Genetic assessment of captive breeding program of Indian Pangolin: implications for conservation and management.

BACKGROUND: Captive breeding programs play a vital role in conservation of threatened species, necessitating an understanding of genetic diversity among captive individuals to ensure long-term genetic viability, appropriate mate selection, and successful reintroduction to native habitats. METHODS AND RESULTS: We did not observe any recent genetic bottleneck, and population showed moderate genetic diversity. The estimated effective population size, representing individuals capable of contributing genetically to future generations, was estimated as 18.6 individuals (11.4-35.1 at 95% CI). Based on the genetic make-up and allelic diversity, we found seventeen pangolins (11 females and 6 males) were genetically unrelated and relatively more potent than others. CONCLUSION: In this study, we evaluated the captive breeding program of the Indian pangolin population at the Pangolin Conservation Breeding Centre in Nandankanan Zoological Park, Bhubaneswar, Odisha. We highlight the significance of genetic monitoring within the captive population of Indian pangolin for preserving genetic diversity and ensuring the long-term survival of the species. We established the genetic profiles of all 29 pangolins and identified 17 pangolins to be prioritized for enhanced breeding and future zoo exchange programs. We appreciate the zoo authorities for promoting genetic assessment of pangolin for better and more effective monitoring of the captive breeding of the endangered Indian pangolin.

Mitochondrial DNA reveals shallow population genetic structure in economically important Cyprinid fish Labeo rohita (Hamilton, 1822) from South and Southeast Asia.

BACKGROUND: Assessment of genetic diversity and population genetic structure is important for species that are economically important, threatened, and are at global conservation priority. Analysis of mitochondrial DNA is broadly used in species identification and population genetics studies due to the availability of sufficient reference data and better evolutionary dynamics for phylogeographic investigation. Labeo rohita (Rohu) is an economically important species cultured under carp polyculture systems in Asia. The present study explores the genetic diversity, phylogeography, and population structure of L. rohita from different countries using cytochrome oxidase subunit I (COI) gene. METHODS AND RESULTS: A total of 17 L. rohita specimens were sampled from River Beas, India. For the genetic study, we amplified and sequenced COI mitochondrial DNA region. The obtained genetic data was combined with 268 COI records available in the NCBI and BOLD databases originating from multiple populations/countries across South and Southeast Asia. As a result, 33 haplotypes were identified that displayed low nucleotide (π = 0.0233) and moderate haplotype diversity (Hd = 0.523). Tajima (D) was found to be negative (P > 0.05), whereas Fu's Fs showed a positive value (P > 0.05). The overall FST value between studied populations was 0.481 (P < 0.05). CONCLUSION: AMOVA analysis indicated higher variation within than among the population examined. The neutrality tests suggested the presence of rare haplotypes and stable demography within studied populations of L. rohita. The Bayesian skyline plot indicated steady population growth until 1 Mya followed by population decline, whereas FST values indicated significant genetic differentiation. High heterogeneity was observed in the Pakistan population which could be indicative of long-term isolation and excessive culturing to meet market demands. The present results are the first global comparative analysis of L. rohita and pave the way forward for detailed genomic and ecological studies aimed at the development of improved stock and effective conservation plans. The study also makes recommendations to conserve the genetic integrity of wild species from aquaculture-reared fishes.

Free-ranging dogs are seriously threatening Himalayan environment: delineating the high-risk areas for curbing free-ranging dog infestation in the Trans-Himalayan region.

It is becoming more widely recognised that free-ranging dogs, which have a nearly global distribution, threatening native wildlife. Their increasing population and spread to new areas is of growing concern for the long-term viability of wildlife species. Hence, it is imperative to understand the factors responsible for their infestation and map areas where native species are most vulnerable. Using the random forests algorithm, we modelled the free-ranging dog infestation in the Trans-Himalayan region to pinpoint the high-risk areas where free-ranging dogs are threatening the native wildlife species. We found that the likelihood of free-ranging dog occurrence is most in valley regions and up to 4000 m, often in proximity to roads. Our results also indicated that free-ranging dog prefers areas with wildlife near to protected areas. The predictor variables, such as potential evapotranspiration of the coldest quarter, distance to protected areas, elevation, distance to roads, and potential evapotranspiration of the driest quarter, significantly influence the distribution of the free-ranging dogs. We found that within the Ladakh region of the Trans-Himalayan area, the high-risk zones for free-ranging dogs are located in and around Hemis National Park, Karakoram Wildlife Sanctuary, and Changthang Wildlife Sanctuary. While, in the Lahaul and Spiti region the high-risk areas encompass Pin Valley National Park, Inderkilla National Park, Khirganga National Park, Kugti Wildlife Sanctuary, and several other protected areas. We identified the potentially high-risk areas for implementing strategies to mitigate the possible impact of free-ranging dogs on native wildlife of the Himalayas. Hence, the identified high priority areas can be used for implementing actions for controlling the population growth and further preventing the infestation of the free-ranging dogs into the new areas.

