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Assessing tiger corridor functionality with landscape genetics and modelling across Terai-Arc landscape, India. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01460-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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2
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Aziz MA, Smith O, Jackson HA, Tollington S, Darlow S, Barlow A, Islam MA, Groombridge JJ. Phylogeography of Panthera tigris in the mangrove forest of the Sundarbans. ENDANGER SPECIES RES 2022. [DOI: 10.3354/esr01188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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3
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Kumari Patel S, Biswas S, Goswami S, Bhatt S, Pandav B, Mondol S. Effects of faecal inorganic content variability on quantifying glucocorticoid and thyroid hormone metabolites in large felines: Implications for physiological assessments in free-ranging animals. Gen Comp Endocrinol 2021; 310:113833. [PMID: 34089705 DOI: 10.1016/j.ygcen.2021.113833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 05/16/2021] [Accepted: 06/01/2021] [Indexed: 11/22/2022]
Abstract
Faecal glucocorticoid (GC) and triiodothyronine (T3) metabolites and their interactions are increasingly used to monitor perceived stress and nutritional challenges in free-ranging animals. However, a number of extrinsic and intrinsic factors including hormone-inert dietary materials, inorganic matters etc. are known to affect reliable hormone metabolite quantifications. In this study, the impacts of inorganic matter (IOM) on faecal GC (fGCMs) and T3 (fT3Ms) metabolite measure were addressed in wild tiger (n = 193 from Terai Arc landscape, India) and captive lion (n = 120 from Sakkarbaug Zoological Garden, Gujarat, India) and possible corrective measures were evaluated. The wild tiger samples contained highly variable IOM content (9-98%, mostly with > 40% IOM) compared to captive Asiatic lion (17-57%, majority with < 40% IOM). Significant correlations were observed between IOM content and tiger fGCM (r = -0.46, p = 0.000), fT3M (r = -0.58, p = 0.000) and lion fT3M measures (r = -0.43, p = 0.003). Two corrective measures viz. removing samples with ≥ 80% IOM and subsequently expressing concentrations as per gram of organic dry matter (instead of total dry matter) reduced IOM influence on tiger fGCM, fT3M and lion fT3M, without affecting lion fGCM measures. The corrective measures changed the interpretations of fT3M data of field-collected tiger samples with no significant changes in fGCM (both tiger and lion) and fT3M (lion) data. As faecal IOM content is common in many wild species, the results emphasize the need to reduce IOM-driven hormone data variation for ecologically relevant interpretations towards species conservation.
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Affiliation(s)
- Shiv Kumari Patel
- Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand 248001 India
| | - Suvankar Biswas
- Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand 248001 India
| | - Sitendu Goswami
- Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand 248001 India
| | - Supriya Bhatt
- Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand 248001 India
| | - Bivash Pandav
- Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand 248001 India
| | - Samrat Mondol
- Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand 248001 India.
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4
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Nittu G, Bhavana PM, Shameer TT, Ramakrishnan B, Archana R, Kaushal KK, Khedkar GD, Mohan G, Jyothi M, Sanil R. Simple Nested Allele-Specific approach with penultimate mismatch for precise species and sex identification of tiger and leopard. Mol Biol Rep 2021; 48:1667-1676. [PMID: 33479828 DOI: 10.1007/s11033-021-06139-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/05/2021] [Indexed: 10/22/2022]
Abstract
Accurate species and sex identification of non-invasive and forensic samples of the tiger and leopard is still confusing when using the allele-specific methods. We designed allele-specific methods with penultimate nucleotide mismatch in a nested manner for the exact identification and double-checking of forensic samples. The mismatch design is a novel concept in species and sex identification, making the allele-specific targeting precise. We developed three sets of markers, a 365 bp outer and a 98 bp inner marker for nested tiger species identification assay, 136 bp leopard specific marker, and carnivore sex identification markers. We validated the method with tissue/blood forensic samples of various felids and herbivorous available in our lab and on known fecal samples from Vandalur Zoo. We also collected 37 scat samples at diverse stages of deterioration from the Mudumalai Tiger Reserve, Tamil Nadu, India. The 365 bp targeted markers resulted in 70.2% (n = 22; 22/37) amplification success, while the 98 bp FAM-labelled marker amplified 89% (n = 33; 33/37) scat samples independently. The 136 bp leopard markers answered four scat samples (11%) unrequited by the tiger specific markers. We evaluated species and the sex identification with these markers in another 190 non-invasive samples provided by the Mudumalai Tiger Reserve authorities. Among which 56.3% (n = 107) of samples were recognized as tiger (64 male and 43 female) and 38.9% (n = 74) as leopard (41 male and 33 female). The method supersedes any other previous methods in this regard by its high accuracy and simplicity.
