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Liang HM, Yang KT, Cheng YT, Chang SC, Lin CY, Tsai MY, Lin DY, Hung KH. Genetic Diversity and Population Structure in Captive Populations of Formosan Sambar Deer ( Rusa unicolor swinhoei). Animals (Basel) 2023; 13:3106. [PMID: 37835712 PMCID: PMC10571969 DOI: 10.3390/ani13193106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
Formosan sambar deer (Rusa unicolor swinhoei) are of great economic significance in Taiwan, resulting in a substantial increase in deer farming to meet the high demand for velvet antlers. Inbreeding depression and reduced genetic variability can lead to the deterioration of captive populations. In this study, 239 Formosan sambar deer were genotyped using 13 microsatellites to analyze their genetic diversity and population genetic structure. Our results indicate a high-resolution power of these microsatellites in individual discrimination and parentage analysis. However, captive populations exhibit a low level of genetic diversity, likely because of inbreeding and bottleneck effects. Both principal coordinate analysis (PCoA) and STRUCTURE analyses revealed two distinct and segregated genetic groups within the captive populations and indicated no clear population genetic structure among the captive populations. Introducing new genetic material from the wild through translocation offers a potential solution for mitigating the impact of inbreeding and enhancing genetic diversity. The comprehensive information obtained from these genetic analyses is crucial for the development of effective breeding strategies aimed at preserving and enhancing Formosan sambar deer populations.
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Affiliation(s)
- Hsiao-Mei Liang
- Southern Region Branch, Livestock Research Institute, Ministry of Agriculture, Pingtung 912013, Taiwan; (H.-M.L.); (S.-C.C.)
| | - Kuo-Tai Yang
- Department of Animal Science, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan;
| | - Yu-Tzu Cheng
- Department of Forestry, Pingtung University of Science and Technology, Pingtung 912301, Taiwan;
| | - Shen-Chang Chang
- Southern Region Branch, Livestock Research Institute, Ministry of Agriculture, Pingtung 912013, Taiwan; (H.-M.L.); (S.-C.C.)
| | - Cheng-Yung Lin
- Livestock Management Division, Livestock Research Institute, Ministry of Agriculture, Tainan 71246, Taiwan; (C.-Y.L.); (M.-Y.T.)
| | - Ming-Yang Tsai
- Livestock Management Division, Livestock Research Institute, Ministry of Agriculture, Tainan 71246, Taiwan; (C.-Y.L.); (M.-Y.T.)
| | - Der-Yuh Lin
- Genetics and Physiology Division, Livestock Research Institute, Ministry of Agriculture, Tainan 71246, Taiwan;
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan
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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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3
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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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Cross-amplification of ungulate microsatellite markers in the endemic Indian antelope or blackbuck (Antilope cervicapra) for population monitoring and conservation genetics studies in south Asia. Mol Biol Rep 2021; 48:5151-5160. [PMID: 34213708 DOI: 10.1007/s11033-021-06514-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 06/25/2021] [Indexed: 01/01/2023]
Abstract
The Indian antelope or blackbuck (Antilope cervicapra) is endemic to the Indian subcontinent, inhabiting scrublands and dry grasslands. Most of the blackbuck populations are small, isolated, and threatened by habitat fragmentation and degradation. Management of such disjunct populations requires genetic characterization, which is critical for assessing hazards of stochastic events and inbreeding. Addressing the scarcity of such information on the blackbuck, we describe a novel panel of microsatellite markers that could be used to monitor blackbuck demography and population genetic parameters using non-invasive faecal sampling. We screened microsatellites (n = 40) that had been reported to amplify in bovid and cervid species using faecal samples of the blackbuck collected from Kaimoor Wildlife Sanctuary, Uttar Pradesh, India and its vicinities. We selected 12 markers for amplification using faecal DNA extracts (n = 140) in three multiplex reactions. We observed a mean amplification success rate of 72.4% across loci (92.1-25.7%) with high allele diversity (mean number of alleles/locus = 8.67 ± 1.03). Mean genotyping error rates across the markers were low to moderate (allelic drop-out rate = 0.09; false allele rate = 0.11). The proportions of first- and second-order relatives in the study population were 0.69% and 6.21%, respectively. Based on amplification success, genotyping error rates and the probability of identity (PID), we suggest (i) a panel of five microsatellite markers (cumulative PID = 1.24 × 10-5) for individual identification and population monitoring and (ii) seven additional markers for conservation genetics studies. This study provides essential tools capable of augmenting blackbuck conservation strategies at the landscape level, integral to protecting the scrubland-grassland ecosystem.
