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East Chicago, IN, United States

Mahon A.R.,Central Michigan University | Jerde C.L.,University of Notre Dame | Galaska M.,University of Notre Dame | Bergner J.L.,Central Michigan University | And 4 more authors.
PLoS ONE | Year: 2013

In many North American rivers, populations of multiple species of non-native cyprinid fishes are present, including black carp (Mylpharyngodon piceus), grass carp (Ctenopharyngodon idella), bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix), common carp (Cyprinus carpio), and goldfish (Carassius auratus). All six of these species are found in the Mississippi River basin and tracking their invasion has proven difficult, particularly where abundance is low. Knowledge of the location of the invasion front is valuable to natural resource managers because future ecological and economic damages can be most effectively prevented when populations are low. To test the accuracy of environmental DNA (eDNA) as an early indicator of species occurrence and relative abundance, we applied eDNA technology to the six non-native cyprinid species putatively present in a 2.6 river mile stretch of the Chicago (IL, USA) canal system that was subsequently treated with piscicide. The proportion of water samples yielding positive detections increased with relative abundance of the six species, as indicated by the number of carcasses recovered after poisoning. New markers for black carp, grass carp, and a common carp/goldfish are reported and details of the marker testing to ensure specificity are provided. Source


Lodge D.M.,University of Notre Dame | Turner C.R.,University of Notre Dame | Jerde C.L.,University of Notre Dame | Barnes M.A.,University of Notre Dame | And 6 more authors.
Molecular Ecology | Year: 2012

Three mantras often guide species and ecosystem management: (i) for preventing invasions by harmful species, 'early detection and rapid response'; (ii) for conserving imperilled native species, 'protection of biodiversity hotspots'; and (iii) for assessing biosecurity risk, 'an ounce of prevention equals a pound of cure.' However, these and other management goals are elusive when traditional sampling tools (e.g. netting, traps, electrofishing, visual surveys) have poor detection limits, are too slow or are not feasible. One visionary solution is to use an organism's DNA in the environment (eDNA), rather than the organism itself, as the target of detection. In this issue of Molecular Ecology, Thomsen et al. (2012) provide new evidence demonstrating the feasibility of this approach, showing that eDNA is an accurate indicator of the presence of an impressively diverse set of six aquatic or amphibious taxa including invertebrates, amphibians, a fish and a mammal in a wide range of freshwater habitats. They are also the first to demonstrate that the abundance of eDNA, as measured by qPCR, correlates positively with population abundance estimated with traditional tools. Finally, Thomsen et al. (2012) demonstrate that next-generation sequencing of eDNA can quantify species richness. Overall, Thomsen et al. (2012) provide a revolutionary roadmap for using eDNA for detection of species, estimates of relative abundance and quantification of biodiversity. © 2012 Blackwell Publishing Ltd. Source


Jerde C.L.,University of Notre Dame | Mahon A.R.,University of Notre Dame | Chadderton W.L.,Great Lakes Project | Lodge D.M.,University of Notre Dame
Conservation Letters | Year: 2011

Effective management of rare species, including endangered native species and recently introduced nonindigenous species, requires the detection of populations at low density. For endangered species, detecting the localized distribution makes it possible to identify and protect critical habitat to enhance survival or reproductive success. Similarly, early detection of an incipient invasion by a harmful species increases the feasibility of rapid responses to eradicate the species or contain its spread. Here we demonstrate the efficacy of environmental DNA (eDNA) as a detection tool in freshwater environments. Specifically, we delimit the invasion fronts of two species of Asian carps in Chicago, Illinois, USA area canals and waterways. Quantitative comparisons with traditional fisheries surveillance tools illustrate the greater sensitivity of eDNA and reveal that the risk of invasion to the Laurentian Great Lakes is imminent. © 2011 Wiley Periodicals, Inc. Source


Wegleitner B.J.,Central Michigan University | Jerde C.L.,University of Nevada, Reno | Tucker A.,Great Lakes Project | Chadderton W.L.,Great Lakes Project | Mahon A.R.,Central Michigan University
Conservation Genetics Resources | Year: 2015

The use of environmental DNA is a rapidly evolving approach for surveillance and detection of species. Often water samples are collected in the field and then immediately cooled, filtered, and the resulting filters are stored in freezers to preserve the DNA for subsequent analyses. Recently it was shown that filtered samples could be stored at room temperature for 14 days without any discernable loss in the total DNA. However, for many conservation applications, particularly in remote settings with limited capacity to freeze samples, it would be advantageous to store samples at room temperature for longer periods of time. Here we test for significant loss of DNA yield from storage of polycarbonate track etched filters in Longmire’s lysis buffer at room temperature (20 °C) for 150 days. © 2015, Springer Science+Business Media Dordrecht. Source


Simmons M.,Central Michigan University | Tucker A.,Great Lakes Project | Chadderton W.L.,Great Lakes Project | Jerde C.L.,University of Nevada, Reno | Mahon A.R.,Central Michigan University
Canadian Journal of Fisheries and Aquatic Sciences | Year: 2015

Environmental DNA (eDNA) is useful for delimiting species ranges in aquatic systems, whereby water samples are screened for the presence of DNA from a single species. However, DNA from many species is collected in every sample, and high-throughput sequencing approaches allow for more passive surveillance where a community of species is identified. In this study, we use active (targeted) and passive molecular surveillance approaches to detect species in the Muskingum River Watershed in Ohio, USA. The presence of bighead carp (Hypophthalmichthys nobilis) eDNA in the Muskingum River Watershed was confirmed with active surveillance using digital droplet polymerase chain reaction (ddPCR). The passive surveillance method detected the presence of eDNA from northern snakehead (Channa argus), which was further confirmed with active ddPCR. Whereas active surveillance may be more sensitive to detecting rare DNA, passive surveillance has the capability of detecting unexpected invasive species. Deploying both active and passive surveillance approaches with the same eDNA samples is beneficial for invasive species management. © 2015, National Research Council of Canada. All rights reserved. Source

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