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Affiliation(s)
- George Nittu
- Molecular Biodiversity Lab, Department of Zoology & Wildlife Biology, Government Arts College, Udhagamandalam, The Nilgiris, Tamil Nadu, 643002, India
| | - Pudupet Madhavan Bhavana
- Molecular Biodiversity Lab, Department of Zoology & Wildlife Biology, Government Arts College, Udhagamandalam, The Nilgiris, Tamil Nadu, 643002, India
| | - Thekke Thumbath Shameer
- Molecular Biodiversity Lab, Department of Zoology & Wildlife Biology, Government Arts College, Udhagamandalam, The Nilgiris, Tamil Nadu, 643002, India
| | - Balasundaram Ramakrishnan
- Molecular Biodiversity Lab, Department of Zoology & Wildlife Biology, Government Arts College, Udhagamandalam, The Nilgiris, Tamil Nadu, 643002, India.,Mudumalai Tiger Conservation Foundation, Mudumalai Tiger Reserve, The Nilgiris, Tamil Nadu, India
| | - Rajan Archana
- Molecular Biodiversity Lab, Department of Zoology & Wildlife Biology, Government Arts College, Udhagamandalam, The Nilgiris, Tamil Nadu, 643002, India
| | - Krishan Kumar Kaushal
- Mudumalai Tiger Conservation Foundation, Mudumalai Tiger Reserve, The Nilgiris, Tamil Nadu, India.,Office of the Field Director and Assistant Principal Chief Conservator of Forest, Mudumalai Tiger Reserve & Mukkurthi National Park, Udhagamandalam, The Nilgiris, Tamil Nadu, 643002, India
| | - Gulab Dattarao Khedkar
- Paul Hebert Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, 431 004, India
| | - Govindarajan Mohan
- Molecular Biodiversity Lab, Department of Zoology & Wildlife Biology, Government Arts College, Udhagamandalam, The Nilgiris, Tamil Nadu, 643002, India
| | - Manikkiri Jyothi
- Department of Zoology, Providence College for Women, Coonoor, Tamil Nadu, 643104, India
| | - Raveendranathanpillai Sanil
- Molecular Biodiversity Lab, Department of Zoology & Wildlife Biology, Government Arts College, Udhagamandalam, The Nilgiris, Tamil Nadu, 643002, India.
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5
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Genetic structure of tigers (Panthera tigris tigris) in India and its implications for conservation. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00710] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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6
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Tyagi A, Kumar V, Kittur S, Reddy M, Naidenko S, Ganswindt A, Umapathy G. Physiological stress responses of tigers due to anthropogenic disturbance especially tourism in two central Indian tiger reserves. CONSERVATION PHYSIOLOGY 2019; 7:coz045. [PMID: 31321036 PMCID: PMC6626984 DOI: 10.1093/conphys/coz045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/31/2019] [Accepted: 06/17/2019] [Indexed: 05/10/2023]
Abstract
Tigers continue to face unprecedented threats to their existence due to poaching, habitat loss, habitat fragmentation and anthropogenic disturbances. The present study examines the physiological stress response of tigers due to anthropogenic activities including wildlife tourism in Bandhavgarh Tiger Reserve and Kanha Tiger Reserve using faecal glucocorticoid metabolite (fGCM) measurement. We collected a total of 341 faecal samples from both reserves during tourism and non-tourism periods. Data on various anthropogenic disturbances including tourism activities like number of vehicles and visitors were also collected. We ascertained the species identity and sex of all the samples collected using genetic markers. fGCMs were extracted using a previously reported procedure, and fGCM concentrations were subsequently determined using an established enzyme immunoassay. There was no significant difference in overall mean fGCM concentrations between the two tiger reserves, but within each reserve, concentrations were significantly higher in tigers during the tourism period as compared to the non-tourism period. We also found that the number of tourist vehicles and disturbance level significantly correlated with fGCM concentrations. This study further supports the assumption that unbridled tourism associated with high anthropogenic disturbance can be related to perceived stress and consequently may have an impact on the reproductive fitness of tigers and long-term survival of isolated populations.
