(Q45734771)

15 December 2017

title

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

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15 December 2017

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15 December 2017

8

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15 December 2017

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Micah Dunthorn

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15 December 2017

7

Colomban de Vargas

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15 December 2017

12

Thorsten Stoeck

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15 December 2017

6

Sarah Romac

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15 December 2017

11

Frank Kauff

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15 December 2017

Johannes Otto

2

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15 December 2017

Simon A Berger

3

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15 December 2017

Alexandros Stamatakis

4

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15 December 2017

Biomarks Consortium

9

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15 December 2017

Alexandra Stock

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15 December 2017

publication date

27 January 2014

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Molecular Biology and Evolution

15 December 2017

published in

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15 December 2017

volume

31

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15 December 2017

issue

4

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15 December 2017

page(s)

993-1009

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The Revised Classification of Eukaryotes

15 December 2017

cites work

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https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Phylogeny of the order Choreotrichida (Ciliophora, Spirotricha, Oligotrichea) as inferred from morphology, ultrastructure, ontogenesis, and SSrRNA gene sequences

21 January 2018

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Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Molecular phylogeny of tintinnid ciliates (Tintinnida, Ciliophora).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Spatio-temporal variations in protistan communities along an O/HS gradient in the anoxic Framvaren Fjord (Norway).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Vampires in the oceans: predatory cercozoan amoebae in marine habitats

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Morphology, morphometrics, and molecular characterization of Bryophrya gemmea n. sp. (Ciliophora, Colpodea): implications for the phylogeny and evolutionary scenario for the formation of oral ciliature in the order Colpodida.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Morphology and phylogeny of Bryophryoides ocellatus n. g., n. sp. (Ciliophora, Colpodea) from in situ soil percolates of Idaho, U.S.A.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Biopython: freely available Python tools for computational molecular biology and bioinformatics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Phylogenetic placement of the Cyrtolophosididae Stokes, 1888 (Ciliophora; Colpodea) and neotypification of Aristerostoma marinum Kahl, 1931.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Molecular phylogenetic analysis of class Colpodea (phylum Ciliophora) using broad taxon sampling

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Expanding character sampling for ciliate phylogenetic inference using mitochondrial SSU-rDNA as a molecular marker

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Secretive ciliates and putative asexuality in microbial eukaryotes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Congruence and indifference between two molecular markers for understanding oral evolution in the Marynidae sensu lato (Ciliophora, Colpodea)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Comparing the hyper-variable V4 and V9 regions of the small subunit rDNA for assessment of ciliate environmental diversity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Profile hidden Markov models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

The diversity of microbes: resurgence of the phenotype

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Global dispersal of free-living microbial eukaryote species

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Multiple cosmopolitan ecotypes within a microbial eukaryote morphospecies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

New SSU-rDNA sequences for eleven colpodeans (Ciliophora, Colpodea) and description of Apocyrtolophosis nov. gen.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Morphological and molecular characterization of a new protist family, Sandmanniellidae n. fam. (Ciliophora, Colpodea), with description of Sandmanniella terricola n. g., n. sp. from the Chobe floodplain in Botswana

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Intraclass evolution and classification of the Colpodea (Ciliophora).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Studies on the genus Mesodinium II. Ultrastructural and molecular investigations of five marine species help clarifying the taxonomy

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Small subunit rRNA phylogenies show that the class nassophorea is not monophyletic (Phylum Ciliophora).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Freshwater Foraminiferans Revealed by Analysis of Environmental DNA Samples

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Highly divergent SSU rRNA genes found in the marine ciliates Myrionecta rubra and Mesodinium pulex.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Cultivation-independent analysis reveals a shift in ciliate 18S rRNA gene diversity in a polycyclic aromatic hydrocarbon-polluted soil

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Highly diverse and seasonally dynamic protist community in a pristine peat bog.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Phylogenetic position of Sorogena stoianovitchae and relationships within the class Colpodea (Ciliophora) based on SSU rDNA sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Infrequent marine-freshwater transitions in the microbial world.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

SOAP, cleaning multiple alignments from unstable blocks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Unveiling new microbial eukaryotes in the surface ocean

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Caryotricha minuta (Xu et al., 2008) nov. comb., a unique marine ciliate (Protista, Ciliophora, Spirotrichea), with phylogenetic analysis of the ambiguous genus Caryotricha inferred from the small-subunit rRNA gene sequence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Delimiting operational taxonomic units for assessing ciliate environmental diversity using small-subunit rRNA gene sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

JAGUC--a software package for environmental diversity analyses.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

New insights into the diversity of marine picoeukaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Class Cariacotrichea, a novel ciliate taxon from the anoxic Cariaco Basin, Venezuela.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Protistan microbial observatory in the Cariaco Basin, Caribbean. II. Habitat specialization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Effect of oxygen minimum zone formation on communities of marine protists

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Eukaryotic richness in the abyss: insights from pyrotag sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Short rDNA barcodes for species identification in foraminifera

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

GUIDANCE: a web server for assessing alignment confidence scores.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

An alignment confidence score capturing robustness to guide tree uncertainty

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

General patterns of diversity in major marine microeukaryote lineages

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Molecular characterization and revised systematics of Microdiaphanosoma arcuatum (Ciliophora, Colpodea).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

The molecular diversity of freshwater picoeukaryotes from an oligotrophic lake reveals diverse, distinctive and globally dispersed lineages

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

MrBayes 3: Bayesian phylogenetic inference under mixed models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Large-scale patterns in biodiversity of microbial eukaryotes from the abyssal sea floor

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Molecular phylogeny of the Heterotrichea (Ciliophora, Postciliodesmatophora) based on small subunit rRNA gene sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

New haptophyte lineages and multiple independent colonizations of freshwater ecosystems

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Microbial diversity in the deep sea and the underexplored "rare biosphere"

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Novel eukaryotes from the permanently anoxic Cariaco Basin (Caribbean Sea).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

A molecular approach to identify active microbes in environmental eukaryote clone libraries

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Molecular phylogeny of litostome ciliates (Ciliophora, Litostomatea) with emphasis on free-living haptorian genera

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Molecular phylogenetics of subclass Peritrichia (Ciliophora: Oligohymenophorea) based on expanded analyses of 18S rRNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Molecular and morphological evidence for a sister group relationship of the classes Armophorea and Litostomatea (Ciliophora, Intramacronucleata, Lamellicorticata infraphyl. nov.), with an account on basal litostomateans.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

The European ribosomal RNA database

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Increasing taxon sampling using both unidentified environmental sequences and identified cultures improves phylogenetic inference in the Prorodontida (Ciliophora, Prostomatea).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Genetic diversity of goniomonads: an ancient divergence between marine and freshwater species

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

Insights into the phylogeny of systematically controversial haptorian ciliates (Ciliophora, Litostomatea) based on multigene analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSU055

21 January 2018

Identifiers

DOI

10.1093/MOLBEV/MSU055

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15 December 2017

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