The Revised Classification of Eukaryotes

How Many Species Are There on Earth and in the Ocean?

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Foraminiferal Genera and Their Classification

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The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists

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The Ciliated Protozoa: Characterization, Classification, and Guide to the Literature

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Illustrated Guide to the Protozoa

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The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa.

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Increased Taxon Sampling Greatly Reduces Phylogenetic Error

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Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits

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Phylogeny of some of the major genera of dinoflagellates based on ultrastructure and partial LSU rDNA sequence data, including the erection of three new genera of unarmoured dinoflagellates

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Taxon sampling and the accuracy of phylogenetic analyses

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Missing data and the design of phylogenetic analyses

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Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”

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A photosynthetic alveolate closely related to apicomplexan parasites

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A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota)

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Myosin domain evolution and the primary divergence of eukaryotes

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Discovery of novel intermediate forms redefines the fungal tree of life

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Phylogenomics Reshuffles the Eukaryotic Supergroups

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Die natürlichen Pflanzenfamilien

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On dinoflagellate evolution

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The evolution and diversity of kinetoplastid flagellates

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Genome size differentiates co-occurring populations of the planktonic diatom Ditylum brightwellii(Bacillariophyta)

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A NEW LOOK AT AN ANCIENT ORDER: GENERIC REVISION OF THE BANGIALES (RHODOPHYTA)1

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A multi-locus time-calibrated phylogeny of the brown algae (Heterokonta, Ochrophyta, Phaeophyceae): Investigating the evolutionary nature of the “brown algal crown radiation”

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The Closest Unicellular Relatives of Animals

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Phylogeny and Classification of Phylum Cercozoa (Protozoa)

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An overview of the systematics of the Sordariomycetes based on a four-gene phylogeny

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Myconet Volume 14. Part One. Outline of Ascomycota—2009. Part Two. Notes on Ascomycete Systematics. Nos. 4751–5113

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Archaeorhizomycetes: Unearthing an Ancient Class of Ubiquitous Soil Fungi

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Diversity, Nomenclature, and Taxonomy of Protists

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The Protistan Origins of Animals and Fungi

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DEFINING THE MAJOR LINEAGES OF RED ALGAE (RHODOPHYTA)1

Yoon, H. S., Müller, K. M., Sheath, R. G., Ott, F. D., & Bhattacharya, D. (2006) · Journal of Phycology · doi:10.1111/j.1529-8817.2006.00210.x · Cited by 305 · see citing works

Resolution of Phylogenetic Conflict in Large Data Sets by Increased Taxon Sampling

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Molecular Phylogeny and Evolution of Morphology in the Social Amoebas

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An overview of the systematics of the Sordariomycetes based on a four-gene phylogeny

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Multigene Phylogeny of Choanozoa and the Origin of Animals

Shalchian‐Tabrizi, K., Minge, M. A., Espelund, M., Orr, R. J. S., Ruden, T. A., Jakobsen, K. S., & Cavalier‐Smith, T. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002098 · Cited by 263 · see citing works

A Revised Classification of Naked Lobose Amoebae (Amoebozoa: Lobosa)

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New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes

Miądlikowska, J., Kauff, F., Hofstetter, V., et al. (2006) · Mycologia · doi:10.3852/mycologia.98.6.1088 · Cited by 261 · see citing works

Phylogenomics reveals a new ‘megagroup’ including most photosynthetic eukaryotes

Burki, F., Shalchian‐Tabrizi, K., & Pawlowski, J. W. (2008) · Biology Letters · doi:10.1098/rsbl.2008.0224 · Cited by 256 · see citing works

Ancient origin of the integrin-mediated adhesion and signaling machinery

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Phylogenomic Evidence for Separate Acquisition of Plastids in Cryptophytes, Haptophytes, and Stramenopiles

Baurain, D., Brinkmann, H., Petersen, J., Rodríguez‐Ezpeleta, N., Stechmann, A., Demoulin, V., Roger, A. J., Burger, G., Lang, B. F., & Philippe, H. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq059 · Cited by 248 · see citing works

The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins

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Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life

Parfrey, L. W., Grant, J. R., Tekle, Y. I., Lasek‐Nesselquist, E., Morrison, H. G., Sogin, M. L., Patterson, D. J., & Katz, L. A. (2010) · Systematic Biology · doi:10.1093/sysbio/syq037 · Cited by 232 · see citing works

Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa)

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The Flagellates: Unity, Diversity and Evolution

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Picobiliphytes: A Marine Picoplanktonic Algal Group with Unknown Affinities to Other Eukaryotes

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Molecular phylogeny of choanoflagellates, the sister group to Metazoa

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Evolution of the Apicomplexa: where are we now?