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Affiliation(s)
- Abhinav Tyagi
- Laboratory for the Conservation of Endangered Species, Council for Scientific and Industrial Research—Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana, India
| | - Vinod Kumar
- Laboratory for the Conservation of Endangered Species, Council for Scientific and Industrial Research—Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana, India
| | - Sagar Kittur
- Laboratory for the Conservation of Endangered Species, Council for Scientific and Industrial Research—Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana, India
| | - Mahender Reddy
- Laboratory for the Conservation of Endangered Species, Council for Scientific and Industrial Research—Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana, India
| | - Sergey Naidenko
- A.N. Severtsov Institute of Ecology and Evolution, Leninsky, pr. 33, Moscow, Russia
| | - Andre Ganswindt
- Mammal Research Institute, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Hatfield, South Africa
| | - Govindhaswamy Umapathy
- Laboratory for the Conservation of Endangered Species, Council for Scientific and Industrial Research—Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana, India
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Paul S, Ghosh T, Pandav B, Mohan D, Habib B, Nigam P, Mondol S. Rapid molecular assays for species and sex identification of swamp deer and other coexisting cervids in human-dominated landscapes of the Terai region and upper Gangetic plains, northern India: implications in understanding species distribution and population parameters. J Genet 2019. [DOI: 10.1007/s12041-019-1094-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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8
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Thatte P, Patel K, Ramakrishnan U. Rapid species identification of sloth bears from non-invasive samples: a PCR-based assay. URSUS 2018. [DOI: 10.2192/ursus-d-17-00024.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Prachi Thatte
- National Centre for Biological Sciences, Bellary Road, Bangalore, India 560065
| | - Kaushal Patel
- National Centre for Biological Sciences, Bellary Road, Bangalore, India 560065
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Bellary Road, Bangalore, India 560065
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10
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Double specific nested PCR and diagnostic SNP assay for species identification in lynx fecal critical samples. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-018-0993-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Using non-invasively collected genetic data to estimate density and population size of tigers in the Bangladesh Sundarbans. Glob Ecol Conserv 2017. [DOI: 10.1016/j.gecco.2017.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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12
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Nachtigall PG, Rodrigues-Filho LFS, Sodré DCA, Vallinoto M, Pinhal D. A multiplex PCR approach for the molecular identification and conservation of the Critically Endangered daggernose shark. ENDANGER SPECIES RES 2017. [DOI: 10.3354/esr00798] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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13
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Maroju PA, Yadav S, Kolipakam V, Singh S, Qureshi Q, Jhala Y. Schrodinger's scat: a critical review of the currently available tiger (Panthera Tigris) and leopard (Panthera pardus) specific primers in India, and a novel leopard specific primer. BMC Genet 2016; 17:37. [PMID: 26860950 PMCID: PMC4748499 DOI: 10.1186/s12863-016-0344-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 02/02/2016] [Indexed: 11/26/2022] Open
Abstract
Background Non-invasive sampling has opened avenues for the genetic study of elusive species, which has contributed significantly to their conservation. Where field based identity of non-invasive sample is ambiguous (e.g. carnivore scats), it is essential to establish identity of the species through molecular approaches. A cost effective procedure to ascertain species identity is to use species specific primers (SSP) for PCR amplification and subsequent resolution through agarose gel electrophoresis. However, SSPs if ill designed can often cross amplify non-target sympatric species. Herein we report the problem of cross amplification with currently published SSPs, which have been used in several recent scientific articles on tigers (Panthera tigris) and leopards (Panthera pardus) in India. Since these papers form pioneering research on which future work will be based, an early rectification is required so as to not propagate this error further. Results We conclusively show cross amplification of three of the four SSPs, in sympatric non-target species like tiger SSP amplifying leopard and striped hyena (Hyaena hyaena), and leopard SSP amplifying tiger, lion (Panthera leo persica) and clouded leopard (Neofelis nebulosa), with the same product size. We develop and test a non-cross-amplifying leopard specific primer pair within the mitochondrial cytochrome b region. We also standardize a duplex PCR method to screen tiger and leopard samples simultaneously in one PCR reaction to reduce cost and time. Conclusions These findings suggest the importance of an often overlooked preliminary protocol of conclusive identification of species from non-invasive samples. The cross amplification of published primers in conspecifics suggests the need to revisit inferences drawn by earlier work. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0344-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Sonu Yadav
- Wildlife Institute of India, Chandrabani, Dehradun, 248001, India.
| | | | - Shweta Singh
- Wildlife Institute of India, Chandrabani, Dehradun, 248001, India.
| | - Qamar Qureshi
- Wildlife Institute of India, Chandrabani, Dehradun, 248001, India.
