Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

1. Traditional biodiversity assessment is costly in time, money and taxonomic expertise. Moreover, data are frequently collected in ways (e.g. visual bird lists) that are unsuitable for auditing by neutral parties, which is necessary for dispute resolution. 2. We present protocols for the extraction...

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Detalles Bibliográficos
Autores: Yu, Douglas W., Ji, Yinqiu, Emerson, Brent C., Wang, Xiaoyang, Ye, Chengxi, Yang, Chunyan, Ding, Zhaoli
Tipo de recurso: artículo
Estado:Versión aceptada para publicación
Fecha de publicación:2012
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/193380
Acceso en línea:http://hdl.handle.net/10261/193380
Access Level:acceso abierto
Palabra clave:High‐throughput sequencing metagenetics
OTU picking
Metagenomics
DNA barcoding
454 Genome Sequencer FLX System
Phylogenetic diversity
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spelling Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoringYu, Douglas W.Ji, YinqiuEmerson, Brent C.Wang, XiaoyangYe, ChengxiYang, ChunyanDing, ZhaoliHigh‐throughput sequencing metageneticsOTU pickingMetagenomicsDNA barcoding454 Genome Sequencer FLX SystemPhylogenetic diversity1. Traditional biodiversity assessment is costly in time, money and taxonomic expertise. Moreover, data are frequently collected in ways (e.g. visual bird lists) that are unsuitable for auditing by neutral parties, which is necessary for dispute resolution. 2. We present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. The protocols combine mass trapping of arthropods, mass‐PCR amplification of the COI barcode gene, pyrosequencing and bioinformatic analysis, which together we call ‘metabarcoding’. 3. We construct seven communities of arthropods (mostly insects) and show that it is possible to recover a substantial proportion of the original taxonomic information. We further demonstrate, for the first time, that metabarcoding allows for the precise estimation of pairwise community dissimilarity (beta diversity) and within‐community phylogenetic diversity (alpha diversity), despite the inevitable loss of taxonomic information inherent to metabarcoding. 4. Alpha and beta diversity metrics are the raw materials of ecology and the environmental sciences, facilitating assessment of the state of the environment with a broad and efficient measure of biodiversity.For support, we thank Yunnan Province (20080A001), the Chinese Academy of Sciences (0902281081, KSCX2‐YW‐Z‐1027), the National Natural Science Foundation of China (31170498), and the University of East Anglia.Peer ReviewedBritish Ecological SocietyChinese Academy of SciencesNational Natural Science Foundation of ChinaConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2019201920122019info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Postprintinfo:eu-repo/semantics/acceptedVersionhttp://hdl.handle.net/10261/193380reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttps://doi.org/10.1111/j.2041-210X.2012.00198.xSíinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/1933802026-05-22T06:33:51Z
dc.title.none.fl_str_mv Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring
title Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring
spellingShingle Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring
Yu, Douglas W.
High‐throughput sequencing metagenetics
OTU picking
Metagenomics
DNA barcoding
454 Genome Sequencer FLX System
Phylogenetic diversity
title_short Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring
title_full Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring
title_fullStr Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring
title_full_unstemmed Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring
title_sort Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring
dc.creator.none.fl_str_mv Yu, Douglas W.
Ji, Yinqiu
Emerson, Brent C.
Wang, Xiaoyang
Ye, Chengxi
Yang, Chunyan
Ding, Zhaoli
author Yu, Douglas W.
author_facet Yu, Douglas W.
Ji, Yinqiu
Emerson, Brent C.
Wang, Xiaoyang
Ye, Chengxi
Yang, Chunyan
Ding, Zhaoli
author_role author
author2 Ji, Yinqiu
Emerson, Brent C.
Wang, Xiaoyang
Ye, Chengxi
Yang, Chunyan
Ding, Zhaoli
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Chinese Academy of Sciences
National Natural Science Foundation of China
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv High‐throughput sequencing metagenetics
OTU picking
Metagenomics
DNA barcoding
454 Genome Sequencer FLX System
Phylogenetic diversity
topic High‐throughput sequencing metagenetics
OTU picking
Metagenomics
DNA barcoding
454 Genome Sequencer FLX System
Phylogenetic diversity
description 1. Traditional biodiversity assessment is costly in time, money and taxonomic expertise. Moreover, data are frequently collected in ways (e.g. visual bird lists) that are unsuitable for auditing by neutral parties, which is necessary for dispute resolution. 2. We present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. The protocols combine mass trapping of arthropods, mass‐PCR amplification of the COI barcode gene, pyrosequencing and bioinformatic analysis, which together we call ‘metabarcoding’. 3. We construct seven communities of arthropods (mostly insects) and show that it is possible to recover a substantial proportion of the original taxonomic information. We further demonstrate, for the first time, that metabarcoding allows for the precise estimation of pairwise community dissimilarity (beta diversity) and within‐community phylogenetic diversity (alpha diversity), despite the inevitable loss of taxonomic information inherent to metabarcoding. 4. Alpha and beta diversity metrics are the raw materials of ecology and the environmental sciences, facilitating assessment of the state of the environment with a broad and efficient measure of biodiversity.
publishDate 2012
dc.date.none.fl_str_mv 2012
2019
2019
2019
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Postprint
info:eu-repo/semantics/acceptedVersion
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/193380
url http://hdl.handle.net/10261/193380
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv https://doi.org/10.1111/j.2041-210X.2012.00198.x
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv British Ecological Society
publisher.none.fl_str_mv British Ecological Society
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.81155

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