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      Molecular Detection of Vertebrates in Stream Water: A Demonstration Using Rocky Mountain Tailed Frogs and Idaho Giant Salamanders

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          Abstract

          Stream ecosystems harbor many secretive and imperiled species, and studies of vertebrates in these systems face the challenges of relatively low detection rates and high costs. Environmental DNA (eDNA) has recently been confirmed as a sensitive and efficient tool for documenting aquatic vertebrates in wetlands and in a large river and canal system. However, it was unclear whether this tool could be used to detect low-density vertebrates in fast-moving streams where shed cells may travel rapidly away from their source. To evaluate the potential utility of eDNA techniques in stream systems, we designed targeted primers to amplify a short, species-specific DNA fragment for two secretive stream amphibian species in the northwestern region of the United States (Rocky Mountain tailed frogs, Ascaphus montanus, and Idaho giant salamanders, Dicamptodon aterrimus). We tested three DNA extraction and five PCR protocols to determine whether we could detect eDNA of these species in filtered water samples from five streams with varying densities of these species in central Idaho, USA. We successfully amplified and sequenced the targeted DNA regions for both species from stream water filter samples. We detected Idaho giant salamanders in all samples and Rocky Mountain tailed frogs in four of five streams and found some indication that these species are more difficult to detect using eDNA in early spring than in early fall. While the sensitivity of this method across taxa remains to be determined, the use of eDNA could revolutionize surveys for rare and invasive stream species. With this study, the utility of eDNA techniques for detecting aquatic vertebrates has been demonstrated across the majority of freshwater systems, setting the stage for an innovative transformation in approaches for aquatic research.

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          R: A language and environment for statistical computing

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            Emerging infectious disease and the loss of biodiversity in a Neotropical amphibian community.

            Pathogens rarely cause extinctions of host species, and there are few examples of a pathogen changing species richness and diversity of an ecological community by causing local extinctions across a wide range of species. We report the link between the rapid appearance of a pathogenic chytrid fungus Batrachochytrium dendrobatidis in an amphibian community at El Copé, Panama, and subsequent mass mortality and loss of amphibian biodiversity across eight families of frogs and salamanders. We describe an outbreak of chytridiomycosis in Panama and argue that this infectious disease has played an important role in amphibian population declines. The high virulence and large number of potential hosts of this emerging infectious disease threaten global amphibian diversity.
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              Light Limitation in a Stream Ecosystem: Responses by Primary Producers and Consumers

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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2011
                26 July 2011
                : 6
                : 7
                : e22746
                Affiliations
                [1 ]Fish and Wildlife Resources, University of Idaho, Moscow, Idaho, United States of America
                [2 ]United States Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, Idaho, United States of America
                Smithsonian's National Zoological Park, United States of America
                Author notes

                Conceived and designed the experiments: CSG DSP RSA LPW. Performed the experiments: CSG RSA. Analyzed the data: CSG DSP RSA LPW. Contributed reagents/materials/analysis tools: CSG DSP LPW. Wrote the paper: CSG DSP RSA LPW.

                Article
                PONE-D-11-08686
                10.1371/journal.pone.0022746
                3144250
                21818382
                2f1e6fcc-cf6d-4bac-9b66-70c0ea1270b2
                This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
                History
                : 15 May 2011
                : 4 July 2011
                Page count
                Pages: 5
                Categories
                Research Article
                Biology
                Ecology
                Freshwater Ecology
                Zoology
                Herpetology

                Uncategorized
                Uncategorized

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