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14
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Kitpipit T, Chotigeat W, Linacre A, Thanakiatkrai P. Forensic animal DNA analysis using economical two-step direct PCR. Forensic Sci Med Pathol 2014; 10:29-38. [PMID: 24435950 DOI: 10.1007/s12024-013-9521-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2013] [Indexed: 11/25/2022]
Abstract
Wildlife forensic DNA analysis by amplification of a mitochondrial locus followed by DNA sequencing is routine, yet suffers from being costly and time-consuming. To address these disadvantages we report on a low-cost two-step direct PCR assay to efficiently analyze 12 forensically relevant mammalian sample types without DNA extraction. A cytochrome oxidase I degenerate-universal primer pair was designed and validated for the developed assay. The 12 sample types, which included bone, horn, feces, and urine, were amplified successfully by the assay using a pre-direct PCR dilution protocol. The average amplification success rate was as high as 92.5 % (n = 350), with an average PCR product concentration of 220.71 ± 180.84 ng/μL. Differences in amplification success rate and PCR product quantity between sample types were observed; however, most samples provided high quality sequences, permitting a 100 % nucleotide similarity to their respective species via BLAST database queries. The combination of PBS and Phire(®) Hot Start II DNA polymerase gave comparable amplification success rate and amplicon quantity with the proprietary commercial kits (P > 0.05, n = 350) but at considerably lower cost. The stability of the assay was tested by successfully amplifying samples that had been stored for up to 12 months. Our data indicate that this low-cost two-step direct amplification assay has the potential to be a valuable tool for the forensic DNA community.
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Affiliation(s)
- Thitika Kitpipit
- Forensic Science Program, Department of Applied Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand,
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15
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Joshi A, Vaidyanathan S, Mondol S, Edgaonkar A, Ramakrishnan U. Connectivity of tiger (Panthera tigris) populations in the human-influenced forest mosaic of Central India. PLoS One 2013; 8:e77980. [PMID: 24223132 PMCID: PMC3819329 DOI: 10.1371/journal.pone.0077980] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 09/06/2013] [Indexed: 11/22/2022] Open
Abstract
Today, most wild tigers live in small, isolated Protected Areas within human dominated landscapes in the Indian subcontinent. Future survival of tigers depends on increasing local population size, as well as maintaining connectivity between populations. While significant conservation effort has been invested in increasing tiger population size, few initiatives have focused on landscape-level connectivity and on understanding the effect different landscape elements have on maintaining connectivity. We combined individual-based genetic and landscape ecology approaches to address this issue in six protected areas with varying tiger densities and separation in the Central Indian tiger landscape. We non-invasively sampled 55 tigers from different protected areas within this landscape. Maximum-likelihood and Bayesian genetic assignment tests indicate long-range tiger dispersal (on the order of 650 km) between protected areas. Further geo-spatial analyses revealed that tiger connectivity was affected by landscape elements such as human settlements, road density and host-population tiger density, but not by distance between populations. Our results elucidate the importance of landscape and habitat viability outside and between protected areas and provide a quantitative approach to test functionality of tiger corridors. We suggest future management strategies aim to minimize urban expansion between protected areas to maximize tiger connectivity. Achieving this goal in the context of ongoing urbanization and need to sustain current economic growth exerts enormous pressure on the remaining tiger habitats and emerges as a big challenge to conserve wild tigers in the Indian subcontinent.
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Affiliation(s)
- Aditya Joshi
- Post-graduate Program in Wildlife Biology and Conservation, Wildlife Conservation Society-India Program, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Srinivas Vaidyanathan
- Foundation for Ecological Research, Advocacy & Learning, Pondicherry Campus, Auroville Post, Tamil Nadu, India
| | - Samrat Mondol
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Advait Edgaonkar
- Indian Institute of Forest Management, Nehru nagar, Bhopal, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
- * E-mail:
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Baumgardt JA, Goldberg CS, Reese KP, Connelly JW, Musil DD, Garton EO, Waits LP. A method for estimating population sex ratio for sage-grouse using noninvasive genetic samples. Mol Ecol Resour 2013; 13:393-402. [PMID: 23347565 DOI: 10.1111/1755-0998.12069] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 12/04/2012] [Accepted: 12/12/2012] [Indexed: 11/27/2022]
Abstract
Population sex ratio is an important metric for wildlife management and conservation, but estimates can be difficult to obtain, particularly for sexually monomorphic species or for species that differ in detection probability between the sexes. Noninvasive genetic sampling (NGS) using polymerase chain reaction (PCR) has become a common method for identifying sex from sources such as hair, feathers or faeces, and is a potential source for estimating sex ratio. If, however, PCR success is sex-biased, naively using NGS could lead to a biased sex ratio estimator. We measured PCR success rates and error rates for amplifying the W and Z chromosomes from greater sage-grouse (Centrocercus urophasianus) faecal samples, examined how success and error rates for sex identification changed in response to faecal sample exposure time, and used simulation models to evaluate precision and bias of three sex assignment criteria for estimating population sex ratio with variable sample sizes and levels of PCR replication. We found PCR success rates were higher for females than males and that choice of sex assignment criteria influenced the bias and precision of corresponding sex ratio estimates. Our simulations demonstrate the importance of considering the interplay between the sex bias of PCR success, number of genotyping replicates, sample size, true population sex ratio and accuracy of assignment rules for designing future studies. Our results suggest that using faecal DNA for estimating the sex ratio of sage-grouse populations has great potential and, with minor adaptations and similar marker evaluations, should be applicable to numerous species.
