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 | |
State | Published - 1 Jan 2019 |
Keywords
- Algae
- amoebae
- biodiversity
- ciliate
- ecology
- flagellate
- fungus
- microbiology
- parasite
- plankton
- protozoa
- systematics
- taxonomy
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Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. / Adl, Sina M.; Bass, David; Lane, Christopher E. et al.
In: Journal of Eukaryotic Microbiology, Vol. 66, No. 1, 01.01.2019, p. 4-119.Research output: Contribution to journal › Article › peer-review
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 -