Por favor, use este identificador para citar o enlazar a este item:
http://hdl.handle.net/10261/130332
COMPARTIR / EXPORTAR:
SHARE CORE BASE | |
Visualizar otros formatos: MARC | Dublin Core | RDF | ORE | MODS | METS | DIDL | DATACITE | |
Campo DC | Valor | Lengua/Idioma |
---|---|---|
dc.contributor.author | Dunthorn, Micah | - |
dc.contributor.author | Massana, Ramon | - |
dc.contributor.author | BioMarKs Consortium | - |
dc.contributor.author | Stoeck, Thorsten | - |
dc.date.issued | 2014-01 | - |
dc.identifier | doi: 10.1093/molbev/msu055 | - |
dc.identifier | issn: 0737-4038 | - |
dc.identifier | e-issn: 1537-1719 | - |
dc.identifier.citation | Molecular Biology and Evolution 31(4): 993-1009 (2014) | - |
dc.identifier.uri | http://hdl.handle.net/10261/130332 | - |
dc.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 | - |
dc.description.abstract | Nucleotide 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 Author | - |
dc.description.sponsorship | This 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. | - |
dc.publisher | Society for Molecular Biology and Evolution | - |
dc.rights | openAccess | - |
dc.subject | Ciliophora | - |
dc.subject | Colpodea | - |
dc.subject | Marine-freshwater transitions | - |
dc.subject | Phylogenetics | - |
dc.subject | SSU rDNA | - |
dc.subject | SSU | - |
dc.subject | rDNA | - |
dc.title | Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context | - |
dc.type | artículo | - |
dc.identifier.doi | 10.1093/molbev/msu055 | - |
dc.relation.publisherversion | https://doi.org/10.1093/molbev/msu055 | - |
dc.date.updated | 2016-03-21T13:48:23Z | - |
dc.description.version | Peer Reviewed | - |
dc.language.rfc3066 | eng | - |
dc.contributor.funder | German Research Foundation | - |
dc.relation.csic | Sí | - |
dc.identifier.funder | http://dx.doi.org/10.13039/501100001659 | es_ES |
dc.type.coar | http://purl.org/coar/resource_type/c_6501 | es_ES |
item.cerifentitytype | Publications | - |
item.grantfulltext | open | - |
item.openairecristype | http://purl.org/coar/resource_type/c_18cf | - |
item.fulltext | With Fulltext | - |
item.openairetype | artículo | - |
Aparece en las colecciones: | (ICM) Artículos |
Ficheros en este ítem:
Fichero | Descripción | Tamaño | Formato | |
---|---|---|---|---|
Dunthorn_et_al_2014.pdf | 632,09 kB | Adobe PDF | Visualizar/Abrir |
CORE Recommender
SCOPUSTM
Citations
78
checked on 24-abr-2024
WEB OF SCIENCETM
Citations
76
checked on 21-feb-2024
Page view(s)
203
checked on 24-abr-2024
Download(s)
157
checked on 24-abr-2024
Google ScholarTM
Check
Altmetric
Altmetric
NOTA: Los ítems de Digital.CSIC están protegidos por copyright, con todos los derechos reservados, a menos que se indique lo contrario.