Open Access

Journal of Eukaryotic Microbiology, volume 66, issue 1, pages 4-119

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

Sina Adl ¹

David I. Bass ^{2, 3}

CHRISTOPHER E. LANE ⁴

Gertraud Burger ^{5, 6}

Conrad L. Schoch ⁷

ALEXEY V. SMIRNOV ⁸

Sabine Agatha ⁹

Cédric Berney ¹⁰

Matthew Brown ^{11, 12}

Fabien Burki ¹³

Paco Cárdenas ¹⁴

Ivan Čepička ¹⁵

Lyudmila Chistyakova ¹⁶

Javier Del Campo ¹⁷

Micah Dunthorn ^{18, 19}

B. Edvardsen ²⁰

Yana Eglit ²¹

Laure Guillou ²²

Vladimir Hampl ²³

Aaron A Heiss ²⁴

MONA HOPPENRATH ²⁵

T. D. James ²⁶

Anna Karnkowska ²⁷

Sergei A Karpov ^{8, 27}

Eunsoo Kim ²⁴

Martin Kolisko ⁵

Aleksandr A Kudryavtsev ^{8, 28}

Daniel J. G. Lahr ²⁹

Enrique Lara ^{30, 31}

Line Le Gall ³²

Denis H. Lynn ^{33, 34}

David Mann ^{35, 36}

Ramunas Stepanauskas ¹⁷

Edward D. Mitchell ^{30, 37}

CHRISTINE MORROW ³⁸

Jong Soo Park ³⁹

J. W. Pawlowski ⁴⁰

Martha J Powell ⁴¹

Daniel J Richter ⁴²

Sonja Rueckert ⁴³

Lora Shadwick ⁴⁴

SATOSHI SHIMANO ⁴⁵

Frederick W. Spiegel ⁴⁴

Guifré Torruella ⁴⁶

Mostafa S. Elshahed ⁴⁷

Vasily V. Zlatogursky ^{8, 48}

Qianqian Zhang ⁴⁹

Show full list: 47 authors

Hide authors affiliations

Department of Soil Sciences College of Agriculture and Bioresources, University of Saskatchewan Saskatoon S7N 5A8 SK Canada |

Department of Life Sciences The Natural History Museum Cromwell Road London SW7 5BD United Kingdom |

Centre for Environment, Fisheries and Aquaculture Science (CEFAS) Barrack Road, The Nothe Weymouth Dorset DT4 8UB United Kingdom |

⁴

Department of Biological Sciences University of Rhode Island Kingston Rhode Island 02881 USA |

⁵

Institute of Parasitology, Biology Centre Czech Academy of Sciences České Budějovice 37005 Czechia |

⁶

Faculty of Science University of South Bohemia České Budějovice 37005 Czechia |

⁷

National Institute for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda Maryland 20892 USA |

⁸

Department of Invertebrate Zoology Faculty of Biology Saint Petersburg State University Saint Petersburg 199034 Russia |

⁹

Department of Biosciences University of Salzburg Hellbrunnerstrasse 34 Salzburg A‐5020 Austria |

¹⁰

CNRS, UMR 7144 (AD2M), Groupe Evolution des Protistes et Ecosystèmes Pélagiques Station Biologique de Roscoff Place Georges Teissier Roscoff 29680 France |

¹¹

Department of Biological Sciences Mississippi State University Starkville 39762 Mississippi USA |

¹²

Institute for Genomics, Biocomputing & Biotechnology Mississippi State University Starkville 39762 Mississippi USA |

¹³

Department of Organismal Biology Program in Systematic Biology Science for Life Laboratory Uppsala University Uppsala 75236 Sweden |

¹⁴

Pharmacognosy, Department of Medicinal Chemistry Uppsala University BMC Box 574 Uppsala SE‐75123 Sweden |

¹⁵

Department of Zoology Faculty of Science Charles University Vinicna 7 Prague 128 44 Czechia |

¹⁶

Core Facility Centre for Culture Collection of Microorganisms Saint Petersburg State University Saint Petersburg 198504 Russia |

