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Kolekar A, Hockings K, Metcalfe K, Gubbi S. Identifying Priority Areas for the Indian Leopard ( Panthera pardus fusca) Within a Shared Landscape. Ecol Evol 2024; 14:e70404. [PMID: 39398637 PMCID: PMC11467164 DOI: 10.1002/ece3.70404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 09/05/2024] [Accepted: 09/10/2024] [Indexed: 10/15/2024] Open
Abstract
Habitat loss is one of the primary drivers of large felid decline. The leopard (Panthera pardus), a generalist large felid species, has the behavioural and dietary flexibility to exploit different habitat types of varying human influence. Understanding habitat selection in a shared landscape is critical for the development of conservation strategies and managing negative human-leopard interactions. The development of conservation policy requires data on large spatial scales, which is mostly lacking, especially within shared landscapes in India. This study aims to determine habitat selection by Indian leopards and the anthropogenic, environmental, and climatic variables contributing to this selection. Leopard occurrence records were obtained from an occupancy survey conducted in the five administrative districts in Karnataka (28,375 km2). 267 randomly selected 30 km2 grids were each walked for 10 km and all leopard signs were recorded. Environment variables were chosen to reflect land use, climatic, topographic, and human disturbances that could affect habitat selection at a resolution of 0.1 km2. The mean ensemble model was projected to the state of Karnataka. Habitat selection predicted by the ensemble model was driven by proximity to forest cover and rocky outcrops, higher precipitation, and negatively by distance to cropland and roads. Protected Areas and Reserved Forests in the study covered 47% of the predicted habitat, while 25% is within human-use areas such as human habitation and croplands. This study predicts that half of the habitat selected by leopards is outside of protected areas and reserved forests. The selection of human-use areas is predicted because of the availability of cover from irrigated croplands and the proximity to natural cover that provides refuge. Livestock density did not drive large-scale habitat selection. The preservation of natural cover and rocky outcrops that provide refuge between protected areas is paramount for leopard conservation.
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Affiliation(s)
- Aparna Kolekar
- Holématthi Nature FoundationBengaluruIndia
- Centre for Ecology and Conservation, College of Life and Environmental SciencesUniversity of ExeterCornwallUK
| | - Kimberley Hockings
- Centre for Ecology and Conservation, College of Life and Environmental SciencesUniversity of ExeterCornwallUK
| | - Kristian Metcalfe
- Centre for Ecology and Conservation, College of Life and Environmental SciencesUniversity of ExeterCornwallUK
| | - Sanjay Gubbi
- Centre for Ecology and Conservation, College of Life and Environmental SciencesUniversity of ExeterCornwallUK
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2
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Joshi BD, Singh SK, Singh VK, Jabin G, Ghosh A, Dalui S, Singh A, Priyambada P, Dolker S, Mukherjee T, Sharief A, Kumar V, Singh H, Thapa A, Sharma CM, Dutta R, Bhattacharjee S, Singh I, Mehar BS, Chandra K, Sharma LK, Thakur M. From poops to planning: A broad non-invasive genetic survey of large mammals from the Indian Himalayan Region. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158679. [PMID: 36099955 DOI: 10.1016/j.scitotenv.2022.158679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
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.
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Affiliation(s)
- Bheem Dutt Joshi
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Sujeet Kumar Singh
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India; Present address: Amity Institute of Forestry and Wildlife, Amity University, Noida 201303, Uttar Pradesh, India
| | - Vinaya Kumar Singh
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Gul Jabin
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Avijit Ghosh
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Supriyo Dalui
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Abhishek Singh
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | | | - Stanzin Dolker
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Tanoy Mukherjee
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Amira Sharief
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Vineet Kumar
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Hemant Singh
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Avantika Thapa
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | | | - Ritam Dutta
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | | | - Inder Singh
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Balram Singh Mehar
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Kailash Chandra
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Lalit Kumar Sharma
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
| | - Mukesh Thakur
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India.
