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Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1006/tpbi.2002.1593openalex-snapshot
Ancient Phylogenetic Relationships
inferredcites →https://doi.org/10.1007/978-1-59745-581-7_1openalex-snapshot
From Gene-Scale to Genome-Scale Phylogenetics: the Data Flood In, but the Challenges Remain
inferredcites →https://doi.org/10.1007/978-3-642-60458-4_21openalex-snapshot
Molecular Systematics: 1994–1995
inferredcites →https://doi.org/10.1007/s00018-005-4539-zopenalex-snapshot
Lateral gene transfer in eukaryotes
inferredcites →https://doi.org/10.1007/s00239-002-2424-zopenalex-snapshot
Phylogeny of Choanozoa, Apusozoa, and Other Protozoa and Early Eukaryote Megaevolution
inferredcites →https://doi.org/10.1007/s002940050241openalex-snapshot
The evolution of the Calvin cycle from prokaryotic to eukaryotic chromosomes: a case study of functional redundancy in ancient pathways through endosymbiosis
inferredcites →https://doi.org/10.1016/0303-2647(81)90050-2openalex-snapshot
Eukaryote kingdoms: Seven or nine?
inferredcites →https://doi.org/10.1016/0378-1119(88)90066-2openalex-snapshot
The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions
inferredcites →https://doi.org/10.1016/j.cub.2004.08.038openalex-snapshot
The real ‘kingdoms’ of eukaryotes
inferredcites →https://doi.org/10.1016/j.cub.2005.06.040openalex-snapshot
Monophyly of Primary Photosynthetic Eukaryotes: Green Plants, Red Algae, and Glaucophytes
inferredcites →https://doi.org/10.1016/j.cub.2007.07.036openalex-snapshot
Toward Resolving the Eukaryotic Tree: The Phylogenetic Positions of Jakobids and Cercozoans
inferredcites →https://doi.org/10.1016/j.cub.2008.05.042openalex-snapshot
Multiple Genes of Apparent Algal Origin Suggest Ciliates May Once Have Been Photosynthetic
inferredcites →https://doi.org/10.1016/j.cub.2008.11.067openalex-snapshot
The Puzzle of Plastid Evolution
inferredcites →https://doi.org/10.1016/j.cub.2008.12.032openalex-snapshot
Evolution: Revisiting the Root of the Eukaryote Tree
inferredcites →https://doi.org/10.1016/j.cub.2009.02.043openalex-snapshot
Another acquisition of a primary photosynthetic organelle is underway in Paulinella chromatophora
inferredcites →https://doi.org/10.1016/j.ejop.2007.12.001openalex-snapshot
Ultrastructure and molecular phylogeny of Stephanopogon minuta: An enigmatic microeukaryote from marine interstitial environments
inferredcites →https://doi.org/10.1016/j.gene.2007.07.023openalex-snapshot
Genome history in the symbiotic hybrid Euglena gracilis
inferredcites →https://doi.org/10.1016/j.protis.2004.12.003openalex-snapshot
The Katablepharids are a Distant Sister Group of the Cryptophyta: A Proposal for Katablepharidophyta Divisio Nova/Kathablepharida Phylum Novum Based on SSU rDNA and Beta-Tubulin Phylogeny
inferredcites →https://doi.org/10.1016/j.protis.2008.07.002openalex-snapshot
Phylogeny of Novel Naked Filose and Reticulose Cercozoa: Granofilosea cl. n. and Proteomyxidea Revised
inferredcites →https://doi.org/10.1016/j.tig.2006.02.003openalex-snapshot
Phylogenomics: the beginning of incongruence?
inferredcites →https://doi.org/10.1016/j.tree.2008.02.004openalex-snapshot
The eukaryotic tree of life: endosymbiosis takes its TOL
inferredcites →https://doi.org/10.1016/j.tree.2008.11.003openalex-snapshot
Chromalveolate plastids: direct descent or multiple endosymbioses?
inferredcites →https://doi.org/10.1016/j.zool.2005.09.006openalex-snapshot
Magic bullets and golden rules: Data sampling in molecular phylogenetics
inferredcites →https://doi.org/10.1016/s0168-9525(98)01494-2openalex-snapshot
You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes
inferredcites →https://doi.org/10.1016/s0960-9822(03)00602-xopenalex-snapshot
The root of the eukaryote tree pinpointed
inferredcites →https://doi.org/10.1046/j.1529-8817.2001.01126.xopenalex-snapshot
PRIMARY AND SECONDARY ENDOSYMBIOSIS AND THE ORIGIN OF PLASTIDS
inferredcites →https://doi.org/10.1046/j.1529-8817.2003.02082.xopenalex-snapshot
THE MESOZOIC RADIATION OF EUKARYOTIC ALGAE: THE PORTABLE PLASTID HYPOTHESIS1
inferredcites →https://doi.org/10.1046/j.1529-8817.2003.02185.xopenalex-snapshot
THE SYMBIOTIC BIRTH AND SPREAD OF PLASTIDS: HOW MANY TIMES AND WHODUNIT?
inferredcites →https://doi.org/10.1073/pnas.0806251106openalex-snapshot
Simultaneous Bayesian gene tree reconstruction and reconciliation analysis
inferredcites →https://doi.org/10.1073/pnas.0807880106openalex-snapshot
Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”
inferredcites →https://doi.org/10.1073/pnas.182432999openalex-snapshot
Evolutionary analysis of Arabidopsis , cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus
inferredcites →https://doi.org/10.1073/pnas.242379899openalex-snapshot
The single, ancient origin of chromist plastids
inferredcites →https://doi.org/10.1073/pnas.96.2.580openalex-snapshot
Microsporidia are related to Fungi: Evidence from the largest subunit of RNA polymerase II and other proteins
inferredcites →https://doi.org/10.1080/10635150290069913openalex-snapshot
An Approximately Unbiased Test of Phylogenetic Tree Selection
inferredcites →https://doi.org/10.1080/10635150290102339openalex-snapshot
Increased Taxon Sampling Greatly Reduces Phylogenetic Error
inferredcites →https://doi.org/10.1080/10635150390132911openalex-snapshot
Is Sparse Taxon Sampling a Problem for Phylogenetic Inference?
