English   español  
Please use this identifier to cite or link to this item: http://hdl.handle.net/10261/130332
Share/Impact:
Statistics
logo share SHARE logo core CORE   Add this article to your Mendeley library MendeleyBASE

Visualizar otros formatos: MARC | Dublin Core | RDF | ORE | MODS | METS | DIDL
Exportar a otros formatos:
Title

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

AuthorsDunthorn, Micah; Massana, Ramon ; BioMarKs Consortium; Stoeck, Thorsten
KeywordsCiliophora
Colpodea
Marine-freshwater transitions
Phylogenetics
SSU rDNA
SSU
rDNA
Issue DateJan-2014
PublisherSociety for Molecular Biology and Evolution
CitationMolecular Biology and Evolution 31(4): 993-1009 (2014)
AbstractNucleotide 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
DescriptionDunthorn, Micah ... et al.-- 17 pages, 4 figures, 3 tables, 1 appendix, supplementary material http://mbe.oxfordjournals.org/content/31/4/993/suppl/DC1
Publisher version (URL)http://dx.doi.org/10.1093/molbev/msu055
URIhttp://hdl.handle.net/10261/130332
DOI10.1093/molbev/msu055
Identifiersdoi: 10.1093/molbev/msu055
issn: 0737-4038
e-issn: 1537-1719
Appears in Collections:(ICM) Artículos
Files in This Item:
There are no files associated with this item.
Show full item record
Review this work
 

Related articles:


WARNING: Items in Digital.CSIC are protected by copyright, with all rights reserved, unless otherwise indicated.