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Abstract
AbstractObserving and quantifying primate behavior in the wild is challenging. Human presence affects primate behavior and habituation of new, especially terrestrial, individuals is a time-intensive process that carries with it ethical and health concerns, especially during the recent pandemic when primates are at even greater risk than usual. As a result, wildlife researchers, including primatologists, have increasingly turned to new technologies to answer questions and provide important data related to primate conservation. Tools and methods should be chosen carefully to maximize and improve the data that will be used to answer the research questions. We review here the role of four indirect methods—camera traps, acoustic monitoring, drones, and portable field labs—and improvements in machine learning that offer rapid, reliable means of combing through large datasets that these methods generate. We describe key applications and limitations of each tool in primate conservation, and where we anticipate primate conservation technology moving forward in the coming years.
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Whole genome survey of big cats (Genus: Panthera) identifies novel microsatellites of utility in conservation genetic study. Sci Rep 2021; 11:14164. [PMID: 34238947 PMCID: PMC8266911 DOI: 10.1038/s41598-021-92781-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 06/14/2021] [Indexed: 02/06/2023] Open
Abstract
Big cats (Genus: Panthera) are among the most threatened mammal groups of the world, owing to hunting, habitat loss, and illegal transnational trade. Conservation genetic studies and effective curbs on poaching are important for the conservation of these charismatic apex predators. A limited number of microsatellite markers exists for Panthera species and researchers often cross-amplify domestic cat microsatellites to study these species. We conducted data mining of seven Panthera genome sequences to discover microsatellites for conservation genetic studies of four threatened big cat species. A total of 32 polymorphic microsatellite loci were identified in silico and tested with 152 big cats, and were found polymorphic in most of the tested species. We propose a set of 12 novel microsatellite markers for use in conservation genetics and wildlife forensic investigations of big cat species. Cumulatively, these markers have a high discriminatory power of one in a million for unrelated individuals and one in a thousand for siblings. Similar PCR conditions of these markers increase the prospects of achieving efficient multiplex PCR assays. This study is a pioneering attempt to synthesise genome wide microsatellite markers for big cats.
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Parchizadeh J, Belant JL. Human-caused mortality of large carnivores in Iran during 1980–2021. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01618] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Ghosh T, Sharma A, Mondol S. Optimisation and application of a forensic microsatellite panel to combat Greater-one horned rhinoceros (Rhinoceros unicornis) poaching in India. Forensic Sci Int Genet 2021; 52:102472. [PMID: 33548856 DOI: 10.1016/j.fsigen.2021.102472] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 11/28/2022]
Abstract
The Greater one-horned (GoH) rhinoceros is one of the most charismatic endemic megaherbivores of the Indian subcontinent. Threatened by poaching, habitat loss and disease, the species is found only in small areas of its historical distribution. Increasing demands for rhino horns in chinese traditional medicine has put the existing population under continuing threat, and large profits and low conviction rates make poaching difficult to contain. DNA forensics such as the RhoDIS-Africa program has helped in combating illegal rhino horn trade, but the approach is yet to be optimised for Indian GoH rhinoceros. Here we followed the International Society for Forensic Genetics (ISFG) guidelines to establish a 14 dinucleotide microsatellite panel for Indian GoH rhinoceros DNA profiling. Selected from a large initial pool (n = 34), the microsatellite markers showed high polymorphism, stable peak characteristics, consistent allele calls and produced precise, reproducible genotypes from different types of rhino samples. The panel also showed low genotyping error and produced high statistical power during individual identification (PIDsibs value of 1.2*10-4). As part of the official RhoDIS-India program, we used this panel to match poached rhino carcass with seized contraband as scientific evidence in court procedure. This program now moves to generate detailed allele-frequency maps of all GoH rhinoceros populations in India and Nepal for development of a genetic database and identification of poaching hotspots and trade routes across the subcontinent and beyond.
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Affiliation(s)
- Tista Ghosh
- Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand, 248001, India
| | - Amit Sharma
- World Wide Fund for Nature-India, 172B Lodhi Estate, New Delhi, 110003, India
| | - Samrat Mondol
- Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand, 248001, India.