inferredcites →https://doi.org/10.1080/10635150500234583openalex-snapshot
Can Incomplete Taxa Rescue Phylogenetic Analyses from Long-Branch Attraction?
inferredcites →https://doi.org/10.1080/10635150500234609openalex-snapshot
An Empirical Assessment of Long-Branch Attraction Artefacts in Deep Eukaryotic Phylogenomics
inferredcites →https://doi.org/10.1080/10635150600697358openalex-snapshot
Resolution of Phylogenetic Conflict in Large Data Sets by Increased Taxon Sampling
inferredcites →https://doi.org/10.1080/10635150701397643openalex-snapshot
Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies
inferredcites →https://doi.org/10.1080/10635150701472164openalex-snapshot
Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments
inferredcites →https://doi.org/10.1080/10635150801910436openalex-snapshot
Testing Congruence in Phylogenomic Analysis
inferredcites →https://doi.org/10.1080/10635150802429642openalex-snapshot
A Rapid Bootstrap Algorithm for the RAxML Web Servers
inferredcites →https://doi.org/10.1080/106351598260987openalex-snapshot
Taxonomic Sampling, Phylogenetic Accuracy, and Investigator Bias
inferredcites →https://doi.org/10.1093/bib/bbn013openalex-snapshot
Recent developments in the MAFFT multiple sequence alignment program
inferredcites →https://doi.org/10.1093/bioinformatics/12.6.543openalex-snapshot
SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny
inferredcites →https://doi.org/10.1093/bioinformatics/17.12.1246openalex-snapshot
CONSEL: for assessing the confidence of phylogenetic tree selection
inferredcites →https://doi.org/10.1093/bioinformatics/btg034openalex-snapshot
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
inferredcites →https://doi.org/10.1093/bioinformatics/btg180openalex-snapshot
MrBayes 3: Bayesian phylogenetic inference under mixed models
inferredcites →https://doi.org/10.1093/bioinformatics/bti079openalex-snapshot
HyPhy: hypothesis testing using phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/bti191openalex-snapshot
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/bti263openalex-snapshot
ProtTest: selection of best-fit models of protein evolution
inferredcites →https://doi.org/10.1093/bioinformatics/btn230openalex-snapshot
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony
inferredcites →https://doi.org/10.1093/gbe/evp022openalex-snapshot
Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates
inferredcites →https://doi.org/10.1093/molbev/msh137openalex-snapshot
Genome-Scale Phylogeny and the Detection of Systematic Biases
inferredcites →https://doi.org/10.1093/molbev/msh182openalex-snapshot
Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments
inferredcites →https://doi.org/10.1093/molbev/msi121openalex-snapshot
More Genes or More Taxa? The Relative Contribution of Gene Number and Taxon Number to Phylogenetic Accuracy
inferredcites →https://doi.org/10.1093/molbev/msj068openalex-snapshot
Comprehensive Multigene Phylogenies of Excavate Protists Reveal the Evolutionary Positions of “Primitive” Eukaryotes
inferredcites →https://doi.org/10.1093/molbev/msl032openalex-snapshot
Genome Architecture Drives Protein Evolution in Ciliates
inferredcites →https://doi.org/10.1093/molbev/msm089openalex-snapshot
Phylogenomic Analysis Supports the Monophyly of Cryptophytes and Haptophytes and the Association of Rhizaria with Chromalveolates
inferredcites →https://doi.org/10.1093/molbev/msn075openalex-snapshot
Plastid-Derived Genes in the Nonphotosynthetic Alveolate Oxyrrhis marina
inferredcites →https://doi.org/10.1093/nar/22.22.4673openalex-snapshot
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
inferredcites →https://doi.org/10.1093/nar/30.1.183openalex-snapshot
The European database on small subunit ribosomal RNA
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025647openalex-snapshot
Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids
inferredcites →https://doi.org/10.1093/sysbio/27.4.401openalex-snapshot
Cases in which Parsimony or Compatibility Methods will be Positively Misleading
inferredcites →https://doi.org/10.1098/rsbl.2008.0224openalex-snapshot
Phylogenomics reveals a new ‘megagroup’ including most photosynthetic eukaryotes
inferredcites →https://doi.org/10.1098/rspb.2006.3515openalex-snapshot
Telonemia, a new protist phylum with affinity to chromist lineages
inferredcites →https://doi.org/10.1098/rstb.2006.1843openalex-snapshot
Eukaryotic organisms in Proterozoic oceans
inferredcites →https://doi.org/10.1098/rstb.2006.1845openalex-snapshot
The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation
inferredcites →https://doi.org/10.1099/00207713-52-5-1901openalex-snapshot
Insights into the diversity of choreotrich and oligotrich ciliates (Class: Spirotrichea) based on genealogical analyses of multiple loci.