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Singh B, Kumar A, Uniyal VP, Gupta SK. Phylogeography and population genetic structure of red muntjacs: evidence of enigmatic Himalayan red muntjac from India. BMC Ecol Evol 2021; 21:49. [PMID: 33757420 PMCID: PMC7989103 DOI: 10.1186/s12862-021-01780-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/11/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Identifying factors shaping population genetic structure across continuous landscapes in the context of biogeographic boundaries for lineage diversification has been a challenging goal. The red muntjacs cover a wide range across multiple vegetation types, making the group an excellent model to study South and Southeast Asian biogeography. Therefore, we analysed mitogenomes and microsatellite loci, confirming the number of red muntjac lineages from India, gaining insights into the evolutionary history and phylogeography of red muntjacs. RESULTS Our results indicated the Northwestern population of red muntjac or the Himalayan red muntjac (M. aureus) in India as genetically diverse and well-structured, with significant genetic differentiation implying a low level of gene flow. The phylogenetic, population genetic structure, as well as species delimitation analyses, confirm the presence of the lineage from Western Himalayan in addition to the previously identified red muntjac lineages. Relatively low genetic diversity was observed in M. aureus compared to M. vaginalis, M. malabaricus and M. muntjak. The M. aureus and M. vaginalis lineages have split during the late Pleistocene, ~ 1.01 million years ago (Mya), making M. aureus the youngest lineage; whereas, M. malabaricus split earlier, ~ 2.2 Mya and appeared as the oldest lineage among red muntjacs. CONCLUSIONS Pronounced climate fluctuations during the Quaternary period were pivotal in influencing the current spatial distribution of forest-dwelling species' restriction to Northwestern India. Our finding confirms the distinct Himalayan red muntjac (M. aureus) within the red muntjac group from Northwestern India that should be managed as an Evolutionary Significant Unit (ESU). We recommend a reassessment of the conservation status of red muntjacs for effective conservation and management.
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Affiliation(s)
- Bhim Singh
- Wildlife Institute of India, Chandrabani, Dehradun, 248001, UK, India
| | - Ajit Kumar
- Wildlife Institute of India, Chandrabani, Dehradun, 248001, UK, India
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Ghazi MG, Sharma SP, Tuboi C, Angom S, Gurumayum T, Nigam P, Hussain SA. Population genetics and evolutionary history of the endangered Eld's deer (Rucervus eldii) with implications for planning species recovery. Sci Rep 2021; 11:2564. [PMID: 33510319 PMCID: PMC7844053 DOI: 10.1038/s41598-021-82183-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 01/18/2021] [Indexed: 01/30/2023] Open
Abstract
Eld's deer (Rucervus eldii) with three recognised subspecies (R. e. eldii, R. e. thamin, and R. e. siamensis) represents one of the most threatened cervids found in Southeast Asia. The species has experienced considerable range contractions and local extinctions owing to habitat loss and fragmentation, hunting, and illegal trade across its distribution range over the last century. Understanding the patterns of genetic variation is crucial for planning effective conservation strategies. This study investigated the phylogeography, divergence events and systematics of Eld's deer subspecies using the largest mtDNA dataset compiled to date. We also analysed the genetic structure and demographic history of R. e. eldii using 19 microsatellite markers. Our results showed that R. e. siamensis exhibits two divergent mtDNA lineages (mainland and Hainan Island), which diverged around 0.2 Mya (95% HPD 0.1-0.2), possibly driven by the fluctuating sea levels of the Early Holocene period. The divergence between R. e. eldii and R. e. siamensis occurred around 0.4 Mya (95% HPD 0.3-0.5), potentially associated with the adaptations to warm and humid climate with open grassland vegetation that predominated the region. Furthermore, R. e. eldii exhibits low levels of genetic diversity and small contemporary effective population size (median = 7, 4.7-10.8 at 95% CI) with widespread historical genetic bottlenecks which accentuates its vulnerability to inbreeding and extinction. Based on the observed significant evolutionary and systematic distance between Eld's deer and other species of the genus Rucervus, we propose to classify Eld's deer (Cervus eldii) in the genus Cervus, which is in congruent with previous phylogenetic studies. This study provides important conservation implications required to direct the ongoing population recovery programs and planning future conservation strategies.
