The cost of sympatry: spatio-temporal patterns in leopard dietary and physiological responses to tiger competition gradient in Rajaji Tiger Reserve, Uttarakhand, India.

Apex predators have critical roles in maintaining the structure of ecosystem functioning by controlling intraguild subordinate populations. Such dominant-subordinate interactions involve agonistic interactions including direct or indirect impacts on the subordinates. As these indirect effects are often mediated through physiological processes, it is important to quantify such responses to better understand population parameters. We used a large carnivore intraguild system involving tiger (Panthera tigris) and leopard (Panthera pardus) to understand the dietary and physiological responses under a spatio-temporal gradient of tiger competition pressures in Rajaji Tiger Reserve (RTR) between 2015 and 2020. We conducted systematic faecal sampling in the winters of 2015 and 2020 from the park to assess diet and physiological measures. Analyses of leopard-confirmed faeces suggest a dietary-niche separation as a consequence of tiger competition. In 2020, we found an increased occurrence of large-bodied prey species without tiger competition in western-RTR. Physiological measures followed the dietary responses where leopards with large-sized prey in the diet showed higher fT3M and lower fGCM measures in western-RTR. In contrast, eastern-RTR leopards showed lower levels of fT3M and fGCM in 2020, possibly due to intense competition from tigers. Overall, these patterns strongly indicate a physiological cost of sympatry where competition with dominant tigers resulted in elevated nutritional stress. We recommend expansion of leopard monitoring and population estimation efforts to buffers, developing appropriate plans for human-leopard conflict mitigation and intensive efforts to understand leopard population dynamics patterns to ensure their persistence during the ongoing Anthropocene.

Heronry distribution and site preference dynamics of tree-nesting colonial waterbirds in Tamil Nadu.

Anthropogenic disturbance and climate change have significantly affected the distribution of wetlands globally and particularly in Asian countries. Various types of wetlands are harboured across all the biogeographic zones in India. These wetlands provide vital ecological services and are rich in biodiversity. However, anthropogenic pressures continue to be a threat to these wetlands by affecting the flora and fauna that depend on them. Tree-nesting colonial waterbirds are vulnerable to these pressures as their colonies are typically located in wetlands and associated areas. Disturbances to these areas have resulted in the loss or shifting of many heronries. The present study was conducted in the Indian state of Tamil Nadu during the period of 2017-2019 to document the existing and previously unknown heronries of the landscape. A total of 101 heronries were documented in 22 districts. The Little Cormorant was the most dominant species, occurring in 79% of the sites, with relative abundances of 24% and 26% during 2017-2018 and 2018-2019, respectively. A total of 23 tree species were utilized by the birds for nesting and Vachellia nilotica trees were used for nesting in about 25% of the heronries. 19% of the heronries were situated inside protected areas and 81% were located outside protected areas. Out of the 58 active nesting sites reported in 2005, 43 have been lost or are no longer active. Species distribution modelling with presence only data indicated that the sites with a high probability of occurrence were confined to the major waterbodies and rivers. Spatial correlation showed that the heronries were dispersed randomly across the landscape. The population dynamics within heronries and colonial nesting waterbirds' response to various environmental factors must be monitored continuously to conserve these heronries.

Tracking forest loss and fragmentation between 1930 and 2020 in Asian elephant (Elephas maximus) range in Nepal.

Forest cover is the primary determinant of elephant distribution, thus, understanding forest loss and fragmentation is crucial for elephant conservation. We assessed deforestation and patterns of forest fragmentation between 1930 and 2020 in Chure Terai Madhesh Lanscape (CTML) which covers the entire elephant range in Nepal. Forest cover maps and fragmentation matrices were generated using multi-source data (Topographic maps and Landsat satellite images of 1930, 1975, 2000, and 2020) and spatiotemporal change was quantified. At present, 19,069 km2 forest cover in CTML is available as the elephant habitat in Nepal. Overall, 21.5% of elephant habitat was lost between 1930 and 2020, with a larger (12.3%) forest cover loss between 1930 and 1975. Area of the large forests (Core 3) has decreased by 43.08% whereas smaller patches (Core 2, Core 1, edge and patch forests) has increased multifold between 1930 and 2020. The continued habitat loss and fragmentation probably fragmented elephant populations during the last century and made them insular with long-term ramifications for elephant conservation and human-elephant conflict. Given the substantial loss in forest cover and high levels of fragmentation, improving the resilience of elephant populations in Nepal would urgently require habitat and corridor restoration to enable the movement of elephants.

