenotypes throughout the Mammalia.

Sunda clouded leopard Neofelis diardi densities and human activities in the humid evergreen rainforests of Sumatra

Most species of wild felids are threatened, but for many little is known about their status in the wild. For the cryptic and elusive Vulnerable Sunda clouded leopard Neofelis diardi, key metrics such as abundance and occupancy have been challenging to obtain. We conducted an intensive survey for this species on the Indonesian island of Sumatra. We deployed camera traps across four study areas that varied in elevation and threats, for a total of 28,404 trap nights, resulting in 114 independent clouded leopard photographs, in which we identified 18 individuals. Using a Bayesian spatially explicit capture–recapture analysis, we estimated clouded leopard density to be 0.8–2.4 individuals/100 km2. The highest predicted occurrence of people was at lower altitudes and closer to the forest edge, where we categorized more than two-thirds of people recorded by camera traps as bird poachers, 12.5% each as ungulate/tiger poachers and non-timber collectors, and < 2% as fishers. Our findings provide important insights into the status of this little known species in Sumatra. We recommend that the large volume of camera-trap data from other Sumatran landscapes be used for an island-wide assessment of the clouded leopard population, to provide up-to-date and reliable information for guiding future conservation planning.

Coloration in Mammals

Mammalian colors and color patterns are some of the most diverse and conspicuous traits found in nature and have been widely studied from genetic/developmental and evolutionary perspectives. In this review we first discuss the proximate causes underlying variation in pigment type (i.e., color) and pigment distribution (i.e., color pattern) and highlight both processes as having a distinct developmental basis. Then, using multiple examples, we discuss ultimate factors that have driven the evolution of coloration differences in mammals, which include background matching, intra- and interspecific signaling, and physiological influences. Throughout, we outline bridges between developmental and functional investigatory approaches that help broaden knowledge of mammals' memorable external appearances, and we point out areas for future interdisciplinary research.

Melanism evolution in the cat family is influenced by intraspecific communication under low visibility

Melanism in the cat family has been associated with functions including camouflage, thermoregulation and parasite resistance. Here we investigate a new hypothesis proposing that the evolution of melanism in cats has additionally been influenced by communication functions of body markings. To evaluate this hypothesis, we assembled a species-level data set of morphological (body marks: white marks on the backs of ears) and ecological (circadian activity: arrhythmic/nocturnal, and environmental preference: open/closed) characteristics that could be associated with communication via body markings, and combined these data with a dated molecular phylogeny. Next, we tested the association between melanism and communication, first by relating species’ body marks with their ecological conditions, using a Bayesian implementation of the threshold model. Second, to explore the evolution of characteristics potentially influencing melanism in cat species, we modeled their evolution relative to melanism using models of coordinated vs. independent character changes. Our results suggest that white marks are associated with intraspecific communication between individuals that have non-melanistic phenotypes, as well as towards melanistic individuals (without white marks). The absence of white marks in a melanistic individual tends to be a limiting condition for intraspecific visual communication at night, resulting in an evolutionary dilemma for these species, i.e. to be almost invisible at night, but not to communicate visually. The comparative analysis of several evolutionary models indicated more support for the evolution of melanism being coordinated with the evolution of arrhythmic activity and white marks on the backs of ears.

Carnivore hotspots in Peninsular Malaysia and their landscape attributes

Mammalian carnivores play a vital role in ecosystem functioning. However, they are prone to extinction because of low population densities and growth rates, and high levels of persecution or exploitation. In tropical biodiversity hotspots such as Peninsular Malaysia, rapid conversion of natural habitats threatens the persistence of this vulnerable group of animals. Here, we carried out the first comprehensive literature review on 31 carnivore species reported to occur in Peninsular Malaysia and updated their probable distribution. We georeferenced 375 observations of 28 species of carnivore from 89 unique geographic locations using records spanning 1948 to 2014. Using the Getis-Ord Gi*statistic and weighted survey records by IUCN Red List status, we identified hotspots of species that were of conservation concern and built regression models to identify environmental and anthropogenic landscape factors associated with Getis-Ord Gi* z scores. Our analyses identified two carnivore hotspots that were spatially concordant with two of the peninsula's largest and most contiguous forest complexes, associated with Taman Negara National Park and Royal Belum State Park. A cold spot overlapped with the southwestern region of the Peninsula, reflecting the disappearance of carnivores with higher conservation rankings from increasingly fragmented natural habitats. Getis-Ord Gi* z scores were negatively associated with elevation, and positively associated with the proportion of natural land cover and distance from the capital city. Malaysia contains some of the world's most diverse carnivore assemblages, but recent rates of forest loss are some of the highest in the world. Reducing poaching and maintaining large, contiguous tracts of lowland forests will be crucial, not only for the persistence of threatened carnivores, but for many mammalian species in general.