Morrison, D. A. (2009) · Trends in Parasitology · doi:10.1016/j.pt.2009.05.010 · Cited by 205 · see citing works

Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae

Geiser, D. M., Gueidan, C., Miądlikowska, J., et al. (2006) · Mycologia · doi:10.3852/mycologia.98.6.1053 · Cited by 199 · see citing works

An outline for the reclassification of the Chytridiales, and for a new order, the Spizellomycetales

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The simple-septate basidiomycetes: a synopsis

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Phylogeny of Novel Naked Filose and Reticulose Cercozoa: Granofilosea cl. n. and Proteomyxidea Revised

Bass, D., Chao, E. E. Y., Nikolaev, S. I., et al. (2008) · Protist · doi:10.1016/j.protis.2008.07.002 · Cited by 186 · see citing works

ON THE IDENTITY OFKARLODINIUM VENEFICUMAND DESCRIPTION OFKARLODINIUM ARMIGERSP. NOV. (DINOPHYCEAE), BASED ON LIGHT AND ELECTRON MICROSCOPY, NUCLEAR‐ENCODED LSU RDNA, AND PIGMENT COMPOSITION1

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The Environmental Clade LKM11 and Rozella Form the Deepest Branching Clade of Fungi

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Toward Resolving the Eukaryotic Tree: The Phylogenetic Positions of Jakobids and Cercozoans

Rodríguez‐Ezpeleta, N., Brinkmann, H., Burger, G., Roger, A. J., Gray, M. W., Philippe, H., & Lang, B. F. (2007) · Current Biology · doi:10.1016/j.cub.2007.07.036 · Cited by 182 · see citing works

Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists

Burki, F., Kudryavtsev, A. A., Matz, M. V., Aglyamova, G. V., Bulman, S. R., Fiers, M. W. E. J., Keeling, P. J., & Pawlowski, J. W. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-377 · Cited by 180 · see citing works

Comprehensive Multigene Phylogenies of Excavate Protists Reveal the Evolutionary Positions of “Primitive” Eukaryotes

Simpson, A. G. B., Inagaki, Y., & Roger, A. J. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj068 · Cited by 178 · see citing works

A phylogenetic overview of the Agaricomycotina

Hibbett, D. S. (2006) · Mycologia · doi:10.3852/mycologia.98.6.917 · Cited by 176 · see citing works

New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes

Miądlikowska, J., Kauff, F., Hofstetter, V., et al. (2006) · Mycologia · doi:10.1080/15572536.2006.11832636 · Cited by 175 · see citing works

A nuclear phylogeny of the Florideophyceae (Rhodophyta) inferred from combined EF2, small subunit and large subunit ribosomal DNA: Establishing the new red algal subclass Corallinophycidae

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An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences

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On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes

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Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains

Torruella, G., Derelle, R., Paps, J., Lang, B. F., Roger, A. J., Shalchian-Tabrizi, K., & Ruiz-Trillo, I. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/msr185 · Cited by 169 · see citing works

Molecular phylogenetics of the gomphoid-phalloid fungi with an establishment of the new subclass Phallomycetidae and two new orders

Hosaka, K., Bates, S. T., Beever, R. E., et al. (2006) · Mycologia · doi:10.3852/mycologia.98.6.949 · Cited by 169 · see citing works

Phylogenetic Validation of the Genera Angomonas and Strigomonas of Trypanosomatids Harboring Bacterial Endosymbionts with the Description of New Species of Trypanosomatids and of Proteobacterial Symbionts

Teixeira, M. M. G., Borghesan, T. C., Ferreira, R. C., et al. (2011) · Protist · doi:10.1016/j.protis.2011.01.001 · Cited by 165 · see citing works

Ultrastructural and molecular phylogenetic delineation of a new order, the Rhizophydiales (Chytridiomycota)

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Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates

Burki, F., Inagaki, Y., Bråte, J., Archibald, J. M., Keeling, P. J., Cavalier‐Smith, T., Sakaguchi, M., Hashimoto, T., Horák, A., Kumar, S., et al. (2009) · Genome Biology and Evolution · doi:10.1093/gbe/evp022 · Cited by 159 · see citing works

