Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

Sina M Adl; David Bass; Christopher E Lane; Julius Lukeš; Conrad L Schoch; Alexey Smirnov; Sabine Agatha; Cedric Berney; Matthew W Brown; Fabien Burki; Paco Cárdenas; Ivan Čepička; Lyudmila Chistyakova; Javier Del Campo; Micah Dunthorn; Bente Edvardsen; Yana Eglit; Laure Guillou; Vladimír Hampl; Aaron A Heiss; Mona Hoppenrath; Timothy Y James; Anna Karnkowska; Sergey Karpov; Eunsoo Kim; Martin Kolisko; Alexander Kudryavtsev; Daniel J G Lahr; Enrique Lara; Line Le Gall; Denis H Lynn; David G Mann; Ramon Massana; Edward A D Mitchell; Christine Morrow; Jong Soo Park; Jan W Pawlowski; Martha J Powell; Daniel J Richter; Sonja Rueckert; Lora Shadwick; Satoshi Shimano; Frederick W Spiegel; Guifré Torruella; Noha Youssef; Vasily Zlatogursky; Qianqian Zhang

doi:10.1111/jeu.12691

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

J Eukaryot Microbiol. 2019 Jan;66(1):4-119. doi: 10.1111/jeu.12691.

Authors

Sina M Adl¹, David Bass^{2

3}, Christopher E Lane⁴, Julius Lukeš^{5

6}, Conrad L Schoch⁷, Alexey Smirnov⁸, Sabine Agatha⁹, Cedric Berney¹⁰, Matthew W Brown^{11

12}, Fabien Burki¹³, Paco Cárdenas¹⁴, Ivan Čepička¹⁵, Lyudmila Chistyakova¹⁶, Javier Del Campo¹⁷, Micah Dunthorn^{18

19}, Bente Edvardsen²⁰, Yana Eglit²¹, Laure Guillou²², Vladimír Hampl²³, Aaron A Heiss²⁴, Mona Hoppenrath²⁵, Timothy Y James²⁶, Anna Karnkowska²⁷, Sergey Karpov^{8

27}, Eunsoo Kim²⁴, Martin Kolisko⁵, Alexander Kudryavtsev^{8

28}, Daniel J G Lahr²⁹, Enrique Lara^{30

31}, Line Le Gall³², Denis H Lynn^{33

34}, David G Mann^{35

36}, Ramon Massana¹⁷, Edward A D Mitchell^{30

37}, Christine Morrow³⁸, Jong Soo Park³⁹, Jan W Pawlowski⁴⁰, Martha J Powell⁴¹, Daniel J Richter⁴², Sonja Rueckert⁴³, Lora Shadwick⁴⁴, Satoshi Shimano⁴⁵, Frederick W Spiegel⁴⁴, Guifré Torruella⁴⁶, Noha Youssef⁴⁷, Vasily Zlatogursky^{8

48}, Qianqian Zhang⁴⁹

Affiliations

¹ Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, S7N 5A8, SK, Canada.
² Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom.
³ 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.

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.

Keywords: Algae; amoebae; biodiversity; ciliate; ecology; flagellate; fungus; microbiology; parasite; plankton; protozoa; systematics; taxonomy.

Publication types

Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Biodiversity*
Eukaryota / classification*
Phylogeny*
Terminology as Topic*

Grants and funding

R03 AI124092/AI/NIAID NIH HHS/United States