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Ahmad K, Shankar Pacha A, Yahya Naqash R, Kumar Peddamma S, Yellapu S, Hudson S, Singh Baghel D, Nigam P, Mondol S. Evolutionary insights on critically endangered Kashmir red deer or hangul ( Cervus hanglu hanglu) through a mitogenomic lens. PeerJ 2023; 11:e15746. [PMID: 37872949 PMCID: PMC10590573 DOI: 10.7717/peerj.15746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 06/22/2023] [Indexed: 10/25/2023] Open
Abstract
Background The Kashmir red deer or Hangul (Cervus hanglu hanglu) is the only Tarim red deer species endemic to India. With a current estimated population size of fewer than 200 individuals, this critically endangered species is confined to the greater Dachigam landscape in Jammu and Kashmir. Poaching, habitat loss and fragmentation, resource competition with livestock, and small population size are the major conservation challenges for this species. Methods Blood sampling was conducted from two wild Hangul individuals during radio-collaring operations at Dachigam National Park, Kashmir in 2013 and 2020, respectively. Using next-generation sequencing approach, we sequenced the 16,351 bp long mitogenome of two wild-caught Hangul individuals (1 M:1 F at ~14× and ~10× coverage, respectively) from Dachigam National Park. Results The annotated sequences were identical with an AT-rich composition, including 13 protein-coding genes (11,354 bp), 22 tRNA genes (1,515 bp), two ribosomal genes (2,526 bp) and a non-coding control region (917 bp) in a conserved order like other red deer species. Bayesian phylogenetic reconstruction of the red deer complex revealed two major groups: the elaphoid and the wapitoid clades. Hangul formed a distinct clade with its other subspecies C. hanglu yarkandensis and is sister to the Hungarian red deer (C. elaphus hippelaphus). Divergence time analyses suggested that the Tarim deer species group separated ~1.55 Mya from their common ancestors and Hangul diverged ~0.75 Mya from closely related C. yarkandensis, corroborating with the known paleobiogeographic events related to refugia during glaciations in the Pleistocene era. This study provides baseline information on Hangul mitogenome for further research on phylogeography and other population parameters and helps in developing suitable conservation plans for this species.
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Affiliation(s)
- Khursheed Ahmad
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Ankit Shankar Pacha
- Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, Uttarakhand, India
| | - Rashid Yahya Naqash
- Department of Wildlife Protection, Jammu & Kashmir Government, Srinagar, Jammu and Kashmir, India
| | | | | | - Shenu Hudson
- Nucleome Informatics Pvt. Ltd., Hyderabad, Telangana, India
| | | | - Parag Nigam
- Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, Uttarakhand, India
| | - Samrat Mondol
- Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, Uttarakhand, India
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Jabin G, Dolker S, Joshi BD, Singh SK, Chandra K, Sharma LK, Thakur M. Lahaul–Zanskar–Sham Valley Corridor in Indian Trans Himalayan Region Facilitates Dispersal and Gene Flow in Himalayan Ibex. BIOLOGY 2023; 12:biology12030382. [PMID: 36979074 PMCID: PMC10045165 DOI: 10.3390/biology12030382] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023]
Abstract
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.
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Affiliation(s)
- Gul Jabin
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata 700019, West Bengal, India
| | - Stanzin Dolker
- Zoological Survey of India, New Alipore, Kolkata 700053, West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata 700019, West Bengal, India
| | - 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
| | - 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
- Correspondence:
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Singh VK, Joshi BD, Dalui S, Ghosh A, Jabin G, Sharief A, Kumar V, Singh H, Singh SK, Chandra K, Sharma LK, Thakur M. Genetic diversity and population structure of Himalayan tahr (Hemitragus jemlahicus) from Western Himalaya. MAMMALIA 2023. [DOI: 10.1515/mammalia-2022-0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Abstract
Himalayan tahr is a group-living animal of high-altitude Himalaya, distributed all across the subalpine range that also formed an important prey base for large carnivores in Himalaya. The species is threatened due to habitat fragmentation, illegal poaching, and anthropogenic activities. We undertook population genetic assessment of Himalayan tahr from Western Himalaya and observed comparable genetic diversity at both mitochondrial and nuclear microsatellite loci. Bayesian skyline plots showed stable demography in the past several thousand years. We identified 27 unique individuals with a select panel of seven loci and the Bayesian structure analysis inferred two genetic clusters. The present study is the first report on the population genetic make-up of Himalayan tahr and can be used for long-term genetic monitoring of the species.
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Affiliation(s)
- Vinaya Kumar Singh
- Zoological Survey of India , New Alipore , Kolkata 700053 , West Bengal , India
| | - Bheem Dutt Joshi
- Zoological Survey of India , New Alipore , Kolkata 700053 , West Bengal , India
| | - Supriyo Dalui
- Zoological Survey of India , New Alipore , Kolkata 700053 , West Bengal , India
| | - Avijit Ghosh
- Zoological Survey of India , New Alipore , Kolkata 700053 , West Bengal , India
| | - Gul Jabin
- 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
| | - Sujeet Kumar Singh
- Zoological Survey of India , New Alipore , Kolkata 700053 , West Bengal , India
- Amity Institute of Forestry and Wildlife, Amity University , Sector-125 , Noida 201303 , 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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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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Genetic diversity and population structure of the northern red muntjac (Muntiacus vaginalis) in Indian Himalayan region. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00254-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Singh VK, Joshi BD, Bhat GJ, Singh SK, Chandra K, Sharma LK, Thakur M. Population genetics of Sambar (Rusa unicolor) from the Western Himalayas: preliminary findings. Mol Biol Rep 2021; 49:811-816. [PMID: 34668102 DOI: 10.1007/s11033-021-06845-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/15/2021] [Indexed: 11/29/2022]
Abstract
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.