Population genetics of Sambar (Rusa unicolor) from the Western Himalayas: preliminary findings.

BACKGROUND: The sambar (Rusa unicolor) is one of the largest deer distributed across diverse habitats of India and threatened due to habitat loss, changes in the land-use patterns, illegal poaching, and anthropogenic disturbances. Here, we report the first population genetics account of sambar deer from the Western Himalayas. METHODS AND RESULTS: We observed relatively compromised genetic diversity (π = 0.0008 ± 0.0006 at mtDNA and Ho = 0.499 ± 0.056 at nDNA). We identified 60 unique individuals using a select panel of seven loci (PID sib cum 1.60E-03). Bayesian skyline plot showed a stable demographic history since the past 8 kyr with a decline in recent years. The population lacked genetic structuring, likely due to the contiguous distribution and large dispersal patterns of sambar. CONCLUSION: The preliminary findings are valuable in exploring the utility of genetic diversity in monitoring the sambar population, estimating density following capture-recapture analysis, and aid to the conservation planning of sambar in large landscapes.

Population genetic attributes of common leopard (Panthera pardus fusca) from Uttarkashi, Western Himalayas.

BACKGROUND: The common leopard (Panthera pardus fusca), which persists in most of its historic range, is experiencing steady population decline due to habitat loss, anthrophonic disturbances, illegal poaching for their body parts, and retaliatory killings in response to the leopard-human conflicts. METHODS AND RESULTS: We analysed 143 scats samples and identified 32 unique leopards following a selected panel of seven loci with cumulative PID sibs 5.30E-04. We observed moderate genetic diversity at nuclear (Ho = 0.600 ± 0.06) and mitochondrial markers (Hd = 0.569 ± 0.009; π = 0.001 ± 0.0002) and found sub-structuring in the leopard population at Uttarkashi, Western Himalayas. CONCLUSIONS: The present study exhibits the utility of non-invasive genetics in monitoring the leopard population and paves the path to investigate population genetic parameters in further studies.

Mitochondrial cytochrome b indicates the presence of two paraphyletic diverged lineages of the blue sheep Pseudois nayaur across the Indian Himalaya: conservation implications.

BACKGROUND: Populations exhibit signatures of local adaptive traits due to spatial and environmental heterogeneity resulting in microevolution. The blue sheep is widely distributed across the high Asian mountains and are the snow leopard's principal prey species. These mountains differ in their evolutionary history due to differential glaciation and deglaciation periods, orography, and rainfall patterns, and such factors causes diversification in species. METHODS AND RESULTS: Therefore, we assess the phylogeographic status of blue sheep using the mitochondrial cytochrome b gene (220 bp) across the Indian Himalayan region (IHR) and its relationship with other populations. Of the observed five haplotypes, two and three were from the western Himalayas (WH) and eastern Himalayas (EH) respectively. One of the haplotypes from WH was shared with the population of Pamir plateau, suggesting historical maternal connectivity between these areas. The phylogenetic analyses split the blue sheep into two paraphyletic clades, and western and eastern populations of IHR were within the Pamir and Tibetan plateau clades, respectively. We observed a relatively higher mean sequence divergence in the EH population than in the WH. CONCLUSION: We propose five 'Evolutionary Significant Units' across the blue sheep distribution range based on observed variation in the species' ecological requirements, orography, climatic conditions, and maternal lineages, viz.; Western Himalaya-Pamir plateau (WHPP); Eastern Himalaya-Tibetan plateau (EHTP); Qilian mountains; Helan mountains and Hengduan mountains population. Despite the small sample size, population divergence was observed across the IHR, therefore, we suggest a transboundary, collaborative study on comparative morphology, anatomy, ecology, behaviour, and population genetics using harmonized different genetic markers for identifying the overall taxonomic status of the blue sheep across its range for planning effective conservation strategies.

Genetic monitoring of Himalayan goral (Naemorhedus goral) from Western Himalayas, India.