¹⁷

Institut de Ciències del Mar, CSIC Passeig Marítim de la Barceloneta, 37‐49 Barcelona 08003 Catalonia Spain |

¹⁸

Department of Ecology University of Kaiserslautern Erwin‐Schroedinger Street Kaiserslautern D‐67663 Germany |

¹⁹

Department of Eukaryotic Microbiology University of Duisburg‐Essen Universitätsstrasse 5 Essen D‐45141 Germany |

²⁰

Department of Biosciences University of Oslo P.O. Box 1066 Blindern Oslo 0316 Norway |

²¹

Department of Biology Dalhousie University Halifax B3H 4R2 NS Canada |

²²

Sorbonne Université, Université Pierre et Marie Curie ‐ Paris 6, CNRS, UMR 7144 (AD2M) Station Biologique de Roscoff Place Georges Teissier, CS90074 Roscoff 29688 France |

²³

Department of Parasitology Faculty of Science Charles University, BIOCEV Průmyslová 595 Vestec 252 42 Czechia |

²⁴

Department of Invertebrate Zoology American Museum of Natural History New York City New York 10024 USA |

²⁵

Senckenberg am Meer, DZMB – German Centre for Marine Biodiversity Research Wilhelmshaven 26382 Germany |

²⁶

Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor Michigan 48109 USA |

²⁷

Department of Molecular Phylogenetics and Evolution University of Warsaw Warsaw 02‐089 Poland |

²⁸

Laboratory of Parasitic Worms and Protistology Zoological Institute RAS Saint Petersburg 199034 Russia |

²⁹

Department of Zoology Institute of Biosciences University of Sao Paulo Matao Travessa 14 Cidade Universitaria Sao Paulo 05508‐090 Sao Paulo Brazil |

³⁰

Laboratory of Soil Biodiversity University of Neuchâtel Rue Emile‐Argand 11 Neuchâtel 2000 Switzerland |

³¹

Real Jardín Botánico, CSIC Plaza de Murillo 2 Madrid 28014 Spain |

³²

Institut de Systématique, Évolution, Biodiversité, Muséum National d'Histoire Naturelle Sorbonne Universités 57 rue Cuvier, CP 39 Paris 75005 France |

³³

Department of Integrative Biology University of Guelph Summerlee Science Complex Guelph ON N1G 2W1 Canada |

³⁴

Department of Zoology University of British Columbia 4200‐6270 University Blvd. Vancouver BC V6T 1Z4 Canada |

³⁵

Royal Botanic Garden Edinburgh EH3 5LR United Kingdom |

³⁶

Institute for Agrifood Research and Technology C/Poble Nou km 5.5 Sant Carles de La Ràpita E‐43540 Spain |

³⁷

Jardin Botanique de Neuchâtel Chemin du Perthuis‐du‐Sault 58 Neuchâtel 2000 Switzerland |

³⁸

Department of Natural Sciences National Museums Northern Ireland 153 Bangor Road Holywood BT18 OEU United Kingdom |

³⁹

Department of Oceanography and Kyungpook Institute of Oceanography School of Earth System Sciences Kyungpook National University Daegu Korea |

⁴⁰

Department of Genetics and Evolution University of Geneva 1211 Geneva 4 Switzerland |

⁴¹

Department of Biological Sciences The University of Alabama Tuscaloosa Alabama 35487 USA |

⁴²

Institut de Biologia Evolutiva (CSIC‐Universitat Pompeu Fabra) Passeig Marítim de la Barceloneta 37‐49 Barcelona 08003 Catalonia Spain |

⁴³

School of Applied Sciences Edinburgh Napier University Edinburgh EH11 4BN United Kingdom |

⁴⁴

Department of Biological Sciences University of Arkansas Fayetteville Arkansas AR 72701 USA |

⁴⁵

Science Research Centre Hosei University 2‐17‐1 Fujimi Chiyoda‐ku Tokyo 102‐8160 Japan |

