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

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. HeissMona 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

Life Sciences

Research output: Contribution to journal › Article › peer-review

588 Scopus citations

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.

Original language	English
Pages (from-to)	4-119
Number of pages	116
Journal	Journal of Eukaryotic Microbiology
Volume	66
Issue number	1
DOIs	https://doi.org/10.1111/jeu.12691
State	Published - 1 Jan 2019

Keywords

Algae
amoebae
biodiversity
ciliate
ecology
flagellate
fungus
microbiology
parasite
plankton
protozoa
systematics
taxonomy

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10.1111/jeu.12691

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Adl, S. M., Bass, D., Lane, C. E., Lukeš, J., Schoch, C. L., Smirnov, A., Agatha, S., Berney, C., Brown, M. W., Burki, F., Cárdenas, P., Čepička, I., Chistyakova, L., del Campo, J., Dunthorn, M., Edvardsen, B., Eglit, Y., Guillou, L., Hampl, V., ... Zhang, Q. (2019). Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. Journal of Eukaryotic Microbiology, 66(1), 4-119. https://doi.org/10.1111/jeu.12691

@article{a33e3cc5dab3433f938eab50b3b49f32,

title = "Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes",

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",

author = "Adl, {Sina M.} and David Bass and Lane, {Christopher E.} and Julius Luke{\v s} and Schoch, {Conrad L.} and Alexey Smirnov and Sabine Agatha and Cedric Berney and Brown, {Matthew W.} and Fabien Burki and Paco C{\'a}rdenas and Ivan {\v C}epi{\v c}ka and Lyudmila Chistyakova and {del Campo}, Javier and Micah Dunthorn and Bente Edvardsen and Yana Eglit and Laure Guillou and Vladim{\'i}r Hampl and Heiss, {Aaron A.} and Mona Hoppenrath and James, {Timothy Y.} and Anna Karnkowska and Sergey Karpov and Eunsoo Kim and Martin Kolisko and Alexander Kudryavtsev and Lahr, {Daniel J.G.} and Enrique Lara and {Le Gall}, Line and Lynn, {Denis H.} and Mann, {David G.} and Ramon Massana and Mitchell, {Edward A.D.} and Christine Morrow and Park, {Jong Soo} and Pawlowski, {Jan W.} and Powell, {Martha J.} and Richter, {Daniel J.} and Sonja Rueckert and Lora Shadwick and Satoshi Shimano and Spiegel, {Frederick W.} and Guifr{\'e} Torruella and Noha Youssef and Vasily Zlatogursky and Qianqian Zhang",

note = "Funding Information: 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{\textquoteright} 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 {"}Atracci{\'o}n de talen-tos{"} from the Consejer{\'i}a de Educaci{\'o}n, 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 Pin{\'o}s postdoctoral programme of the Government of Catalonia{\textquoteright}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. Funding Information: After the first author, D. Bass, C.E Lane, J. Luke{\v s}, 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{\textquoteright} 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 TaxMArc 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 {"}Atracci{\'o}n de talentos{"} from the Consejer{\'i}a de Educaci{\'o}n, 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 Pin{\'o}s 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 I{\~n}aki Ruiz-Trillo (ICREA - Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Catalonia, Spain) with the Holozoa; David S. Hibbett (Biology Department, Clark University, Worcester, MA USA, and Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA) with the Holomycota; Isabelle Florent (Institut de Syst{\'e}matique, {\'E}volution, Biodiversit{\'e}, Mus{\'e}um National d'Histoire Naturelle, Sorbonne Universit{\'e}s, Paris, France) with Apicomplexa; Shauna Murray (Climate Change Cluster, University of Technology Sydney, Australia), Albert Re{\~n}{\'e} (Dept. Biologia Marina i Oceanografia, Institut de Ci{\`e}ncies del Mar, CMIMA (CSIC), Barcelona, Spain) and Nicolas Chom{\'e}rat (IFREMER, ODE/UL/LER Bretagne Occidentale, Concarneau, France) for dinoflagellate primers and barcoding; Urban Tillmann (Alfred Wegener Institut, Helmholz-Zentrum f{\"u}r 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. Publisher Copyright: {\textcopyright} 2019 International Society of Protistologists",