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Affiliation(s)
| | - Surya Prasad Sharma
- Wildlife Institute of India, Chandrabani, Post Box #18, Dehra Dun, Uttarakhand, 248002, India
| | - Chongpi Tuboi
- Wildlife Institute of India, Chandrabani, Post Box #18, Dehra Dun, Uttarakhand, 248002, India
| | - Sangeeta Angom
- Wildlife Institute of India, Chandrabani, Post Box #18, Dehra Dun, Uttarakhand, 248002, India
| | - Tennison Gurumayum
- Wildlife Institute of India, Chandrabani, Post Box #18, Dehra Dun, Uttarakhand, 248002, India
| | - Parag Nigam
- Wildlife Institute of India, Chandrabani, Post Box #18, Dehra Dun, Uttarakhand, 248002, India
| | - Syed Ainul Hussain
- Wildlife Institute of India, Chandrabani, Post Box #18, Dehra Dun, Uttarakhand, 248002, India.
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Davies C, Wright W, Wedrowicz F, Pacioni C, Hogan FE. Delineating genetic management units of sambar deer (Rusa unicolor) in south-eastern Australia, using opportunistic tissue sampling and targeted scat collection. WILDLIFE RESEARCH 2021. [DOI: 10.1071/wr19235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Angom S, Tuboi C, Ghazi MGU, Badola R, Hussain SA. Demographic and genetic structure of a severely fragmented population of the endangered hog deer (Axis porcinus) in the Indo-Burma biodiversity hotspot. PLoS One 2020; 15:e0210382. [PMID: 32027650 PMCID: PMC7004368 DOI: 10.1371/journal.pone.0210382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 12/17/2019] [Indexed: 11/29/2022] Open
Abstract
The population of the globally endangered hog deer (Axis porcinus) has declined severely across its geographic range. Intensive monitoring of its demographic and genetic status is necessary. We examined the demographic and genetic structure of a small hog deer population in Keibul Lamjao National Park (KLNP), located on the western fringe of the Indo-Burma biodiversity hotspot for conservation planning. The distribution pattern of hog deer in the Park was derived based on the presence/absence of faecal pellets in 1 km × 1 km grids. We used double-observer distance sampling method to derive the hog deer abundance and population structure and compared with previous data to derive the population trend. We determined the genetic diversity of the population through microsatellite screening and bottleneck detection. The overall pellet density was 0.34 ± 0.02 pellets km-2 restricted to only 22.34 ± 0.20 km2 area of the park. The estimated density of the deer in the park was 1.82–4.32 individuals km-2. The population showed a declining trend from 2006–08 (p < 0.05, R2 = 0.916) with 8% annum-1 and an increasing trend from 2003–2018 (p < 0.05, R2 = 0.9304) with 10% annum-1. The adult male-to-female ratio and fawn-to-doe ratio were 36.2 ± 1.9 males per 100 females and 16.5 ± 0.4 fawns per 100 females, respectively. The molecular examination suggested that the mean number of alleles at 23 loci was 2.70 ± 0.18, the observed heterozygosity (Ho) ranged from 0.26 to 0.63 (mean 0.42 ± 0.02), the expected heterozygosity (He) ranged from 0.23 to 0.73 (χ = 0.51 ± 0.03), and the polymorphic information content (PIC) ranged from 0.2 to 0.67 (χ = 0.43 ± 0.03) indicating a moderate level of genetic diversity. Although no bottleneck in the population was observed, the loss of genetic diversity may affect the evolutionary potential of the species at the site by limiting the selection flexibility. Conservation planning coupled with scientific management regime will help in the long term persistence of the population in the region.
