EU project SponGES
Published September 26, 2018 | Version v1
Journal article Open

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

Creators

  • 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; Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Barrack Road, The Nothe, Weymouth, Dorset, DT4 8UB, United Kingdom
  • 3. Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, 02881, USA
  • 4. Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceské Budejovice, 37005, Czechia; Faculty of Science, University of South Bohemia, Ceské Budejovice, 37005, Czechia
  • 5. National Institute for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, 20892, USA
  • 6. Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
  • 7. Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, Salzburg, A-5020, Austria
  • 8. CNRS, UMR 7144 (AD2M), Groupe Evolution des Protistes et Ecosystemes Pelagiques, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France
  • 9. Department of Biological Sciences, Mississippi State University, Starkville, 39762, Mississippi, USA; Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Starkville, 39762, Mississippi, USA
  • 10. Department of Organismal Biology, Program in Systematic Biology, Science for Life Laboratory, Uppsala University, Uppsala, 75236, Sweden
  • 11. Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC Box 574, Uppsala, SE-75123, Sweden
  • 12. Department of Zoology, Faculty of Science, Charles University, Vinicna 7, Prague, 128 44, Czechia
  • 13. Core Facility Centre for Culture Collection of Microorganisms, Saint Petersburg State University, Saint Petersburg, 198504, Russia
  • 14. Institut de Ciencies del Mar, CSIC, Passeig Marıtim de la Barceloneta, 37-49, Barcelona, 08003, Catalonia, Spain
  • 15. Department of Ecology, University of Kaiserslautern, Erwin-Schroedinger Street, Kaiserslautern, D-67663, Germany; Department of Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstrasse 5, Essen, D-45141, Germany
  • 16. Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, Oslo, 0316, Norway
  • 17. Department of Biology, Dalhousie University, Halifax, B3H 4R2, NS, Canada
  • 18. Sorbonne Universite, Universite Pierre et Marie Curie - Paris 6, CNRS, UMR 7144 (AD2M), Station Biologique de Roscoff, Place Georges Teis- sier, CS90074, Roscoff, 29688, France
  • 19. Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Pruumyslová 595, Vestec, 252 42, Czechia
  • 20. Department of Invertebrate Zoology, American Museum of Natural History, New York City, New York, 10024, USA
  • 21. Senckenberg am Meer, DZMB – German Centre for Marine Biodiversity Research, Wilhelmshaven, 26382, Germany
  • 22. Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
  • 23. Department of Molecular Phylogenetics and Evolution, University of Warsaw, Warsaw, 02-089, Poland
  • 24. Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia; Laboratory of Parasitic Worms and Protistology, Zoological Institute RAS, Saint Petersburg, 199034, Russia
  • 25. Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceské Budejovice, 37005, Czechia
  • 26. Department of Zoology, Institute of Biosciences, University of Sao Paulo, Matao Travessa 14 Cidade Universitaria, Sao Paulo, 05508-090, Sao Paulo, Brazil
  • 27. Laboratory of Soil Biodiversity, University of Neuchatel, Rue Emile-Argand 11, Neuchatel, 2000, Switzerland; Real Jardín Botánico, CSIC, Plaza de Murillo 2, Madrid, 28014, Spain
  • 28. Institut de Systématique, Évolution, Biodiversité, Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier, CP 39, Paris, 75005, France
  • 29. Department of Integrative Biology, University of Guelph, Summerlee Science Complex, Guelph, ON, N1G 2W1, Canada;Department of Zoology, University of British Columbia, 4200-6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
  • 30. Royal Botanic Garden, Edinburgh, EH3 5LR, United Kingdom; Institute for Agrifood Research and Technology, C/Poble Nou km 5.5, Sant Carles de La Ràpita, E-43540, Spain
  • 31. Institut de Ciéncies del Mar, CSIC, Passeig Marítim de la Barceloneta, 37-49, Barcelona, 08003, Catalonia, Spain
  • 32. Laboratory of Soil Biodiversity, University of Neuchatel, Rue Emile-Argand 11, Neuchatel, 2000, Switzerland; Jardin Botanique de Neuchatel, Chemin du Perthuis-du-Sault 58, Neuchatel, 2000, Switzerland
  • 33. Department of Natural Sciences, National Museums Northern Ireland, 153 Bangor Road, Holywood, BT18 OEU, United Kingdom
  • 34. Department of Oceanography and Kyungpook Institute of Oceanography, School of Earth System Sciences, Kyungpook National University, Daegu, Korea
  • 35. Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland
  • 36. Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, 35487, USA
  • 37. Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marıtim de la Barceloneta 37-49, Barcelona, 08003, Catalonia, Spain
  • 38. School of Applied Sciences, Edinburgh Napier University, Edinburgh, EH11 4BN, United Kingdom
  • 39. Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, AR 72701, USA
  • 40. Science Research Centre, Hosei University, 2-17-1 Fujimi, Chiyoda-ku, Tokyo, 102-8160, Japan
  • 41. Laboratoire Evolution et Systématique, Université Paris-XI, Orsay, 91405, France
  • 42. Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, 74074, USA
  • 43. Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia; Department of Organismal Biology, Systematic Biology Program, Uppsala University, Uppsala, SE-752 36, Sweden
  • 44. Yantai Institute of Coastal Zone Research, Chinese Academy of Science, Yantai, 264003, China

