An environmental DNA marker for detecting nonnative brown trout ( Salmo trutta )
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TECHNICAL NOTE
An environmental DNA marker for detecting nonnative brown trout (Salmo trutta) K. J. Carim1 • T. M. Wilcox1,2 • M. Anderson3 • D. J. Lawrence4 • M. K. Young1 K. S. McKelvey1 • M. K. Schwartz1
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Received: 16 December 2015 / Accepted: 19 May 2016 Ó Springer Science+Business Media Dordrecht (outside the USA) 2016
Abstract Brown trout (Salmo trutta) are widely introduced in western North America where their presence has led to declines of several native species. To assist conservation efforts aimed at early detection and eradication of this species, we developed a quantitative PCR marker to detect the presence of brown trout DNA in environmental samples. The marker strongly amplified brown trout eDNA, and produced no amplification of eDNA from 17 other species commonly found in western North America. We field tested this marker and demonstrated positive detections in field samples where brown trout presence was known. Keywords Salmonids eDNA Invasive species qPCR Brown trout (Salmo trutta), salmonid fish native to Europe, northern Africa, and northern and central Asia, have been widely introduced across the globe, including North America. In the western U.S., their presence is associated with the decline of native fish species, including Bonneville Electronic supplementary material The online version of this article (doi:10.1007/s12686-016-0548-5) contains supplementary material, which is available to authorized users. & K. J. Carim [email protected] 1
Rocky Mountain Research Station, United States Department of Agriculture, Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT, USA
2
Division of Biological Sciences, University of Montana, Missoula, MT, USA
3
Arizona Department of Game and Fish, Phoenix, AZ, USA
4
National Fish and Wildlife Foundation, Washington, DC, USA
cutthroat trout (Oncorhynchus clarkii utah) and Apache trout (O. gilae apache) (McHugh and Budy 2005; U.S. Fish and Wildlife Service 2009). Determining the presence and distribution of nonnative brown trout is critical for recovery efforts aimed at protecting native fish species or for evaluating the efficacy of chemical and mechanical removal of brown trout before reintroduction of native fish populations. Environmental DNA (eDNA) sampling is gaining popularity as a sensitive method for detection of rare or invading aquatic species (Biggs et al. 2015; Dejean et al., 2012; Siggsgaard et al. 2015; Rees et al. 2014; Wilcox et al. 2016) and for delimiting species distributions (McKelvey et al. 2016). Here, we describe a quantitative PCR (qPCR) marker for eDNA-based detection of brown trout. First, we compiled DNA sequences published on GenBank of the cytochrome b (cytb) region of the mitochondrial genome for brown trout and 13 other salmonids commonly found in the western U.S. (Table S1). We used these sequences and the DECIPHER package (Wright et al. 2013) in R v. 3.0.1 (R Core Team 2014) to develop a forward and reverse primer set specific to brown trout: forward primer 50 -CGCCCGA
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