inferredcites →https://doi.org/10.1099/ijs.0.02114-0openalex-snapshot
Insights into the diversity of choreotrich and oligotrich ciliates (Class: Spirotrichea) based on genealogical analyses of multiple loci
inferredcites →https://doi.org/10.1099/ijs.0.02578-0openalex-snapshot
Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota)
inferredcites →https://doi.org/10.1111/j.0022-3646.2003.03-084.xopenalex-snapshot
WEIGHING THE EVIDENCE FOR A SINGLE ORIGIN OF PLASTIDS1
inferredcites →https://doi.org/10.1111/j.1529-8817.2005.00091.xopenalex-snapshot
DO PLASTID‐RELATED CHARACTERS SUPPORT THE CHROMALVEOLATE HYPOTHESIS?1
inferredcites →https://doi.org/10.1111/j.1550-7408.1999.tb04614.xopenalex-snapshot
Principles of Protein and Lipid Targeting in Secondary Symbiogenesis: Euglenoid, Dinoflagellate, and Sporozoan Plastid Origins and the Eukaryote Family Tree 1 , 2
inferredcites →https://doi.org/10.1111/j.1550-7408.1999.tb06070.xopenalex-snapshot
Malawimonas jakobiformis n. gen., n. sp. (Malawimonadidae n. fam.): A Jakoba‐like Heterotrophic Nanoflagellate with Discoidal Mitochondrial Cristae
inferredcites →https://doi.org/10.1111/j.1550-7408.2005.00053.xopenalex-snapshot
The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists
inferredcites →https://doi.org/10.1111/j.1550-7408.2005.00087.xopenalex-snapshot
Ultrastructural Description ofBreviata anathema, N. Gen., N. Sp., the Organism Previously Studied as “Mastigamoeba invertens”
inferredcites →https://doi.org/10.1111/j.1550-7408.2008.00356.xopenalex-snapshot
The Zooflagellates Stephanopogon and Percolomonas are a Clade (Class Percolatea: Phylum Percolozoa)
inferredcites →https://doi.org/10.1111/j.1550-7408.2008.00371.xopenalex-snapshot
Chromalveolates and the Evolution of Plastids by Secondary Endosymbiosis 1
inferredcites →https://doi.org/10.1111/j.1550-7408.2008.00379.xopenalex-snapshot
Untangling the Phylogeny of Amoeboid Protists1
inferredcites →https://doi.org/10.1126/science.1172983openalex-snapshot
Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms
inferredcites →https://doi.org/10.1146/annurev.arplant.59.032607.092915openalex-snapshot
Plastid Evolution
inferredcites →https://doi.org/10.1146/annurev.genom.9.081307.164407openalex-snapshot
Phylogenetic Inference Using Whole Genomes
inferredcites →https://doi.org/10.1186/1471-2148-6-34openalex-snapshot
A high density of ancient spliceosomal introns in oxymonad excavates
inferredcites →https://doi.org/10.1186/1471-2148-6-8openalex-snapshot
Stable evolutionary signal in a Yeast protein interaction network
inferredcites →https://doi.org/10.1186/1471-2148-8-14openalex-snapshot
Broadly sampled multigene trees of eukaryotes
inferredcites →https://doi.org/10.1186/1471-2148-8-30openalex-snapshot
The cyanobacterial endosymbiont of the unicellular algae Rhopalodia gibba shows reductive genome evolution
inferredcites →https://doi.org/10.1186/1471-2148-8-95openalex-snapshot
Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?
inferredcites →https://doi.org/10.1371/journal.pgen.0020220openalex-snapshot
Evaluating Support for the Current Classification of Eukaryotic Diversity
inferredcites →https://doi.org/10.1371/journal.pone.0000790openalex-snapshot
Phylogenomics Reshuffles the Eukaryotic Supergroups
inferredcites →https://doi.org/10.1371/journal.pone.0002621openalex-snapshot
EEF2 Analysis Challenges the Monophyly of Archaeplastida and Chromalveolata
inferredcites →https://doi.org/10.1525/bio.2009.59.6.5openalex-snapshot
Molecular Data Are Transforming Hypotheses on the Origin and Diversification of Eukaryotes
inferredcites →https://doi.org/10.2307/2412923openalex-snapshot
Cases in which Parsimony or Compatibility Methods Will be Positively Misleading
inferredcites →https://doi.org/10.3724/sp.j.1002.2008.08016openalex-snapshot
Taxon sampling and the accuracy of phylogenetic analyses
inferredcites →https://doi.org/10.3724/sp.j.1002.2008.08040openalex-snapshot
Missing data and the accuracy of Bayesian phylogenetics
inferredcites →https://doi.org/10.5860/choice.39-2183openalex-snapshot
MacClade 4.0: analysis of phylogeny and character evolution
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Phylogeny of North America’s largest cicada radiation redefines Tibicinoides and Okanagana (Hemiptera: Auchenorrhyncha: Cicadidae: Tibicininae)
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Protist Systematics
inferred← citeshttps://doi.org/10.1002/9781118735893.ch14openalex-snapshot
Metatranscriptomics of Soil Eukaryotic Communities
inferred← citeshttps://doi.org/10.1002/bies.201200143openalex-snapshot
Multicellularity arose several times in the evolution of eukaryotes (Response to DOI 10.1002/bies.201100187)
inferred← citeshttps://doi.org/10.1002/bies.201700198openalex-snapshot
Microbial Diversity in the Eukaryotic SAR Clade: Illuminating the Darkness Between Morphology and Molecular Data
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The Evolutionary Origin of Animals and Fungi
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Lateral Gene Transfer in Evolution
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Gene Transfer and the Chimeric Nature of Eukaryotic Genomes
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Metatranscriptomics of Soil Eukaryotic Communities
inferred← citeshttps://doi.org/10.1007/978-1-4939-8728-3_3openalex-snapshot
Characterization of Eukaryotic Microbiome Using 18S Amplicon Sequencing
inferred← citeshttps://doi.org/10.1007/978-1-61779-442-1_2openalex-snapshot
Rho GTPases: Deciphering the Evolutionary History of a Complex Protein Family
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The Chloroplast and Photosynthetic Eukaryotes