High frequency of an otherwise rare phenotype in a small and isolated tiger population.

Most endangered species exist today in small populations, many of which are isolated. Evolution in such populations is largely governed by genetic drift. Empirical evidence for drift affecting striking phenotypes based on substantial genetic data are rare. Approximately 37% of tigers (Panthera tigris) in the Similipal Tiger Reserve (in eastern India) are pseudomelanistic, characterized by wide, merged stripes. Camera trap data across the tiger range revealed the presence of pseudomelanistic tigers only in Similipal. We investigated the genetic basis for pseudomelanism and examined the role of drift in driving this phenotype's frequency. Whole-genome data and pedigree-based association analyses from captive tigers revealed that pseudomelanism cosegregates with a conserved and functionally important coding alteration in Transmembrane Aminopeptidase Q (Taqpep), a gene responsible for similar traits in other felid species. Noninvasive sampling of tigers revealed a high frequency of the Taqpep p.H454Y mutation in Similipal (12 individuals, allele frequency = 0.58) and absence from all other tiger populations (395 individuals). Population genetic analyses confirmed few (minimal number) tigers in Similipal, and its genetic isolation, with poor geneflow. Pairwise FST (0.33) at the mutation site was high but not an outlier. Similipal tigers had low diversity at 81 single nucleotide polymorphisms (mean heterozygosity = 0.28, SD = 0.27). Simulations were consistent with founding events and drift as possible drivers for the observed stark difference of allele frequency. Our results highlight the role of stochastic processes in the evolution of rare phenotypes. We highlight an unusual evolutionary trajectory in a small and isolated population of an endangered species.

Patterns and determinants of elephant attacks on humans in Nepal.

Attacks on humans by Asian elephant (Elephas maximus) is an extreme form of human-elephant conflict. It is a serious issue in southern lowland Nepal where elephant-related human fatalities are higher than other wildlife. Detailed understanding of elephant attacks on humans in Nepal is still lacking, hindering to devising appropriate strategies for human-elephant conflict mitigation. This study documented spatiotemporal pattern of elephant attacks on humans, factors associated with the attacks, and human/elephant behavior contributing to deaths of victims when attacked. We compiled all the documented incidences of elephant attacks on humans in Nepal for last 20 years across Terai and Chure region of Nepal. We also visited and interviewed 412 victim families (274 fatalities and 138 injuries) on elephant attacks. Majority of the victims were males (87.86%) and had low level of education. One fourth of the elephant attacks occurred while chasing the elephants. Solitary bulls or group of subadult males were involved in most of the attack. We found higher number of attacks outside the protected area. People who were drunk and chasing elephants using firecrackers were more vulnerable to the fatalities. In contrast, chasing elephants using fire was negatively associated with the fatalities. Elephant attacks were concentrated in proximity of forests primarily affecting the socioeconomically marginalized communities. Integrated settlement, safe housing for marginalized community, and community grain house in the settlement should be promoted to reduce the confrontation between elephants and humans in entire landscape for their long-term survival.

Effects of faecal inorganic content variability on quantifying glucocorticoid and thyroid hormone metabolites in large felines: Implications for physiological assessments in free-ranging animals.

Faecal glucocorticoid (GC) and triiodothyronine (T3) metabolites and their interactions are increasingly used to monitor perceived stress and nutritional challenges in free-ranging animals. However, a number of extrinsic and intrinsic factors including hormone-inert dietary materials, inorganic matters etc. are known to affect reliable hormone metabolite quantifications. In this study, the impacts of inorganic matter (IOM) on faecal GC (fGCMs) and T3 (fT3Ms) metabolite measure were addressed in wild tiger (n = 193 from Terai Arc landscape, India) and captive lion (n = 120 from Sakkarbaug Zoological Garden, Gujarat, India) and possible corrective measures were evaluated. The wild tiger samples contained highly variable IOM content (9-98%, mostly with > 40% IOM) compared to captive Asiatic lion (17-57%, majority with < 40% IOM). Significant correlations were observed between IOM content and tiger fGCM (r = -0.46, p = 0.000), fT3M (r = -0.58, p = 0.000) and lion fT3M measures (r = -0.43, p = 0.003). Two corrective measures viz. removing samples with ≥ 80% IOM and subsequently expressing concentrations as per gram of organic dry matter (instead of total dry matter) reduced IOM influence on tiger fGCM, fT3M and lion fT3M, without affecting lion fGCM measures. The corrective measures changed the interpretations of fT3M data of field-collected tiger samples with no significant changes in fGCM (both tiger and lion) and fT3M (lion) data. As faecal IOM content is common in many wild species, the results emphasize the need to reduce IOM-driven hormone data variation for ecologically relevant interpretations towards species conservation.