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Affiliation(s)
- J A Baumgardt
- Fish and Wildlife Sciences, University of Idaho, Moscow, ID 83844, USA.
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17
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Dutta T, Sharma S, Maldonado JE, Wood TC, Panwar HS, Seidensticker J. Fine-scale population genetic structure in a wide-ranging carnivore, the leopard (Panthera pardus fusca)in central India. DIVERS DISTRIB 2012. [DOI: 10.1111/ddi.12024] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
| | | | - Jesús E. Maldonado
- Smithsonian Conservation Biology Institute; National Zoological Park; Washington; DC; 20013-7012; USA
| | - Thomas C. Wood
- Department of Environmental Science and Policy; George Mason University; 4400 University Dr, David King Hall MSN 5F2; Fairfax; VA; 22030; USA
| | - H. S. Panwar
- Peace Institute Charitable Trust; 178-F, Pocket-4,Mayur Vihar, Phase-I; Delhi; 110091; India
| | - John Seidensticker
- Smithsonian Conservation Biology Institute; National Zoological Park; Washington; DC; 20013-7012; USA
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Sharma S, Dutta T, Maldonado JE, Wood TC, Panwar HS, Seidensticker J. Spatial genetic analysis reveals high connectivity of tiger (Panthera tigris) populations in the Satpura-Maikal landscape of Central India. Ecol Evol 2012; 3:48-60. [PMID: 23403813 PMCID: PMC3568842 DOI: 10.1002/ece3.432] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 10/21/2012] [Accepted: 10/29/2012] [Indexed: 01/28/2023] Open
Abstract
We investigated the spatial genetic structure of the tiger meta-population in the Satpura–Maikal landscape of central India using population- and individual-based genetic clustering methods on multilocus genotypic data from 273 individuals. The Satpura–Maikal landscape is classified as a global-priority Tiger Conservation Landscape (TCL) due to its potential for providing sufficient habitat that will allow the long-term persistence of tigers. We found that the tiger meta-population in the Satpura–Maikal landscape has high genetic variation and very low genetic subdivision. Individual-based Bayesian clustering algorithms reveal two highly admixed genetic populations. We attribute this to forest connectivity and high gene flow in this landscape. However, deforestation, road widening, and mining may sever this connectivity, impede gene exchange, and further exacerbate the genetic division of tigers in central India.
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Affiliation(s)
- Sandeep Sharma
- Smithsonian Conservation Biology Institute, National Zoological Park Washington, District of Columbia, 20013-7012 ; Environmental Science & Policy Department, George Mason University Fairfax, Virginia, 22030-4444
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Pinhal D, Shivji MS, Nachtigall PG, Chapman DD, Martins C. A streamlined DNA tool for global identification of heavily exploited coastal shark species (genus Rhizoprionodon). PLoS One 2012; 7:e34797. [PMID: 22496864 PMCID: PMC3322161 DOI: 10.1371/journal.pone.0034797] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 03/08/2012] [Indexed: 11/18/2022] Open
Abstract
Obtaining accurate species-specific landings data is an essential step toward achieving sustainable shark fisheries. Globally distributed sharpnose sharks (genus Rhizoprionodon) exhibit life-history characteristics (rapid growth, early maturity, annual reproduction) that suggests that they could be fished in a sustainable manner assuming an investment in monitoring, assessment and careful management. However, obtaining species-specific landings data for sharpnose sharks is problematic because they are morphologically very similar to one another. Moreover, sharpnose sharks may also be confused with other small sharks (either small species or juveniles of large species) once they are processed (i.e., the head and fins are removed). Here we present a highly streamlined molecular genetics approach based on seven species-specific PCR primers in a multiplex format that can simultaneously discriminate body parts from the seven described sharpnose shark species commonly occurring in coastal fisheries worldwide. The species-specific primers are based on nucleotide sequence differences among species in the nuclear ribosomal internal transcribed spacer 2 locus (ITS2). This approach also distinguishes sharpnose sharks from a wide range of other sharks (52 species) and can therefore assist in the regulation of coastal shark fisheries around the world.
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Affiliation(s)
- Danillo Pinhal
- Departament of Genetics, UNESP - São Paulo State University, Botucatu, São Paulo, Brazil.