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Gubbi S, Sharma K, Kumara V. Every hill has its leopard: patterns of space use by leopards ( Panthera pardus) in a mixed use landscape in India. PeerJ 2020; 8:e10072. [PMID: 33083134 PMCID: PMC7548080 DOI: 10.7717/peerj.10072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/09/2020] [Indexed: 11/20/2022] Open
Abstract
Understanding abundance and distribution of species is often necessary for wildlife conservation. However, elusive species such as the leopard (Panthera pardus) that have wide geographical distribution and typically low abundance pose a constant challenge to conservationists due to logistical and methodological constraints. Although leopard abundance has been estimated at the scale of protected areas or other smaller regions, reliable information describing leopard distribution over large spatial scales remains largely unavailable. Knowledge about space use by leopards within landscapes could help improve conservation management, reduce human-wildlife conflict, and also facilitate population status monitoring. We carried out occupancy surveys across c. 24,000 km2 in southern India in a landscape that consisted a mosaic of leopards’ natural habitats and highly human-dominated areas. We investigated the effects of key ecological and anthropogenic variables in determining leopard space use patterns. We addressed imperfect detections obtained using sign surveys conducted on spatially replicated transects within sampling units by modeling detection as a function of spatial auto-correlation and covariates. Our results show that the probability of site-use by leopards across the landscape varied between 0.02 (95% CI [0.01–0.09]) and 0.99 (95% CI [0.99–1.0]) across the study area. The best model (AIC weight = 0.97) showed that the probability of leopard space use was affected by the proportion of natural habitats and the presence of large wild prey in the sampling unit. Given that India is undergoing rapid modifications due to economic changes and demand for natural resources, we emphasize the need for landscape-based approach for conserving and monitoring leopards. We argue that leopards are an indicator of functional ecosystems represented by scrub, deciduous forest and rocky outcrops that do not always get prioritized for conservation, unlike densely forested habitats. Similarly, conservation of natural large wild prey, especially outside the protected area system, should assume greater importance, which could also have a positive impact on reducing human-leopard conflict.
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Affiliation(s)
- Sanjay Gubbi
- Nature Conservation Foundation, Mysore, Karnataka, India.,Department of Wildlife and Management, Kuvempu University, Shankaraghatta, Karnataka, India.,Holématthi Nature Foundation, Bengaluru, Karnataka, India
| | - Koustubh Sharma
- Nature Conservation Foundation, Mysore, Karnataka, India.,Snow Leopard Trust, Seattle, WA, USA
| | - Vijaya Kumara
- Department of Wildlife and Management, Kuvempu University, Shankaraghatta, Karnataka, India
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8
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Leopard activity patterns in a small montane protected area highlight the need for integrated, collaborative landscape conservation. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01182] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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9
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Bourret V, Albert V, April J, Côté G, Morissette O. Past, present and future contributions of evolutionary biology to wildlife forensics, management and conservation. Evol Appl 2020; 13:1420-1434. [PMID: 32684967 PMCID: PMC7359848 DOI: 10.1111/eva.12977] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/27/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022] Open
Abstract
Successfully implementing fundamental concepts into concrete applications is challenging in any given field. It requires communication, collaboration and shared will between researchers and practitioners. We argue that evolutionary biology, through research work linked to conservation, management and forensics, had a significant impact on wildlife agencies and department practices, where new frameworks and applications have been implemented over the last decades. The Quebec government's Wildlife Department (MFFP: Ministère des Forêts, de la Faune et des Parcs) has been proactive in reducing the “research–implementation” gap, thanks to prolific collaborations with many academic researchers. Among these associations, our department's outstanding partnership with Dr. Louis Bernatchez yielded significant contributions to harvest management, stocking programmes, definition of conservation units, recovery of threatened species, management of invasive species and forensic applications. We discuss key evolutionary biology concepts and resulting concrete examples of their successful implementation that derives directly or indirectly from this successful partnership. While old and new threats to wildlife are bringing new challenges, we expect recent developments in eDNA and genomics to provide innovative solutions as long as the research–implementation bridge remains open.
