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      Detecting the movement and spawning activity of bigheaded carps with environmental DNA

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          Abstract

          Bigheaded carps are invasive fishes threatening to invade the Great Lakes basin and establish spawning populations, and have been monitored using environmental DNA ( eDNA). Not only does eDNA hold potential for detecting the presence of species, but may also allow for quantitative comparisons like relative abundance of species across time or space. We examined the relationships among bigheaded carp movement, hydrography, spawning and eDNA on the Wabash River, IN, USA. We found positive relationships between eDNA and movement and eDNA and hydrography. We did not find a relationship between eDNA and spawning activity in the form of drifting eggs. Our first finding demonstrates how eDNA may be used to monitor species abundance, whereas our second finding illustrates the need for additional research into eDNA methodologies. Current applications of eDNA are widespread, but the relatively new technology requires further refinement.

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          Environmental and Economic Costs of Nonindigenous Species in the United States

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

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              A Bayesian state-space formulation of dynamic occupancy models.

              Species occurrence and its dynamic components, extinction and colonization probabilities, are focal quantities in biogeography and metapopulation biology, and for species conservation assessments. It has been increasingly appreciated that these parameters must be estimated separately from detection probability to avoid the biases induced by non-detection error. Hence, there is now considerable theoretical and practical interest in dynamic occupancy models that contain explicit representations of metapopulation dynamics such as extinction, colonization, and turnover as well as growth rates. We describe a hierarchical parameterization of these models that is analogous to the state-space formulation of models in time series, where the model is represented by two components, one for the partially observable occupancy process and another for the observations conditional on that process. This parameterization naturally allows estimation of all parameters of the conventional approach to occupancy models, but in addition, yields great flexibility and extensibility, e.g., to modeling heterogeneity or latent structure in model parameters. We also highlight the important distinction between population and finite sample inference; the latter yields much more precise estimates for the particular sample at hand. Finite sample estimates can easily be obtained using the state-space representation of the model but are difficult to obtain under the conventional approach of likelihood-based estimation. We use R and WinBUGS to apply the model to two examples. In a standard analysis for the European Crossbill in a large Swiss monitoring program, we fit a model with year-specific parameters. Estimates of the dynamic parameters varied greatly among years, highlighting the irruptive population dynamics of that species. In the second example, we analyze route occupancy of Cerulean Warblers in the North American Breeding Bird Survey (BBS) using a model allowing for site-specific heterogeneity in model parameters. The results indicate relatively low turnover and a stable distribution of Cerulean Warblers which is in contrast to analyses of counts of individuals from the same survey that indicate important declines. This discrepancy illustrates the inertia in occupancy relative to actual abundance. Furthermore, the model reveals a declining patch survival probability, and increasing turnover, toward the edge of the range of the species, which is consistent with metapopulation perspectives on the genesis of range edges. Given detection/non-detection data, dynamic occupancy models as described here have considerable potential for the study of distributions and range dynamics.
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                Author and article information

                Journal
                Mol Ecol Resour
                Mol Ecol Resour
                10.1111/(ISSN)1755-0998
                MEN
                Molecular Ecology Resources
                John Wiley and Sons Inc. (Hoboken )
                1755-098X
                1755-0998
                09 May 2016
                July 2016
                : 16
                : 4 ( doiID: 10.1111/men.2016.16.issue-4 )
                : 957-965
                Affiliations
                [ 1 ] U.S. Geological Survey Upper Midwest Environmental Sciences Center La Crosse WI USA
                [ 2 ] Department of Forestry and Natural Resources Purdue University West Lafayette IN USA
                [ 3 ]Present address: US Fish and Wildlife Service Northeast Fishery Center Lamar PA USA
                [ 4 ]Present address: Center for Fisheries, Aquaculture and Aquatic Science Southern Illinois University Carbondale IL USA
                [ 5 ]Present address: Wisconsin Department of Natural Resources Rhinelander WI USA
                Author notes
                [*] [* ]Correspondence: Richard A. Erickson, Fax: 608‐783‐6066; E‐mail: rerickson@ 123456usgs.gov
                [†]

                These authors contributed equally to this work.

                [‡]

                These authors also contributed equally to this work.

                Author information
                http://orcid.org/0000-0003-4649-482X
                Article
                MEN12533
                10.1111/1755-0998.12533
                6680351
                27087387
                73565898-d4b3-4539-b6f1-5a59c58d25be
                © 2016 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 28 August 2015
                : 04 April 2016
                : 07 April 2016
                Page count
                Pages: 9
                Funding
                Funded by: U.S. Environmental Protection Agency – Great Lakes Restoration Initiative
                Funded by: U.S. Geological Survey
                Funded by: Indiana Department of Natural Resources
                Categories
                Resource Article
                RESOURCE ARTICLES
                Molecular and Statistical Advances
                Custom metadata
                2.0
                men12533
                July 2016
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.6.7 mode:remove_FC converted:05.08.2019

                Ecology
                asian carp,bigheaded carp,environmental monitoring,fisheries management,invasive species detection

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