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Al Hikmani H, van Oosterhout C, Birley T, Labisko J, Jackson HA, Spalton A, Tollington S, Groombridge JJ. Can genetic rescue help save Arabia's last big cat? Evol Appl 2024; 17:e13701. [PMID: 38784837 PMCID: PMC11113348 DOI: 10.1111/eva.13701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/01/2024] [Accepted: 04/10/2024] [Indexed: 05/25/2024] Open
Abstract
Genetic diversity underpins evolutionary potential that is essential for the long-term viability of wildlife populations. Captive populations harbor genetic diversity potentially lost in the wild, which could be valuable for release programs and genetic rescue. The Critically Endangered Arabian leopard (Panthera pardus nimr) has disappeared from most of its former range across the Arabian Peninsula, with fewer than 120 individuals left in the wild, and an additional 64 leopards in captivity. We (i) examine genetic diversity in the wild and captive populations to identify global patterns of genetic diversity and structure; (ii) estimate the size of the remaining leopard population across the Dhofar mountains of Oman using spatially explicit capture-recapture models on DNA and camera trap data, and (iii) explore the impact of genetic rescue using three complementary computer modeling approaches. We estimated a population size of 51 (95% CI 32-79) in the Dhofar mountains and found that 8 out of 25 microsatellite alleles present in eight loci in captive leopards were undetected in the wild. This includes two alleles present only in captive founders known to have been wild-sourced from Yemen, which suggests that this captive population represents an important source for genetic rescue. We then assessed the benefits of reintroducing novel genetic diversity into the wild population as well as the risks of elevating the genetic load through the release of captive-bred individuals. Simulations indicate that genetic rescue can improve the long-term viability of the wild population by reducing its genetic load and realized load. The model also suggests that the genetic load has been partly purged in the captive population, potentially making it a valuable source population for genetic rescue. However, the greater loss of its genetic diversity could exacerbate genomic erosion of the wild population during a rescue program, and these risks and benefits should be carefully evaluated. An important next step in the recovery of the Arabian leopard is to empirically validate these conclusions, implement and monitor a genomics-informed management plan, and optimize a strategy for genetic rescue as a tool to recover Arabia's last big cat.
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Affiliation(s)
- Hadi Al Hikmani
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
- Office for Conservation of the EnvironmentDiwan of Royal CourtMuscatOman
- The Royal Commission for AlUlaAlUlaSaudi Arabia
| | - Cock van Oosterhout
- School of Environmental SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - Thomas Birley
- School of Environmental SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - Jim Labisko
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
- Centre for Biodiversity and Environment Research, Research Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
- Island Biodiversity and Conservation CentreUniversity of SeychellesVictoriaSeychelles
- Department of Life SciencesThe Natural History MuseumLondonUK
| | - Hazel A. Jackson
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
| | | | - Simon Tollington
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
- School of Animal Rural and Environmental SciencesNottingham Trent UniversityNottinghamUK
| | - Jim J. Groombridge
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, Division of Human and Social SciencesUniversity of KentCanterburyKentUK
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Current Genetic Structure Analysis of Leopard Cats Reveals a Weak Disparity Trend in Subpopulations in Beijing, China. BIOLOGY 2022; 11:biology11101478. [PMID: 36290381 PMCID: PMC9598953 DOI: 10.3390/biology11101478] [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] [Received: 08/02/2022] [Revised: 10/02/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022]
Abstract
Simple Summary Habitat fragmentation is an important factor leading to the decline in the leopard cat population in Beijing. Habitat loss may further result in population shrinkage, which increases the risk of inbreeding and genetic decline. To reveal the segregation effects of highway construction and infrastructure expansion on population genetic variation, this study analyzed the genetic structure of leopard cats in five nature reserves in the mountain surroundings of Beijing. The results showed that a mild disparity trend exists in Baihuashan and Songshan subpopulations, due to habitat segregation and dispersal difficulties. We suggest that the genetic structures of the leopard cat population be monitored every 5 years to detect any changes. If needed, individuals can be artificially exchanged among different subpopulations to maintain the viability of this wild cat in Beijing. Abstract In the face of habitat shrinkage and segregation, the survival of wild cats looks bleak. Interpreting their population genetic structure during habitat fragmentation is critical in planning effective management strategies. To reveal the segregation effects of road construction and human settlements on the population genetic structure, we analyzed non-invasive fecal DNA samples from leopard cats (Prionailurus bengalensis) from five nature reserves in mountainous areas around Beijing. We focused on microsatellite markers. A total of 112 individual leopard cats were identified among 601 samples of scat, and moderate population genetic diversity was detected. Microsatellite-marker-based genetic differentiation (Fst) and gene flow (Nm) showed a weak trend toward discrepancies in the Baihuashan and Songshan subpopulations, which indicated habitat fragmentation effects on individual dispersal. Because the segregated subpopulations may suffer a high risk of genetic diversity loss, we suggest that their genetic structure be monitored with more molecular markers to detect any changes, and that female individuals be artificially introduced as needed to maintain the viability of the leopard cat subpopulations in Beijing.