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On the Approximation of the Kolmogorov Complexity for DNA Sequences
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Algae from Secondary Endosymbiosis
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Definition und Abgrenzung der Pilze
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The Single Primary Endosymbiotic Event
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Analysis of the Genome of Cyanophora paradoxa: An Algal Model for Understanding Primary Endosymbiosis
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Photosynthetic Paulinella: Recapitulation of Primary Plastid Establishment
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Origins of Mitochondria and Plastids
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Phylogenomics in Algal Research: Current Trends and Future Perspectives
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Protistan Skeletons: A Geologic History of Evolution and Constraint
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Timing the Origins of Multicellular Eukaryotes Through Phylogenomics and Relaxed Molecular Clock Analyses
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A Novel Clade of Unique Eukaryotic Ribonucleotide Reductase R2 Subunits is Exclusive to Apicomplexan Parasites
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An 18S rRNA Workflow for Characterizing Protists in Sewage, with a Focus on Zoonotic Trichomonads
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Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria
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Large-Scale Pairwise Alignments on GPU Clusters: Exploring the Implementation Space
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Origin of eukaryotic cells: 40 years on
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Diversity and Evolution of Algae
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The Evolution of Algae by Secondary and Tertiary Endosymbiosis
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Protist Diversification
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Plant Systematics: An Overview
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Mitochondrial NADH:ubiquinone oxidoreductase (complex I) in eukaryotes: A highly conserved subunit composition highlighted by mining of protein databases
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Alternative cytoskeletal landscapes: cytoskeletal novelty and evolution in basal excavate protists
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Circuit Assembly: The Repulsive Side of Lamination
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Split Genes: Another Surprise from Giardia
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Red and Green Algal Monophyly and Extensive Gene Sharing Found in a Rich Repertoire of Red Algal Genes
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Evolution: Rooting the Eukaryotic Tree of Life
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An Alternative Root for the Eukaryote Tree of Life
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Phylogenomics of neglected flagellated protists supports a revised eukaryotic tree of life
inferred← citeshttps://doi.org/10.1016/j.ejop.2011.10.003openalex-snapshot
A genomic survey shows that the haloarchaeal type tyrosyl tRNA synthetase is not a synapomorphy of opisthokonts
inferred← citeshttps://doi.org/10.1016/j.ejop.2013.01.001openalex-snapshot
The flagellar apparatus of Breviata anathema, a eukaryote without a clear supergroup affinity
inferred← citeshttps://doi.org/10.1016/j.ejop.2014.12.001openalex-snapshot
Mixed heterolobosean and novel gregarine lineage genes from culture ATCC 50646: Long-branch artefacts, not lateral gene transfer, distort α-tubulin phylogeny
inferred← citeshttps://doi.org/10.1016/j.epsl.2011.05.030openalex-snapshot
Agglutinated tests in post-Sturtian cap carbonates of Namibia and Mongolia
inferred← citeshttps://doi.org/10.1016/j.funbio.2017.07.006openalex-snapshot
Are Thraustochytrids algae?
inferred← citeshttps://doi.org/10.1016/j.jbior.2015.05.002openalex-snapshot
Class I PI 3-kinases: Function and evolution
inferred← citeshttps://doi.org/10.1016/j.margen.2017.10.001openalex-snapshot
Novel subfamilies of actin-regulating proteins
inferred← citeshttps://doi.org/10.1016/j.marmicro.2011.06.007openalex-snapshot
Multigene phylogenetic analyses including diverse radiolarian species support the “Retaria” hypothesis — The sister relationship of Radiolaria and Foraminifera
inferred← citeshttps://doi.org/10.1016/j.mbs.2012.11.009openalex-snapshot
C-curve: A novel 3D graphical representation of DNA sequence based on codons
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A biomechanical analysis of the early eukaryotic fossil Valeria and new occurrence of organic-walled microfossils from the Paleo-Mesoproterozoic Ruyang Group
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Subulatomonas tetraspora nov. gen. nov. sp. is a Member of a Previously Unrecognized Major Clade of Eukaryotes
inferred← citeshttps://doi.org/10.1016/j.protis.2011.11.002openalex-snapshot
Diversity, Evolution and Molecular Systematics of the Psalteriomonadidae, the Main Lineage of Anaerobic/Microaerophilic Heteroloboseans (Excavata: Discoba)
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Evolution of the Chloroplast Genome in Photosynthetic Euglenoids: A Comparison of Eutreptia viridis and Euglena gracilis (Euglenophyta)
inferred← citeshttps://doi.org/10.1016/j.protis.2012.08.002openalex-snapshot
Amoeba Stages in the Deepest Branching Heteroloboseans, Including Pharyngomonas: Evolutionary and Systematic Implications