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Affiliation(s)
- Sangeeta Angom
- Wildlife Institute of India, Dehra Dun, Uttarakhand, India
| | - Chongpi Tuboi
- Wildlife Institute of India, Dehra Dun, Uttarakhand, India
| | | | - Ruchi Badola
- Wildlife Institute of India, Dehra Dun, Uttarakhand, India
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9
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Davies C, Wright W, Wedrowicz F, Hogan FE. A DNA toolbox for non-invasive genetic studies of sambar deer (Rusa unicolor). AUSTRALIAN MAMMALOGY 2020. [DOI: 10.1071/am18032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Invasive sambar deer (Rusa unicolor) are having significant detrimental impacts on natural environments in south-eastern Australia. Little, however, is known about their ecology, limiting evidence-based management strategies directed at reducing deer impacts. Genetic data, generated from DNA isolated from deer scats, can be used to fill ecological knowledge gaps. This study outlines a non-invasive genetic sampling strategy by which good-quality DNA from a single deer scat can be used to determine (1) species of origin, (2) sex and (3) a unique DNA profile. DNA from deer tissue and sambar deer scat samples were used to develop and optimise molecular methods to collect reliable genetic information. A DNA toolbox is presented that describes how to find, collect and store scat samples, isolate DNA and use molecular markers to generate informative genetic data. Generating genetic data using this approach will support studies aimed at acquiring ecological knowledge about sambar deer. Such knowledge will be critical for developing evidence-based recommendations to improve on-ground management decisions for sambar deer.
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10
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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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Kumar VP, Shukla M, Rajpoot A, Thakur M, Nigam P, Kumar D, Mehta AK, Goyal SP. DNA barcoding as a tool for robust identification of cervids of India and its utility in wildlife forensics. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:250-255. [PMID: 33474133 PMCID: PMC7800678 DOI: 10.1080/23802359.2018.1438858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA barcoding has become a popular method of choice for identification of specimen based on molecular techniques. Here, we present preliminary findings on generating robust DNA barcode library of Cervids of India. The dataset comprising the DNA barcode library of seven deer species included in the genus Cervus, Axis and Muntiacus classified under family Cervidae. Mitochondrial Cytochrome C Oxidase subunit I gene of ca. 710 bp accepted widely as DNA barcode region, was used for generating species specific signature from 31 known samples of seven Indian deer species. Expectedly, the NJ tree clustered three genera i.e. Cervus, Axis and Muntiacus of Cervids of India into three clades. Further, the intra- and interspecies distances based on Kimura 2 parameter model also supported the results. The average intra- and interspecies sequence divergence were 0.011 (±0.09) and 0.65 (±0.14), respectively. The present study has exhibited that DNA barcoding has discriminating power to delineate boundaries among the closely related species. The data generated are of high importance to the law enforcement agencies in effective identification of species in wildlife offence cases. The similar approach can be utilized for generating DNA barcodes for other Indian mammals for making effective management and conservation action decisions.
