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A fecal sequel: Testing the limits of a genetic assay for bat species identification

DNA metabarcoding assays are powerful tools for delving into the DNA in wildlife feces, giving unprecedented ability to detect species, understand natural history, and identify pathogens for a range of applications in management, conservation, and research. Next-generation sequencing technology is d...

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Autores principales: Walker, Faith M., Tobin, Abby, Simmons, Nancy B., Sobek, Colin J., Sanchez, Daniel E., Chambers, Carol L., Fofanov, Viacheslav Y.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6855431/
https://www.ncbi.nlm.nih.gov/pubmed/31725795
http://dx.doi.org/10.1371/journal.pone.0224969
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author Walker, Faith M.
Tobin, Abby
Simmons, Nancy B.
Sobek, Colin J.
Sanchez, Daniel E.
Chambers, Carol L.
Fofanov, Viacheslav Y.
author_facet Walker, Faith M.
Tobin, Abby
Simmons, Nancy B.
Sobek, Colin J.
Sanchez, Daniel E.
Chambers, Carol L.
Fofanov, Viacheslav Y.
author_sort Walker, Faith M.
collection PubMed
description DNA metabarcoding assays are powerful tools for delving into the DNA in wildlife feces, giving unprecedented ability to detect species, understand natural history, and identify pathogens for a range of applications in management, conservation, and research. Next-generation sequencing technology is developing rapidly, which makes it especially important that predictability and reproducibility of DNA metabarcoding assays are explored together with the post-depositional ecology of the target taxon’s fecal DNA. Here, we defined the constraints of an assay called ‘Species from Feces’ used by government agencies, research groups, and non-governmental organizations to identify bat species from guano. We tested assay sensitivity by examining how time and humidity affect the ability to recover and successfully sequence DNA in guano, assessing whether a fecal pellet from a rare bat species could be detected in a background of feces from other bat species, and evaluating the efficacy of Species from Feces as a survey tool for bat roosts in temperate and tropical areas. We found that the assay performs well with feces over two years old in dry, cool environments, and fails by 12 months at 100% relative humidity. We also found that it reliably identifies rare DNA, has great utility for surveying roosts in temperate and tropical regions, and detects more bat species than do visual surveys. We attribute the success of Species from Feces to characteristics of the assay paired with application in taxa that are particularly well-suited for fecal DNA survival. In a time of rapid evolution of DNA metabarcoding approaches and their use with feces, this study illustrates the strengths and limitations of applied assays.
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spelling pubmed-68554312019-11-22 A fecal sequel: Testing the limits of a genetic assay for bat species identification Walker, Faith M. Tobin, Abby Simmons, Nancy B. Sobek, Colin J. Sanchez, Daniel E. Chambers, Carol L. Fofanov, Viacheslav Y. PLoS One Research Article DNA metabarcoding assays are powerful tools for delving into the DNA in wildlife feces, giving unprecedented ability to detect species, understand natural history, and identify pathogens for a range of applications in management, conservation, and research. Next-generation sequencing technology is developing rapidly, which makes it especially important that predictability and reproducibility of DNA metabarcoding assays are explored together with the post-depositional ecology of the target taxon’s fecal DNA. Here, we defined the constraints of an assay called ‘Species from Feces’ used by government agencies, research groups, and non-governmental organizations to identify bat species from guano. We tested assay sensitivity by examining how time and humidity affect the ability to recover and successfully sequence DNA in guano, assessing whether a fecal pellet from a rare bat species could be detected in a background of feces from other bat species, and evaluating the efficacy of Species from Feces as a survey tool for bat roosts in temperate and tropical areas. We found that the assay performs well with feces over two years old in dry, cool environments, and fails by 12 months at 100% relative humidity. We also found that it reliably identifies rare DNA, has great utility for surveying roosts in temperate and tropical regions, and detects more bat species than do visual surveys. We attribute the success of Species from Feces to characteristics of the assay paired with application in taxa that are particularly well-suited for fecal DNA survival. In a time of rapid evolution of DNA metabarcoding approaches and their use with feces, this study illustrates the strengths and limitations of applied assays. Public Library of Science 2019-11-14 /pmc/articles/PMC6855431/ /pubmed/31725795 http://dx.doi.org/10.1371/journal.pone.0224969 Text en © 2019 Walker et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Walker, Faith M.
Tobin, Abby
Simmons, Nancy B.
Sobek, Colin J.
Sanchez, Daniel E.
Chambers, Carol L.
Fofanov, Viacheslav Y.
A fecal sequel: Testing the limits of a genetic assay for bat species identification
title A fecal sequel: Testing the limits of a genetic assay for bat species identification
title_full A fecal sequel: Testing the limits of a genetic assay for bat species identification
title_fullStr A fecal sequel: Testing the limits of a genetic assay for bat species identification
title_full_unstemmed A fecal sequel: Testing the limits of a genetic assay for bat species identification
title_short A fecal sequel: Testing the limits of a genetic assay for bat species identification
title_sort fecal sequel: testing the limits of a genetic assay for bat species identification
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6855431/
https://www.ncbi.nlm.nih.gov/pubmed/31725795
http://dx.doi.org/10.1371/journal.pone.0224969
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