Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes Sina Adl, David Bass, Christopher Lane, Julius Lukeš, Conrad Schoch, Alexey Smirnov, Sabine Agatha, Cédric Berney, Matthew Brown, Fabien Burki, et al.
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Sina Adl, David Bass, Christopher Lane, Julius Lukeš, Conrad Schoch, et al.. Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. Journal of Eukaryotic Microbiology, Wiley, 2019, 66, pp.4-119. 10.1111/jeu.12691. hal-02167105
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ORIGINAL ARTICLE Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes
Sina M. Adla,* , David Bassb,c , Christopher E. Laned, Julius Lukes e,f , Conrad L. Schochg, Alexey Smirnovh, Sabine Agathai, Cedric Berneyj , Matthew W. Brownk,l, Fabien Burkim,PacoCardenas n , Ivan Cepi cka o, Lyudmila Chistyakovap, Javier del Campoq, Micah Dunthornr,s , Bente Edvardsent , Yana Eglitu, Laure Guillouv, Vladim ır Hamplw, Aaron A. Heissx, Mona Hoppenrathy, Timothy Y. Jamesz, Anna Karn- kowskaaa, Sergey Karpovh,ab, Eunsoo Kimx, Martin Koliskoe, Alexander Kudryavtsevh,ab, Daniel J.G. Lahrac, Enrique Laraad,ae , Line Le Gallaf , Denis H. Lynnag,ah , David G. Mannai,aj, Ramon Massanaq, Edward A.D. Mitchellad,ak , Christine Morrowal, Jong Soo Parkam , Jan W. Pawlowskian, Martha J. Powellao, Daniel J. Richterap, Sonja Rueckertaq, Lora Shadwickar, Satoshi Shimanoas, Frederick W. Spiegelar, Guifre Torruellaat , Noha Youssefau, Vasily Zlatogurskyh,av & Qianqian Zhangaw a Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, S7N 5A8, SK, Canada b Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom c Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Barrack Road, The Nothe, Weymouth, Dorset, DT4 8UB, United Kingdom d Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, 02881, USA e Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Cesk e Budejovice, 37005, Czechia f Faculty of Science, University of South Bohemia, Cesk e Budejovice, 37005, Czechia g National Institute for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, 20892, USA h Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia i Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, Salzburg, A-5020, Austria j CNRS, UMR 7144 (AD2M), Groupe Evolution des Protistes et Ecosystemes Pelagiques, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France k Department of Biological Sciences, Mississippi State University, Starkville, 39762, Mississippi, USA l Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Starkville, 39762, Mississippi, USA m Department of Organismal Biology, Program in Systematic Biology, Science for Life Laboratory, Uppsala University, Uppsala, 75236, Sweden n Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC Box 574, Uppsala, SE-75123, Sweden o Department of Zoology, Faculty of Science, Charles University, Vinicna 7, Prague, 128 44, Czechia p Core Facility Centre for Culture Collection of Microorganisms, Saint Petersburg State University, Saint Petersburg, 198504, Russia q Institut de Ciencies del Mar, CSIC, Passeig Mar ıtim de la Barceloneta, 37-49, Barcelona, 08003, Catalonia, Spain r Department of Ecology, University of Kaiserslautern, Erwin-Schroedinger Street, Kaiserslautern, D-67663, Germany s Department of Eukaryotic Microbiology, University of Duisburg-Essen, Universitatsstrasse€ 5, Essen, D-45141, Germany t Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, Oslo, 0316, Norway u Department of Biology, Dalhousie University, Halifax, B3H 4R2, NS, Canada v 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 w Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Pr umyslova 595, Vestec, 252 42, Czechia x Department of Invertebrate Zoology, American Museum of Natural History, New York City, New York, 10024, USA y Senckenberg am Meer, DZMB – German Centre for Marine Biodiversity Research, Wilhelmshaven, 26382, Germany z Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA aa Department of Molecular Phylogenetics and Evolution, University of Warsaw, Warsaw, 02-089, Poland ab Laboratory of Parasitic Worms and Protistology, Zoological Institute RAS, Saint Petersburg, 199034, Russia ac Department of Zoology, Institute of Biosciences, University of Sao Paulo, Matao Travessa 14 Cidade Universitaria, Sao Paulo, 05508-090, Sao Paulo, Brazil ad Laboratory of Soil Biodiversity, University of Neuchatel,^ Rue Emile-Argand 11, Neuchatel,^ 2000, Switzerland ae Real Jard ın Botanico, CSIC, Plaza de Murillo 2, Madrid, 28014, Spain af Institut de Systematique, Evolution, Biodiversite, Museum National d’Histoire Naturelle, Sorbonne Universites, 57 rue Cuvier, CP 39, Paris, 75005, France ag Department of Integrative Biology, University of Guelph, Summerlee Science Complex, Guelph, ON, N1G 2W1, Canada ah Department of Zoology, University of British Columbia, 4200-6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada ai Royal Botanic Garden, Edinburgh, EH3 5LR, United Kingdom aj Institute for Agrifood Research and Technology, C/Poble Nou km 5.5, Sant Carles de La Rapita, E-43540, Spain ak Jardin Botanique de Neuchatel,^ Chemin du Perthuis-du-Sault 58, Neuchatel,^ 2000, Switzerland al Department of Natural Sciences, National Museums Northern Ireland, 153 Bangor Road, Holywood, BT18 OEU, United Kingdom
© 2018 The Authors Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists 4 Journal of Eukaryotic Microbiology 2019, 66, 4–119 This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Adl et al. Classification of Eukaryotes am Department of Oceanography and Kyungpook Institute of Oceanography, School of Earth System Sciences, Kyungpook National University, Daegu, Korea an Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland ao Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, 35487, USA ap Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Mar ıtim de la Barceloneta 37-49, Barcelona, 08003, Catalonia, Spain aq School of Applied Sciences, Edinburgh Napier University, Edinburgh, EH11 4BN, United Kingdom ar Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, AR 72701, USA as Science Research Centre, Hosei University, 2-17-1 Fujimi, Chiyoda-ku, Tokyo, 102-8160, Japan at Laboratoire Evolution et Systematique, Universite Paris-XI, Orsay, 91405, France au Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, 74074, USA av Department of Organismal Biology, Systematic Biology Program, Uppsala University, Uppsala, SE-752 36, Sweden aw Yantai Institute of Coastal Zone Research, Chinese Academy of Science, Yantai, 264003, China