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Affiliation(s)
- Ved P Kumar
- Wildlife Forensic Cell, Wildlife Institute of India, Dehradun, Uttarakhand, India.,Department of Zoology, Veer Kunwar Singh University, Arrah, Bihar, India
| | - Malay Shukla
- Wildlife Forensic Cell, Wildlife Institute of India, Dehradun, Uttarakhand, India.,Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, Gujarat, India
| | - Ankita Rajpoot
- Molecular Systematics Laboratory, Zoological Survey of India, Northern Regional Centre, Dehradun, Uttarakhand, India
| | - Mukesh Thakur
- Molecular Systematics Division,Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | - Parag Nigam
- Wildlife Forensic Cell, Wildlife Institute of India, Dehradun, Uttarakhand, India
| | - Dhyanendra Kumar
- Department of Zoology, Veer Kunwar Singh University, Arrah, Bihar, India
| | - Anil Kumar Mehta
- Institute of Forensic Science, Gujarat Forensic Sciences University, Gandhinagar, Gujarat, India
| | - Surendra P Goyal
- Department of Zoology, Veer Kunwar Singh University, Arrah, Bihar, India
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Understanding predation behaviour of the tiger (Panthera tigris tigris) in Ranthambore tiger Reserve, Rajasthan, India: use of low-cost gel based molecular sexing of prey hairs from scats. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-017-0963-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Mantellatto AMB, Caparroz R, Christofoletti MD, Piovezan U, Duarte JMB. Genetic diversity of the pampas deer (Ozotoceros bezoarticus) population in the Brazilian Pantanal assessed by combining fresh fecal DNA analysis and a set of heterologous microsatellite loci. Genet Mol Biol 2017; 40:774-780. [PMID: 28981561 PMCID: PMC5738621 DOI: 10.1590/1678-4685-gmb-2016-0323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/20/2017] [Indexed: 11/29/2022] Open
Abstract
The pampas deer (Ozotoceros bezoarticus) is close to being
classified as ‘globally threatened’, with the largest population occurring in
the Brazilian Pantanal. Since capture is stressful to these animals,
non-invasive sampling methods such as the use of feces can provide reliable
sources of DNA. The aim of this study was to use fecal samples to evaluate the
genetic variability of the Brazilian Pantanal population of pampas deer. Six
heterologous microsatellite markers were used to screen 142 stool specimens.
Seventy-four deer were identified, of which 50 adults were used to determine the
genetic characteristics of the population. The Pantanal population showed high
genetic diversity (mean number of alleles per locus = 11.5, expected
heterozygosity = 0.75). This is the first investigation to characterize a South
American deer species using fecal DNA and demonstrates the usefulness and
efficiency of this approach, as well as the feasibility of obtaining information
that could not have been easily obtained by traditional DNA sampling. Our
findings suggest that management strategies for this species may be much more
effective if applied now when the population still shows high genetic
variability.
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Affiliation(s)
- Aline Meira Bonfim Mantellatto
- Núcleo de Pesquisa e Conservação de Cervídeos, Departamento de Zootecnia, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Jaboticabal, SP, Brazil
| | - Renato Caparroz
- Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Maurício Durante Christofoletti
- Núcleo de Pesquisa e Conservação de Cervídeos, Departamento de Zootecnia, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Jaboticabal, SP, Brazil
| | - Ubiratan Piovezan
- Centro de Pesquisas Agropecuárias do Pantanal (CPAP), Embrapa, Corumbá, MS, Brazil
| | - José Maurício Barbanti Duarte
- Núcleo de Pesquisa e Conservação de Cervídeos, Departamento de Zootecnia, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Jaboticabal, SP, Brazil
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Kumar VP, Sharma LK, Shukla M, Sathyakumar S. Pragmatic perspective on conservation genetics and demographic history of the last surviving population of Kashmir red deer (Cervus elaphus hanglu) in India. PLoS One 2015; 10:e0117069. [PMID: 25671567 PMCID: PMC4324630 DOI: 10.1371/journal.pone.0117069] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/18/2014] [Indexed: 11/30/2022] Open