inferred← citeshttps://doi.org/10.1016/j.protis.2013.02.003openalex-snapshot
Multigene Phylogenetic Reconstruction of the Tubulinea (Amoebozoa) Corroborates Four of the Six Major Lineages, while Additionally Revealing that Shell Composition Does not Predict Phylogeny in the Arcellinida
inferred← citeshttps://doi.org/10.1016/j.protis.2013.05.005openalex-snapshot
The Microtubular Cytoskeleton of the Apusomonad Thecamonas, a Sister Lineage to the Opisthokonts
inferred← citeshttps://doi.org/10.1016/j.protis.2014.05.002openalex-snapshot
DNA Barcoding in Amoebozoa and Challenges: The Example of Cochliopodium
inferred← citeshttps://doi.org/10.1016/j.protis.2014.07.008openalex-snapshot
Evidence of Parasexual Activity in “Asexual Amoebae” Cochliopodium spp. (Amoebozoa): Extensive Cellular and Nuclear Fusion
inferred← citeshttps://doi.org/10.1016/j.protis.2016.01.001openalex-snapshot
Description of Lecythium terrestris sp. nov. (Chlamydophryidae, Cercozoa), a Soil Dwelling Protist Feeding on Fungi and Algae
inferred← citeshttps://doi.org/10.1016/j.protis.2017.04.004openalex-snapshot
Evolutionary Relationship of the Scale-Bearing Kraken (incertae sedis, Monadofilosa, Cercozoa, Rhizaria): Combining Ultrastructure Data and a Two-Gene Phylogeny
inferred← citeshttps://doi.org/10.1016/j.pt.2011.11.002openalex-snapshot
Double peaks reveal rare diplomonad sex
inferred← citeshttps://doi.org/10.1016/j.resmic.2011.05.001openalex-snapshot
Tetrahymena thermophila, a unicellular eukaryote with separate germline and somatic genomes
inferred← citeshttps://doi.org/10.1016/j.tplants.2013.09.007openalex-snapshot
Assessing the bacterial contribution to the plastid proteome
inferred← citeshttps://doi.org/10.1016/j.tree.2011.11.010openalex-snapshot
Sequencing our way towards understanding global eukaryotic biodiversity
inferred← citeshttps://doi.org/10.1016/j.tree.2012.08.011openalex-snapshot
Transcriptomics and microbial eukaryote diversity: a way forward
inferred← citeshttps://doi.org/10.1016/j.tree.2012.09.005openalex-snapshot
Metagenomics will highlight and drive links to taxonomic data: reply to Murray
inferred← citeshttps://doi.org/10.1016/j.virol.2013.04.018openalex-snapshot
Evaluation of higher plant virus resistance genes in the green alga, Chlorella variabilis NC64A, during the early phase of infection with Paramecium bursaria chlorella virus-1
inferred← citeshttps://doi.org/10.1016/j.xgen.2026.101254openalex-snapshot
A protein interactome for the last eukaryotic common ancestor illuminates the biochemical basis of modern genetic diseases
inferred← citeshttps://doi.org/10.1016/j.ympev.2012.11.013openalex-snapshot
Evolutionary implications of intron–exon distribution and the properties and sequences of the RPL10A gene in eukaryotes
inferred← citeshttps://doi.org/10.1016/j.ympev.2013.10.007openalex-snapshot
Dinoflagellate phylogeny revisited: Using ribosomal proteins to resolve deep branching dinoflagellate clades
inferred← citeshttps://doi.org/10.1016/j.ympev.2013.11.013openalex-snapshot
Sampling strategies for improving tree accuracy and phylogenetic analyses: A case study in ciliate protists, with notes on the genus Paramecium
inferred← citeshttps://doi.org/10.1016/j.ympev.2013.11.016openalex-snapshot
The impact of automated filtering of BLAST-determined homologs in the phylogenetic detection of horizontal gene transfer from a transcriptome assembly
inferred← citeshttps://doi.org/10.1016/j.ympev.2014.04.020openalex-snapshot
Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages
inferred← citeshttps://doi.org/10.1016/j.ympev.2014.08.011openalex-snapshot
Multigene phylogeny resolves deep branching of Amoebozoa
inferred← citeshttps://doi.org/10.1016/j.ympev.2014.11.011openalex-snapshot
Phylogeny, divergence times, and historical biogeography of the angiosperm family Saxifragaceae
inferred← citeshttps://doi.org/10.1016/j.ympev.2015.07.004openalex-snapshot
Multiple origins of Heliozoa from flagellate ancestors: New cryptist subphylum Corbihelia, superclass Corbistoma, and monophyly of Haptista, Cryptista, Hacrobia and Chromista
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.04.033openalex-snapshot
Reducing long-branch effects in multi-protein data uncovers a close relationship between Alveolata and Rhizaria
inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108289openalex-snapshot
An expanded phylogenomic analysis of Heterolobosea reveals the deep relationships, non-canonical genetic codes, and cryptic flagellate stages in the group
inferred← citeshttps://doi.org/10.1017/s0031182010001708openalex-snapshot
Eukaryotic systematics: a user's guide for cell biologists and parasitologists
inferred← citeshttps://doi.org/10.1038/cti.2016.91openalex-snapshot
Embracing the gut microbiota: the new frontier for inflammatory and infectious diseases
inferred← citeshttps://doi.org/10.1038/ismej.2013.116openalex-snapshot
Vampires in the oceans: predatory cercozoan amoebae in marine habitats
inferred← citeshttps://doi.org/10.1038/ismej.2014.146openalex-snapshot
Alternatives to vitamin B1 uptake revealed with discovery of riboswitches in multiple marine eukaryotic lineages
inferred← citeshttps://doi.org/10.1038/nature18297openalex-snapshot
Environmental Breviatea harbour mutualistic Arcobacter epibionts
inferred← citeshttps://doi.org/10.1038/s41586-025-09808-zopenalex-snapshot
Dated gene duplications elucidate the evolutionary assembly of eukaryotes
inferred← citeshttps://doi.org/10.1038/s41598-022-15372-7openalex-snapshot
New insights on the evolutionary relationships between the major lineages of Amoebozoa
inferred← citeshttps://doi.org/10.1038/srep04780openalex-snapshot
