LETTER “Sight-unseen” detection of rare aquatic species using environmental DNA Christopher L. Jerde 1 , Andrew R. Mahon 1 , W. Lindsay Chadderton 2 , & David M. Lodge 1 1 Center for Aquatic Conservation, Department of Biological Sciences, University of Notre Dame 2 Great Lakes Project, The Nature Conservancy Keywords Asian carp; early detection; environmental DNA; Great Lakes; invasive species; surveillance. Correspondence Christopher L. Jerde, Center for Aquatic Conservation, University of Notre Dame, P.O. Box 369, Notre Dame, IN 46556-0369. Tel: (574) 631-2665; fax: (574) 631-7413. E-mail: cjerde@nd.edu Received 27 July 2010 Accepted 23 November 2010 Editor Corey Bradshaw doi: 10.1111/j.1755-263X.2010.00158.x Abstract Effective management of rare species, including endangered native species and recently introduced nonindigenous species, requires the detection of popula- tions at low density. For endangered species, detecting the localized distribu- tion 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 environ- mental DNA (eDNA) as a detection tool in freshwater environments. Specifi- cally, we delimit the invasion fronts of two species of Asian carps in Chicago, Illinois, USA area canals and waterways. Quantitative comparisons with tradi- tional fisheries surveillance tools illustrate the greater sensitivity of eDNA and reveal that the risk of invasion to the Laurentian Great Lakes is imminent. Introduction In the absence of tools to detect rare species, uncertainty about when, where, and for how long a management action should be implemented often results in inaction or ineffective use of management resources (Thompson 2004; Lodge et al. 2006). Detection probabilities for rare species are typically low in all environments, but par- ticularly in aquatic environments where organisms are hidden beneath the water’s surface. Fish surveillance pro- grams, for example, traditionally employ nets or elec- trofishing gear. Because these tools usually have low capture probabilities per target organism, they are re- liable indicators of occurrence only for species present at moderate-to-high abundance (Magnuson et al. 1994). In contrast, for rare species, the low detection probabil- ity of these tools often leads to an error in inference— concluding a species is absent when it is actually present (Gu & Swihart 2004). In the case of rare species, the only solutions are to increase sampling effort or change to a detection tool with greater detection probability (McDonald 2004). However with traditional surveillance tools, increases in sampling effort sufficient to achieve a usefully high detection probability for rare species are of- ten infeasible. Here we describe the application of environmental DNA (eDNA) as an effective surveillance method for rare fishes in a large river and canal complex. We show that it is more sensitive than traditional tools, has no risk of harming the species under study (Beja-Pereira et al. 2009), and effort can feasibly be increased for species management. The eDNA surveillance method exploits an advantage of aquatic environments: the aqueous envi- ronment suspends sloughed tissues, making it easy to sample and detect DNA from even rare organisms that are present but invisible to traditional tools. This conser- vation application of the eDNA method was inspired by previous identification of whales (Megaptera novaeangliae, Conservation Letters 00 (2011) 1–8 Copyright and Photocopying: c  2011 Wiley Periodicals, Inc. 1