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Affiliation(s)
- Vinaya Kumar Singh
- Zoological Survey of India, New Alipore, Kolkata, 700053, West Bengal, India
| | - Bheem Dutt Joshi
- Zoological Survey of India, New Alipore, Kolkata, 700053, West Bengal, India
| | - Gul Jabin Bhat
- 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.,Amity Institute of Forestry and Wildlife, Amity University, Sector-125, Noida, 201303, 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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Genetic monitoring of Himalayan goral (Naemorhedus goral) from Western Himalayas, India. Mol Biol Rep 2021; 48:7609-7615. [PMID: 34599485 DOI: 10.1007/s11033-021-06716-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/27/2021] [Indexed: 10/20/2022]
Abstract
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.
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Mukherjee T, Sharma V, Sharma LK, Thakur M, Joshi BD, Sharief A, Thapa A, Dutta R, Dolker S, Tripathy B, Chandra K. Landscape-level habitat management plan through geometric reserve design for critically endangered Hangul (Cervus hanglu hanglu). THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 777:146031. [PMID: 33676208 DOI: 10.1016/j.scitotenv.2021.146031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Hangul (Cervus hanglu hanglu), the only red deer subspecies surviving in the Indian subcontinent, is of top conservation priority with global importance. Unfortunately, it has lost much of its historical distribution range, and it is now confined to Dachigam landscape within the Kashmir valley of India. The Government of India initiated a recovery plan in 2008 to augment their numbers through ex-situ conservation programs. However, it was necessary to identify potential hangul habitats in Kashmir valley for adopting landscape-level conservation planning for the species. Based on geometric aspects of reserve design, we modeled hangul habitat using an ensemble approach to identify hangul habitats. The present model indicates that the conifer and broadleaf mixed forests were the most suitable habitats. Only 9% of the total study landscape was found suitable for the species. We identified corridors among the suitable habitat blocks, which may be vital for the species' long-term genetic viability. We suggest reorganizing the existing management of Dachigam National Park (NP) following the landscape level and habitat block-level management planning based on the core principles of geometric reserve design. We recommend that the identified patch (PID-6) in the southern region of the landscape to be converted into a Conservation Reserve or merged with the Overa-Aru Wildlife Sanctuary. This habitat patch PID-6 may be a stepping stone habitat and vital for maintaining the species landscape connectivity and metapopulation dynamics.
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Affiliation(s)
| | - Vandana Sharma
- Indian Institute of Remote Sensing, Dehradun 248001, India
| | | | | | | | | | | | - Ritam Dutta
- Zoological Survey of India, Kolkata 700053, India
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Dutt Joshi B, Jabin G, Sharief A, Kumar V, Mukherjee T, Kumar M, Singh A, Kumar Singh S, Chandra K, Sharma LK, Thakur M. Genetic evidence for allopatric speciation of the Siberian ibex Capra sibirica in India. ENDANGER SPECIES RES 2020. [DOI: 10.3354/esr01034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Montane systems, formed by a series of climatic oscillations and temporal topographic metamorphoses, have broken up the contiguous distribution of widespread species and accelerated allopatric speciation. We used a partial fragment of the mitochondrial cytochrome b (cytb) gene to address speciation across the entire range of the Siberian ibex Capra sibirica. We demonstrated that the Siberian ibex is a polytypic species, plausibly formed by a combination of at least 2 species and/or 3 to 4 sub-species. Bayesian phylogeny showed that the Indian-Tajikistan (I-T) clade is adequately diverged from the other clades based on the mean intra-specific distance criterion, and warrants recognition as a distinct species. We provide pragmatic evidence for the endorsement of the I-T clade as a distinct species of Siberian ibex and urge prioritization of the conservation of this species at global and regional scales.
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Affiliation(s)
- B Dutt Joshi
- Zoological Survey of India, New Alipore, Kolkata, 700053 West Bengal, India
| | - G Jabin
- Zoological Survey of India, New Alipore, Kolkata, 700053 West Bengal, India
- Department of Zoology, University of Calcutta, Kolkata, 700019 West Bengal, India
| | - A Sharief
- Zoological Survey of India, New Alipore, Kolkata, 700053 West Bengal, India
| | - V Kumar
- Zoological Survey of India, New Alipore, Kolkata, 700053 West Bengal, India
| | - T Mukherjee
- Zoological Survey of India, New Alipore, Kolkata, 700053 West Bengal, India
| | - M Kumar
- Zoological Survey of India, New Alipore, Kolkata, 700053 West Bengal, India
| | - A Singh
- Zoological Survey of India, New Alipore, Kolkata, 700053 West Bengal, India
| | - S Kumar Singh
- Zoological Survey of India, New Alipore, Kolkata, 700053 West Bengal, India
| | - K Chandra
- Zoological Survey of India, New Alipore, Kolkata, 700053 West Bengal, India
| | - LK Sharma
- Zoological Survey of India, New Alipore, Kolkata, 700053 West Bengal, India
| | - M Thakur
- Zoological Survey of India, New Alipore, Kolkata, 700053 West Bengal, India
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Shukla MA, Joshi BD, Kumar VP, Mehta AK, Goyal SP. Investigating the genetic diversity and presence of forensically informative nucleotide sequences in Indian antelope (Antilope cervicapra) using multiple genes of the mitochondrial genome. Mol Biol Rep 2019; 46:6187-6195. [PMID: 31486977 DOI: 10.1007/s11033-019-05054-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 08/29/2019] [Indexed: 10/26/2022]
Abstract
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.