⁴⁶

Laboratoire Evolution et Systématique, Université Paris‐XI Orsay 91405 France |

⁴⁷

Department of Microbiology and Molecular Genetics Oklahoma State University Stillwater Oklahoma 74074 USA |

⁴⁸

Department of Organismal Biology Systematic Biology Program Uppsala University Uppsala SE‐752 36 Sweden |

⁴⁹

Yantai Institute of Coastal Zone Research Chinese Academy of Science Yantai 264003 China |

Publication type: Journal Article

Publication date: 2019-01-01

Wiley

Journal: Journal of Eukaryotic Microbiology

scimago Q3

SJR: 0.656

CiteScore: 4.3

Impact factor: 2.1

ISSN: 10665234, 15507408

DOI: 10.1111/jeu.12691

Copy DOI

PubMed ID: 30257078

Microbiology

Abstract

This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.

Found

	5 10 15 20 25 30 35 40 45 50
European Journal of Protistology	European Journal of Protistology, 46, 4.8% European Journal of Protistology 46 publications, 4.8%
Journal of Eukaryotic Microbiology	Journal of Eukaryotic Microbiology, 38, 3.96% Journal of Eukaryotic Microbiology 38 publications, 3.96%
Scientific Reports	Scientific Reports, 24, 2.5% Scientific Reports 24 publications, 2.5%
Protist	Protist, 21, 2.19% Protist 21 publications, 2.19%
Frontiers in Microbiology	Frontiers in Microbiology, 20, 2.09% Frontiers in Microbiology 20 publications, 2.09%
Microorganisms	Microorganisms, 16, 1.67% Microorganisms 16 publications, 1.67%
Science of the Total Environment	Science of the Total Environment, 15, 1.56% Science of the Total Environment 15 publications, 1.56%
Frontiers in Marine Science	Frontiers in Marine Science, 13, 1.36% Frontiers in Marine Science 13 publications, 1.36%
Molecular Phylogenetics and Evolution	Molecular Phylogenetics and Evolution, 11, 1.15% Molecular Phylogenetics and Evolution 11 publications, 1.15%
Environmental Microbiology	Environmental Microbiology, 11, 1.15% Environmental Microbiology 11 publications, 1.15%
Diversity	Diversity, 10, 1.04% Diversity 10 publications, 1.04%
Soil Biology and Biochemistry	Soil Biology and Biochemistry, 9, 0.94% Soil Biology and Biochemistry 9 publications, 0.94%
Genome Biology and Evolution	Genome Biology and Evolution, 9, 0.94% Genome Biology and Evolution 9 publications, 0.94%
Microbial Ecology	Microbial Ecology, 8, 0.83% Microbial Ecology 8 publications, 0.83%
Biological Reviews	Biological Reviews, 8, 0.83% Biological Reviews 8 publications, 0.83%
International Journal of Systematic and Evolutionary Microbiology	International Journal of Systematic and Evolutionary Microbiology, 7, 0.73% International Journal of Systematic and Evolutionary Microbiology 7 publications, 0.73%
Water Research	Water Research, 7, 0.73% Water Research 7 publications, 0.73%
Current Biology	Current Biology, 7, 0.73% Current Biology 7 publications, 0.73%
Open Biology	Open Biology, 6, 0.63% Open Biology 6 publications, 0.63%
Pathogens	Pathogens, 6, 0.63% Pathogens 6 publications, 0.63%
Frontiers in Cell and Developmental Biology	Frontiers in Cell and Developmental Biology, 6, 0.63% Frontiers in Cell and Developmental Biology 6 publications, 0.63%
International Journal for Parasitology	International Journal for Parasitology, 6, 0.63% International Journal for Parasitology 6 publications, 0.63%
Water Biology and Security	Water Biology and Security, 6, 0.63% Water Biology and Security 6 publications, 0.63%
Journal of Phycology	Journal of Phycology, 6, 0.63% Journal of Phycology 6 publications, 0.63%
Molecular Biology and Evolution	Molecular Biology and Evolution, 6, 0.63% Molecular Biology and Evolution 6 publications, 0.63%
Proceedings of the National Academy of Sciences of the United States of America	Proceedings of the National Academy of Sciences of the United States of America, 6, 0.63% Proceedings of the National Academy of Sciences of the United States of America 6 publications, 0.63%
eLife	eLife, 6, 0.63% eLife 6 publications, 0.63%
Journal of Plankton Research	Journal of Plankton Research, 5, 0.52% Journal of Plankton Research 5 publications, 0.52%
PeerJ	PeerJ, 5, 0.52% PeerJ 5 publications, 0.52%
	5 10 15 20 25 30 35 40 45 50

