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      Using eDNA to detect the distribution and density of invasive crayfish in the Honghe-Hani rice terrace World Heritage site

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          Abstract

          The Honghe-Hani landscape in China is a UNESCO World Natural Heritage site due to the beauty of its thousands of rice terraces, but these structures are in danger from the invasive crayfish Procambarus clarkii. Crayfish dig nest holes, which collapse terrace walls and destroy rice production. Under the current control strategy, farmers self-report crayfish and are issued pesticide, but this strategy is not expected to eradicate the crayfish nor to prevent their spread since farmers are not able to detect small numbers of crayfish. Thus, we tested whether environmental DNA (eDNA) from paddy-water samples could provide a sensitive detection method. In an aquarium experiment, Real-time Quantitative polymerase chain reaction (qPCR) successfully detected crayfish, even at a simulated density of one crayfish per average-sized paddy (with one false negative). In a field test, we tested eDNA and bottle traps against direct counts of crayfish. eDNA successfully detected crayfish in all 25 paddies where crayfish were observed and in none of the 7 paddies where crayfish were absent. Bottle-trapping was successful in only 68% of the crayfish-present paddies. eDNA concentrations also correlated positively with crayfish counts. In sum, these results suggest that single samples of eDNA are able to detect small crayfish populations, but not perfectly. Thus, we conclude that a program of repeated eDNA sampling is now feasible and likely reliable for measuring crayfish geographic range and for detecting new invasion fronts in the Honghe Hani landscape, which would inform regional control efforts and help to prevent the further spread of this invasive crayfish.

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          Most cited references 28

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          Environmental DNA for wildlife biology and biodiversity monitoring.

          Extraction and identification of DNA from an environmental sample has proven noteworthy recently in detecting and monitoring not only common species, but also those that are endangered, invasive, or elusive. Particular attributes of so-called environmental DNA (eDNA) analysis render it a potent tool for elucidating mechanistic insights in ecological and evolutionary processes. Foremost among these is an improved ability to explore ecosystem-level processes, the generation of quantitative indices for analyses of species, community diversity, and dynamics, and novel opportunities through the use of time-serial samples and unprecedented sensitivity for detecting rare or difficult-to-sample taxa. Although technical challenges remain, here we examine the current frontiers of eDNA, outline key aspects requiring improvement, and suggest future developments and innovations for research. Copyright © 2014 Elsevier Ltd. All rights reserved.
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            The ecology of environmental DNA and implications for conservation genetics

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              Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples

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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                15 May 2017
                2017
                : 12
                : 5
                Affiliations
                [1 ]State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
                [2 ]Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, China
                [3 ]Institute of Ecology and Geobotany, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
                [4 ]Public Technical Service Center, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, China
                [5 ]Kunming Biological Diversity Regional Center of Instruments, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
                [6 ]School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, United Kingdom
                University of Hyogo, JAPAN
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Conceptualization: CYY DWY.

                • Data curation: WC CYY GGZ.

                • Formal analysis: WC CYY DWY.

                • Funding acquisition: CYY YPG DWY.

                • Investigation: WC ZXM GGZ.

                • Methodology: WC CYY.

                • Project administration: CYY.

                • Resources: CYY YPG.

                • Software: WZW.

                • Supervision: CYY DWY.

                • Validation: CYY YPG DWY.

                • Visualization: LW WZW.

                • Writing – original draft: WC CYY.

                • Writing – review & editing: CYY DWY.

                Article
                PONE-D-17-02981
                10.1371/journal.pone.0177724
                5432173
                28505200
                © 2017 Cai et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                Page count
                Figures: 6, Tables: 0, Pages: 13
                Product
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 31400470
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 41661144002
                Award Recipient :
                Funded by: Ministry of Science and Technology of the People's Republic of China (CN)
                Award ID: 2012FY110800
                Award Recipient :
                Funded by: State Key Laboratory of Genetic Resources and Evolution at the Kunming Institute of Zoology
                Award ID: GREKF13-13, GREKF14-13 and GREKF16-09
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100002855, Ministry of Science and Technology of the People's Republic of China;
                Award ID: 2016YFC1201100
                Award Recipient :
                Support was provided by the National Natural Science Foundation of China [ http://www.nsfc.gov.cn] to CYY and DWY; the Ministry of Science and Technology of the People's Republic of China [ http://www.most.gov.cn] to DWY and GYP; and the Chinese Academy of Sciences [ http://www.cas.cn] to DWY and YPG.
                Categories
                Research Article
                Biology and Life Sciences
                Organisms
                Animals
                Invertebrates
                Arthropoda
                Crustaceans
                Crayfish
                Biology and Life Sciences
                Organisms
                Plants
                Grasses
                Rice
                Research and Analysis Methods
                Experimental Organism Systems
                Plant and Algal Models
                Rice
                Biology and Life Sciences
                Agriculture
                Agrochemicals
                Pesticides
                Biology and Life Sciences
                Agriculture
                Pest Control
                Pesticides
                Biology and life sciences
                Molecular biology
                Molecular biology techniques
                Molecular biology assays and analysis techniques
                DNA filter assay
                Research and analysis methods
                Molecular biology techniques
                Molecular biology assays and analysis techniques
                DNA filter assay
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Research and Analysis Methods
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Research and analysis methods
                Extraction techniques
                DNA extraction
                Ecology and Environmental Sciences
                Species Colonization
                Invasive Species
                People and Places
                Geographical Locations
                Asia
                China
                Custom metadata
                All relevant data are within the paper and its Supporting Information files.

                Uncategorized

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