Single cell genome analysis of an uncultured heterotrophic stramenopile
inferred← citeshttps://doi.org/10.1073/pnas.1110633108openalex-snapshot
Estimating the timing of early eukaryotic diversification with multigene molecular clocks
inferred← citeshttps://doi.org/10.1073/pnas.1421374112openalex-snapshot
Genomic perspectives on the birth and spread of plastids
inferred← citeshttps://doi.org/10.1083/jcb.201103171openalex-snapshot
Functional evolution of nuclear structure
inferred← citeshttps://doi.org/10.1093/bib/bbw034openalex-snapshot
Heterogeneous molecular processes among the causes of how sequence similarity scores can fail to recapitulate phylogeny
inferred← citeshttps://doi.org/10.1093/gbe/evad058openalex-snapshot
Maturases and Group II Introns in the Mitochondrial Genomes of the Deepest Jakobid Branch
inferred← citeshttps://doi.org/10.1093/gbe/evt001openalex-snapshot
Chloroplast Phylogenomics Indicates that Ginkgo biloba Is Sister to Cycads
inferred← citeshttps://doi.org/10.1093/gbe/evt019openalex-snapshot
A Broad Phylogenetic Survey Unveils the Diversity and Evolution of Telomeres in Eukaryotes
inferred← citeshttps://doi.org/10.1093/gbe/evt113openalex-snapshot
In Silico Resurrection of the Major Vault Protein Suggests It Is Ancestral in Modern Eukaryotes
inferred← citeshttps://doi.org/10.1093/gbe/evt179openalex-snapshot
Horizontal Gene Transfer is a Significant Driver of Gene Innovation in Dinoflagellates
inferred← citeshttps://doi.org/10.1093/gbe/evu187openalex-snapshot
Six Subgroups and Extensive Recent Duplications Characterize the Evolution of the Eukaryotic Tubulin Protein Family
inferred← citeshttps://doi.org/10.1093/gbe/evw196openalex-snapshot
Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low-Copy Nuclear Genes
inferred← citeshttps://doi.org/10.1093/molbev/msq200openalex-snapshot
Evolution of the Actin Gene Family in Testate Lobose Amoebae (Arcellinida) is Characterized by Two Distinct Clades of Paralogs and Recent Independent Expansions
inferred← citeshttps://doi.org/10.1093/molbev/msr108openalex-snapshot
Large-Scale Phylogenomic Analyses Indicate a Deep Origin of Primary Plastids within Cyanobacteria
inferred← citeshttps://doi.org/10.1093/molbev/msr295openalex-snapshot
Rooting the Eukaryotic Tree with Mitochondrial and Bacterial Proteins
inferred← citeshttps://doi.org/10.1093/molbev/mss001openalex-snapshot
Collodictyon--An Ancient Lineage in the Tree of Eukaryotes
inferred← citeshttps://doi.org/10.1093/molbev/msv340openalex-snapshot
Evolutionary Origins of Rhizarian Parasites
inferred← citeshttps://doi.org/10.1093/molbev/msx075openalex-snapshot
Single Cell Transcriptomics, Mega-Phylogeny, and the Genetic Basis of Morphological Innovations in Rhizaria
inferred← citeshttps://doi.org/10.1093/molbev/msx147openalex-snapshot
Evolutionary History of Chemosensory-Related Gene Families across the Arthropoda
inferred← citeshttps://doi.org/10.1093/pcp/pct200openalex-snapshot
Calcium-Dependent Protein Kinases in Plants: Evolution, Expression and Function
inferred← citeshttps://doi.org/10.1093/sysbio/syab027openalex-snapshot
Six-State Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses
inferred← citeshttps://doi.org/10.1093/sysbio/syab036openalex-snapshot
Phylogenomic Insights into the Origin of Primary Plastids
inferred← citeshttps://doi.org/10.1093/sysbio/sys001openalex-snapshot
Overcoming Deep Roots, Fast Rates, and Short Internodes to Resolve the Ancient Rapid Radiation of Eupolypod II Ferns
inferred← citeshttps://doi.org/10.1093/sysbio/sys026openalex-snapshot
Turning the Crown Upside Down: Gene Tree Parsimony Roots the Eukaryotic Tree of Life
inferred← citeshttps://doi.org/10.1093/sysbio/sys027openalex-snapshot
Phylogeny and Biogeography of the Core Babblers (Aves: Timaliidae)
inferred← citeshttps://doi.org/10.1093/sysbio/sys036openalex-snapshot
Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny
inferred← citeshttps://doi.org/10.1093/sysbio/sys049openalex-snapshot
Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
inferred← citeshttps://doi.org/10.1093/sysbio/syt008openalex-snapshot
Is Permanent Parasitism Reversible?—Critical Evidence from Early Evolution of House Dust Mites
inferred← citeshttps://doi.org/10.1093/sysbio/syu126openalex-snapshot
Taxon-Rich Phylogenomic Analyses Resolve the Eukaryotic Tree of Life and Reveal the Power of Subsampling by Sites
inferred← citeshttps://doi.org/10.1098/rsos.171707openalex-snapshot
Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes
inferred← citeshttps://doi.org/10.1098/rspb.2011.0289openalex-snapshot
The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms
inferred← citeshttps://doi.org/10.1098/rspb.2013.1755openalex-snapshot
Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads
inferred← citeshttps://doi.org/10.1099/ijs.0.054221-0openalex-snapshot
Applications of next-generation sequencing to unravelling the evolutionary history of algae
inferred← citeshttps://doi.org/10.1101/240929openalex-snapshot
Proposal for practical multi-kingdom classification of eukaryotes based on monophyly and comparable divergence time criteria
inferred← citeshttps://doi.org/10.1101/cshperspect.a016139openalex-snapshot
On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks
inferred← citeshttps://doi.org/10.1101/gr.228429.117openalex-snapshot
Genome-reconstruction for eukaryotes from complex natural microbial communities
inferred← citeshttps://doi.org/10.1104/pp.111.173500openalex-snapshot
Plastid Origin and Evolution: New Models Provide Insights into Old Problems
inferred← citeshttps://doi.org/10.1104/pp.112.193896openalex-snapshot