	50 100 150 200 250
Elsevier	Elsevier, 249, 25.96% Elsevier 249 publications, 25.96%
Springer Nature	Springer Nature, 143, 14.91% Springer Nature 143 publications, 14.91%
Wiley	Wiley, 115, 11.99% Wiley 115 publications, 11.99%
MDPI	MDPI, 73, 7.61% MDPI 73 publications, 7.61%
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 63, 6.57% Cold Spring Harbor Laboratory 63 publications, 6.57%
Frontiers Media S.A.	Frontiers Media S.A., 57, 5.94% Frontiers Media S.A. 57 publications, 5.94%
Oxford University Press	Oxford University Press, 45, 4.69% Oxford University Press 45 publications, 4.69%
Taylor & Francis	Taylor & Francis, 20, 2.09% Taylor & Francis 20 publications, 2.09%
American Society for Microbiology	American Society for Microbiology, 14, 1.46% American Society for Microbiology 14 publications, 1.46%
Pleiades Publishing	Pleiades Publishing, 12, 1.25% Pleiades Publishing 12 publications, 1.25%
The Royal Society	The Royal Society, 10, 1.04% The Royal Society 10 publications, 1.04%
Pensoft Publishers	Pensoft Publishers, 8, 0.83% Pensoft Publishers 8 publications, 0.83%
Microbiology Society	Microbiology Society, 7, 0.73% Microbiology Society 7 publications, 0.73%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 7, 0.73% Public Library of Science (PLoS) 7 publications, 0.73%
Cambridge University Press	Cambridge University Press, 6, 0.63% Cambridge University Press 6 publications, 0.63%
Proceedings of the National Academy of Sciences (PNAS)	Proceedings of the National Academy of Sciences (PNAS), 6, 0.63% Proceedings of the National Academy of Sciences (PNAS) 6 publications, 0.63%
eLife Sciences Publications	eLife Sciences Publications, 6, 0.63% eLife Sciences Publications 6 publications, 0.63%
Magnolia Press	Magnolia Press, 6, 0.63% Magnolia Press 6 publications, 0.63%
The Company of Biologists	The Company of Biologists, 5, 0.52% The Company of Biologists 5 publications, 0.52%
EDP Sciences	EDP Sciences, 5, 0.52% EDP Sciences 5 publications, 0.52%
PeerJ	PeerJ, 5, 0.52% PeerJ 5 publications, 0.52%
American Association for the Advancement of Science (AAAS)	American Association for the Advancement of Science (AAAS), 5, 0.52% American Association for the Advancement of Science (AAAS) 5 publications, 0.52%
American Chemical Society (ACS)	American Chemical Society (ACS), 3, 0.31% American Chemical Society (ACS) 3 publications, 0.31%
F1000 Research	F1000 Research, 3, 0.31% F1000 Research 3 publications, 0.31%
Geological Society of London	Geological Society of London, 3, 0.31% Geological Society of London 3 publications, 0.31%
Inter-Research Science Center	Inter-Research Science Center, 3, 0.31% Inter-Research Science Center 3 publications, 0.31%
SciELO	SciELO, 3, 0.31% SciELO 3 publications, 0.31%
Annual Reviews	Annual Reviews, 3, 0.31% Annual Reviews 3 publications, 0.31%
The Russian Academy of Sciences	The Russian Academy of Sciences, 3, 0.31% The Russian Academy of Sciences 3 publications, 0.31%
	50 100 150 200 250