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Affiliation(s)
- Vincent Bourret
- Direction générale de la protection de la faune Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Vicky Albert
- Direction générale de la protection de la faune Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Julien April
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Guillaume Côté
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Olivier Morissette
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
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10
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Bhatt S, Biswas S, Karanth K, Pandav B, Mondol S. Genetic analyses reveal population structure and recent decline in leopards ( Panthera pardus fusca) across the Indian subcontinent. PeerJ 2020; 8:e8482. [PMID: 32117616 PMCID: PMC7006512 DOI: 10.7717/peerj.8482] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/29/2019] [Indexed: 11/21/2022] Open
Abstract
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.
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Affiliation(s)
- Supriya Bhatt
- Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, India
| | - Suvankar Biswas
- Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, India
| | - Krithi Karanth
- Centre for Wildlife Studies, Bengaluru, India.,Nicholas School of Environment, Duke University, Durham, United States of America
| | - Bivash Pandav
- Endangered Species Management, Wildlife Institute of India, Dehradun, India
| | - Samrat Mondol
- Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, India
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11
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Testing microsatellite loci for individual identification of captive African grey parrots (Psittacus erithacus): a molecular tool for parentage analysis that will aid in monitoring legal trade. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-019-01127-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Utility and Applicability of a Universal Set of Primers in Identifying the Sex of South and Southeast Asian Mammals. Zool Stud 2019; 58:e19. [PMID: 31966320 DOI: 10.6620/zs.2019.58-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 06/21/2019] [Indexed: 11/18/2022]
Abstract
Sex identification of individuals is an important task in wildlife forensics as well as in conservation biology. It helps scientists understand population sex ratios with respect to maintaining genetic diversity, managing inbreeding depression and preventing the demographic consequences of sex-biased poaching. The literature on the use of mammalian molecular sex markers indicates that the success of accurate sex identification is variable across species. Very little is known about the effectiveness of such markers on the mammals of South and Southeast Asia. Therefore, we selected and tested three sets of universal primers for low-cost gel-based sex identification of mammals. We amplified different sets of markers-SRY (157 bp) and 12S rRNA (384 bp); Y-53-SRY (225 bp) and ZFX/ZFY (P1/P2; 445); SRY (157 bp) and 12S rRNA (151 bp)-to be used with different types (tissue, hair and skin) of samples from 20 mammalian species. All three sets of primers amplified the sex-specific fragment in a range of samples from hair to tissue. With an increasing number of field studies using non-invasively collected samples, this proposed low-cost gel- based method of molecular sexing may be applied in various aspects of the ecology and biology of South and Southeast Asian mammals, their conservation and forensics. We suggest that at least two sets of primers be used for any biological samples to avoid ambiguity.
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13
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Karmacharya D, Sherchan AM, Dulal S, Manandhar P, Manandhar S, Joshi J, Bhattarai S, Bhatta TR, Awasthi N, Sharma AN, Bista M, Silwal NR, Pokharel P, Lamichhane RR, Sharma N, Llewellyn B, Wultsch C, Kelly MJ, Gour D, Waits L, Hero JM, Hughes J. Species, sex and geo-location identification of seized tiger (Panthera tigris tigris) parts in Nepal-A molecular forensic approach. PLoS One 2018; 13:e0201639. [PMID: 30138352 PMCID: PMC6107122 DOI: 10.1371/journal.pone.0201639] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 07/19/2018] [Indexed: 11/19/2022] Open
Abstract
Tiger (Panthera tigris) populations are in danger across their entire range due to habitat loss, poaching and the demand for tiger parts. The Bengal tiger (Panthera tigris tigris) is an endangered apex predator with a population size estimated to be less than 200 in Nepal. In spite of strict wildlife protection laws, illegal trade of tiger parts is increasing; and Nepal has become one of the major sources and transit routes for poached wildlife parts. Identification of wildlife parts is often challenging for law enforcement officials due to inadequate training and lack of available tools. Here, we describe a molecular forensic approach to gain insight into illegally trafficked tiger parts seized across Nepal. We created Nepal's first comprehensive reference genetic database of wild tigers through the Nepal Tiger Genome Project (2011-2013). This database has nuclear DNA microsatellite genotype and sex profiles, including geo-spatial information, of over 60% (n = 120) of the wild tigers of Nepal. We analyzed 15 putative cases of confiscated poached tiger parts and all were confirmed to be of tiger. Ten samples were identified as male and five were female. We determined probable geo-source location for 9 of the 14 samples with 6-8 nuclear DNA microsatellite loci using inferences from four different statistical assignment methods. Six samples were assigned to Bardia National Park and one of these was an exact match to a female tiger previously profiled in our fecal DNA reference database. Two tiger samples were assigned to Shuklaphanta Wildlife Reserve and one to Chitwan National Park. We are unable to definitively assign five tiger samples which could be offspring dispersers or might have come from tiger population outside of Nepal. Our study revealed that the western region, particularly Bardia National Park, is a poaching hotspot for illegal tiger trade in Nepal. We present feasibility of using molecular forensic based evidence to incriminate criminals in a court of law in the fight against wildlife crime.
