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.

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.

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.

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.

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.

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.

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.

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.

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.

From poops to planning: A broad non-invasive genetic survey of large mammals from the Indian Himalayan Region.

Large forested landscapes often harbour significant amount of biodiversity and support mankind by rendering various livelihood opportunities and ecosystem services. Their periodic assessment for health and ecological integrity is essential for timely mitigation of any negative impact of human use due to over harvesting of natural resources or unsustainable developmental activities. In this context, monitoring of mega fauna may provide reasonable insights about the connectivity and quality of forested habitats. In the present study, we conducted a largest non-invasive genetic survey to explore mammalian diversity and genetically characterized 13 mammals from the Indian Himalayan Region (IHR). We analyzed 4806 faecal samples using 103 autosomal microsatellites and with three mitochondrial genes, we identified 37 species of mammal. We observed low to moderate level of genetic variability and most species exhibited stable demographic history. We estimated an unbiased population genetic account (PGAunbias) for 13 species that may be monitored after a fixed time interval to understand species performance in response to the landscape changes. The present study has been evident to show pragmatic permeability with the representative sampling in the IHR in order to facilitate the development of species-oriented conservation and management programmes.

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.

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.

Landscape use and co-occurrence pattern of snow leopard (Panthera uncia) and its prey species in the fragile ecosystem of Spiti Valley, Himachal Pradesh.

The snow leopard (Panthera uncia) plays a vital role in maintaining the integrity of the high mountain ecosystem by regulating prey populations and maintaining plant community structure. Therefore, it is necessary to understand the role of the snow leopard and its interaction with prey species. Further, elucidating landscape use and co-occurrence of snow leopard and its prey species can be used to assess the differential use of habitat, allowing them to coexist. We used camera trapping and sign survey to study the interactions of snow leopard and its prey species (Siberian Ibex- Capra sibrica and Blue sheep-Pseudois nayaur) in the Spiti valley Himachal Pradesh. Using the occupancy modelling, we examined whether these prey and predator species occur together more or less frequently than would be expected by chance. To understand this, we have used ten covariates considering the ecology of the studied species. Our results suggest habitat covariates, such as LULC16 (barren area), LULC10 (grassland), ASP (aspect), SLP (slope) and DW (distance to water), are important drivers of habitat use for the snow leopard as well as its prey species. Furthermore, we found that the snow leopard detection probability was high if the site was used by its prey species, i.e., ibex and blue sheep. Whereas, in the case of the prey species, the probability of detection was low when the predator (snow leopard) was present and detected. Besides this, our results suggested that both species were less likely to detect together than expected if they were independent (Snow leopard-Ibex, Delta = 0.29, and snow leopard-blue sheep, Delta = 0.28, both the values are <1, i.e., avoidance). Moreover, despite the predation pressure, the differential anti-predation habitat selection and restriction of temporal activities by the prey species when snow leopard is present allows them to co-exist. Therefore, considering the strong link between the habitat use by the snow leopard and its prey species, it is imperative to generate quantitative long-term data on predator-prey densities and the population dynamics of its prey species 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.

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.

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.

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.

Non-protected areas demanding equitable conservation strategies as of protected areas in the Central Himalayan region.

The present study aims to explore the mammalian diversity of Darjeeling district using camera traps along with questionnaire survey in protected area (PA) and non- protected area (Non-PA). We also attempted to understand the influence of habitat variables on mammalian species richness using the generalized linear mixed models (GLMM). A total of 30 mammal species were recorded of which 21 species were detected through camera trapping with the most abundant records of barking deer (Muntiacus muntjak) and least of the elusive Chinese pangolin (Manis pentadactyla) and red panda (Ailurus fulgens). Additionally, melanistic forms of four mammals were also recorded. The mammalian species richness, their capture rate and naïve occupancy did not differ significantly among the PA and Non-PA. The GLMM revealed that the proportions of oak and bamboo in the forest, percentage canopy cover and camera trap operational days (wAICc = 0.145, wBIC = 0.603) were significant predictors of species richness in the study. We suggest Non-PA forest of Darjeeling should be given equal conservation importance as to the PA. Landscape based conservation planning will be imperative for achieving long term conservation goals in the study area.