year = "2019",

month = jan,

day = "1",

doi = "10.1111/jeu.12691",

language = "English",

volume = "66",

pages = "4--119",

journal = "Journal of Eukaryotic Microbiology",

issn = "1066-5234",

publisher = "Wiley-Blackwell Publishing Ltd",

number = "1",

}

Adl, SM, Bass, D, Lane, CE, Lukeš, J, Schoch, CL, Smirnov, A, Agatha, S, Berney, C, Brown, MW, Burki, F, Cárdenas, P, Čepička, I, Chistyakova, L, del Campo, J, Dunthorn, M, Edvardsen, B, Eglit, Y, Guillou, L, Hampl, V, Heiss, AA, Hoppenrath, M, James, TY, Karnkowska, A, Karpov, S, Kim, E, Kolisko, M, Kudryavtsev, A, Lahr, DJG, Lara, E, Le Gall, L, Lynn, DH, Mann, DG, Massana, R, Mitchell, EAD, Morrow, C, Park, JS, Pawlowski, JW, Powell, MJ, Richter, DJ, Rueckert, S, Shadwick, L, Shimano, S, Spiegel, FW, Torruella, G, Youssef, N, Zlatogursky, V & Zhang, Q 2019, 'Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes', Journal of Eukaryotic Microbiology, vol. 66, no. 1, pp. 4-119. https://doi.org/10.1111/jeu.12691

TY - JOUR

T1 - Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

AU - Adl, Sina M.

AU - Bass, David

AU - Lane, Christopher E.

AU - Lukeš, Julius

AU - Schoch, Conrad L.

AU - Smirnov, Alexey

AU - Agatha, Sabine

AU - Berney, Cedric

AU - Brown, Matthew W.

AU - Burki, Fabien

AU - Cárdenas, Paco

AU - Čepička, Ivan

AU - Chistyakova, Lyudmila

AU - del Campo, Javier

AU - Dunthorn, Micah

AU - Edvardsen, Bente

AU - Eglit, Yana

AU - Guillou, Laure

AU - Hampl, Vladimír

AU - Heiss, Aaron A.

AU - Hoppenrath, Mona

AU - James, Timothy Y.

AU - Karnkowska, Anna

AU - Karpov, Sergey

AU - Kim, Eunsoo

AU - Kolisko, Martin

AU - Kudryavtsev, Alexander

AU - Lahr, Daniel J.G.

AU - Lara, Enrique

AU - Le Gall, Line

AU - Lynn, Denis H.

AU - Mann, David G.

AU - Massana, Ramon

AU - Mitchell, Edward A.D.

AU - Morrow, Christine

AU - Park, Jong Soo

AU - Pawlowski, Jan W.

AU - Powell, Martha J.

AU - Richter, Daniel J.

AU - Rueckert, Sonja

AU - Shadwick, Lora

AU - Shimano, Satoshi

AU - Spiegel, Frederick W.

AU - Torruella, Guifré

AU - Youssef, Noha

AU - Zlatogursky, Vasily

AU - Zhang, Qianqian

N1 - Funding Information: 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 talen-tos" 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. Funding Information: After the first author, D. Bass, C.E Lane, J. Lukeš, 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 TaxMArc 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 Iñaki Ruiz-Trillo (ICREA - Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Catalonia, Spain) with the Holozoa; David S. Hibbett (Biology Department, Clark University, Worcester, MA USA, and Radcliffe Institute for Advanced Study, Harvard University, Cambridge, 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, Australia), Albert Reñé (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. Publisher Copyright: © 2019 International Society of Protistologists

PY - 2019/1/1

Y1 - 2019/1/1

N2 - 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.

AB - 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.

KW - Algae

KW - amoebae

KW - biodiversity

KW - ciliate

KW - ecology

KW - flagellate

KW - fungus

KW - microbiology

KW - parasite

KW - plankton

KW - protozoa

KW - systematics

KW - taxonomy

UR - http://www.scopus.com/inward/record.url?scp=85060143843&partnerID=8YFLogxK

U2 - 10.1111/jeu.12691

DO - 10.1111/jeu.12691

M3 - Article

C2 - 30257078

AN - SCOPUS:85060143843

SN - 1066-5234

VL - 66

SP - 4

EP - 119

JO - Journal of Eukaryotic Microbiology

JF - Journal of Eukaryotic Microbiology

IS - 1

ER -

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

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Keywords

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