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Affiliation(s)
- Dibesh Karmacharya
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
- School of Environment, Griffith University, Gold Coast, Queensland, Australia
| | | | - Santosh Dulal
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Prajwol Manandhar
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | | | - Jyoti Joshi
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Susmita Bhattarai
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Tarka R. Bhatta
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Nagendra Awasthi
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Ajay N. Sharma
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Manisha Bista
- Center for Molecular Dynamics Nepal, Thapathali-11, Kathmandu, Nepal
| | - Nawa R. Silwal
- Central Investigation Bureau (CIB), Pillar 4, Nepal Police, Kathmandu, Nepal
| | - Pravin Pokharel
- Central Investigation Bureau (CIB), Pillar 4, Nepal Police, Kathmandu, Nepal
| | - Rom R. Lamichhane
- Bio-Diversity Section, Ministry of Forest and Soil Conservation, Kathmandu, Nepal
| | - Netra Sharma
- Environment Team, U.S. Agency for International Development (USAID), Kathmandu, Nepal
| | - Bronwyn Llewellyn
- Environment Team, U.S. Agency for International Development (USAID), Kathmandu, Nepal
| | - Claudia Wultsch
- Sackler Institute for Comparative Genomics, American Natural History Museum, New York, New York, United States of America
| | - Marcella J. Kelly
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Digpal Gour
- Laboratory for Ecological, Evolutionary and Conservation Genetics, University of Idaho, Moscow, Idaho, United States of America
| | - Lisette Waits
- Laboratory for Ecological, Evolutionary and Conservation Genetics, University of Idaho, Moscow, Idaho, United States of America
| | - Jean-Marc Hero
- School of Science and Engineering, University of the Sunshine Coast, Sunshine Coast, Queensland, Australia
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, United Kingdom
| | - Jane Hughes
- School of Environment, Griffith University, Gold Coast, Queensland, Australia
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14
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Coetzer WG, Downs CT, Perrin MR, Willows-Munro S. Testing of microsatellite multiplexes for individual identification of Cape Parrots ( Poicephalus robustus): paternity testing and monitoring trade. PeerJ 2017; 5:e2900. [PMID: 28344897 PMCID: PMC5363265 DOI: 10.7717/peerj.2900] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 12/12/2016] [Indexed: 12/04/2022] Open
Abstract
Background Illegal trade in rare wildlife species is a major threat to many parrot species around the world. Wildlife forensics plays an important role in the preservation of endangered or threatened wildlife species. Identification of illegally harvested or traded animals through DNA techniques is one of the many methods used during forensic investigations. Natural populations of the South African endemic Cape Parrot (Poicephalus robustus) are negatively affected by the removal of eggs and chicks for the pet trade. Methods In this study, 16 microsatellite markers specifically designed for the South African endemic Cape Parrot (P. robustus) are assessed for their utility in forensic casework. Using these 16 loci, the genetic diversity of a subset of the captive Cape Parrot population was also assessed and compared to three wild Cape Parrot populations. Results It was determined that the full 16 locus panel has sufficient discriminatory power to be used in parentage analyses and can be used to determine if a bird has been bred in captivity and so can be legally traded or if it has been illegally removed from the wild. In cases where birds have been removed from the wild, this study suggests that a reduced 12 locus microsatellite panel has sufficient power to assign confiscated birds to geographic population of origin. Discussion The level of genetic diversity observed within the captive Cape Parrot population was similar to that observed in the wild populations, which suggests that the captive population is not suffering from decreased levels of genetic diversity. The captive Cape Parrots did however have double the number of private alleles compared to that observed in the most genetically diverse wild population. This is probably due to the presence of rare alleles present in the founder population, which has not been lost due to genetic drift, as many of the individuals tested in this study are F1–F3 wild descendants. The results from this study provide a suit of markers that can be used to aid conservation and law enforcement authorities to better control legal and illegal trade of this South African endemic.