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Ghimire P. Conservation of Tiger Panthera tigris in Nepal: a review of current efforts and challenges. JOURNAL OF THREATENED TAXA 2022. [DOI: 10.11609/jott.7011.14.9.21769-21775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The Tiger Panthera tigris is one of the most charismatic and well known Asian big cats. In the lowlands of Nepal, Tigers along with the Greater One-Horned Rhinoceros Rhinoceros unicornis and the Asiatic Elephant Elephas maximus serve as flagship species gathering global conservation attention. Current surveys estimate a population of 235 tigers in Nepal. Tigers in Nepal are strictly protected in five protected areas located in the lowlands and their adjoining forest areas which cover 7,668.20 km2. However, over the last century, tiger population and their distribution range drastically declined with the species heading towards extinction. The long-term survival of this charismatic species is challenging largely due to the loss and fragmentation of habitat, climate change, increasing human-wildlife interface and poaching for illegal trade of body parts. In response to this, the Government of Nepal along with conservation agencies and local communities have proceeded to execute various conservation initiatives both at national and international level. This paper tries to scrutinize the current status of tiger population, conservation efforts, and existing challenges to conserve tiger species in Nepal.
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Cho S, Pandey P, Hyun JY, Marchenkova T, Vitkalova A, Petrov T, Jeong D, Lee J, Kim DY, Li Y, Darman Y, Min MS, Kim KS, Bardyuk V, Lee H. Efficient and cost-effective non-invasive population monitoring as a method to assess the genetic diversity of the last remaining population of Amur leopard (Panthera pardus orientalis) in the Russia Far East. PLoS One 2022; 17:e0270217. [PMID: 35793341 PMCID: PMC9258825 DOI: 10.1371/journal.pone.0270217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 06/07/2022] [Indexed: 11/18/2022] Open
Abstract
Small populations of the endangered species are more vulnerable to extinction and hence require periodic genetic monitoring to establish and revisit the conservation strategies. The Amur leopard is critically endangered with about 100 individuals in the wild. In this study, we developed a simple and cost-effective noninvasive genetic monitoring protocol for Amur leopards. Also, we investigated the impact of fecal sample's age, storage, and collection season on microsatellite genotyping success and data quality. We identified 89 leopard scats out of the 342 fecal samples collected from Land of the Leopard between 2014-2019. Microsatellite genotyping using 12 markers optimized in 3 multiplex PCR reactions reveals presence of at least 24 leopard individuals (18 males and 6 females). There was a significant difference in the success rate of genotyping depending on the time from feces deposition to collection (p = 0.014, Fisher's exact test), with better genotyping success for samples having <2 weeks of environmental exposure. Amur leopard genetic diversity was found low (Ho- 0.33, HE- 0.35, and NA- 2.57) with no visible population substructure and recent bottleneck signature. Although a historical bottleneck footprint was observed. Mitochondrial DNA diversity was also found low with two haplotypes differing by a point mutation reported in 1,769 bp of investigated sequence covering parts of cytochrome b gene (846 bp), NADH-5 gene (611 bp) and control region (312 bp). We recommend periodic genetic monitoring of wild Amur leopards following the proposed methodology to achieve cost effectiveness and efficiency.