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A reliable method for individual identification and gender determination of wild leopards (Panthera pardus fusca) using non-invasive samples. CONSERV GENET RESOUR 2012. [DOI: 10.1007/s12686-012-9618-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Chaves PB, Graeff VG, Lion MB, Oliveira LR, Eizirik E. DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples. Mol Ecol Resour 2011; 12:18-35. [PMID: 21883979 DOI: 10.1111/j.1755-0998.2011.03056.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although species assignment of scats is important to study carnivore biology, there is still no standardized assay for the identification of carnivores worldwide, which would allow large-scale routine assessments and reliable cross-comparison of results. Here, we evaluate the potential of two short mtDNA fragments [ATP6 (126 bp) and cytochrome oxidase I gene (COI) (187 bp)] to serve as standard markers for the Carnivora. Samples of 66 species were sequenced for one or both of these segments. Alignments were complemented with archival sequences and analysed with three approaches (tree-based, distance-based and character-based). Intraspecific genetic distances were generally lower than between-species distances, resulting in diagnosable clusters for 86% (ATP6) and 85% (COI) of the species. Notable exceptions were recently diverged species, most of which could still be identified using diagnostic characters and uniqueness of haplotypes or by reducing the geographic scope of the comparison. In silico analyses were also performed for a 110-bp cytochrome b (cytb) segment, whose identification success was lower (70%), possibly due to the smaller number of informative sites and/or the influence of misidentified sequences obtained from GenBank. Finally, we performed case studies with faecal samples, which supported the suitability of our two focal markers for poor-quality DNA and allowed an assessment of prey DNA co-amplification. No evidence of prey DNA contamination was found for ATP6, while some cases were observed for COI and subsequently eliminated by the design of more specific primers. Overall, our results indicate that these segments hold good potential as standard markers for accurate species-level identification in the Carnivora.
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Affiliation(s)
- Paulo B Chaves
- Programa de Pós-Graduação em Zoologia, Pontifícia Universidade Católica do Rio Grande do Sul, Faculdade de Biociências, Av. Ipiranga, 6681, 90619-900 Porto Alegre, RS, Brazil
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Kitpipit T, Tobe SS, Kitchener AC, Gill P, Linacre A. The development and validation of a single SNaPshot multiplex for tiger species and subspecies identification--implications for forensic purposes. Forensic Sci Int Genet 2011; 6:250-7. [PMID: 21723800 DOI: 10.1016/j.fsigen.2011.06.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 02/22/2011] [Accepted: 06/01/2011] [Indexed: 11/26/2022]
Abstract
The tiger (Panthera tigris) is currently listed on Appendix I of the Convention on the International Trade in Endangered Species of Wild Fauna and Flora; this affords it the highest level of international protection. To aid in the investigation of alleged illegal trade in tiger body parts and derivatives, molecular approaches have been developed to identify biological material as being of tiger in origin. Some countries also require knowledge of the exact tiger subspecies present in order to prosecute anyone alleged to be trading in tiger products. In this study we aimed to develop and validate a reliable single assay to identify tiger species and subspecies simultaneously; this test is based on identification of single nucleotide polymorphisms (SNPs) within the tiger mitochondrial genome. The mitochondrial DNA sequence from four of the five extant putative tiger subspecies that currently exist in the wild were obtained and combined with DNA sequence data from 492 tiger and 349 other mammalian species available on GenBank. From the sequence data a total of 11 SNP loci were identified as suitable for further analyses. Five SNPs were species-specific for tiger and six amplify one of the tiger subspecies-specific SNPs, three of which were specific to P. t. sumatrae and the other three were specific to P. t. tigris. The multiplex assay was able to reliably identify 15 voucher tiger samples. The sensitivity of the test was 15,000 mitochondrial DNA copies (approximately 0.26 pg), indicating that it will work on trace amounts of tissue, bone or hair samples. This simple test will add to the DNA-based methods currently being used to identify the presence of tiger within mixed samples.
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Affiliation(s)
- Thitika Kitpipit
- Centre of Forensic Science, WestChem, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, G1 1XW, United Kingdom
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Borthakur U, Barman RD, Das C, Basumatary A, Talukdar A, Ahmed MF, Talukdar BK, Bharali R. Noninvasive genetic monitoring of tiger (Panthera tigris tigris) population of Orang National Park in the Brahmaputra floodplain, Assam, India. EUR J WILDLIFE RES 2010. [DOI: 10.1007/s10344-010-0471-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Mukherjee S, Krishnan A, Tamma K, Home C, Navya R, Joseph S, Das A, Ramakrishnan U. Ecology driving genetic variation: a comparative phylogeography of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis) in India. PLoS One 2010; 5:e13724. [PMID: 21060831 PMCID: PMC2966403 DOI: 10.1371/journal.pone.0013724] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 09/28/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Comparative phylogeography links historical population processes to current/ecological processes through congruent/incongruent patterns of genetic variation among species/lineages. Despite high biodiversity, India lacks a phylogeographic paradigm due to limited comparative studies. We compared the phylogenetic patterns of Indian populations of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis). Given similarities in their distribution within India, evolutionary histories, body size and habits, congruent patterns of genetic variation were expected. METHODOLOGY/PRINCIPAL FINDINGS We collected scats from various biogeographic zones in India and analyzed mtDNA from 55 jungle cats (460 bp NADH5, 141 bp cytochrome b) and 40 leopard cats (362 bp NADH5, 202 bp cytochrome b). Jungle cats revealed high genetic variation, relatively low population structure and demographic expansion around the mid-Pleistocene. In contrast, leopard cats revealed lower genetic variation and high population structure with a F(ST) of 0.86 between North and South Indian populations. Niche-model analyses using two approaches (BIOCLIM and MaxEnt) support absence of leopard cats from Central India, indicating a climate associated barrier. We hypothesize that high summer temperatures limit leopard cat distribution and that a rise in temperature in the peninsular region of India during the LGM caused the split in leopard cat population in India. CONCLUSIONS/SIGNIFICANCE Our results indicate that ecological variables describing a species range can predict genetic patterns. Our study has also resolved the confusion over the distribution of the leopard cat in India. The reciprocally monophyletic island population in the South mandates conservation attention.