BACKGROUND: Himalayan goral (Naemorhedus goral), solitary cliff-dwelling species and are distributed throughout the Indian Himalayan region. Its populations across the range are facing severe threats due to habitat loss, fragmentation and changes in the land-use patterns by various anthropogenic activities. METHODS AND RESULTS: We carried out genetic analyses of Himalayan goral using the mitochondrial control regions and microsatellite loci (n = 10) in the Uttarkashi district of Uttarakhand. We reported a moderate genetic diversity at nuclear (Ho 0.602 ± 0.057) and mitochondrial markers (Hd-0.6931 ± 0.053; π-0.0048 ± 001). Bayesian skyline plot indicates a sharp decline in the goral population in the last 100 years. CONCLUSIONS: Our results indicate the population of Himalayan goral in Uttarkashi is under panmictic condition, plausibly due to long-ranging behaviour. The present study laid the foundation for future non-invasive genetics monitoring and detailed population genetic assessment of goral from the entire range in the Western Himalayas.

Pangolin Indexing System: implications in forensic surveillance of large seizures.

Demand for pangolin scales in East Asia has increased dramatically in the past two decades, raising concern to the pangolin survival and bringing them to the brink of local extinction. Enumerating the number of individuals from the seized pangolin scales primarily goes undocumented, mostly due to the unavailability of the appropriate methods. In this study, we developed a Pangolin Indexing System, a multi-locus STR panel of eight dinucleotide microsatellites that showed promising results in individualization and assignment of scales into Chinese and Indian pangolins. The combined power of exclusion was 0.83 and 0.99 for Chinese and Indian pangolin. The select panel of eight polymorphic STRs exhibited the cumulative probability of identity 3.7 × 10-9 for Indian pangolin and 3.6 × 10-7 for Chinese pangolin and identified 51 unique genotypes from the 74 scales selected from the four pangolin seizures. The study demonstrated the first report of cross-species validation of STRs developed from Malayan pangolin to Indian pangolin and showed the potential application of Pangolin Indexing System in screening of large seizures through DNA profiling from the scales of Indian and Chinese pangolin.

Investigating the genetic diversity and presence of forensically informative nucleotide sequences in Indian antelope (Antilope cervicapra) using multiple genes of the mitochondrial genome.

Indian antelope or Blackbuck (Antilope cervicapra) is one of the widely distributed endemic species in India among wild bovids and a majority of preferred habitats are in human-dominated landscapes. Poaching threats and habitat degradation are major factors for the decline in Blackbuck population from its distribution range. Till date, there is no detailed study using molecular techniques in India on Blackbuck, except a few studies entailing phylogenetic scenario based on inadequate sampling and DNA sequences restricted over limited geographic areas. In view of this, the present study is aimed to screen the Blackbuck samples from a large part of its distribution range and to investigate the genetic diversity as well as to identify the forensically informative nucleotide sequences (FINS) for species identification. We relied on multi-genes approach using three genes of mtDNA genome viz. Cytochrome Oxidase I, Cytochrome b and 16S rRNA and identified the FINS in the Blackbuck population along with conspecific sequences divergence and genetic diversity indices. In all three genes, we observed 8 to 17 haplotypes with the intra-species sequence divergence of 0.004-0.016. Inter-species sequence divergence with the other closely related species of the Blackbuck was 0.0225-0.033. We report the presence of FINS across three genes from 12 to 18 and found more informative nucleotide sites using Cytochrome Oxidase I genes compared to Cytochrome b and 16S rRNA gene. We did not observe the presence of geographic-specific FINS amongst Blackbuck population that can be used to assign individuals to geographic origin. Besides, in the phylogenetic tree, samples from different locations did not cluster into geographic-specific clade and exhibited mixed homology for these sequences. We suggest exploring the feasibility of using nuclear markers for population assignment.

Species dilemma of musk deer (Moschus spp) in India: molecular data on cytochrome c oxidase I suggests distinct genetic lineage in Uttarakhand compared to other Moschus species.