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Affiliation(s)
- Malay Ashvinkumar Shukla
- Laboratory of Forensic Biology and Biotechnology, Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, Gujarat, 382007, India.,Wildlife Institute of India, Post Box # 18, Chandrabani, Dehradun, Uttarakhand, 248001, India
| | - Bheem Dutt Joshi
- Wildlife Institute of India, Post Box # 18, Chandrabani, Dehradun, Uttarakhand, 248001, India
| | - Ved Prakash Kumar
- Wildlife Institute of India, Post Box # 18, Chandrabani, Dehradun, Uttarakhand, 248001, India
| | - Anil Kumar Mehta
- Laboratory of Forensic Biology and Biotechnology, Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, Gujarat, 382007, India
| | - Surendra Prakash Goyal
- Wildlife Institute of India, Post Box # 18, Chandrabani, Dehradun, Uttarakhand, 248001, India.
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Khatri H, Ghosh A, Jabin G, Basu S, Singh SK, Chandra K, Sharma LK, Thakur M. Mass mortality of birds on railway track genetically identified as critically endangered Red-headed Vulture (Sarcogyps calvus) in Ranipur Wildlife Sanctuary, Uttar Pradesh, India. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-019-01088-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Genetic analysis of endangered hog deer (Axis porcinus) reveals two distinct lineages from the Indian subcontinent. Sci Rep 2018; 8:16308. [PMID: 30397218 PMCID: PMC6218551 DOI: 10.1038/s41598-018-34482-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/16/2018] [Indexed: 11/08/2022] Open
Abstract
The hog deer (Axis porcinus) is threatened by habitat alteration, fragmentation, and poaching, which have led to a drastic decline of its wild population. Two subspecies of A. porcinus have been described from its distribution range. A. p. porcinus is reported to occur from Pakistan along the Himalayan foothills through Nepal, India and Myanmar, and A. p. annamiticus is found in Thailand, Indo-China, Laos, Cambodia, and Vietnam. However, the current distribution range of A. p. annamiticus is still unclear. We used the partial control region (CR) of mitochondrial DNA (mtDNA) and seven microsatellite loci to investigate the intra-species structure, differentiation, and demographic history of hog deer populations from three landscapes, the Terai Arc, Northeast, and Indo-Burma (Keibul Lamjao National Park (KLNP), Manipur, India) landscapes. We also carried out divergence time estimation using the complete mitogenome. The level of variation was ~4%, and the time of divergence of the KLNP population and the other Indian populations was about 0.22 Mya, i.e., during the last glaciation periods of the Late Pleistocene/Early Holocene. The KLNP haplotypes of the control region were shared with the Southeast Asian subspecies, A. p. annamiticus. The results of the investigations of the microsatellite loci supported the mtDNA results unambiguously. Two genetically distinct lineages are found in India: one is found from the Terai Arc to Assam (A. p. porcinus) and the other in Manipur (A. p. annamiticus). The genetic diversity in KLNP was low and exhibited a higher degree of genetic differentiation compared with major Indian populations. The Bayesian skyline plots indicated that after a long phase of historic demographic stability, the populations of both the lineages of hog deer suffered pronounced declines during the period from ~800 years BP to 5000 years BP. In summary, our finding provided evidence that the KLNP population is probably a prime, isolated and sustaining stock of A. p. annamiticus and should be managed as evolutionarily significant units (ESUs).
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Thakur M, Fernandes M, Sathyakumar S, Singh SK, Vijh RK, Han J, Wu DD, Zhang YP. Understanding the cryptic introgression and mixed ancestry of Red Junglefowl in India. PLoS One 2018; 13:e0204351. [PMID: 30307994 PMCID: PMC6188471 DOI: 10.1371/journal.pone.0204351] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/06/2018] [Indexed: 11/19/2022] Open
Abstract
Red Junglefowls (RJFs), the wild progenitor of modern day chickens (DCs), are
believed to be in genetic endangerment due to introgression of domestic genes
through opportunistic matings with domestic or feral chickens. Previous studies
from India reported rare hybridization of RJFs in the wild. However, RJF
population genetic structure, pattern of gene flow and their admixture with DC
populations are poorly understood at the landscape level. We conducted this
study with a large sample size, covering the predicted natural distribution
range of RJFs in India. We documented strong evidence of directional gene flow
from DCs to free-ranging wild RJFs, with the Northeastern RJF population
exhibiting the most genetic variants in their nuclear and mitochondrial genomes,
indicating it to be the ancestral population from which early radiation may have
occurred. The results provide evidence that landscape features do not act as a
barrier to gene flow and the distribution pattern could not be explored due to
physical sharing or exchange of wild birds in the past when forests were
continuous across RJF range in India.
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Affiliation(s)
- Mukesh Thakur
- Wildlife Institute of India, Chandrabani, Dehradun,Uttarakhand,
India
- State Key Laboratory of Genetic Resources and Evolution and Yunnan
Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of
Zoology, Chinese Academy of Sciences, Kunming, Yunnan, P.R.