What is Cryptosporidium? Reappraising its biology and phylogenetic affinities

Barta, J. R., & Thompson, R. C. A. (2006) · Trends in Parasitology · doi:10.1016/j.pt.2006.08.001 · Cited by 159 · see citing works

Critical Taxonomic Revision of Parabasalids with Description of one New Genus and three New Species

Čepička, I., Hampl, V., & Kulda, J. (2010) · Protist · doi:10.1016/j.protis.2009.11.005 · Cited by 158 · see citing works

A phylogenetic hypothesis of Ustilaginomycotina based on multiple gene analyses and morphological data

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Deep Phylogeny and Evolution of Slime Moulds (Mycetozoa)

Fiore‐Donno, A. M., Nikolaev, S. I., Nelson, M., et al. (2009) · Protist · doi:10.1016/j.protis.2009.05.002 · Cited by 151 · see citing works

Untangling the Phylogeny of Amoeboid Protists1

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Marine gregarines: evolutionary prelude to the apicomplexan radiation?

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Molecular Evolutionary Analyses of Nuclear‐Encoded Small Subunit Ribosomal RNA Identify an Independent Rhizopod Lineage Containing the Euglyphina and the Chlorarachniophyta

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Phylogeny of the "Forgotten" Cellular Slime Mold, Fonticula alba, Reveals a Key Evolutionary Branch within Opisthokonta

Brown, M. W., Spiegel, F. W., & Silberman, J. D. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp185 · Cited by 149 · see citing works

Morphology, Ultrastructure and Life Cycle of Vitrella brassicaformis n. sp., n. gen., a Novel Chromerid from the Great Barrier Reef

Obornı́k, M., Modrý, D., Lukeš, M., Černotíková‐Stříbrná, E., Cihlář, J., Tesařová, M., Kotabová, E., Vancová, M., Prášil, O., & Lukeš, J. (2011) · Protist · doi:10.1016/j.protis.2011.09.001 · Cited by 148 · see citing works

Supraordinal taxa of Ascomycota

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Phylogenomic analyses predict sistergroup relationship of nucleariids and Fungi and paraphyly of zygomycetes with significant support

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Novel Cultured Protists Identify Deep-branching Environmental DNA Clades of Cercozoa: New Genera Tremula, Micrometopion, Minimassisteria, Nudifila, Peregrinia

Howe, A. T., Bass, D., Scoble, J. M., Lewis, R., Vickerman, K., Arndt, H., & Cavalier‐Smith, T. (2011) · Protist · doi:10.1016/j.protis.2010.10.002 · Cited by 139 · see citing works

Evolution: Revisiting the Root of the Eukaryote Tree

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Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae

Geiser, D. M., Gueidan, C., Miądlikowska, J., et al. (2006) · Mycologia · doi:10.1080/15572536.2006.11832633 · Cited by 131 · see citing works

A phylogenetic hypothesis of Ustilaginomycotina based on multiple gene analyses and morphological data

Begerow, D., Stoll, M., & Bauer, R. (2006) · Mycologia · doi:10.1080/15572536.2006.11832620 · Cited by 130 · see citing works

Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life

Verbruggen, H., Maggs, C. A., Saunders, G. W., Gall, L. L., Yoon, H. S., & Clerck, O. D. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-16 · Cited by 129 · see citing works

Congruence between nuclear and mitochondrial genes in Demospongiae: A new hypothesis for relationships within the G4 clade (Porifera: Demospongiae)

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Hyaloraphidium curvatum: A Linear Mitochondrial Genome, tRNA Editing, and an Evolutionary Link to Lower Fungi

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COI Barcoding of Nebelid Testate Amoebae (Amoebozoa: Arcellinida): Extensive Cryptic Diversity and Redefinition of the Hyalospheniidae Schultze

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Molecular phylogenetics of the gomphoid-phalloid fungi with an establishment of the new subclass Phallomycetidae and two new orders

Hosaka, K., Bates, S. T., Beever, R. E., et al. (2006) · Mycologia · doi:10.1080/15572536.2006.11832624 · Cited by 119 · see citing works

Morphology and development of rumen fungi: Neocallimastix sp., Piromyces communis, and Orpinomyces bovis gen.nov., sp.nov.

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AMPHIDINIUM REVISITED. I. REDEFINITION OF AMPHIDINIUM (DINOPHYCEAE) BASED ON CLADISTIC AND MOLECULAR PHYLOGENETIC ANALYSES1

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For common community phylogenetic analyses, go ahead and use synthesis phylogenies

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Phylogenomic Insights into Animal Evolution

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