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Affiliation(s)
- Willem G Coetzer
- School of Life Science, University of KwaZulu-Natal , Pietermaritzburg , South Africa
| | - Colleen T Downs
- School of Life Science, University of KwaZulu-Natal , Pietermaritzburg , South Africa
| | - Mike R Perrin
- School of Life Science, University of KwaZulu-Natal , Pietermaritzburg , South Africa
| | - Sandi Willows-Munro
- School of Life Science, University of KwaZulu-Natal , Pietermaritzburg , South Africa
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Aarnes SG, Hagen SB, Andreassen R, Schregel J, Knappskog PM, Hailer F, Stenhouse G, Janke A, Eiken HG. Y-chromosomal testing of brown bears (Ursus arctos): Validation of a multiplex PCR-approach for nine STRs suitable for fecal and hair samples. Forensic Sci Int Genet 2015; 19:197-204. [PMID: 26264959 DOI: 10.1016/j.fsigen.2015.07.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/27/2015] [Accepted: 07/26/2015] [Indexed: 11/15/2022]
Abstract
High-resolution Y-chromosomal markers have been applied to humans and other primates to study population genetics, migration, social structures and reproduction. Y-linked markers allow the direct assessment of the genetic structure and gene flow of uniquely male inherited lineages and may also be useful for wildlife conservation and forensics, but have so far been available only for few wild species. Thus, we have developed two multiplex PCR reactions encompassing nine Y-STR markers identified from the brown bear (Ursus arctos) and tested them on hair, fecal and tissue samples. The multiplex PCR approach was optimized and analyzed for species specificity, sensitivity and stutter-peak ratios. The nine Y-STRs also showed specific STR-fragments for male black bears and male polar bears, while none of the nine markers produced any PCR products when using DNA from female bears or males from 12 other mammals. The multiplex PCR approach in two PCR reactions could be amplified with as low as 0.2 ng template input. Precision was high in DNA templates from hairs, fecal scats and tissues, with standard deviations less than 0.14 and median stutter ratios from 0.04 to 0.63. Among the eight di- and one tetra-nucleotide repeat markers, we detected simple repeat structures in seven of the nine markers with 9-25 repeat units. Allelic variation was found for eight of the nine Y-STRs, with 2-9 alleles for each marker and a total of 36 alleles among 453 male brown bears sampled mainly from Northern Europe. We conclude that the multiplex PCR approach with these nine Y-STRs would provide male bear Y-chromosomal specificity and evidence suited for samples from conservation and wildlife forensics.
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Affiliation(s)
| | | | - Rune Andreassen
- Faculty of Health Sciences, Oslo and Akershus University College, Oslo Norway
| | | | | | - Frank Hailer
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK
| | - Gordon Stenhouse
- Foothills Research Institute, 1176 Switzer Drive, Box 6330, Hinton, AB T7V 1X6, Canada
| | - Axel Janke
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Goethe University Frankfurt, Institute for Ecology, Evolution & Diversity, Frankfurt am Main, Germany
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