Abstract
The hangul (Cervus elaphus hanglu) is of great conservation concern because it represents the easternmost and only hope for an Asiatic survivor of the red deer species in the Indian subcontinent. Despite the rigorous conservation efforts of the Department of Wildlife Protection in Jammu & Kashmir, the hangul population has experienced a severe decline in numbers and range contraction in the past few decades. The hangul population once abundant in the past has largely become confined to the Dachigam landscape, with a recent population estimate of 218 individuals. We investigated the genetic variability and demographic history of the hangul population and found that it has shown a relatively low diversity estimates when compared to other red deer populations of the world. Neutrality tests, which are used to evaluate demographic effects, did not support population expansion, and the multimodal pattern of mismatch distribution indicated that the hangul population is under demographic equilibrium. Furthermore, the hangul population did not exhibit any signature of bottleneck footprints in the past, and Coalescent Bayesian Skyline plot analysis revealed that the population had not experienced any dramatic changes in the effective population size over the last several thousand years. We observed a strong evidence of sub-structuring in the population, wherein the majority of individuals were assigned to different clusters in Bayesian cluster analysis. Population viability analysis demonstrated insignificant changes in the mean population size, with a positive growth rate projected for the next hundred years. We discuss the phylogenetic status of hangul for the first time among the other red deer subspecies of the world and strongly recommend to upgrade hangul conservation status under IUCN that should be discrete from the other red deer subspecies of the world to draw more conservation attention from national and international bodies.
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Affiliation(s)
- Ved P Kumar
- Wildlife Institute of India, Chandrabani, Dehradun 248 001, Uttarakhand, India
| | - Lalit K Sharma
- Wildlife Institute of India, Chandrabani, Dehradun 248 001, Uttarakhand, India
| | - Malay Shukla
- Gujarat Forensic Sciences University, Gandhinagar 382007, Gujarat, India
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Hoffmann GS, Johannesen J, Griebeler EM. Species cross-amplification, identification and genetic variation of 17 species of deer (Cervidae) with microsatellite and mitochondrial DNA from antlers. Mol Biol Rep 2014; 42:1059-67. [PMID: 25424838 DOI: 10.1007/s11033-014-3845-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 11/22/2014] [Indexed: 11/26/2022]
Abstract
Strong anthropogenic impact has caused 28 of the currently recognized 55 species of deer (Cervidae) to be listed on the IUCN Red List. Particular threats to vulnerable species include habitat deterioration and hybridization with alien, introduced species. The scarcity of many species has severely hampered genetic analyses of their populations, including the detection of loci for cross-species amplification. Because deer antlers are shed and re-grown annually, antlers offer the possibility for non-invasive genetic sampling of large individual numbers, and may provide material for reference genotyping from historical samples stored in zoos, museums and trophy collections of rare and extinct species/populations. In this paper, we report cross-species amplification of 19 nuclear microsatellite loci and the amplification of 16S mtDNA for barcoding from nearly a third of all deer species worldwide based on high quality DNA extracted from antler bone up to 40 years old. Phylogenetic analysis based on mtDNA of seventeen species and five subspecies corroborate previously published phylogenetic data, thus confirming the specific resolution of the DNA extraction methodology.