Description

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.

Notes

ACKNOWLEDGEMENTS. After the first author, D. Bass, C.E Lane, J. Lukes, C. L. Schoch and A. Smirnov have contributed equally and are to be considered second authors; subsequent authors are listed alphabetically and are to be considered third authors. We were saddened and hurt by the untimely loss of two dear colleagues, D.H. Lynn and J. Clamp, both ciliatologists. Research support was provided as follows: SMA by NSERC 249889-2007; DB by NERC NE/H009426/1 and NE/H000887/1; MWB by NSF 1456054; FB by a Fellowship from Science for Life Laboratory and VR/2017-04563; PC by EU-Horizon 2020 research and innovation program through the SponGES project 679849 (This document reflects only the authors' view and the Executive Agency for Small and Medium-sized Enterprises (EASME) is not responsible for any use that may be made of the information it contains); IC by CSF 18-18699S; BE by RCN Tax- MArc 268286/GMR; LG by ANR HAPAR (ANR-14-CE02- 0007); VH MK JL by ERDF; MEYS with ERC 771592 CZ 1.05/1.1.00/02.0109 BIOCEV; SK by RSF 16-14-10302; MK by CSF GA18-28103S; CEL by NSF 1541510 and NIH- AI124092; EL by CAM: 2017-T1/AMB-5210; and by grant 2017-T1/AMB-5210 from the program "Atracción de talentos" from the Consejería de Educación, Juventud y Deporte, Comunidad de Madrid; JL by ERC CZ LL1601 and OPVVV 16_019/0000759; MP by NSF DEB-1455611; DJR by the Beatriu de Pinós postdoctoral programme of the Government of Catalonia's Secretariat for Universities and Research of the Ministry of Economy and Knowledge; CLS by the intramural research program of the National Library of Medicine, National Institutes of Health; AS by RSF 17-14-01391 and RFBR 16-04-01454 NY by NSF DEB 1557102; VZ by RFBR 16-34-60102 mol-a-dk; UniEuk and EukRef by the Gordon and Betty Moore Foundation. We thank numerous colleagues who were consulted ad hoc throughout this process. In addition, we specifically thank Alexander Ereskovsky (CNRS, Station marine d'Endoume, Marseille, France) for help with the sponges; and Inaki Ruiz-Trillo (ICREA - Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Catalonia, Spain) with the Holozoa; David S. Hibbett (Biology Depart- ment, Clark University, Worcester, MA USA, and Radcliffe Institute for Advanced Study, Harvard University, Cam- bridge, MA) with the Holomycota; Isabelle Florent (Institut de Systématique, Évolution, Biodiversité, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris, France) with Apicomplexa; Shauna Murray (Climate Change Cluster, University of Technology Sydney, Aus-tralia), Albert René (Dept. Biologia Marina i Oceanografia, Institut de Ciències del Mar, CMIMA (CSIC), Barcelona, Spain) and Nicolas Chomérat (IFREMER, ODE/UL/LER Bretagne Occidentale, Concarneau, France) for dinoflagellate primers and barcoding; Urban Tillmann (Alfred Wegener Institut, Helmholz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany) and Per Juel Hansen (Marine Biological Section, Dept. of Biology, University of Copenhagen, Denmark) for the dinoflagellate literature and functional assignments; William Bourland (Biology, Boise State University) for discussions on ciliates; Alastair Simpson (Dalhousie University) for discussions on higher level ranking and structure; Angela Mele (Philadelphia) for the cover art.

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Is identical to
https://onlinelibrary.wiley.com/doi/full/10.1111/jeu.12691 (URL)

Funding

SponGES – Deep-sea Sponge Grounds Ecosystems of the North Atlantic: an integrated approach towards their preservation and sustainable exploitation 679849
European Commission