Musk deer are of high conservation priority owing to poaching pressure because of its musk pod. Representation of musk deer status using genetics is poorly documented in India, and it is not confirmed as to how many species of musk deer are present. We characterize for the first time, the genetic diversity of musk deer from Uttarakhand using Cytochrome Oxidase sub-unit (COI) gene (486 bp) and compared with the data available for other species. Results revealed the presence of six haplotypes in the Uttarakhand population amongst 17 sequences. Of these, 12 sequences shared the single haplotype. The intra-species sequences divergence was 0.003-0.017, whereas divergence with other species of musk deer was 0.071-0.081. Bayesian phylogenetic tree revealed that samples from Uttarakhand formed a separate clade with respect to other species of musk deer, whereas three species distributed in China clustered in the same clade and showed low sequences divergence, i.e., 0.002-0.061. Because of different ecomorph reported, we suggest using the barcoding based approach for inter and intra-species distinction and delineating species boundaries across the range for effective conservation. Besides, systematic classification, DNA barcoding would also help in dealing wildlife offence cases for disposal of the legal report in court.

Phylogeography of the Small Indian Civet and Origin of Introductions to Western Indian Ocean Islands.

The biogeographic dynamics affecting the Indian subcontinent, East and Southeast Asia during the Plio-Pleistocene has generated complex biodiversity patterns. We assessed the molecular biogeography of the small Indian civet (Viverricula indica) through mitogenome and cytochrome b + control region sequencing of 89 historical and modern samples to (1) establish a time-calibrated phylogeography across the species' native range and (2) test introduction scenarios to western Indian Ocean islands. Bayesian phylogenetic analyses identified 3 geographic lineages (East Asia, sister-group to Southeast Asia and the Indian subcontinent + northern Indochina) diverging 3.2-2.3 million years ago (Mya), with no clear signature of past demographic expansion. Within Southeast Asia, Balinese populations separated from the rest 2.6-1.3 Mya. Western Indian Ocean populations were assigned to the Indian subcontinent + northern Indochina lineage and had the lowest mitochondrial diversity. Approximate Bayesian computation did not distinguish between single versus multiple introduction scenarios. The early diversification of the small Indian civet was likely shaped by humid periods in the Late Pliocene-Early Pleistocene that created evergreen rainforest barriers, generating areas of intra-specific endemism in the Indian subcontinent, East, and Southeast Asia. Later, Pleistocene dispersals through drier conditions in South and Southeast Asia were likely, giving rise to the species' current natural distribution. Our molecular data supported the delineation of only 4 subspecies in V. indica, including an endemic Balinese lineage. Our study also highlighted the influence of prefirst millennium AD introductions to western Indian Ocean islands, with Indian and/or Arab traders probably introducing the species for its civet oil.

Mid-Pleistocene Transitions Forced Himalayan ibex to Evolve Independently after Split into an Allopatric Refugium.

Pleistocene glaciations had profound impact on the spatial distribution and genetic makeup of species in temperate ecosystems. While the glacial period trapped several species into glacial refugia and caused abrupt decline in large populations, the interglacial period facilitated population growth and range expansion leading to allopatric speciation. Here, we analyzed 40 genomes of four species of ibex and found that Himalayan ibex in the Pamir Mountains evolved independently after splitting from its main range about 0.1 mya following the Pleistocene species pump concept. Demographic trajectories showed Himalayan ibex experienced two historic bottlenecks, one each c. 0.8-0.5 mya and c. 50-30 kya, with an intermediate large population expansion c. 0.2-0.16 mya coinciding with Mid-Pleistocene Transitions. We substantiate with multi-dimensional evidence that Himalayan ibex is an evolutionary distinct phylogenetic species of Siberian ibex which need to be prioritized as Capra himalayensis for taxonomic revision and conservation planning at a regional and global scale.

Lahaul-Zanskar-Sham Valley Corridor in Indian Trans Himalayan Region Facilitates Dispersal and Gene Flow in Himalayan Ibex.

Wildlife corridors that connect mosaic habitats in heterogeneous mountainous landscapes can be of high significance as they facilitate the genetic and demographic stability of free-ranging populations. Peripheral populations of widespread species are usually ignored in conservation planning. However, these populations retain locally common alleles and are genetic reservoir under the changing climatic conditions. Capra sibirica has widespread distribution, and its southern peripheral population is distributed in the Indian trans-Himalayan region (ITR). In the present study, we studied the spatial distribution and genetic make-up of Himalayan ibex from the ITR following the landscape genetics approach. We obtained 16 haplotypes at the mitochondrial d-loop region and found a stable demography in the past with a recent decline. With 10 nuclear microsatellites, we ascertained 111 unique individuals assigned into two clusters following Bayesian and non-Bayesian clustering analysis with several admixed individuals. We also recorded 25 first-generation migrants that reflected relatively high dispersal and gene-flow across the range. We identified a 19,835 sq.km suitable area with 13,311 sq.km in Ladakh and 6524 sq.km in Lahaul-Spiti. We identified a novel movement corridor for Himalayan ibex across the Lahaul-Zanskar-Sham valley (L-Z-SV) that displayed a fairly good conductance with low genetic divergence among the samples collected on the L-Z-SV corridor. We propose declaring a protected area in the Lahaul and Kargil districts to prioritize dedicated conservation efforts for the Himalayan ibex and other sympatric ungulates that impart a major role in the diet of large carnivore and balancing ecosystem services in the trans-Himalayan region.