China
- * E-mail: (MT); (SS)
| | - Merwyn Fernandes
- Wildlife Institute of India, Chandrabani, Dehradun,Uttarakhand,
India
| | - Sambandam Sathyakumar
- Wildlife Institute of India, Chandrabani, Dehradun,Uttarakhand,
India
- * E-mail: (MT); (SS)
| | - Sujeet K. Singh
- Wildlife Institute of India, Chandrabani, Dehradun,Uttarakhand,
India
| | - Ramesh Kumar Vijh
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), G.T. Road Bye
Pass, Near Basant Vihar, Karnal, Haryana, India
| | - Jianlin Han
- CAAS—ILRI Joint Laboratory on Livestock and Forage Genetic Resources,
Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS),
Beijing, P.R. China
- International Livestock Research Institute (ILRI), Nairobi,
Kenya
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan
Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of
Zoology, Chinese Academy of Sciences, Kunming, Yunnan, P.R.
China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan
Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of
Zoology, Chinese Academy of Sciences, Kunming, Yunnan, P.R.
China
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Schmid S, Neuenschwander S, Pitteloud C, Heckel G, Pajkovic M, Arlettaz R, Alvarez N. Spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus revealed by museum genomics. Ecol Evol 2018; 8:1480-1495. [PMID: 29435226 PMCID: PMC5792620 DOI: 10.1002/ece3.3699] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/06/2017] [Accepted: 11/10/2017] [Indexed: 12/14/2022] Open
Abstract
Analyzing genetic variation through time and space is important to identify key evolutionary and ecological processes in populations. However, using contemporary genetic data to infer the dynamics of genetic diversity may be at risk of a bias, as inferences are performed from a set of extant populations, setting aside unavailable, rare, or now extinct lineages. Here, we took advantage of new developments in next-generation sequencing to analyze the spatial and temporal genetic dynamics of the grasshopper Oedaleus decorus, a steppic Southwestern-Palearctic species. We applied a recently developed hybridization capture (hyRAD) protocol that allows retrieving orthologous sequences even from degraded DNA characteristic of museum specimens. We identified single nucleotide polymorphisms in 68 historical and 51 modern samples in order to (i) unravel the spatial genetic structure across part of the species distribution and (ii) assess the loss of genetic diversity over the past century in Swiss populations. Our results revealed (i) the presence of three potential glacial refugia spread across the European continent and converging spatially in the Alpine area. In addition, and despite a limited population sample size, our results indicate (ii) a loss of allelic richness in contemporary Swiss populations compared to historical populations, whereas levels of expected heterozygosities were not significantly different. This observation is compatible with an increase in the bottleneck magnitude experienced by central European populations of O. decorus following human-mediated land-use change impacting steppic habitats. Our results confirm that application of hyRAD to museum samples produces valuable information to study genetic processes across time and space.
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Affiliation(s)
- Sarah Schmid
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | | | - Camille Pitteloud
- Department of Environmental Systems ScienceEidgenössische Technische Hochschule ZürichZürichSwitzerland
| | - Gerald Heckel
- Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| | - Mila Pajkovic
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Raphaël Arlettaz
- Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| | - Nadir Alvarez
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Natural History Museum of GenevaGenevaSwitzerland
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15
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Noor A, Mir ZR, Veeraswami GG, Habib B. Activity patterns and spatial co-occurrence of sympatric mammals in the moist temperate forest of the Kashmir Himalaya, India. FOLIA ZOOLOGICA 2017. [DOI: 10.25225/fozo.v66.i4.a4.2017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Athar Noor
- Wildlife Institute of India, P.O. Box 18, Chandrabani, Dehradun, Uttarakhand 248001, India:, , ,
| | - Zaffar Rais Mir
- Wildlife Institute of India, P.O. Box 18, Chandrabani, Dehradun, Uttarakhand 248001, India:, , ,
| | - Gopi Govindan Veeraswami
- Wildlife Institute of India, P.O. Box 18, Chandrabani, Dehradun, Uttarakhand 248001, India:, , ,
| | - Bilal Habib
- Wildlife Institute of India, P.O. Box 18, Chandrabani, Dehradun, Uttarakhand 248001, India:, , ,
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16
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Kumar VP, Thakur M, Rajpoot A, Joshi BD, Nigam P, Ahmad K, Kumar D, Goyal SP. Resolving the phylogenetic status and taxonomic relationships of the Hangul (Cervus elaphus hanglu) in the family Cervidae. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:835-842. [PMID: 27937071 DOI: 10.1080/24701394.2016.1197217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The Hangul (Cervus elaphus hanglu) is a "Least Concern" deer species, and it is the only survivor of the Red Deer group in the Indian subcontinent. The phylogenetic status of the Hangul relative to the other members of the family Cervidae is not known because sequence data are not available in public databases. Therefore, this study was carried out to determine the phylogenetic status and delineate the genetic boundaries of the Hangul with respect to the other Red Deer subspecies on the basis of cytochrome b gene sequence data (ca 421 bp). There are three major monophyletic groups of the Red Deer in the phylogenetic tree, which are referred to as the western (Hap-01 to Hap-10), eastern (Hap-11 to Hap-20) and tarim (Hap-21 to Hap-25) groups. The overall haplotype diversity and per-site nucleotide diversity were 0.9771 (±0.0523) and 0.0388 (±0.00261), respectively. In the phylogenetic tree, the Hangul clustered with the tarim group (Yarkand and Bactrian Red Deer) with a strong bootstrap support (92%) and was found to be genetically closer to the Bactrian Red Deer than to the Yarkand Red Deer. Our molecular analysis supported the idea that the Hangul diverged from the Bactrian Red Deer and migrated to India from Tajikistan approximately 1.2 MYA.