Sequencing and annotation of the endangered wild buffalo (Bubalus arnee) mitogenome for taxonomic assessment.

The wild water buffalo (Bubalus arnee) is one of the most endangered and least studied large bovid in the Indian subcontinent. India retains 90% of the estimated global population of >4000 individuals as two fragmented populations in Assam and Chhattisgarh, both threatened by habitat loss and degradation, hunting, disease from livestock, and hybridization with the domestic buffalos. Small, fragmented population size and potential hybridisation pressures from co-occurring domestic buffalos are the major conservation challenges. For the first time, we sequenced the 16,357 bp long mitogenome of three opportunistically collected wild water buffalo samples from Assam (n = 1) and Chhattishgarh (n = 2). The annotated sequence has a base composition of 26.4% T, 26.6% C, 33.1% A and 13.9% G depicting an AT-rich mitogenome composition, including 13 protein-coding genes (11,361 bp), 22 transfer RNA (tRNA) (1514 bp), two ribosomal genes (2525 bp), and a non-coding control region (928 bp). The gene order is conserved with other bovid species. Comparative mitogenome analyses showed both populations are genetically similar but significantly different from domestic buffalo. We also identified structural differences in seven tRNA secondary structures between both species. The genetic distance between wild buffalo and other bovids varied between 0.103 and 0.122. Multiple Bayesian phylogenetic trees showed that both wild and domestic water buffalo formed sister clades which were paraphyletic to other potentially sympatric species of genus Bos. This study provides baseline information on wild buffalo mitogenome for further research on phylogeny, phylogeography and hybrid assessment and help conserving this endangered species.

Genetic analyses reveal population structure and recent decline in leopards (Panthera pardus fusca) across the Indian subcontinent.

BACKGROUND: Large carnivores maintain the stability and functioning of ecosystems. Currently, many carnivore species face declining population sizes due to natural and anthropogenic pressures. The leopard, Panthera pardus, is probably the most widely distributed and highly adaptable large felid globally, still persisting in most of its historic range. However, we lack subspecies-level data on country or regional scale on population trends, as ecological monitoring approaches are difficult to apply on such wide-ranging species. We used genetic data from leopards sampled across the Indian subcontinent to investigate population structure and patterns of demographic decline. METHODS: We collected faecal samples from the Terai-Arc landscape of northern India and identified 56 unique individuals using a panel of 13 microsatellite markers. We merged this data with already available 143 leopard individuals and assessed genetic structure at country scale. Subsequently, we investigated the demographic history of each identified subpopulations and compared genetic decline analyses with countrywide local extinction probabilities. RESULTS: Our genetic analyses revealed four distinct subpopulations corresponding to Western Ghats, Deccan Plateau-Semi Arid, Shivalik and Terai region of the north Indian landscape, each with high genetic variation. Coalescent simulations with microsatellite loci revealed a possibly human-induced 75-90% population decline between ∼120-200 years ago across India. Population-specific estimates of genetic decline are in concordance with ecological estimates of local extinction probabilities in these subpopulations obtained from occupancy modeling of the historic and current distribution of leopards in India. CONCLUSIONS: Our results confirm the population decline of a widely distributed, adaptable large carnivore. We re-iterate the relevance of indirect genetic methods for such species in conjunction with occupancy assessment and recommend that detailed, landscape-level ecological studies on leopard populations are critical to future conservation efforts. Our approaches and inference are relevant to other widely distributed, seemingly unaffected carnivores such as the leopard.