Environmental predictors may change at fine scale habitat suitability modelling: implications for conservation of Kashmir musk deer in three protected areas of Uttarakhand, India.

The Kashmir musk deer (Moschus cupreus, hereafter KMD) is one of the top conservation priority species which is facing population decline due to poaching, habitat loss, and climate change. Therefore, the long-term survival and viability of KMD populations in their natural habitat require conservation and management of suitable habitats. Hence, the present study attempted to assess the suitable habitat of KMD in three protected areas (PAs) of the Western Himalayan region of Uttarakhand using the Maxent modelling algorithm. Our results suggest that Kedarnath wildlife sanctuary (KWLS) possesses the maximum highly suitable habitats (22.55%) of KMD, followed by Govind Pashu Vihar National Park & Sanctuary (GPVNP&S; 8.33%) and Gangotri National Park (GNP; 5%). Among the environmental variables, altitude was the major contributing factor governing the distribution of KMD in KWLS. In contrast, human footprint in GPVNP&S and precipitation in GNP were the major contributing factors governing the distribution of KMD in these respective PAs. The response curve indicated that habitats with less disturbance falling in the altitudinal zone of 2000-4000 m were the most suitable habitat range for the distribution of KMD in all three PAs. However, in the case of GNP suitable habitat of KMD increases with an increase in the value of variables bio_13 (precipitation of wettest month). Further, based on our results, we believe that the predictors of suitable habitat change are site specific and cannot be generalized in the entire distribution range of the species. Therefore, the present study will be helpful in making proper habitat management actions at fine scale for the conservation of KMD.

Landscape genetics identified conservation priority areas for blue sheep (Pseudois nayaur) in the Indian Trans-Himalayan Region.

The trans-Himalayan region of India, although have xeric features, still supports a unique assemblage of biodiversity, including some of the charismatic and endemic species. In the present study, we studied blue sheep (Pseudois nayaur) across the distribution range in the Western trans Himalayas of India and found about 18,775 km2 area suitable for blue sheep. The explicit Bayesian based spatial and non-spatial population structure analysis assigned blue sheep into two genetic populations, i.e., Ladakh and Lahaul-Spiti. We found relatively high genetic divergence in blue sheep which is also supported by the low current flow in Circuitscape model. With the multiple evidences, we explain landscape resistance facilitated by the landscape heterogeneity, and large patches of unsuitable habitats forced population divergence and poor functional connectivity. We found that blue sheep population has been demographically stable in the past, but showed a slight decline within the last few decades. This study is the first range-wide attempt to exhibit landscape features in shaping the spatial distribution, genetic structure and demography patterns of blue sheep in Western Himalayas, and will be of use in the conservation and management planning of blue sheep.

Empirical Data Suggest That the Kashmir Musk Deer (Moschus cupreus, Grubb 1982) Is the One Musk Deer Distributed in the Western Himalayas: An Integration of Ecology, Genetics and Geospatial Modelling Approaches.

Insufficient research has been conducted on musk deer species across their distribution range, primarily because of their elusive behaviour and the fact they occupy remote high-altitude habitats in the Himalayas above 2500 m. The available distribution records, primarily derived from ecological studies with limited photographic and indirect evidence, fail to provide comprehensive information on the species distribution. Consequently, uncertainties arise when attempting to determine the presence of specific taxonomic units of musk deer in the Western Himalayas. This lack of knowledge hampers species-oriented conservation efforts, as there need to be more species-specific initiatives focused on monitoring, protecting, and combatting the illegal poaching of musk deer for their valuable musk pods. We used transect surveys (220 trails), camera traps (255 cameras), non-invasive DNA sampling (40 samples), and geospatial modelling (279 occurrence records) to resolve the taxonomic ambiguity, and identify the suitable habitat of musk deer (Moschus spp.) in Uttarkashi District of Uttarakhand and the Lahaul-Pangi landscape of Himachal Pradesh. All the captured images and DNA-based identification results confirmed the presence of only Kashmir musk deer (KDM) (Moschus cupreus) in Uttarakhand and Himachal Pradesh. The results suggest that KMD inhabit a narrow range of suitable habitats (6.9%) of the entire Western Himalayas. Since all evidence indicates that only KMD are present in the Western Himalayas, we suggest that the presence of other species of musk deer (Alpine musk deer and Himalayan musk deer) was wrongly reported. Therefore, future conservation plans and management strategies must focus only on KMD in the Western Himalayas.