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Affiliation(s)
- Ved P Kumar
- a Wildlife Institute of India , Chandrabani , Dehradun , Uttarakhand , India.,b Department of Zoology, Veer Kunwar Singh University , Arrah , Bihar , India
| | - Mukesh Thakur
- c Amity Institute of Wildlife Sciences, Amity University , Noida , Uttar Pradesh , India
| | - Ankita Rajpoot
- d Zoological Survey of India, NRC , Dehradun , Uttarakhand , India
| | - Bhim Dutt Joshi
- a Wildlife Institute of India , Chandrabani , Dehradun , Uttarakhand , India
| | - Parag Nigam
- a Wildlife Institute of India , Chandrabani , Dehradun , Uttarakhand , India
| | - Khursheed Ahmad
- e Centre for Mountain Wildlife Sciences, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology , Srinagar , Jammu & Kashmir , India
| | - Dhyanendra Kumar
- b Department of Zoology, Veer Kunwar Singh University , Arrah , Bihar , India
| | - Surendra P Goyal
- a Wildlife Institute of India , Chandrabani , Dehradun , Uttarakhand , India
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17
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Ahmad K, Kumar VP, Joshi BD, Raza M, Nigam P, Khan AA, Goyal SP. Genetic diversity of the Tibetan antelope (Pantholops hodgsonii) population of Ladakh, India, its relationship with other populations and conservation implications. BMC Res Notes 2016; 9:477. [PMID: 27769305 PMCID: PMC5073904 DOI: 10.1186/s13104-016-2271-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 10/08/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Tibetan antelope (Pantholops hodgsonii), or chiru, is an endangered antelope, distributed in China [Xinjiang, Xizang, Qinghai, Zhuolaihu Lake (Breeding habitat)], and India (Aksai Chin and Ladakh). There is a global demand for the species prized wool, which is used in weaving shahtoosh shawls. Over the years, the population of the Tibetan antelope has drastically declined from more than a million to a few thousand individuals, mainly due to poaching. Field studies undertaken in Ladakh, India also indicated winter migration of the population to Tibet. Migration between winter and calving habitats is well established to be female-biased across the Qinghai Tibetan Plateau (QTP). For effective conservation planning, genetic characterization is considered the best way to understand the likely impact of threats for ensuring the long-term viability of the population. In this regard, genetic characteristics of all Chinese populations are well-studied using mitochondrial and microsatellite markers, but information is lacking for the Indian population. Therefore, using the control region marker, we document for the first time the genetic variation of the Indian population of the Tibetan antelope, the extent of migration and its relationships with other populations of China. RESULTS The partial fragment of control region (259 bp) marker was successfully amplified in 30 Tibetan antelope samples that were collected from the Chang Chenmo Valley in eastern Ladakh, India. We also retrieved control region sequences (n = 88) available in the public domain from GenBank of different Chinese populations. Low levels of nucleotide (π; 0.004) and haplotype (hd; 0.543) diversity were observed in the Indian population when compared to Chinese populations (π = 0.01357-0.02048 and hd = 0.889-0.986). Commonly used indices (Tajima's D and Fu's Fs) were analyzed for inferring the demographic history of the Indian populations, and all values were negative indicating population expansion or demographic equilibrium, though nonsignificant. We observed five haplotypes in the Indian population, and these were not reported in previously studied populations of QTP. Bayesian-based phylogenetic analysis indicates the presence of four clades, however, the posterior probability support for three of these clades is weak (<0.5). Of these, the Indian population formed a distinct clade, whereas the Chinese populations exhibited shared haplotypes, and no geographic structure was observed. Median-joining network analysis was conducted for 46 haplotypes in the overall population, except the samples from India which showed a star-like topology. The Indian population is separated by one median vector from the Chinese population. CONCLUSIONS The present study revealed the presence of different sub-clades in the Bayesian phylogenetic tree and five new haplotypes only in the Indian population or sampling location. Furthermore, in the phylogenetic tree, Indian haplotypes of Tibetan antelopes were clustered with the haplotype reported in the Chinese population of the Xinjiang region. Median-joining network analysis showed shared haplotypes pattern in all populations of QTP except the samples from India which showed new haplotypes. Given the presence of low nucleotide and haplotype diversity in eastern Ladakh populations and limited information available for populations of the western side in its range, we suggest to include genetic studies of Tibetan antelope populations around Aksai Chin (Fig. 1) under the proposed transboundary agenda between India and China and assess relationships with other populations. Such understanding would enable the planning of conservation strategies for ensuring long-term survival of westernmost populations in its range, and if required, it would establish connectivity with the other populations.
