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.

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.

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.

Digging out the keys in the heap of seized pangolin scales: up scaling pangolin conservation using wildlife forensics.

Pangolins, despite banned through legislative measures, are threatened by heavy illegal poaching for the demand of meat and scales in the making of Traditional East Asian Medicines (TEAM), resulting in severe decline of the population sizes across the distribution range. Species assignment from the confiscated scales is pre-requisite to enforce the appropriate national and international law and legislations in the successful prosecution of the cases in the court of law. In the present study, we characterised the morphological features in voucher specimens of the Indian pangolin (Manis crassicaudata) and Chinese pangolin (Manis pentadactyla) and used the identified keys to establish the species identity from the confiscated scales. We investigated intra and inter genetic variations by sequencing 624 scales of pangolin for cytb gene and obtained unique haplotypes to Indian and Chinese pangolins by comparing sequences with all eight pangolin species. Scales from the voucher specimens, which varied in the size, shape and weight, were measured for morphological features to establish species signature of Indian and Chinese pangolins. The cumulative success of species assignment using morphological features from the confiscated scales was 98.33% and 100% from the large and caudal scales, respectively. The present study has generated reference signature of Indian and Chinese pangolins from the scales and facilitates the law enforcements for taking spot decision by ascertaining species identity from the seized scales.

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.

Identifying the tick Amblyomma javanense (Acari: Ixodidae) from Chinese pangolin: generating species barcode, phylogenetic status and its implication in wildlife forensics.

Zoonotic diseases transmitted through ticks and other ectoparasites often travel across the globe with illegally traded wildlife parts and products. In this study, we analyzed a confiscated case of pangolin scales and observed a few dead ticks attached. On genetic analysis, the pangolin scales were identified to be originated from Chinese pangolin (Manis pentadactyla), an IUCN listed Critically Endangered species, and ticks were identified as Amblyomma javanense. Here, we provide the first authentic physical record of A. javanense from India as a parasite of Chinese pangolin and also generated its species DNA barcode that may be useful for biologists working on ticks in species validation and constructing phylogenies across the globe.

DNA barcodes and ethnomedicinal use of Sharpnose guitarfish Glaucostegus granulatus by the locals at Keylong, Lahaul and Spiti, Himachal Pradesh.

Illegal trade of fishes is common and has been in practice since ages for the support of livelihood and as dietary supplements. However, several species are protected in the Wildlife (Protection) Act, 1972 of India and their trade is restricted under CITES. In this article, we report trade of Sharpnose guitarfish (Glaucostegus granulatus) for the ethnomedicinal remedy, identified using DNA barcoding in the Keylong district of Lahaul and Spiti, Himachal Pradesh. This study provides the first DNA barcode of Sharpnose guitarfish. In order to handle wildlife offense cases we emphasize that a large reference database for other fishes in trade is needed.

Resolving the trans-boundary dispute of elephant poaching between India and Nepal.

In Kangchenjunga Landscape (KL), which is shared by three countries - Bhutan, India, and Nepal, the wild elephants migrate from east of Jhapa (Nepal), through West Bengal (India) and Sibsoo (Bhutan) to further east in Assam (India). The route Jhapa-WB-Sibsoo-Assam is a known route for elephant movements where maximum causalities have been reported in the past. The present study was undertaken to ascertain the individual identity of a poached elephant in Jhapa, Nepal and ivory which was suspected to be from the same individual elephant confiscated in Siliguri, India. We undertook STR profiling of the confiscated specimens with nine polymorphic STRs. The forensic parameters has established the fact that the two analyzed samples of elephant were not identical and belong to two different individuals. The present study highlights the necessity of transboundary research for elephant conservation and monitoring their movements in Kangchenjunga Landscape and emphasizes the use of forensic genetics in curbing illegal wildlife trade.