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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...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2015
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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. |
format | Online Article Text |
id | pubmed-4744776 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
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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