Placing Environmental Next-Generation Sequencing Amplicons from Microbial Eukaryotes into a Phylogenetic Context

Correction: A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

(2014) Linda A. Amaral-Zettler et al.   PLoS One

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

(2013) William A. Bourland et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

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

(2013) Wilhelm Foissner et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Vampires in the oceans: predatory cercozoan amoebae in marine habitats

(2013) Cédric Berney et al.   ISME Journal

General Patterns of Diversity in Major Marine Microeukaryote Lineages

(2013) Massimo C. Pernice et al.   PLoS One

454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes

(2013) Elianne Egge et al.   PLoS One

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

(2012) Micah Dunthorn et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Effect of oxygen minimum zone formation on communities of marine protists

(2012) William Orsi et al.   ISME Journal

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

(2012) Ramiro Logares et al.   ISME Journal

Comparing the Hyper-Variable V4 and V9 Regions of the Small Subunit rDNA for Assessment of Ciliate Environmental Diversity

(2012) Micah Dunthorn et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Studies on the Genus Mesodinium II. Ultrastructural and Molecular Investigations of Five Marine Species Help Clarifying the Taxonomy

(2012) Lydia Garcia-Cuetos et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

The Revised Classification of Eukaryotes

(2012) Sina M. Adl et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay

(2012) Lucie Bittner et al.   MOLECULAR ECOLOGY

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

(2012) Q. Zhang et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Molecular Phylogeny of Tintinnid Ciliates (Tintinnida, Ciliophora)

(2012) Charles Bachy et al.   PROTIST

Meta-analyses of environmental sequence data identify anoxia and salinity as parameters shaping ciliate communities

(2012) Dominik Forster et al.   SYSTEMATICS AND BIODIVERSITY

Diversity and endemism of ciliates inhabiting Neotropical phytotelmata

(2012) Micah Dunthorn et al.   SYSTEMATICS AND BIODIVERSITY

Evaluating molecular support for and against the monophyly of the Peritrichia and phylogenetic relationships within the Mobilida (Ciliophora, Oligohymenophorea)

(2012) Zifeng Zhan et al.   ZOOLOGICA SCRIPTA

Morphology and phylogeny of a new woodruffiid ciliate, Etoschophrya inornata sp. n. (Ciliophora, Colpodea, Platyophryida), with an account on evolution of platyophryids

(2012) William A. Bourland et al.   ZOOLOGICA SCRIPTA

New haptophyte lineages and multiple independent colonizations of freshwater ecosystems

(2012) Marianne Simon et al.   Environmental Microbiology Reports

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

(2011) W. Orsi et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

(2011) William Orsi et al.   ISME Journal

Molecular Characterization and Revised Systematics of Microdiaphanosoma arcuatum (Ciliophora, Colpodea)

(2011) PABLO QUINTELA-ALONSO et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Intraclass Evolution and Classification of the Colpodea (Ciliophora)

(2011) WILHELM FOISSNER et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Eukaryotic Richness in the Abyss: Insights from Pyrotag Sequencing

(2011) Jan Pawlowski et al.   PLoS One

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

(2011) Béatrice Lecroq et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

JAGUC — A SOFTWARE PACKAGE FOR ENVIRONMENTAL DIVERSITY ANALYSES

(2011) MARKUS E. NEBEL et al.   Journal of Bioinformatics and Computational Biology

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

(2010) Anke Behnke et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2010) Peter Vďačný et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Spatio-temporal variations in protistan communities along an O2/H2S gradient in the anoxic Framvaren Fjord (Norway)

(2010) Anke Behnke et al.   FEMS MICROBIOLOGY ECOLOGY

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

(2010) Jon Bråte et al.   ISME Journal

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

(2010) WILLIAM A. BOURLAND et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Short rDNA Barcodes for Species Identification in Foraminifera

(2010) JAN PAWLOWSKI et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty

(2010) O. Penn et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2010) VIOLA NOLTE et al.   MOLECULAR ECOLOGY

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

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

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

(2010) Zhenzhen Yi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2010) Angélique Gobet et al.   NUCLEIC ACIDS RESEARCH

GUIDANCE: a web server for assessing alignment confidence scores

(2010) O. Penn et al.   NUCLEIC ACIDS RESEARCH

Expanding Character Sampling for Ciliate Phylogenetic Inference Using Mitochondrial SSU-rDNA as a Molecular Marker

(2010) Micah Dunthorn et al.   PROTIST

Highly Diverse and Seasonally Dynamic Protist Community in a Pristine Peat Bog

(2010) Enrique Lara et al.   PROTIST

Secretive ciliates and putative asexuality in microbial eukaryotes

(2010) Micah Dunthorn et al.   TRENDS IN MICROBIOLOGY

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

(2010) Markus Nebel et al.   Environmental Microbiology Reports

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

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

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

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Rapid diversification of mating systems in ciliates

(2009) SUJAL S. PHADKE et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

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

(2009) Thorsten Stoeck et al.   BMC BIOLOGY

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

(2009) Julie A. Huber et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2009) M. Miao et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

(2009) M. Dunthorn et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Morphological and Molecular Characterization of a New Protist Family, Sandmanniellidae n. fam. (Ciliophora, Colpodea), with Description ofSandmanniella terricolan. g., n. sp. from the Chobe Floodplain in Botswana

(2009) WILHELM FOISSNER et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Small Subunit rRNA Phylogenies Show that the Class Nassophorea is Not Monophyletic (Phylum Ciliophora)

(2009) JUN GONG et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

New Insights into the Diversity of Marine Picoeukaryotes

(2009) Fabrice Not et al.   PLoS One

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

(2009) F. Scheckenbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Infrequent marine–freshwater transitions in the microbial world

(2009) Ramiro Logares et al.   TRENDS IN MICROBIOLOGY

Unveiling new microbial eukaryotes in the surface ocean

(2008) Ramon Massana et al.   CURRENT OPINION IN MICROBIOLOGY

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

(2007) Micah Dunthorn et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION