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Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding

Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture...

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Autores principales: Evans, Nathan T., Olds, Brett P., Renshaw, Mark A., Turner, Cameron R., Li, Yiyuan, Jerde, Christopher L., Mahon, Andrew R., Pfrender, Michael E., Lamberti, Gary A., Lodge, David M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4744776/
https://www.ncbi.nlm.nih.gov/pubmed/26032773
http://dx.doi.org/10.1111/1755-0998.12433
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author Evans, Nathan T.
Olds, Brett P.
Renshaw, Mark A.
Turner, Cameron R.
Li, Yiyuan
Jerde, Christopher L.
Mahon, Andrew R.
Pfrender, Michael E.
Lamberti, Gary A.
Lodge, David M.
author_facet Evans, Nathan T.
Olds, Brett P.
Renshaw, Mark A.
Turner, Cameron R.
Li, Yiyuan
Jerde, Christopher L.
Mahon, Andrew R.
Pfrender, Michael E.
Lamberti, Gary A.
Lodge, David M.
author_sort Evans, Nathan T.
collection PubMed
description Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. Our objective was to determine whether environmental DNA (eDNA) sampling and metabarcoding analysis can be used to accurately measure species diversity in aquatic assemblages with differing structures. We manipulated the density and relative abundance of eight fish and one amphibian species in replicated 206‐L mesocosms. Environmental DNA was filtered from water samples, and six mitochondrial gene fragments were Illumina‐sequenced to measure species diversity in each mesocosm. Metabarcoding detected all nine species in all treatment replicates. Additionally, we found a modest, but positive relationship between species abundance and sequencing read abundance. Our results illustrate the potential for eDNA sampling and metabarcoding approaches to improve quantification of aquatic species diversity in natural environments and point the way towards using eDNA metabarcoding as an index of macrofaunal species abundance.
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spelling pubmed-47447762016-02-18 Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding Evans, Nathan T. Olds, Brett P. Renshaw, Mark A. Turner, Cameron R. Li, Yiyuan Jerde, Christopher L. Mahon, Andrew R. Pfrender, Michael E. Lamberti, Gary A. Lodge, David M. Mol Ecol Resour RESOURCE ARTICLES Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. Our objective was to determine whether environmental DNA (eDNA) sampling and metabarcoding analysis can be used to accurately measure species diversity in aquatic assemblages with differing structures. We manipulated the density and relative abundance of eight fish and one amphibian species in replicated 206‐L mesocosms. Environmental DNA was filtered from water samples, and six mitochondrial gene fragments were Illumina‐sequenced to measure species diversity in each mesocosm. Metabarcoding detected all nine species in all treatment replicates. Additionally, we found a modest, but positive relationship between species abundance and sequencing read abundance. Our results illustrate the potential for eDNA sampling and metabarcoding approaches to improve quantification of aquatic species diversity in natural environments and point the way towards using eDNA metabarcoding as an index of macrofaunal species abundance. John Wiley and Sons Inc. 2015-06-18 2016-01 /pmc/articles/PMC4744776/ /pubmed/26032773 http://dx.doi.org/10.1111/1755-0998.12433 Text en © 2015 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs (http://creativecommons.org/licenses/by-nc-nd/4.0/) License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.
spellingShingle RESOURCE ARTICLES
Evans, Nathan T.
Olds, Brett P.
Renshaw, Mark A.
Turner, Cameron R.
Li, Yiyuan
Jerde, Christopher L.
Mahon, Andrew R.
Pfrender, Michael E.
Lamberti, Gary A.
Lodge, David M.
Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding
title Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding
title_full Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding
title_fullStr Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding
title_full_unstemmed Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding
title_short Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding
title_sort quantification of mesocosm fish and amphibian species diversity via environmental dna metabarcoding
topic RESOURCE ARTICLES
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4744776/
https://www.ncbi.nlm.nih.gov/pubmed/26032773
http://dx.doi.org/10.1111/1755-0998.12433
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