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Affiliation(s)
- G Sebastian Hoffmann
- Department of Ecology, Institute of Zoology, Johannes Gutenberg-University of Mainz, 55099, Mainz, Germany,
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Mukesh, Sharma LK, Kumar VP, Charoo SA, Mohan N, Goyal SP, Sathyakumar S. Loss of genetic diversity and inbreeding in Kashmir red deer (Cervus elaphus hanglu) of Dachigam National Park, Jammu & Kashmir, India. BMC Res Notes 2013; 6:326. [PMID: 24060051 PMCID: PMC3751512 DOI: 10.1186/1756-0500-6-326] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 08/13/2013] [Indexed: 11/10/2022] Open
Abstract
Background Hangul (Cervus elaphus hanglu), the eastern most subspecies of red deer, is now confined only to the mountains in the Kashmir region of Jammu & Kashmir State of India. It is of great conservation significance as this is the last and only hope for Asiatic survivor of the red deer species in India. Wild population of free ranging hangul deer inhabiting in and around Dachigam National Park was genetically assessed in order to account for constitutive genetic attributes of hangul population using microsatellite markers. Results In a pool of 36 multi-locus genotypes, 30 unique individuals were identified based on six microsatellite loci. The estimated cumulative probability of identity assuming all individuals were siblings (PID sibs) was 0.009 (9 in 1000). Altogether, 49 different alleles were observed with mean (± s.e.) allelic number of 8.17 ± 1.05, ranging from 5 to 11 per locus. The observed heterozygosity ranged between 0.08 and 0.83, with mean 0.40 ± 0.11 and the inbreeding coefficient ranged between −0.04 and 0.87 with mean 0.38 ± 0.15. Majority of loci (5/6) were found to be informative (PIC value > 0.5). All loci deviated from Hardy-Weinberg equilibrium except Ca-38 (P > 0.05) and none of the pairs of loci showed significant linkage disequilibrium except the single pair of Ca-30 and Ca-43 (P < 0.05). Conclusions The preliminary findings revealed that hangul population is significantly inbred and exhibited a low genetic diversity in comparison to other deer populations of the world. We suggest prioritizing the potential individuals retaining high heterozygosity for ex situ conservation and genetic monitoring of the hangul population should be initiated covering the entire distribution range to ensure the long term survival of hangul. We speculate further ignoring genetics attributes may lead to a detrimental effect which can negatively influence the reproductive fitness and survivorship of the hangul population in the wild.
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Zhang P, Kuang YY, Wu HL, Li L, Ge YF, Wan QH, Fang SG. The Père David's deer MHC class I genes show unexpected diversity patterns, with monomorphic classical genes but polymorphic nonclassical genes and pseudogenes. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2012; 318:294-307. [PMID: 22821865 DOI: 10.1002/jez.b.22445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Père David's deer (Elaphurus davidianus) is a highly inbred species that arose from 11 founders but now comprises a population of about 3,000 individuals, making it interesting to investigate the adaptive variation of this species from the major histocompatibility complex (MHC) perspective. In this study, we isolated Elda-MHC class I loci using magnetic bead-based cDNA hybridization, and examined the molecular variations of these loci using single-strand conformation polymorphism (SSCP) and sequence analysis. We obtained seven MHC class I genes, which we designated F1, F12, G2, I7, AF, I8, and C1. Our analyses of stop codons, phylogenetic trees, amino acid conservation, and G+C content revealed that F1, F12, G2, and I7 were classical genes, AF was a nonclassical gene, and I8 and C1 were pseudogenes. Our subsequent molecular examinations showed that the diversity pattern in the Père David's deer was unusual. Most mammals have more polymorphic classical class I loci vs. the nonclassical and neutral genes. In contrast, the Père David's deer was found to be monomorphic at classical genes F1, F12, G2, and I7, dimorphic at the nonclassical AF gene, dimorphic at pseudogene I8, and tetramorphic at pseudogene C1. The adverse polymorphism patterns of Elda-I genes might provide evidence for selection too faster deplete MHC variation than drift in the bottlenecked populations, while the postbottleneck tetramorphism of the C1 pseudogene appears to be evidence of strong historical balancing selection.