Analysis of Porphyra Membrane Transporters Demonstrates Gene Transfer among Photosynthetic Eukaryotes and Numerous Sodium-Coupled Transport Systems
inferred← citeshttps://doi.org/10.1109/asap.2013.6567598openalex-snapshot
A distributed CPU-GPU framework for pairwise alignments on large-scale sequence datasets
inferred← citeshttps://doi.org/10.1111/1462-2920.12143openalex-snapshot
Soil metatranscriptomics for mining eukaryotic heavy metal resistance genes
inferred← citeshttps://doi.org/10.1111/cla.12191openalex-snapshot
Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae)
inferred← citeshttps://doi.org/10.1111/j.1095-8312.2012.01962.xopenalex-snapshot
Time to regulate microbial eukaryote nomenclature
inferred← citeshttps://doi.org/10.1111/j.1529-8817.2012.01169.xopenalex-snapshot
MOLECULAR EVOLUTION OF GLUTAMINE SYNTHETASE II AND III IN THE CHROMALVEOLATES1
inferred← citeshttps://doi.org/10.1111/j.1529-8817.2012.01194.xopenalex-snapshot
ANALYSIS OF ALEXANDRIUM TAMARENSE (DINOPHYCEAE) GENES REVEALS THE COMPLEX EVOLUTIONARY HISTORY OF A MICROBIAL EUKARYOTE1
inferred← citeshttps://doi.org/10.1111/j.1550-7408.2011.00571.xopenalex-snapshot
Sorosphaerula nom. n. for the Plasmodiophorid Genus Sorosphaera J. Schröter 1886 (Rhizaria: Endomyxa: Phytomyxea: Plasmodiophorida)
inferred← citeshttps://doi.org/10.1111/j.1550-7408.2012.00644.xopenalex-snapshot
The Revised Classification of Eukaryotes
inferred← citeshttps://doi.org/10.1111/j.1759-6831.2012.00188.xopenalex-snapshot
Evolution of the life cycle in land plants
inferred← citeshttps://doi.org/10.1111/j.1759-6831.2012.00237.xopenalex-snapshot
Horizontal gene transfer in the evolution of photosynthetic eukaryotes
inferred← citeshttps://doi.org/10.1111/jeu.12031openalex-snapshot
Heat Shock Protein 90 of B onamia ostreae: Characterization and Possible Correlation with Infection of the Flat O yster, O strea edulis
inferred← citeshttps://doi.org/10.1111/jeu.12837openalex-snapshot
Description of Imasa heleensis, gen. nov., sp. nov. (Imasidae, fam. nov.), a Deep‐Branching Marine Malawimonad and Possible Key Taxon in Understanding Early Eukaryotic Evolution
inferred← citeshttps://doi.org/10.1111/mec.14520openalex-snapshot
Taxon sampling effects on the quantification and comparison of community phylogenetic diversity
inferred← citeshttps://doi.org/10.1111/tpj.12145openalex-snapshot
Evolution of microtubule organizing centers across the tree of eukaryotes
inferred← citeshttps://doi.org/10.1126/science.1213561openalex-snapshot
Cyanophora paradoxa Genome Elucidates Origin of Photosynthesis in Algae and Plants
inferred← citeshttps://doi.org/10.1128/aem.00163-16openalex-snapshot
Biochemical and Structural Characterizations of Two Dictyostelium Cellobiohydrolases from the Amoebozoa Kingdom Reveal a High Level of Conservation between Distant Phylogenetic Trees of Life
inferred← citeshttps://doi.org/10.1128/ec.00155-12openalex-snapshot
Dynamics and Innovations within Oomycete Genomes: Insights into Biology, Pathology, and Evolution
inferred← citeshttps://doi.org/10.1128/ec.00326-10openalex-snapshot
Do Red and Green Make Brown?: Perspectives on Plastid Acquisitions within Chromalveolates
inferred← citeshttps://doi.org/10.1146/annurev-micro-090110-102808openalex-snapshot
Origin and Diversification of Eukaryotes
inferred← citeshttps://doi.org/10.1155/2012/134839openalex-snapshot
Diversity of Eukaryotic Translational Initiation Factor eIF4E in Protists
inferred← citeshttps://doi.org/10.1155/2016/3262813openalex-snapshot
Circular Helix-Like Curve: An Effective Tool of Biological Sequence Analysis and Comparison
inferred← citeshttps://doi.org/10.1159/000324505openalex-snapshot
Evolution of Patchily Distributed Proteins Shared between Eukaryotes and Prokaryotes: Dictyostelium as a Case Study
inferred← citeshttps://doi.org/10.1186/1471-2148-10-377openalex-snapshot
Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists
inferred← citeshttps://doi.org/10.1186/1471-2148-11-105openalex-snapshot
Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids
inferred← citeshttps://doi.org/10.1186/1471-2148-11-268openalex-snapshot
A holistic phylogeny of the coronin gene family reveals an ancient origin of the tandem-coronin, defines a new subfamily, and predicts protein function
inferred← citeshttps://doi.org/10.1186/1471-2148-11-7openalex-snapshot
Comparative genomics of proteins involved in RNA nucleocytoplasmic export
inferred← citeshttps://doi.org/10.1186/1471-2148-12-95openalex-snapshot
Evolution of the eukaryotic dynactin complex, the activator of cytoplasmic dynein
inferred← citeshttps://doi.org/10.1186/1471-2148-13-140openalex-snapshot
Evolution of protein indels in plants, animals and fungi
inferred← citeshttps://doi.org/10.1186/1471-2148-13-37openalex-snapshot
Horizontal gene transfer of epigenetic machinery and evolution of parasitism in the malaria parasite Plasmodium falciparum and other apicomplexans
inferred← citeshttps://doi.org/10.1186/1756-0500-4-330openalex-snapshot
An extended phylogenetic analysis reveals ancient origin of "non-green" phosphoribulokinase genes from two lineages of "green" secondary photosynthetic eukaryotes: Euglenophyta and Chlorarachniophyta
inferred← citeshttps://doi.org/10.1186/1756-0500-5-88openalex-snapshot
Evolution of the eukaryotic ARP2/3 activators of the WASP family: WASP, WAVE, WASH, and WHAMM, and the proposed new family members WAWH and WAML
inferred← citeshttps://doi.org/10.1186/s12862-018-1283-1openalex-snapshot
A practical implementation of large transcriptomic data analysis to resolve cryptic species diversity problems in microbial eukaryotes
inferred← citeshttps://doi.org/10.1186/s13630-016-0042-4openalex-snapshot
Eight unique basal bodies in the multi-flagellated diplomonad Giardia lamblia
