From metabarcoding to metaphylogeography: separating the wheat from the chaff

Metabarcoding is by now a well‐established method for biodiversity assessment in terrestrial, freshwater, and marine environments. Metabarcoding data sets are usually used for α‐ and β‐diversity estimates, that is, interspecies (or inter‐MOTU [molecular operational taxonomic unit]) patterns. However...

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Autores: Turon, Xavier, Antich, Adrià, Palacín Cabañas, Cruz, Præbel, Kim, Wangensteen Fuentes, Owen S. (Simon)
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2020
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:2445/170898
Acceso en línea:https://hdl.handle.net/2445/170898
Access Level:acceso abierto
Palabra clave:Marcadors genètics
Biodiversitat
Genetic markers
Biodiversity
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spelling From metabarcoding to metaphylogeography: separating the wheat from the chaffTuron, XavierAntich, AdriàPalacín Cabañas, CruzPræbel, KimWangensteen Fuentes, Owen S. (Simon)Marcadors genèticsBiodiversitatGenetic markersBiodiversityMetabarcoding is by now a well‐established method for biodiversity assessment in terrestrial, freshwater, and marine environments. Metabarcoding data sets are usually used for α‐ and β‐diversity estimates, that is, interspecies (or inter‐MOTU [molecular operational taxonomic unit]) patterns. However, the use of hypervariable metabarcoding markers may provide an enormous amount of intraspecies (intra‐MOTU) information mostly untapped so far. The use of cytochrome oxidase (COI) amplicons is gaining momentum in metabarcoding studies targeting eukaryote richness. COI has been for a long time the marker of choice in population genetics and phylogeographic studies. Therefore, COI metabarcoding data sets may be used to study intraspecies patterns and phylogeographic features for hundreds of species simultaneously, opening a new field that we suggest to name metaphylogeography. The main challenge for the implementation of this approach is the separation of erroneous sequences from true intra‐MOTU variation. Here, we develop a cleaning protocol based on changes in entropy of the different codon positions of the COI sequence, together with co‐occurrence patterns of sequences. Using a data set of community DNA from several benthic littoral communities in the Mediterranean and Atlantic seas, we first tested by simulation on a subset of sequences a two‐step cleaning approach consisting of a denoising step followed by a minimal abundance filtering. The procedure was then applied to the whole data set. We obtained a total of 563 MOTUs that were usable for phylogeographic inference. We used semiquantitative rank data instead of read abundances to perform AMOVAs and haplotype networks. Genetic variability was mainly concentrated within samples, but with an important between seas component as well. There were intergroup differences in the amount of variability between and within communities in each sea. For two species, the results could be compared with traditional Sanger sequence data available for the same zones, giving similar patterns. Our study shows that metabarcoding data can be used to infer intra‐ and interpopulation genetic variability of many species at a time, providing a new method with great potential for basic biogeography, connectivity and dispersal studies, and for the more applied fields of conservation genetics, invasion genetics, and design of protected areas.The Ecological Society of America2020202020202020info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion19 p.application/pdfhttps://hdl.handle.net/2445/170898Articles publicats en revistes (Biologia Evolutiva, Ecologia i Ciències Ambientals)reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésReproducció del document publicat a: https://doi.org/10.1002/eap.2036Ecological Applications, 2020, p. e02036https://doi.org/10.1002/eap.2036cc by-nc-nd (c) Turon et al., 2020http://creativecommons.org/licenses/by-nc-nd/3.0/es/info:eu-repo/semantics/openAccessoai:recercat.cat:2445/1708982026-05-29T05:05:01Z
dc.title.none.fl_str_mv From metabarcoding to metaphylogeography: separating the wheat from the chaff
title From metabarcoding to metaphylogeography: separating the wheat from the chaff
spellingShingle From metabarcoding to metaphylogeography: separating the wheat from the chaff
Turon, Xavier
Marcadors genètics
Biodiversitat