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Affiliation(s)
- Sujoo Cho
- Research Institute for Veterinary Science and Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
- Tiger and Leopard Conservation Fund in Korea, Seoul, South Korea
| | - Puneet Pandey
- Research Institute for Veterinary Science and Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
- Tiger and Leopard Conservation Fund in Korea, Seoul, South Korea
- ENPROTEC India Foundation, Uttar Pradesh, India
| | - Jee Yun Hyun
- Research Institute for Veterinary Science and Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
- Tiger and Leopard Conservation Fund in Korea, Seoul, South Korea
| | - Taisia Marchenkova
- Federal State Budgetary Institution Joint Directorate of Kedrovaya Pad’ State Biosphere Nature Reserve and Land of the Leopard National Park, Ministry of Natural Resources and Environment of the Russian Federation, Vladivostok, Primorsky Krai, Russia
| | - Anna Vitkalova
- Federal State Budgetary Institution Joint Directorate of Kedrovaya Pad’ State Biosphere Nature Reserve and Land of the Leopard National Park, Ministry of Natural Resources and Environment of the Russian Federation, Vladivostok, Primorsky Krai, Russia
| | - Timophey Petrov
- Federal State Budgetary Institution Joint Directorate of Kedrovaya Pad’ State Biosphere Nature Reserve and Land of the Leopard National Park, Ministry of Natural Resources and Environment of the Russian Federation, Vladivostok, Primorsky Krai, Russia
| | - Daecheol Jeong
- Research Institute for Veterinary Science and Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
- Tiger and Leopard Conservation Fund in Korea, Seoul, South Korea
| | - Jangmi Lee
- Research Institute for Veterinary Science and Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
- Tiger and Leopard Conservation Fund in Korea, Seoul, South Korea
| | - Dong Youn Kim
- Research Institute for Veterinary Science and Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
- Tiger and Leopard Conservation Fund in Korea, Seoul, South Korea
| | - Ying Li
- Research Institute for Veterinary Science and Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
- Tiger and Leopard Conservation Fund in Korea, Seoul, South Korea
- College of Geography and Ocean Science, Yanbian University, Yanji, Jilin, China
| | - Yury Darman
- WWF-Russia, Amur Branch, Vladivostok, Primorsky Krai, Russia
| | - Mi-Sook Min
- Research Institute for Veterinary Science and Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
- Tiger and Leopard Conservation Fund in Korea, Seoul, South Korea
| | - Kyung Seok Kim
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, Iowa, United States of America
| | - Victor Bardyuk
- Federal State Budgetary Institution Joint Directorate of Kedrovaya Pad’ State Biosphere Nature Reserve and Land of the Leopard National Park, Ministry of Natural Resources and Environment of the Russian Federation, Vladivostok, Primorsky Krai, Russia
| | - Hang Lee
- Research Institute for Veterinary Science and Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
- Tiger and Leopard Conservation Fund in Korea, Seoul, South Korea
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Hayward KM, Clemente-Carvalho RBG, Jensen EL, de Groot PVC, Branigan M, Dyck M, Tschritter C, Sun Z, Lougheed SC. Genotyping-in-thousands by sequencing (GT-seq) of non-invasive fecal and degraded samples: a new panel to enable ongoing monitoring of Canadian polar bear populations. Mol Ecol Resour 2022; 22:1906-1918. [PMID: 35007402 PMCID: PMC9305793 DOI: 10.1111/1755-0998.13583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/25/2021] [Accepted: 12/07/2021] [Indexed: 11/26/2022]
Abstract