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Affiliation(s)
- Shomita Mukherjee
- National Centre for Biological Sciences, Bangalore, Karnataka, India.
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Mukherjee S, Cn A, Home C, Ramakrishnan U. An evaluation of the PCR-RFLP technique to aid molecular-based monitoring of felids and canids in India. BMC Res Notes 2010; 3:159. [PMID: 20525407 PMCID: PMC2892506 DOI: 10.1186/1756-0500-3-159] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Accepted: 06/07/2010] [Indexed: 11/11/2022] Open
Abstract
Background The order Carnivora is well represented in India, with 58 of the 250 species found globally, occurring here. However, small carnivores figure very poorly in research and conservation policies in India. This is mainly due to the dearth of tested and standardized techniques that are both cost effective and conducive to small carnivore studies in the field. In this paper we present a non-invasive genetic technique standardized for the study of Indian felids and canids with the use of PCR amplification and restriction enzyme digestion of scat collected in the field. Findings Using existing sequences of felids and canids from GenBank, we designed primers from the 16S rRNA region of the mitochondrial genome and tested these on ten species of felids and five canids. We selected restriction enzymes that would cut the selected region differentially for various species within each family. We produced a restriction digestion profile for the potential differentiation of species based on fragment patterns. To test our technique, we used felid PCR primers on scats collected from various habitats in India, representing varied environmental conditions. Amplification success with field collected scats was 52%, while 86% of the products used for restriction digestion could be accurately assigned to species. We verified this through sequencing. A comparison of costs across the various techniques currently used for scat assignment showed that this technique was the most practical and cost effective. Conclusions The species-specific key developed in this paper provides a means for detailed investigations in the future that focus on elusive carnivores in India and this approach provides a model for other studies in areas of Asia where many small carnivores co-occur.
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Affiliation(s)
- Shomita Mukherjee
- National Centre for Biological Sciences, GKVK Campus, Bellary Road, Bangalore 560 065, Karnataka, India.
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Meganathan PR, Dubey B, Jogayya KN, Whitaker N, Haque I. A novel multiplex PCR assay for the identification of Indian crocodiles. Mol Ecol Resour 2010; 10:744-7. [PMID: 21565084 DOI: 10.1111/j.1755-0998.2010.02834.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Illegal hunting has been a major threat for the survival of wildlife fauna, including the three crocodile species that India harbours: Crocodylus palustris, Crocodylus porosus and Gavialis gangeticus. Although law prevents trade on these species, illicit hunting for trade continues to threaten the survival of these endangered species; conservation strategies therefore require a rapid molecular identification technique for Indian crocodiles. A multiplex polymerase chain reaction (PCR) assay with species-specific primers, considered as one of the most effective molecular techniques, is described herein. The primers were designed to yield species-specific sized amplicons. The assay discriminates the three Indian crocodile species unambiguously within a short time period using only simple agarose gel electrophoresis. We recommend this multiplex PCR assay to be used in the identification of Indian crocodile species.