Occurrence of leucism in Eira barbara (Carnivora, Mustelidae) in Brazil

Abstract The occurrence of anomalous coloration (albinism, leucism and melanism) in mammals is a rare phenomenon in nature, but this phenomenon has been reported for several species of mammals. In this study, we report on the occurrence of leucism in Eira barbara by examining three road-killed individuals and two sightings of live animals in Reserva Particular do Patrimônio Natural Santuário do Caraça, southeastern Brazil. In addition, we examined tayra specimens housed in mammal collections from Brazil and USA. The animals found dead and those sighted had a whitish yellow fur on the body and head, resulting in lighter coloration than the coloring pattern commonly observed in tayras. Despite these lighter color pattern, the specimens showed parts of soft tissue, such as iris and the skin, with pigmentation very similar to that present in individuals with the typical color pattern. This set of factors indicates the specimens recorded were in fact leucistic and not albino. Among the specimens examined in the scientific collections, we found nine individuals from different localities that presented the whitish yellow color pattern. Some studies attribute the higher frequency of cases of leucism due to small populations and / or with some mechanism of reproductive isolation. Thus, analysis of the genetic variability of populations containing individuals with such characteristics should be considered. On the other hand, the occurrence of polymorphic color phenotype in tayras indicates that hypotheses related to the fixation of recessive characteristics, or on possible environmental adaptive advantages of these phenotypes can be tested.

Historical mitochondrial diversity in African leopards (Panthera pardus) revealed by archival museum specimens

Once found throughout Africa and Eurasia, the leopard (Panthera pardus) was recently uplisted from Near Threatened to Vulnerable by the International Union for the Conservation of Nature (IUCN). Historically, more than 50% of the leopard's global range occurred in continental Africa, yet sampling from this part of the species' distribution is only sparsely represented in prior studies examining patterns of genetic variation at the continental or global level. Broad sampling to determine baseline patterns of genetic variation throughout the leopard's historical distribution is important, as these measures are currently used by the IUCN to direct conservation priorities and management plans. By including data from 182 historical museum specimens, faecal samples from ongoing field surveys, and published sequences representing sub-Saharan Africa, we identify previously unrecognized genetic diversity in African leopards. Our mtDNA data indicates high levels of divergence among regional populations and strongly differentiated lineages in West Africa on par with recent studies of other large vertebrates. We provide a reference benchmark of genetic diversity in African leopards against which future monitoring can be compared. These findings emphasize the utility of historical museum collections in understanding the processes that shape present biodiversity. Additionally, we suggest future research to clarify African leopard taxonomy and to differentiate between delineated units requiring monitoring or conservation action.

Mapping black panthers: Macroecological modeling of melanism in leopards (Panthera pardus)

The geographic distribution and habitat association of most mammalian polymorphic phenotypes are still poorly known, hampering assessments of their adaptive significance. Even in the case of the black panther, an iconic melanistic variant of the leopard (Panthera pardus), no map exists describing its distribution. We constructed a large database of verified records sampled across the species’ range, and used it to map the geographic occurrence of melanism. We then estimated the potential distribution of melanistic and non-melanistic leopards using niche-modeling algorithms. The overall frequency of melanism was ca. 11%, with a significantly non-random spatial distribution. Distinct habitat types presented significantly different frequencies of melanism, which increased in Asian moist forests and approached zero across most open/dry biomes. Niche modeling indicated that the potential distributions of the two phenotypes were distinct, with significant differences in habitat suitability and rejection of niche equivalency between them. We conclude that melanism in leopards is strongly affected by natural selection, likely driven by efficacy of camouflage and/or thermoregulation in different habitats, along with an effect of moisture that goes beyond its influence on vegetation type. Our results support classical hypotheses of adaptive coloration in animals (e.g. Gloger’s rule), and open up new avenues for in-depth evolutionary analyses of melanism in mammals.