Genetic monitoring using noninvasive samples provides a complement or alternative to traditional population monitoring methods. However, next‐generation sequencing approaches to monitoring typically require high quality DNA and the use of noninvasive samples (e.g., scat) is often challenged by poor DNA quality and contamination by nontarget species. One promising solution is a highly multiplexed sequencing approach called genotyping‐in‐thousands by sequencing (GT‐seq), which can enable cost‐efficient genomics‐based monitoring for populations based on noninvasively collected samples. Here, we develop and validate a GT‐seq panel of 324 single nucleotide polymorphisms (SNPs) optimized for genotyping of polar bears based on DNA from noninvasively collected faecal samples. We demonstrate (1) successful GT‐seq genotyping of DNA from a range of sample sources, including successful genotyping (>50% loci) of 62.9% of noninvasively collected faecal samples determined to contain polar bear DNA; and (2) that we can reliably differentiate individuals, ascertain sex, assess relatedness, and resolve population structure of Canadian polar bear subpopulations based on a GT‐seq panel of 324 SNPs. Our GT‐seq data reveal spatial‐genetic patterns similar to previous polar bear studies but at lesser cost per sample and through use of noninvasively collected samples, indicating the potential of this approach for population monitoring. This GT‐seq panel provides the foundation for a noninvasive toolkit for polar bear monitoring and can contribute to community‐based programmes – a framework which may serve as a model for wildlife conservation and management for species worldwide.
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Affiliation(s)
- Kristen M Hayward
- Department of Biology, Queen's University, Kingston, Ontario, Canada
| | | | - Evelyn L Jensen
- School of Natural and Environmental Sciences, Newcastle University, Newcastle, United Kingdom
| | | | - Marsha Branigan
- Department of Environment and Natural Resources, Government of the Northwest Territories, Inuvik, Northwest Territories, Canada
| | - Markus Dyck
- Department of Environment, Government of Nunavut, Igloolik, Nunavut, Canada
| | | | - Zhengxin Sun
- Department of Biology, Queen's University, Kingston, Ontario, Canada
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Jiménez J, C. Augustine B, Linden DW, B. Chandler R, Royle JA. Spatial capture-recapture with random thinning for unidentified encounters. Ecol Evol 2021; 11:1187-1198. [PMID: 33598123 PMCID: PMC7863675 DOI: 10.1002/ece3.7091] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 11/08/2022] Open
Abstract
Spatial capture-recapture (SCR) models have increasingly been used as a basis for combining capture-recapture data types with variable levels of individual identity information to estimate population density and other demographic parameters. Recent examples are the unmarked SCR (or spatial count model), where no individual identities are available and spatial mark-resight (SMR) where individual identities are available for only a marked subset of the population. Currently lacking, though, is a model that allows unidentified samples to be combined with identified samples when there are no separate classes of "marked" and "unmarked" individuals and when the two sample types cannot be considered as arising from two independent observation models. This is a common scenario when using noninvasive sampling methods, for example, when analyzing data on identified and unidentified photographs or scats from the same sites.Here we describe a "random thinning" SCR model that utilizes encounters of both known and unknown identity samples using a natural mechanistic dependence between samples arising from a single observation model. Our model was fitted in a Bayesian framework using NIMBLE.We investigate the improvement in parameter estimates by including the unknown identity samples, which was notable (up to 79% more precise) in low-density populations with a low rate of identified encounters. We then applied the random thinning SCR model to a noninvasive genetic sampling study of brown bear (Ursus arctos) density in Oriental Cantabrian Mountains (North Spain).Our model can improve density estimation for noninvasive sampling studies for low-density populations with low rates of individual identification, by making use of available data that might otherwise be discarded.