Genetic markers
Biodiversity
title_short From metabarcoding to metaphylogeography: separating the wheat from the chaff
title_full From metabarcoding to metaphylogeography: separating the wheat from the chaff
title_fullStr From metabarcoding to metaphylogeography: separating the wheat from the chaff
title_full_unstemmed From metabarcoding to metaphylogeography: separating the wheat from the chaff
title_sort From metabarcoding to metaphylogeography: separating the wheat from the chaff
dc.creator.none.fl_str_mv Turon, Xavier
Antich, Adrià
Palacín Cabañas, Cruz
Præbel, Kim
Wangensteen Fuentes, Owen S. (Simon)
author Turon, Xavier
author_facet Turon, Xavier
Antich, Adrià
Palacín Cabañas, Cruz
Præbel, Kim
Wangensteen Fuentes, Owen S. (Simon)
author_role author
author2 Antich, Adrià
Palacín Cabañas, Cruz
Præbel, Kim
Wangensteen Fuentes, Owen S. (Simon)
author2_role author
author
author
author
dc.subject.none.fl_str_mv Marcadors genètics
Biodiversitat
Genetic markers
Biodiversity
topic Marcadors genètics
Biodiversitat
Genetic markers
Biodiversity
description Metabarcoding is by now a well‐established method for biodiversity assessment in terrestrial, freshwater, and marine environments. Metabarcoding data sets are usually used for α‐ and β‐diversity estimates, that is, interspecies (or inter‐MOTU [molecular operational taxonomic unit]) patterns. However, the use of hypervariable metabarcoding markers may provide an enormous amount of intraspecies (intra‐MOTU) information mostly untapped so far. The use of cytochrome oxidase (COI) amplicons is gaining momentum in metabarcoding studies targeting eukaryote richness. COI has been for a long time the marker of choice in population genetics and phylogeographic studies. Therefore, COI metabarcoding data sets may be used to study intraspecies patterns and phylogeographic features for hundreds of species simultaneously, opening a new field that we suggest to name metaphylogeography. The main challenge for the implementation of this approach is the separation of erroneous sequences from true intra‐MOTU variation. Here, we develop a cleaning protocol based on changes in entropy of the different codon positions of the COI sequence, together with co‐occurrence patterns of sequences. Using a data set of community DNA from several benthic littoral communities in the Mediterranean and Atlantic seas, we first tested by simulation on a subset of sequences a two‐step cleaning approach consisting of a denoising step followed by a minimal abundance filtering. The procedure was then applied to the whole data set. We obtained a total of 563 MOTUs that were usable for phylogeographic inference. We used semiquantitative rank data instead of read abundances to perform AMOVAs and haplotype networks. Genetic variability was mainly concentrated within samples, but with an important between seas component as well. There were intergroup differences in the amount of variability between and within communities in each sea. For two species, the results could be compared with traditional Sanger sequence data available for the same zones, giving similar patterns. Our study shows that metabarcoding data can be used to infer intra‐ and interpopulation genetic variability of many species at a time, providing a new method with great potential for basic biogeography, connectivity and dispersal studies, and for the more applied fields of conservation genetics, invasion genetics, and design of protected areas.
publishDate 2020
dc.date.none.fl_str_mv 2020
2020
2020
2020
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/170898
url https://hdl.handle.net/2445/170898
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: https://doi.org/10.1002/eap.2036
Ecological Applications, 2020, p. e02036
https://doi.org/10.1002/eap.2036
dc.rights.none.fl_str_mv cc by-nc-nd (c) Turon et al., 2020
http://creativecommons.org/licenses/by-nc-nd/3.0/es/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc by-nc-nd (c) Turon et al., 2020
http://creativecommons.org/licenses/by-nc-nd/3.0/es/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 19 p.
application/pdf
dc.publisher.none.fl_str_mv The Ecological Society of America
publisher.none.fl_str_mv The Ecological Society of America
dc.source.none.fl_str_mv Articles publicats en revistes (Biologia Evolutiva, Ecologia i Ciències Ambientals)
reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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