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Affiliation(s)
- Pei Zhang
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, PR China
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An J, Choi SK, Sommer J, Louis E, Brenneman R, Zemanová B, Hájková P, Park G, Min MS, Kim KS, Lee H. A core set of microsatellite markers for conservation genetics studies of Korean goral (Naemorhedus caudatus) and its cross-species amplification in Caprinae species. J Vet Sci 2011; 11:351-3. [PMID: 21113106 PMCID: PMC2998748 DOI: 10.4142/jvs.2010.11.4.351] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to screen microsatellites for conservation genetics studies of the species, a total of 23 microsatellite loci from Korean goral (Naemorhedus caudatus), including 15 previously developed loci and 8 new loci in this study, were tested. Eleven microsatellites were screened and subjected to cross-species amplification using a test panel of four Caprinae species, Japanese serows (Capricornis crispus), Chinese gorals (Naemorhedus goral), Northern chamois (Rupicapra rupicapra) and domestic goats (Capra hircus). In addition, all eleven microsatellites (SY3A, SY12A, SY12B, SY48, SY58, SY71, SY76, SY84, SY84B, SY112, and SY129) satisfied the criteria to be a core set of microsatellites. This core set of microsatellites and cross-species amplification of Korean goral microsatellites were found to be helpful for high-resolution studies for conservation and management of Korean goral and other endangered Caprinae species.
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Affiliation(s)
- Junghwa An
- Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science, Seoul National University, Seoul 151-742, Korea
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Mantellatto AMB, Carnelossi EAG, Duarte JMB. Transferability of microsatellite loci from exotic Cervidae to Brazilian brocket deer (Mazama spp, Mammalia: Cervidae). GENETICS AND MOLECULAR RESEARCH 2010; 9:277-82. [PMID: 20198583 DOI: 10.4238/vol9-1gmr720] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Transferability of microsatellite loci between closely related species has been reported in several species. This helps reduce costs involved with the development of primers for newly investigated species. Fifteen microsatellite primers developed for Rangifer tarandus, Cervus elaphus, C. axis, and Moschus berezovskii were tested on five species of Brazilian brocket deer of the genus Mazama (M. americana, M. bororo, M. gouazoubira, M. nana, and M. nemorivaga). These primers were tested with DNA extracted from blood samples of two individuals of each species obtained from the Núcleo de Pesquisa e Conservação de Cervídeos (NUPECCE) of Universidade Estadual Paulista (UNESP). Fourteen of the 15 primers tested amplified microsatellite regions of all five species of Mazama, confirmed by sequencing of the amplified fragments. We conclude that these primers could be used for population studies of brocket deer.
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Affiliation(s)
- A M B Mantellatto
- Departamento de Zootecnia, Núcleo de Pesquisa e Conservação de Cervídeos, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Universidade Estadual Paulista, Jaboticabal, SP, Brasil.
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Guan TL, Zeng B, Peng QK, Yue BS, Zou FD. Microsatellite analysis of the genetic structure of captive forest musk deer populations and its implication for conservation. BIOCHEM SYST ECOL 2009. [DOI: 10.1016/j.bse.2009.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Singh L. Development and exploitation of DNA fingerprinting technology in India. Biotechnol J 2009; 4:335-41. [DOI: 10.1002/biot.200900015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Barbará T, Palma-Silva C, Paggi GM, Bered F, Fay MF, Lexer C. Cross-species transfer of nuclear microsatellite markers: potential and limitations. Mol Ecol 2007; 16:3759-67. [PMID: 17850543 DOI: 10.1111/j.1365-294x.2007.03439.x] [Citation(s) in RCA: 317] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular ecologists increasingly require 'universal' genetic markers that can easily be transferred between species. The distribution of cross-species transferability of nuclear microsatellite loci is highly uneven across taxa, being greater in animals and highly variable in flowering plants. The potential for successful cross-species transfer appears highest in species with long generation times, mixed or outcrossing breeding systems, and where genome size in the target species is small compared to the source. We discuss the implications of these findings and close with an outlook on potential alternative sources of cross-species transferable markers.
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Affiliation(s)
- Thelma Barbará
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey TW9 3DS, UK
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XIA SHAN, ZOU FANGDONG, YUE BISONG. Six microsatellite loci in forest musk deer, Moschus berezovskii. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2005.01158.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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