Ten real‐time <scp>PCR</scp> assays for detection of fish predation at the community level in the San Francisco Estuary–Delta

Brandl, Scott; Schumer, Gregg; Schreier, Brian M.; Conrad, J. Louise; May, Bernie; Baerwald, Melinda R.

doi:10.1111/1755-0998.12305

Cited by 36 publications

(40 citation statements)

References 21 publications

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“…In vitro testing involves applying the assay to tissue-derived DNA from target and non-target species, to empirically demonstrate specificity. It is important to note that trace levels of cross-contamination between tissue samples or DNA extracts can easily confound in vitro testing (Brandl et al 2014). In situ testing involves applying the assay to eDNA samples from environments where the target species is absent and environments where it is present, to empirically demonstrate sensitivity and specificity under natural conditions.…”

Section: Qpcr Assay Design and Validationmentioning

confidence: 99%

Critical considerations for the application of environmental DNA methods to detect aquatic species

et al. 2016

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Summary1. Species detection using environmental DNA (eDNA) has tremendous potential for contributing to the understanding of the ecology and conservation of aquatic species. Detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species. The sensitivity of eDNA methods, however, requires a heightened awareness and attention to quality assurance and quality control protocols. Additionally, the interpretation of eDNA data demands careful consideration of multiple factors. As eDNA methods have grown in application, diverse approaches have been implemented to address these issues. With interest in eDNA continuing to expand, supportive guidelines for undertaking eDNA studies are greatly needed. 2. Environmental DNA researchers from around the world have collaborated to produce this set of guidelines and considerations for implementing eDNA methods to detect aquatic macroorganisms. 3. Critical considerations for study design include preventing contamination in the field and the laboratory, choosing appropriate sample analysis methods, validating assays, testing for sample inhibition and following minimum reporting guidelines. Critical considerations for inference include temporal and spatial processes, limits of correlation of eDNA with abundance, uncertainty of positive and negative results, and potential sources of allochthonous DNA. 4. We present a synthesis of knowledge at this stage for application of this new and powerful detection method.

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Section: Qpcr Assay Design and Validationmentioning

confidence: 99%

Critical considerations for the application of environmental DNA methods to detect aquatic species

et al. 2016

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“…, salamanders (Olson, Briggler, & Williams, 2012;Spear, Groves, Williams, & Waits, 2015), mollusks (Goldberg et al, 2013;Stoeckle, Kuehn, & Geist, 2015), crustaceans , mammals (Padgett-Stewart et al, 2015), lamprey , and bony fishes (Brandl et al, 2015;Mahon et al, 2013;.…”

Section: )mentioning

confidence: 99%

“…Environmental DNA (eDNA) sampling in aquatic environments has been lauded as a highly sensitive and efficient tool for assessing species presence, particularly for aquatic or semi‐aquatic species which are invasive (Dejean et al., ; Goldberg, Sepulveda, Ray, Baumgardt, & Waits, ), native but rare (McKelvey et al., ; Sigsgaard, Carl, Moller, & Thomsen, ; Wilcox et al., ), or cryptic and difficult to survey (Carim, Dysthe, Young, McKelvey, & Schwartz, ; Fukumoto, Ushimaru, & Minamoto, ). It has been applied to an array of taxa including frogs (Dejean et al., ; Ficetola, Miaud, Pompanon, & Taberlet, ; Goldberg, Pilliod, Arkle, & Waits, ), salamanders (Olson, Briggler, & Williams, ; Spear, Groves, Williams, & Waits, ), mollusks (Goldberg et al., ; Stoeckle, Kuehn, & Geist, ), crustaceans (Carim, McKelvey, Young, Wilcox, & Schwartz, ), mammals (Padgett‐Stewart et al., ), lamprey (Carim et al., ), and bony fishes (Brandl et al., ; Mahon et al., ; Wilcox, Carim, McKelvey, Young, & Schwartz, ).…”

Section: Introductionmentioning

confidence: 99%

Repurposing environmental DNA samples—detecting the western pearlshell (Margaritifera falcata) as a proof of concept

Dysthe

Rodgers

Franklin

et al. 2018

Ecology and Evolution

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Information on the distribution of multiple species in a common landscape is fundamental to effective conservation and management. However, distribution data are expensive to obtain and often limited to high‐profile species in a system. A recently developed technique, environmental DNA (eDNA) sampling, has been shown to be more sensitive than traditional detection methods for many aquatic species. A second and perhaps underappreciated benefit of eDNA sampling is that a sample originally collected to determine the presence of one species can be re‐analyzed to detect additional taxa without additional field effort. We developed an eDNA assay for the western pearlshell mussel (Margaritifera falcata) and evaluated its effectiveness by analyzing previously collected eDNA samples that were annotated with information including sample location and deposited in a central repository. The eDNA samples were initially collected to determine habitat occupancy by nonbenthic fish species at sites that were in the vicinity of locations recently occupied by western pearlshell. These repurposed eDNA samples produced results congruent with historical western pearlshell surveys and permitted a more precise delineation of the extent of local populations. That a sampling protocol designed to detect fish was also successful for detecting a freshwater mussel suggests that rapidly accumulating collections of eDNA samples can be repurposed to enhance the efficiency and cost‐effectiveness of aquatic biodiversity monitoring.

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“…Molecular techniques have also been used to assess the diet of piscivores with a focus on marine predators such as pinnipeds (Deagle et al 2009;Marshall et al 2010), squids (Deagle et al 2005) and seabirds (Bowser et al 2013;Jarman et al 2013), but to this point, they have only been scarcely applied in freshwater ecosystems (e.g. Bradford et al 2014;Brandl et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Molecular prey identification in Central European piscivores

Thalinger

Oehm

Mayr

et al. 2015

Molecular Ecology Resources

122

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Diet analysis is an important aspect when investigating the ecology of fish‐eating animals and essential for assessing their functional role in food webs across aquatic and terrestrial ecosystems. The identification of fish remains in dietary samples, however, can be time‐consuming and unsatisfying using conventional morphological analysis of prey remains. Here, we present a two‐step multiplex PCR system, comprised of six assays, allowing for rapid, sensitive and specific detection of fish DNA in dietary samples. This approach encompasses 78 fish and lamprey species native to Central European freshwaters and enables the identification of 31 species, six genera, two families, two orders and two fish family clusters. All targeted taxa were successfully amplified from 25 template molecules, and each assay was specific when tested against a wide range of invertebrates and vertebrates inhabiting aquatic environments. The applicability of the multiplex PCR system was evaluated in a feeding trial, wherein it outperformed morphological prey analysis regarding species‐specific prey identification in faeces of Eurasian otters. Additionally, a wide spectrum of fish species was detected in field‐collected faecal samples and regurgitated pellets of Common Kingfishers and Great Cormorants, demonstrating the broad applicability of the approach. In conclusion, this multiplex PCR system provides an efficient, easy to use and cost‐effective tool for assessing the trophic ecology of piscivores in Central Europe. Furthermore, the multiplex PCRs and the primers described therein will be applicable wherever DNA of the targeted fish species needs to be detected at high sensitivity and specificity.

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Ten real‐time PCR assays for detection of fish predation at the community level in the San Francisco Estuary–Delta

Cited by 36 publications

References 21 publications

Critical considerations for the application of environmental DNA methods to detect aquatic species

Critical considerations for the application of environmental DNA methods to detect aquatic species

Repurposing environmental DNA samples—detecting the western pearlshell (Margaritifera falcata) as a proof of concept

Molecular prey identification in Central European piscivores

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