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Affiliation(s)
- Khursheed Ahmad
- Centre for Mountain Wildlife Sciences, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, Jammu and Kashmir 190006 India
| | - Ved P. Kumar
- Wildlife Forensic and Conservation Genetics Cell, Wildlife Institute of India, Post Box #18, Chandrabani, Dehradun, Uttarakhand 248001 India
| | - Bheem Dutt Joshi
- Wildlife Forensic and Conservation Genetics Cell, Wildlife Institute of India, Post Box #18, Chandrabani, Dehradun, Uttarakhand 248001 India
| | - Mohamed Raza
- Centre for Mountain Wildlife Sciences, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, Jammu and Kashmir 190006 India
| | - Parag Nigam
- Wildlife Health Managment, Wildlife Institute of India, Post Box #18, Chandrabani, Dehradun, Uttarakhand 248001 India
| | - Anzara Anjum Khan
- Centre for Mountain Wildlife Sciences, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, Jammu and Kashmir 190006 India
| | - Surendra P. Goyal
- Wildlife Forensic and Conservation Genetics Cell, Wildlife Institute of India, Post Box #18, Chandrabani, Dehradun, Uttarakhand 248001 India
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18
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Mitochondrial and Nuclear DNA Based Genetic Assessment Indicated Distinct Variation and Low Genetic Exchange Among the Three Subspecies of Swamp Deer (Rucervus duvaucelii). Evol Biol 2016. [DOI: 10.1007/s11692-016-9387-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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19
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Zachos FE, Frantz AC, Kuehn R, Bertouille S, Colyn M, Niedziałkowska M, Pérez-González J, Skog A, Sprĕm N, Flamand MC. Genetic Structure and Effective Population Sizes in European Red Deer (Cervus elaphus) at a Continental Scale: Insights from Microsatellite DNA. J Hered 2016; 107:318-26. [PMID: 26912909 DOI: 10.1093/jhered/esw011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/19/2016] [Indexed: 11/14/2022] Open
Abstract
We analyzed more than 600 red deer (Cervus elaphus) from large parts of its European distribution range at 13 microsatellite loci, presenting the first continent-wide study of this species using nuclear markers. Populations were clearly differentiated (overall F ST = 0.166, Jost's D est = 0.385), and the BAPS clustering algorithm yielded mainly geographically limited and adjacent genetic units. When forced into only 3 genetic clusters our data set produced a very similar geographic pattern as previously found in mtDNA phylogeographic studies: a western group from Iberia to central and parts of Eastern Europe, an eastern group from the Balkans to Eastern Europe, and a third group including the threatened relict populations from Sardinia and Mesola in Italy. This result was also confirmed by a multivariate approach to analyzing our data set, a discriminant analysis of principal components. Calculations of genetic diversity and effective population sizes (linkage disequilibrium approach) yielded the lowest results for Italian (Sardinia, Mesola; N e between 2 and 8) and Scandinavian red deer, in line with known bottlenecks in these populations. Our study is the first to present comparative nuclear genetic data in red deer across Europe and may serve as a baseline for future analyses of genetic diversity and structuring in this widespread ungulate.
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Affiliation(s)
- Frank E Zachos
- From the Natural History Museum Vienna, 1010 Vienna, Austria (Zachos); Musée National d'Histoire Naturelle, L-2160 Münster, Luxembourg (Frantz); Fondation faune-flore, 25, Rue Munster, L-2160 Luxembourg (Frantz); Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technische Universität München, Freising, Germany (Kuehn); Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, NM 88003-8003, USA (Kuehn); Département de l'Etude du Milieu naturel et agricole, Service Public de Wallonie, 23 Avenue Maréchal Juin, 5030 Gembloux, Belgium (Bertouille); CNRS-UMR 6553, Université de Rennes 1, Station Biologique, 35380 Paimpont, France (Colyn); Mammal Research Institute, Polish Academy of Sciences, Białowieza, Poland (Niedziałkowska); Grupo de Biología y Etología, Universidad de Extremadura, 10071 Cáceres, Spain (Perez-Gonzalez); Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, 0316 Oslo, Norway (Skog); Cancer Registry of Norway, 0304 Oslo, Norway (Skog); Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia (Sprĕm); and Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-15, 1348 Louvain-la-Neuve, Belgium (Flamand)
| | - Alain C Frantz
- From the Natural History Museum Vienna, 1010 Vienna, Austria (Zachos); Musée National d'Histoire Naturelle, L-2160 Münster, Luxembourg (Frantz); Fondation faune-flore, 25, Rue Munster, L-2160 Luxembourg (Frantz); Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technische Universität München, Freising, Germany (Kuehn); Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, NM 88003-8003, USA (Kuehn); Département de l'Etude du Milieu naturel et agricole, Service Public de Wallonie, 23 Avenue Maréchal Juin, 5030 Gembloux, Belgium (Bertouille); CNRS-UMR 6553, Université de Rennes 1, Station Biologique, 35380 Paimpont, France (Colyn); Mammal Research Institute, Polish Academy of Sciences, Białowieza, Poland (Niedziałkowska); Grupo de Biología y Etología, Universidad de Extremadura, 10071 Cáceres, Spain (Perez-Gonzalez); Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, 0316 Oslo, Norway (Skog); Cancer Registry of Norway, 0304 Oslo, Norway (Skog); Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia (Sprĕm); and Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-15, 1348 Louvain-la-Neuve, Belgium (Flamand)
| | - Ralph Kuehn