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Affiliation(s)
- José Jiménez
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC‐UCLM‐JCCM)Ronda de Toledo, 12Ciudad Real13071Spain
| | - Ben C. Augustine
- U.S. Geological Survey John Wesley Powell CenterCornell Department of Natural ResourcesIthacaNew York14853USA
| | - Daniel W. Linden
- Greater Atlantic Regional Fisheries OfficeNOAA National Marine Fisheries Service55 Great Republic DriveGloucesterMassachusetts01922USA
| | - Richard B. Chandler
- Warnell School of Forestry and Natural ResourcesUniversity of Georgia180 E. Green StreetAthensGeorgia30602USA
| | - J. Andrew Royle
- U.S. Geological SurveyPatuxent Wildlife Research Center12100 Beech Forest RoadLaurelMaryland20708USA
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Vesterinen EJ, Kaunisto KM, Lilley TM. A global class reunion with multiple groups feasting on the declining insect smorgasbord. Sci Rep 2020; 10:16595. [PMID: 33024156 PMCID: PMC7539006 DOI: 10.1038/s41598-020-73609-9] [Citation(s) in RCA: 5] [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: 03/05/2020] [Accepted: 09/15/2020] [Indexed: 12/05/2022] Open
Abstract
We report a detection of a surprising similarity in the diet of predators across distant phyla. Though just a first glimpse into the subject, our discovery contradicts traditional aspects of biology, as the earliest notions in ecology have linked the most severe competition of resources with evolutionary relatedness. We argue that our finding deserves more research, and propose a plan to reveal more information on the current biodiversity loss around the world. While doing so, we expand the recently proposed conservation roadmaps into a parallel study of global interaction networks.
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Affiliation(s)
- Eero J Vesterinen
- Department of Biology, University of Turku, Turku, Finland.
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | | | - Thomas M Lilley
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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Aziz MA, Islam MA, Groombridge J. Spatial differences in prey preference by tigers across the Bangladesh Sundarbans reveal a need for customised strategies to protect prey populations. ENDANGER SPECIES RES 2020. [DOI: 10.3354/esr01052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Sundarbans is the only mangrove habitat in the world to support tigers Panthera tigris, whose persistence there is believed to be dependent on a very limited number of prey species. Conservation managers therefore need to understand how tigers utilise available prey species on a spatial scale in order to formulate a prey-based protection strategy for this global-priority tiger landscape. A total of 512 scat samples were collected during a survey of 1984 km2 of forest across 4 sample blocks in the 6017 km2 of the Bangladesh Sundarbans. Analysis of scat composition and prey remains reliably identified 5 major prey species, of which spotted deer Axis axis and wild pig Sus scrofa contributed a cumulative biomass of 89% to tiger diet. Tiger preference for prey species was highly skewed towards spotted deer and wild pig, but the relative contribution of these 2 species differed significantly across the 4 study areas, which spanned the Sundarbans, demonstrating important spatial patterns of tiger prey preference across the Sundarbans landscape. Given the comparatively limited number of prey species available to support the dwindling tiger population, different strategies are needed in different parts of the Sundarbans to support tiger populations and to protect spotted deer and wild pig populations from unabated poaching.
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Affiliation(s)
- MA Aziz
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury CT2 7NZ, UK
- Department of Zoology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - MA Islam
- Department of Zoology, University of Dhaka, Dhaka 1000, Bangladesh
| | - J Groombridge
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury CT2 7NZ, UK
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Eriksson CE, Ruprecht J, Levi T. More affordable and effective noninvasive single nucleotide polymorphism genotyping using high‐throughput amplicon sequencing. Mol Ecol Resour 2020; 20:1505-1516. [DOI: 10.1111/1755-0998.13208] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 12/26/2022]
Affiliation(s)
| | - Joel Ruprecht
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
| | - Taal Levi
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
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Donaldson ME, Jackson K, Rico Y, Sayers JB, Ethier DM, Kyle CJ. Development of a massively parallel, genotyping-by-sequencing assay in American badger (Taxidea taxus) highlights the need for careful validation when working with low template DNA. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01146-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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12
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Identifying landscape factors affecting tiger decline in the Bangladesh Sundarbans. Glob Ecol Conserv 2018. [DOI: 10.1016/j.gecco.2018.e00382] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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