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Surveillance of a federally protected freshwater fish using loop-mediated isothermal amplification (LAMP) and eDNA
  • +2
  • Kayla Fast,
  • Anakela Popp,
  • Patrick O’Neil,
  • Stuart McGregor,
  • Michael Sandel
Kayla Fast
University of West Alabama
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Anakela Popp
Georgia Department of Natural Resources
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Patrick O’Neil
Geological Survey of Alabama
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Stuart McGregor
Geological Survey of Alabama
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Michael Sandel
University of West Alabama
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Peer review status:UNDER REVIEW

25 Jun 2020Submitted to Molecular Ecology Resources
27 Jul 2020Assigned to Editor
27 Jul 2020Submission Checks Completed
06 Aug 2020Reviewer(s) Assigned

Abstract

Environmental DNA (eDNA) has increasingly been used in the surveillance of imperiled aquatic species. Despite recent efforts in drawing genetic material from the environment, there are still pitfalls surrounding this field. We created a novel protocol which implements loop-mediated isothermal amplification (LAMP) to detect target DNA. Our methods are applied here in the surveillance of Etheostoma trisella, the Trispot Darter, a freshwater fish that recently received protection under the U.S. Endangered Species Act. Water samples (n = 256) were collected at sites in Alabama and Georgia to determine whether E. trisella still occupies historic sites and whether it inhabits previously unknown areas. We found evidence of E. trisella presence in 69 water samples while 187 were negative. Our LAMP protocol is capable of amplifying low quantities of DNA in the water, and is a robust technique for freshwater species surveillance. Verification of positive results from eDNA experiments is essential to confirm reaction reliability. Application of methods such as ours are necessary for recognizing species under threat that require conservation.