- From the Natural History Museum Vienna, 1010 Vienna, Austria (Zachos); Musée National d'Histoire Naturelle, L-2160 Münster, Luxembourg (Frantz); Fondation faune-flore, 25, Rue Munster, L-2160 Luxembourg (Frantz); Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technische Universität München, Freising, Germany (Kuehn); Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, NM 88003-8003, USA (Kuehn); Département de l'Etude du Milieu naturel et agricole, Service Public de Wallonie, 23 Avenue Maréchal Juin, 5030 Gembloux, Belgium (Bertouille); CNRS-UMR 6553, Université de Rennes 1, Station Biologique, 35380 Paimpont, France (Colyn); Mammal Research Institute, Polish Academy of Sciences, Białowieza, Poland (Niedziałkowska); Grupo de Biología y Etología, Universidad de Extremadura, 10071 Cáceres, Spain (Perez-Gonzalez); Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, 0316 Oslo, Norway (Skog); Cancer Registry of Norway, 0304 Oslo, Norway (Skog); Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia (Sprĕm); and Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-15, 1348 Louvain-la-Neuve, Belgium (Flamand)
| | - Sabine Bertouille
- From the Natural History Museum Vienna, 1010 Vienna, Austria (Zachos); Musée National d'Histoire Naturelle, L-2160 Münster, Luxembourg (Frantz); Fondation faune-flore, 25, Rue Munster, L-2160 Luxembourg (Frantz); Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technische Universität München, Freising, Germany (Kuehn); Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, NM 88003-8003, USA (Kuehn); Département de l'Etude du Milieu naturel et agricole, Service Public de Wallonie, 23 Avenue Maréchal Juin, 5030 Gembloux, Belgium (Bertouille); CNRS-UMR 6553, Université de Rennes 1, Station Biologique, 35380 Paimpont, France (Colyn); Mammal Research Institute, Polish Academy of Sciences, Białowieza, Poland (Niedziałkowska); Grupo de Biología y Etología, Universidad de Extremadura, 10071 Cáceres, Spain (Perez-Gonzalez); Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, 0316 Oslo, Norway (Skog); Cancer Registry of Norway, 0304 Oslo, Norway (Skog); Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia (Sprĕm); and Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-15, 1348 Louvain-la-Neuve, Belgium (Flamand)
| | - Marc Colyn
- From the Natural History Museum Vienna, 1010 Vienna, Austria (Zachos); Musée National d'Histoire Naturelle, L-2160 Münster, Luxembourg (Frantz); Fondation faune-flore, 25, Rue Munster, L-2160 Luxembourg (Frantz); Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technische Universität München, Freising, Germany (Kuehn); Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, NM 88003-8003, USA (Kuehn); Département de l'Etude du Milieu naturel et agricole, Service Public de Wallonie, 23 Avenue Maréchal Juin, 5030 Gembloux, Belgium (Bertouille); CNRS-UMR 6553, Université de Rennes 1, Station Biologique, 35380 Paimpont, France (Colyn); Mammal Research Institute, Polish Academy of Sciences, Białowieza, Poland (Niedziałkowska); Grupo de Biología y Etología, Universidad de Extremadura, 10071 Cáceres, Spain (Perez-Gonzalez); Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, 0316 Oslo, Norway (Skog); Cancer Registry of Norway, 0304 Oslo, Norway (Skog); Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia (Sprĕm); and Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-15, 1348 Louvain-la-Neuve, Belgium (Flamand)
| | - Magdalena Niedziałkowska
- From the Natural History Museum Vienna, 1010 Vienna, Austria (Zachos); Musée National d'Histoire Naturelle, L-2160 Münster, Luxembourg (Frantz); Fondation faune-flore, 25, Rue Munster, L-2160 Luxembourg (Frantz); Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technische Universität München, Freising, Germany (Kuehn); Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, NM 88003-8003, USA (Kuehn); Département de l'Etude du Milieu naturel et agricole, Service Public de Wallonie, 23 Avenue Maréchal Juin, 5030 Gembloux, Belgium (Bertouille); CNRS-UMR 6553, Université de Rennes 1, Station Biologique, 35380 Paimpont, France (Colyn); Mammal Research Institute, Polish Academy of Sciences, Białowieza, Poland (Niedziałkowska); Grupo de Biología y Etología, Universidad de Extremadura, 10071 Cáceres, Spain (Perez-Gonzalez); Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, 0316 Oslo, Norway (Skog); Cancer Registry of Norway, 0304 Oslo, Norway (Skog); Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia (Sprĕm); and Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-15, 1348 Louvain-la-Neuve, Belgium (Flamand)
| | - Javier Pérez-González
- From the Natural History Museum Vienna, 1010 Vienna, Austria (Zachos); Musée National d'Histoire Naturelle, L-2160 Münster, Luxembourg (Frantz); Fondation faune-flore, 25, Rue Munster, L-2160 Luxembourg (Frantz); Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technische Universität München, Freising, Germany (Kuehn); Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, NM 88003-8003, USA (Kuehn); Département de l'Etude du Milieu naturel et agricole, Service Public de Wallonie, 23 Avenue Maréchal Juin, 5030 Gembloux, Belgium (Bertouille); CNRS-UMR 6553, Université de Rennes 1, Station Biologique, 35380 Paimpont, France (Colyn); Mammal Research Institute, Polish Academy of Sciences, Białowieza, Poland (Niedziałkowska); Grupo de Biología y Etología, Universidad de Extremadura, 10071 Cáceres, Spain (Perez-Gonzalez); Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, 0316 Oslo, Norway (Skog); Cancer Registry of Norway, 0304 Oslo, Norway (Skog); Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia (Sprĕm); and Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-15, 1348 Louvain-la-Neuve, Belgium (Flamand)
| | - Anna Skog