Rapid molecular assays for species and sex identification of swamp deer and other coexisting cervids in human-dominated landscapes of the Terai region and upper Gangetic plains, northern India: implications in understanding species distribution and population parameters.

Burgeoning pressures of habitat loss is a major cause of herbivore decline across India, forcing them to coexist with humans in non-protected areas. Their conservation in such landscapes is challenging due to paucity of ecological and demographic information. The northern subspecies of swamp deer, Rucervus duvaucelii duvaucelii, is one such herbivore that lives across human dominated landscapes in Terai region and upper Gangetic plains of north India. Here, we describe species-specific molecular markers and a cervid-specific molecular sexing assay for swamp deer and four other coexisting cervids sambar, chital, barking deer and hog deer. Our markers show species-specific band patterns and a high success rate of 88.21% in large number of field collected referencesamples for all species. Faecal pellets from pilot swamp deer survey samples from upper Ganges basin show 93.81% success rate, and only 5.5% misidentification based on morphological characteristics. Our cervid-specific molecular sexing multiplex assay accurately ascertained 81.15% samples to respective sexes. These molecular approaches provide an easy, quick and cheap option to generate critical information on herbivore population parameters and aid their conservation in this mosaic of protected and non-protected grassland habitats.

Palghat gap reveals presence of two diverged populations of Nilgiri tahr (Nilgiritragus hylocrius) in Western Ghats, India.

Genetic analysis is an important tool in understanding population structure, genetic diversity, and phylogenetics of endangered species likely to be affected by microevolution and anthropogenic factors. Western Ghats landscape is one of the identified biodiversity hotspots in India, and micro-evolutionary processes are observed in this landscape due to the presence of the gaps in the mountain ranges. Nilgiri tahr is endemic to and distributed in this landscape while very little is known about genetic characteristics, population structure and impact of these gaps on the species. In the present study, two different populations of Nilgiri tahr from the north (NPG) and south (SPG) of Palghat gap (PG) were studied using the cytochrome b gene (Cyt b; 310 bp) of mtDNA genome in the Western Ghats, India. Two variable sites were observed in the Cyt b fragment while the mean pairwise genetic distance between these two populations was 0.007. All the samples phylogenetically clustered in either north or south of PG. The presence of shallow divergence indicates the presence of suitable habitat in past which may have facilitated movement between NPG and SPG. A subsequent change in Paleo-climatic conditions and gradual formation of PG may have resulted in population diversification during the Pleistocene. Besides, Forensically Informative Nucleotide Sequence (FINS) observed would help in geo-assigning any individual from NPG or SPG to understand the likely influences on population demography due to poaching.

Influence of connectivity, wild prey and disturbance on occupancy of tigers in the human-dominated western Terai Arc Landscape.

Occupying only 7% of their historical range and confined to forested habitats interspersed in a matrix of human dominated landscapes, tigers (Panthera tigris) typify the problems faced by most large carnivores worldwide. With heads of governments of tiger range countries pledging to reverse the extinction process and setting a goal of doubling wild tiger numbers by 2022, achieving this target would require identifying existing breeding cores, potential breeding habitats and opportunities for dispersal. The Terai Arc Landscape (TAL) represents one region which has recently witnessed recovery of tiger populations following conservation efforts. In this study, we develop a spatially explicit tiger occupancy model with survey data from 2009-10 based on a priori knowledge of tiger biology and specific issues plaguing the western TAL (6,979 km(2)), which occurs in two disjunct units (Tiger Habitat Blocks; THBs). Although the overall occupancy of tigers was 0.588 (SE 0.071), our results clearly indicate that loss in functionality of a regional corridor has resulted in tigers now occupying 17.58% of the available habitat in THB I in comparison to 88.5% in THB II. The current patterns of occupancy were best explained by models incorporating the interactive effect of habitat blocks (AIC w = 0.883) on wild prey availability (AIC w = 0.742) and anthropogenic disturbances (AIC w = 0.143). Our analysis has helped identify areas of high tiger occupancy both within and outside existing protected areas, which highlights the need for a unified control of the landscape under a single conservation unit with the primary focus of managing tigers and associated wildlife. Finally, in the light of global conservation targets and recent legislations in India, our study assumes significance as we identify opportunities to secure (e.g. THB II) and increase (e.g. THB I) tiger populations in the landscape.