Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context

Dunthorn, Micah ... et al.-- 17 pages, 4 figures, 3 tables, 1 appendix, supplementary material http://mbe.oxfordjournals.org/content/31/4/993/suppl/DC1

Detalles Bibliográficos
Autores: Dunthorn, Micah, Massana, Ramon, BioMarKs Consortium, Stoeck, Thorsten
Tipo de recurso: artículo
Fecha de publicación:2014
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/130332
Acceso en línea:http://hdl.handle.net/10261/130332
Access Level:acceso abierto
Palabra clave:Ciliophora
Colpodea
Marine-freshwater transitions
Phylogenetics
SSU rDNA
SSU
rDNA
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spelling Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic contextDunthorn, MicahMassana, RamonBioMarKs ConsortiumStoeck, ThorstenCiliophoraColpodeaMarine-freshwater transitionsPhylogeneticsSSU rDNASSUrDNADunthorn, Micah ... et al.-- 17 pages, 4 figures, 3 tables, 1 appendix, supplementary material http://mbe.oxfordjournals.org/content/31/4/993/suppl/DC1Nucleotide positions in the hypervariable V4 and V9 regions of the small subunit (SSU)-rDNA locus are normally difficult to align and are usually removed before standard phylogenetic analyses. Yet, with next-generation sequencing data, amplicons of these regions are all that are available to answer ecological and evolutionary questions that rely on phylogenetic inferences. With ciliates, we asked how inclusion of the V4 or V9 regions, regardless of alignment quality, affects tree topologies using distinct phylogenetic methods (including PairDist that is introduced here). Results show that the best approach is to place V4 amplicons into an alignment of full-length Sanger SSU-rDNA sequences and to infer the phylogenetic tree with RAxML. A sliding window algorithm as implemented in RAxML shows, though, that not all nucleotide positions in the V4 region are better than V9 at inferring the ciliate tree. With this approach and an ancestral-state reconstruction, we use V4 amplicons from European nearshore sampling sites to infer that rather than being primarily terrestrial and freshwater, colpodean ciliates may have repeatedly transitioned from terrestrial/freshwater to marine environments. © 2014 The AuthorThis work was supported by the Deutsche Forschungsgemeinschaft (DFG, grant DU1319/1-1) to M.D.; DFG (grant STA/860-3) to A.Sta.; European Funding Agencies from the ERAnet program BiodivERsA under the BioMarKs project (grant 2008-6530) to C.dV, T.S., and the BioMarKS Consortium; Carl-Zeiss postdoc grant to A.Sto.; and DFG (grants STO414/3-1 and STO414/3-2) to T.S.Peer ReviewedSociety for Molecular Biology and EvolutionGerman Research FoundationConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]20142016info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501http://hdl.handle.net/10261/130332reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttps://doi.org/10.1093/molbev/msu055Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/1303322026-05-22T06:33:51Z
dc.title.none.fl_str_mv Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context
title Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context
spellingShingle Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context
Dunthorn, Micah
Ciliophora
Colpodea
Marine-freshwater transitions
Phylogenetics
SSU rDNA
SSU
rDNA
title_short Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context
title_full Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context
title_fullStr Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context
title_full_unstemmed Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context
title_sort Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context
dc.creator.none.fl_str_mv Dunthorn, Micah
Massana, Ramon
BioMarKs Consortium
Stoeck, Thorsten
author Dunthorn, Micah
author_facet Dunthorn, Micah
Massana, Ramon
BioMarKs Consortium
Stoeck, Thorsten
author_role author
author2 Massana, Ramon
BioMarKs Consortium
Stoeck, Thorsten
author2_role author
author
author
dc.contributor.none.fl_str_mv German Research Foundation
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Ciliophora
Colpodea
Marine-freshwater transitions
Phylogenetics
SSU rDNA
SSU
rDNA
topic Ciliophora
Colpodea
Marine-freshwater transitions
Phylogenetics
SSU rDNA
SSU
rDNA
description Dunthorn, Micah ... et al.-- 17 pages, 4 figures, 3 tables, 1 appendix, supplementary material http://mbe.oxfordjournals.org/content/31/4/993/suppl/DC1
publishDate 2014
dc.date.none.fl_str_mv 2014
2016
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/130332
url http://hdl.handle.net/10261/130332
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv https://doi.org/10.1093/molbev/msu055
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Society for Molecular Biology and Evolution
publisher.none.fl_str_mv Society for Molecular Biology and Evolution
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
_version_ 1869406854943080448
score 15,811543

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