- From the Natural History Museum Vienna, 1010 Vienna, Austria (Zachos); Musée National d'Histoire Naturelle, L-2160 Münster, Luxembourg (Frantz); Fondation faune-flore, 25, Rue Munster, L-2160 Luxembourg (Frantz); Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technische Universität München, Freising, Germany (Kuehn); Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, NM 88003-8003, USA (Kuehn); Département de l'Etude du Milieu naturel et agricole, Service Public de Wallonie, 23 Avenue Maréchal Juin, 5030 Gembloux, Belgium (Bertouille); CNRS-UMR 6553, Université de Rennes 1, Station Biologique, 35380 Paimpont, France (Colyn); Mammal Research Institute, Polish Academy of Sciences, Białowieza, Poland (Niedziałkowska); Grupo de Biología y Etología, Universidad de Extremadura, 10071 Cáceres, Spain (Perez-Gonzalez); Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, 0316 Oslo, Norway (Skog); Cancer Registry of Norway, 0304 Oslo, Norway (Skog); Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia (Sprĕm); and Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-15, 1348 Louvain-la-Neuve, Belgium (Flamand)
| | - Nikica Sprĕm
- From the Natural History Museum Vienna, 1010 Vienna, Austria (Zachos); Musée National d'Histoire Naturelle, L-2160 Münster, Luxembourg (Frantz); Fondation faune-flore, 25, Rue Munster, L-2160 Luxembourg (Frantz); Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technische Universität München, Freising, Germany (Kuehn); Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, NM 88003-8003, USA (Kuehn); Département de l'Etude du Milieu naturel et agricole, Service Public de Wallonie, 23 Avenue Maréchal Juin, 5030 Gembloux, Belgium (Bertouille); CNRS-UMR 6553, Université de Rennes 1, Station Biologique, 35380 Paimpont, France (Colyn); Mammal Research Institute, Polish Academy of Sciences, Białowieza, Poland (Niedziałkowska); Grupo de Biología y Etología, Universidad de Extremadura, 10071 Cáceres, Spain (Perez-Gonzalez); Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, 0316 Oslo, Norway (Skog); Cancer Registry of Norway, 0304 Oslo, Norway (Skog); Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia (Sprĕm); and Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-15, 1348 Louvain-la-Neuve, Belgium (Flamand)
| | - Marie-Christine Flamand
- From the Natural History Museum Vienna, 1010 Vienna, Austria (Zachos); Musée National d'Histoire Naturelle, L-2160 Münster, Luxembourg (Frantz); Fondation faune-flore, 25, Rue Munster, L-2160 Luxembourg (Frantz); Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technische Universität München, Freising, Germany (Kuehn); Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, NM 88003-8003, USA (Kuehn); Département de l'Etude du Milieu naturel et agricole, Service Public de Wallonie, 23 Avenue Maréchal Juin, 5030 Gembloux, Belgium (Bertouille); CNRS-UMR 6553, Université de Rennes 1, Station Biologique, 35380 Paimpont, France (Colyn); Mammal Research Institute, Polish Academy of Sciences, Białowieza, Poland (Niedziałkowska); Grupo de Biología y Etología, Universidad de Extremadura, 10071 Cáceres, Spain (Perez-Gonzalez); Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, 0316 Oslo, Norway (Skog); Cancer Registry of Norway, 0304 Oslo, Norway (Skog); Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia (Sprĕm); and Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-15, 1348 Louvain-la-Neuve, Belgium (Flamand)
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Volodin IA, Sibiryakova OV, Volodina EV. Sex and age-class differences in calls of Siberian wapiti Cervus elaphus sibiricus. Mamm Biol 2016. [DOI: 10.1016/j.mambio.2015.09.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Conflict bear translocation: investigating population genetics and fate of bear translocation in Dachigam National Park, Jammu and Kashmir, India. PLoS One 2015; 10:e0132005. [PMID: 26267280 PMCID: PMC4534036 DOI: 10.1371/journal.pone.0132005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/09/2015] [Indexed: 11/19/2022] Open
Abstract
The Asiatic black bear population in Dachigam landscape, Jammu and Kashmir is well recognized as one of the highest density bear populations in India. Increasing incidences of bear-human interactions and the resultant retaliatory killings by locals have become a serious threat to the survivorship of black bears in the Dachigam landscape. The Department of Wildlife Protection in Jammu and Kashmir has been translocating bears involved in conflicts, henceforth 'conflict bears' from different sites in Dachigam landscape to Dachigam National Park as a flagship activity to mitigate conflicts. We undertook this study to investigate the population genetics and the fate of bear translocation in Dachigam National Park. We identified 109 unique genotypes in an area of ca. 650 km2 and observed bear population under panmixia that showed sound genetic variability. Molecular tracking of translocated bears revealed that mostly bears (7 out of 11 bears) returned to their capture sites, possibly due to homing instincts or habituation to the high quality food available in agricultural croplands and orchards, while only four bears remained in Dachigam National Park after translocation. Results indicated that translocation success was most likely to be season dependent as bears translocated during spring and late autumn returned to their capture sites, perhaps due to the scarcity of food inside Dachigam National Park while bears translocated in summer remained in Dachigam National Park due to availability of surplus food resources. Thus, the current management practices of translocating conflict bears, without taking into account spatio-temporal variability of food resources in Dachigam landscape seemed to be ineffective in mitigating conflicts on a long-term basis. However, the study highlighted the importance of molecular tracking of bears to understand their movement patterns and socio-biology in tough terrains like Dachigam landscape.
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