Detection of Asian carp DNA as part of a Great Lakes basin-wide surveillance program

Jerde, Christopher L.; Chadderton, W. Lindsay; Mahon, Andrew R.; Renshaw, Mark A.; Corush, Joel B.; Budny, Michelle L.; Mysorekar, Sagar; Lodge, David M.

doi:10.1139/cjfas-2012-0478

Cited by 280 publications

(228 citation statements)

References 13 publications

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“…eDNA is rapidly moving from proof of concept to actual implementation for purposes like surveillance for the early arrival of new or spreading invasive species (e.g., Jerde et al, 2013;Egan et al, 2015) or documenting distributional or population trends for imperiled species (e.g., de Souza et al, 2016). Here we report the first application of eDNA to test for major range expansions of invasive crayfishes into new regions where they were not previously known to occur, but where climatic conditions are anticipated to be suitable for their population establishment and spread Morehouse & Tobler, 2013).…”

Section: Discussionmentioning

confidence: 99%

Environmental DNA (eDNA) detects the invasive crayfishes Orconectes rusticus and Pacifastacus leniusculus in large lakes of North America

et al. 2017

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We report results of a study that made reciprocal comparisons of environmental DNA (eDNA) assays for two major invasive crayfishes between their disparate invasive ranges in North America. Specifically, we tested for range expansions of the signal crayfish Pacifastacus leniusculus (Dana, 1852) into the Laurentian Great Lakes region known to be invaded by the rusty crayfish Orconectes rusticus (Girard, 1852), as well as for the invasion of O. rusticus into large lakes of California and Nevada, US known to be invaded by P. leniusculus. We compared eDNA detections to historic localities for O. rusticus within the Great Lakes, and to recent sampling for presence/absence and relative abundance of P. leniusculus in California and Nevada via overnight sets of baited traps. We successfully detected O. rusticus eDNA at six sites from the Great Lakes and P. leniusculus from six of seven lakes where it was known to occur in California and Nevada, but did not detect any range expansions by either species across the North American continent. eDNA appears suitable to detect benthic arthropods from exceptionally large lakes, and will likely be useful in applications for monitoring of new biological invasions into these and other freshwater and marine habitats.

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Section: Discussionmentioning

confidence: 99%

Environmental DNA (eDNA) detects the invasive crayfishes Orconectes rusticus and Pacifastacus leniusculus in large lakes of North America

et al. 2017

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“…Costa et al 2015;Dong et al 2015;Pal et al 2015), followed by investigations of fish (e.g. Jerde et al 2013;Takahara & Minimoto 2013;Janosik & Johnston 2015;Fig. 3).…”

Section: Organisms Studiedmentioning

confidence: 99%

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

107

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Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil ® and PowerMax ® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil ® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater ® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

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“…Analysis of environmental DNA (eDNA) is likely to become a revolutionary tool to increase both spatial and temporal scales of monitoring datasets for species of concern (Dejean et al 2012;Jerde et al 2011Jerde et al , 2013Lodge et al 2012;Mahon et al 2013;Pilliod et al 2013;Thomsen et al 2012a). The eDNA method detects traces of DNA in cellular or extracellular form from sources such as feces, secreted mucous membranes, gametes, and skin cells (Haile et al 2009;Lydolph et al 2005;Taberlet et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Improving herpetological surveys in eastern North America using the environmental DNA method

Lacoursière‐Roussel

Dubois

Normandeau

et al. 2016

Genome

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Among vertebrates, herpetofauna has the highest proportion of declining species. Detection of environmental DNA (eDNA) is a promising method towards significantly increasing large-scale herpetological conservation efforts. However, the integration of eDNA results within a management framework requires an evaluation of the efficiency of the method in large natural environments and the calibration of eDNA surveys with the quantitative monitoring tools currently used by conservation biologists. Towards this end, we first developed species-specific primers to detect the wood turtle (Glyptemys insculpta) a species at risk in Canada, by quantitative PCR (qPCR). The rate of eDNA detection obtained by qPCR was also compared to the relative abundance of this species in nine rivers obtained by standardized visual surveys in the Province of Québec (Canada). Second, we developed multi-species primers to detect North American amphibian and reptile species using eDNA metabarcoding analysis. An occurrence index based on the distribution range and habitat type was compared with the eDNA metabarcoding dataset from samples collected in seven lakes and five rivers. Our results empirically support the effectiveness of eDNA metabarcoding to characterize herpetological species distributions. Moreover, detection rates provided similar results to standardized visual surveys currently used to develop conservation strategies for the wood turtle. We conclude that eDNA detection rates may provide an effective semiquantitative survey tool, provided that assay calibration and standardization is performed.

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Detection of Asian carp DNA as part of a Great Lakes basin-wide surveillance program

Cited by 280 publications

References 13 publications

Environmental DNA (eDNA) detects the invasive crayfishes Orconectes rusticus and Pacifastacus leniusculus in large lakes of North America

Environmental DNA (eDNA) detects the invasive crayfishes Orconectes rusticus and Pacifastacus leniusculus in large lakes of North America

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Improving herpetological surveys in eastern North America using the environmental DNA method

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