Living with a large predator: Assessing the root causes of Human-brown bear conflict and their spatial patterns in Lahaul valley, Himachal Pradesh.

Brown bear-mediated conflicts have caused immense economic loss to the local people living across the distribution range. In India, limited knowledge is available on the Himalayan brown bear (HBB), making human-brown bear conflict (HBC) mitigation more challenging. In this study, we studied HBC in the Lahaul valley using a semi-structured questionnaire survey by interviewing 398 respondents from 37 villages. About 64.8% of respondents reported conflict in two major groups-crop damage (30.6%) and livestock depredations (6.2%), while 28% reported both. Conflict incidences were relatively high in summer and frequently occurred in areas closer to the forest (<500 m) and between the elevations range of 2700 m to 3000 m above sea level (asl). The dependency of locals on forest resources (70%) for their livelihood makes them vulnerable to HBC. The "upper lower" class respondents were most impacted among the various socioeconomic classes. Two of the four clusters were identified as HBC hot spots in Lahaul valley using SaTscan analysis. We also obtained high HBC in cluster II with a 14.35 km radius. We found that anthropogenic food provisioning for HBB, livestock grazing in bear habitats, and poor knowledge of animal behavior among the communities were the major causes of HBC. We suggest horticulture crop waste management, controlled and supervised grazing, ecotourism, the constitution of community watch groups, and others to mitigate HBC. We also recommend notifying a few HBB abundant sites in the valley as protected areas for the long-term viability of the HBB in the landscape.

Future simulated landscape predicts habitat loss for the Golden Langur (Trachypithecus geei): A range level analysis for an endangered primate.

Trachypithecus geei Khajuria, 1956 or Golden langur are an endangered colobine primate species that are distributed in the transboundary region of Bhutan and India. The species is severely threatened because of increasing habitat fragmentation and isolation across its entire range, especially the populations in Assam, India. The distribution range of the species has not been updated for the last two decades, nor is there any proper evaluation of the habitat requirements for the species. Therefore, we mapped the habitat suitability for the species across its entire distribution and projected its habitat suitability on the simulated landscape for the future (2031). The results indicate that out of the total range extent (66,320 km2), only 12,265 km2 (18.49%) is suitable for the species at present, which will further be reduced to 8884 km2 by the year 2031, indicating major range contraction. These suitable habitats are largely scattered and fragmented in southern range of the species. Among the predictors used, the distance to evergreen and deciduous broadleaf forest was the strongest predictor out of the 35 used for model building. Moreover, land use and land cover were found to be more informative than the climatic variables. Much of the suitable habitats of the species are located outside the protected area network in the landscape. Therefore, we identified landscape configurations and suitable habitat areas for the future conservation and monitoring of Golden Langur in the protected areas of its range.

Multi-species occupancy modeling suggests interspecific interaction among the three ungulate species.

Species with sympatric distribution influence ecosystem dynamics and are impacted by the presence of other co-existing species. Assessing the coexistence and the role of interspecific interactions with the landscape variables is necessary to know the species co-occurrence in space. In the Indian Himalayan region, such studies are completely lacking due to limited efforts being made, mainly because of complex terrains and inaccessible landscape features. We used camera trapping and sign survey in a multi-species occupancy framework to understand the influence of environmental variables on occupancy and detection probability of species-specific and pair-wise interaction of the three ungulates in Uttarkashi. Our results concluded that individual species' occupancy probabilities were related both to the environmental variables and the presence or absence of other interacting species. Our top model showed evidence of interspecific interaction among species pairs, and the occupancy probability of species one varied in the presence or absence of another species. The overall activity patterns were similar among all the three species and were found active throughout the day. The activity overlap between sambar-barking deer (Dhat1 value = 0.85) was considerably higher than barking deer-goral (Dhat1 value = 0.78). The findings of the present study will be useful for the conservation and management of ungulates in the Indian Himalayan and adjoining regions.