inferred← citeshttps://doi.org/10.1186/s40064-016-3146-9openalex-snapshot
Evolutionary analyses of mitochondrial carrier family of dictyostelids
inferred← citeshttps://doi.org/10.1242/jcs.078436openalex-snapshot
Multivesicular bodies in the enigmatic amoeboflagellateBreviata anathemaand the evolution of ESCRT 0
inferred← citeshttps://doi.org/10.13140/rg.2.1.4458.0961openalex-snapshot
STORI: Selectable Taxon Ortholog Retrieval Iteratively
inferred← citeshttps://doi.org/10.1371/currents.tol.c24b6054aebf3602748ac042ccc8f2e9openalex-snapshot
Building a Phylogenomic Pipeline for the Eukaryotic Tree of Life - Addressing Deep Phylogenies with Genome-Scale Data
inferred← citeshttps://doi.org/10.1371/journal.pbio.1001094openalex-snapshot
Gene Gain and Loss during Evolution of Obligate Parasitism in the White Rust Pathogen of Arabidopsis thaliana
inferred← citeshttps://doi.org/10.1371/journal.pone.0020774openalex-snapshot
Phylogeny of Parasitic Parabasalia and Free-Living Relatives Inferred from Conventional Markers vs. Rpb1, a Single-Copy Gene
inferred← citeshttps://doi.org/10.1371/journal.pone.0022269openalex-snapshot
Multiple Independent Fusions of Glucose-6-Phosphate Dehydrogenase with Enzymes in the Pentose Phosphate Pathway
inferred← citeshttps://doi.org/10.1371/journal.pone.0022780openalex-snapshot
Comprehensive Phylogenetic Reconstruction of Amoebozoa Based on Concatenated Analyses of SSU-rDNA and Actin Genes
inferred← citeshttps://doi.org/10.1371/journal.pone.0031165openalex-snapshot
Shedding Light on Vampires: The Phylogeny of Vampyrellid Amoebae Revisited
inferred← citeshttps://doi.org/10.1371/journal.pone.0040635openalex-snapshot
Assessing Whether Alpha-Tubulin Sequences Are Suitable for Phylogenetic Reconstruction of Ciliophora with Insights into Its Evolution in Euplotids
inferred← citeshttps://doi.org/10.1371/journal.pone.0050004openalex-snapshot
When Naked Became Armored: An Eight-Gene Phylogeny Reveals Monophyletic Origin of Theca in Dinoflagellates
inferred← citeshttps://doi.org/10.1371/journal.pone.0050827openalex-snapshot
A Case Study for Effects of Operational Taxonomic Units from Intracellular Endoparasites and Ciliates on the Eukaryotic Phylogeny: Phylogenetic Position of the Haptophyta in Analyses of Multiple Slowly Evolving Genes
inferred← citeshttps://doi.org/10.1371/journal.pone.0062586openalex-snapshot
Two-Gene Phylogeny of Bright-Spored Myxomycetes (Slime Moulds, Superorder Lucisporidia)
inferred← citeshttps://doi.org/10.1371/journal.pone.0075217openalex-snapshot
Molecular Phylogeny of a RING E3 Ubiquitin Ligase, Conserved in Eukaryotic Cells and Dominated by Homologous Components, the Muskelin/RanBPM/CTLH Complex
inferred← citeshttps://doi.org/10.1371/journal.pone.0101158openalex-snapshot
Phylogenomic Analysis of “Red” Genes from Two Divergent Species of the “Green” Secondary Phototrophs, the Chlorarachniophytes, Suggests Multiple Horizontal Gene Transfers from the Red Lineage before the Divergence of Extant Chlorarachniophytes
inferred← citeshttps://doi.org/10.1371/journal.pone.0131821openalex-snapshot
Guanchochroma wildpretii gen. et spec. nov. (Ochrophyta) Provides New Insights into the Diversification and Evolution of the Algal Class Synchromophyceae
inferred← citeshttps://doi.org/10.1371/journal.pone.0270913openalex-snapshot
Illuminating protist diversity in pitcher plants and bromeliad tanks
inferred← citeshttps://doi.org/10.1666/11-138.1openalex-snapshot
Scale microfossils from the mid-Neoproterozoic Fifteenmile Group, Yukon Territory
inferred← citeshttps://doi.org/10.1666/12-157ropenalex-snapshot
Phosphatized acanthomorphic acritarchs and related microfossils from the Ediacaran Doushantuo Formation at Weng'an (South China) and their implications for biostratigraphic correlation
inferred← citeshttps://doi.org/10.17077/etd.6xg42cj3openalex-snapshot
The evolutionary history of meiotic genes
inferred← citeshttps://doi.org/10.18257/raccefyn.277openalex-snapshot
Evolutionary history of the group formerly known as protists using a phylogenomics approach
inferred← citeshttps://doi.org/10.20381/ruor-21873openalex-snapshot
A Phylogenetic Assessment of Flatfish (Order Pleuronectiformes) Intrarelationships Based on Molecular Evidence
inferred← citeshttps://doi.org/10.22452/mjs.vol32no3.2openalex-snapshot
Phylogenomics of Marine Algae
inferred← citeshttps://doi.org/10.23860/thesis-pagano-giovanni-2014openalex-snapshot
STRUCTURE, FUNCTION AND EVOLUTION OF PHOSPHOPROTEIN P0 AND ITS UNIQUE INSERT IN TETRAHYMENA THERMOPHILA
inferred← citeshttps://doi.org/10.2478/prge-2012-0002openalex-snapshot
Gene discovery from a pilot study of the transcriptomes from three diverse microbial eukaryotes: Corallomyxa tenera, Chilodonella uncinata, and Subulatomonas tetraspora
inferred← citeshttps://doi.org/10.25335/m5t75topenalex-snapshot
Evolutionary changes in the euglenoid chloroplast
inferred← citeshttps://doi.org/10.3109/09687688.2010.521201openalex-snapshot
Patterns and processes in the evolution of the eukaryotic endomembrane system
inferred← citeshttps://doi.org/10.32469/10355/66808openalex-snapshot
Homology sequence analysis using GPU acceleration
inferred← citeshttps://doi.org/10.3389/fevo.2014.00066openalex-snapshot
Primary endosymbiosis and the evolution of light and oxygen sensing in photosynthetic eukaryotes
inferred← citeshttps://doi.org/10.3389/fmicb.2011.00153openalex-snapshot
Microbial Eukaryotes in the Human Microbiome: Ecology, Evolution, and Future Directions
inferred← citeshttps://doi.org/10.3389/fmicb.2014.00298openalex-snapshot
Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity
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