Recurrent evolution of melanism in South American felids

Morphological variation in natural populations is a genomic test bed for studying the interface between molecular evolution and population genetics, but some of the most interesting questions involve non-model organisms that lack well annotated reference genomes. Many felid species exhibit polymorphism for melanism but the relative roles played by genetic drift, natural selection, and interspecies hybridization remain uncertain. We identify mutations of Agouti signaling protein (ASIP) or the Melanocortin 1 receptor (MC1R) as independent causes of melanism in three closely related South American species: the pampas cat (Leopardus colocolo), the kodkod (Leopardus guigna), and Geoffroy’s cat (Leopardus geoffroyi). To assess population level variation in the regions surrounding the causative mutations we apply genomic resources from the domestic cat to carry out clone-based capture and targeted resequencing of 299 kb and 251 kb segments that contain ASIP and MC1R, respectively, from 54 individuals (13–21 per species), achieving enrichment of ~500–2500-fold and ~150x coverage. Our analysis points to unique evolutionary histories for each of the three species, with a strong selective sweep in the pampas cat, a distinctive but short melanism-specific haplotype in the Geoffroy’s cat, and reduced nucleotide diversity for both ancestral and melanism-bearing chromosomes in the kodkod. These results reveal an important role for natural selection in a trait of longstanding interest to ecologists, geneticists, and the lay community, and provide a platform for comparative studies of morphological variation in other natural populations.

Color polymorphism in closely related animal species provides an opportunity to study how the balance between natural selection and genetic drift shapes the evolution of appearance and form. The cat family, Felidae, is especially interesting; 13 of 37 extant species exhibit polymorphism for melanism, but evidence for any adaptive role is lacking, in part because the potential benefits of melanism to felid predators are not clear, and in part because the tools for genomic analysis of natural populations are limited. We identify the mutations responsible for melanism in three closely related South American wild felids, the pampas cat, the kodkod, and Geoffroy’s cat, then adapt a new approach for targeted genome sequencing to characterize molecular variation in the region surrounding each melanism mutation. We find that each mutation has developed independently, with strong evidence for natural selection in the black pampas cat, and reduced genetic variation in the entire population of kodkods. Our results demonstrate that some “black cats” are black not by chance, but by selection for a mutation that provides increased fitness.

How the leopard hides its spots: ASIP mutations and melanism in wild cats

The occurrence of melanism (darkening of the background coloration) is documented in 13 felid species, in some cases reaching high frequencies at the population level. Recent analyses have indicated that it arose multiple times in the Felidae, with three different species exhibiting unique mutations associated with this trait. The causative mutations in the remaining species have so far not been identified, precluding a broader assessment of the evolutionary dynamics of melanism in the Felidae. Among these, the leopard (Panthera pardus) is a particularly important target for research, given the iconic status of the ‘black panther’ and the extremely high frequency of melanism observed in some Asian populations. Another felid species from the same region, the Asian golden cat (Pardofelis temminckii), also exhibits frequent records of melanism in some areas. We have sequenced the coding region of the Agouti Signaling Protein (ASIP) gene in multiple leopard and Asian golden cat individuals, and identified distinct mutations strongly associated with melanism in each of them. The single nucleotide polymorphism (SNP) detected among the P. pardus individuals was caused by a nonsense mutation predicted to completely ablate ASIP function. A different SNP was identified in P. temminckii, causing a predicted amino acid change that should also induce loss of function. Our results reveal two additional cases of species-specific mutations implicated in melanism in the Felidae, and indicate that ASIP mutations may play an important role in naturally-occurring coloration polymorphism.