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Affiliation(s)
- P R Meganathan
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30-Gorachand Road, Kolkata 700 014, West Bengal, India Madras Crocodile Bank Trust, Centre for Herpetology, Mamallapuram 603 104, Tamil Nadu, India
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A panel of microsatellites to individually identify leopards and its application to leopard monitoring in human dominated landscapes. BMC Genet 2009; 10:79. [PMID: 19961605 PMCID: PMC2801509 DOI: 10.1186/1471-2156-10-79] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Accepted: 12/04/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Leopards are the most widely distributed of the large cats, ranging from Africa to the Russian Far East. Because of habitat fragmentation, high human population densities and the inherent adaptability of this species, they now occupy landscapes close to human settlements. As a result, they are the most common species involved in human wildlife conflict in India, necessitating their monitoring. However, their elusive nature makes such monitoring difficult. Recent advances in DNA methods along with non-invasive sampling techniques can be used to monitor populations and individuals across large landscapes including human dominated ones. In this paper, we describe a DNA-based method for leopard individual identification where we used fecal DNA samples to obtain genetic material. Further, we apply our methods to non-invasive samples collected in a human-dominated landscape to estimate the minimum number of leopards in this human-leopard conflict area in Western India. RESULTS In this study, 25 of the 29 tested cross-specific microsatellite markers showed positive amplification in 37 wild-caught leopards. These loci revealed varied levels of polymorphism (four-12 alleles) and heterozygosity (0.05-0.79). Combining data on amplification success (including non-invasive samples) and locus specific polymorphisms, we showed that eight loci provide a sibling probability of identity of 0.0005, suggesting that this panel can be used to discriminate individuals in the wild. When this microsatellite panel was applied to fecal samples collected from a human-dominated landscape, we identified 7 individuals, with a sibling probability of identity of 0.001. Amplification success of field collected scats was up to 72%, and genotype error ranged from 0-7.4%. CONCLUSION Our results demonstrated that the selected panel of eight microsatellite loci can conclusively identify leopards from various kinds of biological samples. Our methods can be used to monitor leopards over small and large landscapes to assess population trends, as well as could be tested for population assignment in forensic applications.
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Why the Indian subcontinent holds the key to global tiger recovery. PLoS Genet 2009; 5:e1000585. [PMID: 19680439 PMCID: PMC2716534 DOI: 10.1371/journal.pgen.1000585] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 07/02/2009] [Indexed: 11/29/2022] Open
Abstract
With only ∼3,000 wild individuals surviving restricted to just 7% of their historical range, tigers are now a globally threatened species. Therefore, conservation efforts must prioritize regions that harbor more tigers, as well try to capture most of the remaining genetic variation and habitat diversity. Only such prioritization based on demographic, genetic, and ecological considerations can ensure species recovery and retention of evolutionary flexibility in the face of ongoing global changes. Although scientific understanding of ecological and demographic aspects of extant wild tiger populations has improved recently, little is known about their genetic composition and variability. We sampled 73 individual tigers from 28 reserves spread across a diversity of habitats in the Indian subcontinent to obtain 1,263 bp of mitochondrial DNA and 10 microsatellite loci. Our analyses reveals that Indian tigers retain more than half of the extant genetic diversity in the species. Coalescent simulations attribute this high genetic diversity to a historically large population size of about 58,200 tigers for peninsular India south of the Gangetic plains. Furthermore, our analyses indicate a precipitous, possibly human-induced population crash ∼200 years ago in India, which is in concordance with historical records. Our results suggest that only 1.7% (with an upper limit of 13% and a lower limit of 0.2%) of tiger numbers in historical times remain now. In the global conservation context our results suggest that, based on genetic, demographic, and ecological considerations, the Indian subcontinent holds the key to global survival and recovery of wild tigers. Tiger range and numbers have collapsed globally despite substantial conservation efforts. Genetic data quantifying variation from 73 wild tigers in 28 reserves in the Indian subcontinent suggests historically high numbers for tigers, and simulations reveal a signature of a 200-year-old, possibly human-induced decline. Simulations suggest that only 1.7% of historical tiger numbers now persist in peninsular Indian. Our data also reveal that tigers of the Indian subcontinent retain most of the species' genetic diversity, besides this region harbouring maximum diversity of tiger habitats. Overall, the Indian subcontinent appears to be a global hotspot holding the key to any future recovery of wild tigers from both an ecological and genetic perspective.
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BEJA‐PEREIRA ALBANO, OLIVEIRA RITA, ALVES PAULOC, SCHWARTZ MICHAELK, LUIKART GORDON. Advancing ecological understandings through technological transformations in noninvasive genetics. Mol Ecol Resour 2009; 9:1279-301. [DOI: 10.1111/j.1755-0998.2009.02699.x] [Citation(s) in RCA: 258] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- ALBANO BEJA‐PEREIRA
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
| | - RITA OLIVEIRA
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
- Departamento de Zoologia e Antropologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169‐007 Porto, Portugal
| | - PAULO C. ALVES
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
- Departamento de Zoologia e Antropologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169‐007 Porto, Portugal
| | - MICHAEL K. SCHWARTZ
- USDA Forest Service, Rocky Mountain Research Station, Missoula, MT 59801, USA
| | - GORDON LUIKART
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485‐661 Vairão, Portugal
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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Oliveira R, Castro D, Godinho R, Luikart G, Alves PC. Species identification using a small nuclear gene fragment: application to sympatric wild carnivores from South-western Europe. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9947-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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