Keywords ABSTRACT Algae; amoebae; biodiversity; ciliate; ecol- ogy; flagellate; fungus; microbiology; para- This revision of the classification of eukaryotes follows that of Adl et al., 2012 site; plankton; protozoa; systematics; [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since taxonomy. have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, Correspondence environmental sampling in the intervening years has massively increased the S.M. Adl, Department of Soil Sciences, genetic information at hand. Consequently, we have discovered novel clades, College of Agriculture and Bioresources, exciting new genera and uncovered a massive species level diversity beyond University of Saskatchewan, 51 Campus the morphological species descriptions. Several clades known from environ- Drive, Saskatoon, SK, S7N 5A8 Canada mental samples only have now found their home. Sampling soils, deeper mar- Telephone number: 306 966 6866 ine waters and the deep sea will continue to fill us with surprises. The main e-mail: [email protected] 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 Hap- Received: 2 September 2018; accepted tista and Cryptista. We provide suggested primer sets for DNA sequences September 4, 2018. from environmental samples that are effective for each clade. We have pro- vided a guide to trophic functional guilds in an appendix, to facilitate the inter- doi:10.1111/jeu.12691 pretation of environmental samples, and a standardized taxonomic guide for East Asian users.
THIS revision of the classification of eukaryotes updates background information, and to Adl et al. 2007 for a dis- that of the International Society of Protistologists (Adl cussion. Briefly, we adopted a hierarchical system with- et al. 2012). Since then, there has been a massive out formal rank designations. The hierarchy is increase in DNA sequence information of phylogenetic rel- represented by indented paragraphs. The nomenclatural evance from environmental samples. We now have a priority is given to the oldest name (and its authority) that much better sense of the undescribed biodiversity in our correctly assembled genera or higher groups together environment (De Vargas et al. 2015; Pawlowski et al. into a clade, except where its composition was substan- 2012). While significant, it still remains a partial estimation tially modified. In these cases, we have used a newer as several continents and soils in general are poorly sam- term and its appropriate authorship. In cases where ranks pled, and the deeper ocean is hard to reach. These new were created to include a single lower rank, the higher data clarified phylogenetic relationships and the new infor- ranks were eliminated as superfluous. In this scheme, mation is incorporated in this revision. monotypic taxa are represented by the genus only. Nested clades represent monophyletic lineages as best we know and para- or polyphyletic groups are so Systematics indicated. We assembled the classification according to the princi- This system of hierarchical nameless ranks, that ples outlined elsewhere, and we refer the reader to the ignores endings of clade names, has proved its utility in introductions of both Adl et al. 2005 and 2012 for providing name stability as we reconstructed a new
© 2018 The Authors Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists Journal of Eukaryotic Microbiology 2019, 66, 4–119 5 Classification of Eukaryotes Adl et al.
Nomenclature This committee of the Society has had the responsibility of arbitrating nomenclature for protists in general. Histori- cally, the task was simpler as most groups fell under one or the other of the two Codes of Nomenclature (al- gae and some other protists under the “International Code of Nomenclature for algae, fungi, and plants”, and protozoa under the “International Code of Zoological Nomenclature”), and few were described under both Codes. The Society was represented on the relevant committees. Notwithstanding that both Codes are incom- patible, some have proposed to provide parallel classifica- tions in each Code, while others proposed to adopt a modern unified code of nomenclature. Since the rear- rangement of the classification along monophyletic lin- eages during the 1990s, many clades now include a mixture of taxa from both Codes. Several taxa, such as diatoms, are described in parallel under both Codes with different names. This situation created and perpetuates anomalies, such as the recent redescription of the dic- tyostellid amoebae with the botanical Code (Sheikh et al. 2018) for genera that are unarguably in Amoebozoa gov- erned by the Zoological Code. Issues such as these have been thoroughly discussed in the past (Adl et al. 2007; Lahr et al. 2012). It has been the responsibility of this committee to discuss and arbitrate published Figure 1 Overview of the diversity of protists among eukaryotes. phylogenetic hypotheses, proposals for new names and Amoebozoa, Nucletmycea, and Holozoa together form the Amorphea; name changes. Underlying these discussions are princi- The Diaphoretickes includes Crypista, Chloroplastida and Embryo- ples of nomenclatural priority in the spirit of the codes phyta, Rhodophyceae, Haptista, Rhizaria, Alveolata (Apicomplexa, of nomenclature. Dinoflagellata, Ciliata), Stramenopiles and Phaeophyta. A classification is unlike a phylogenetic tree in a publica- tion, where the discovery of new clades, branches, or robust nodes ultimately leads to proposing new names. phylogenetic classification during the past 20 years. Newly named clades and nodes have their utility in phylo- Clade names in this system do not change when their genetic analysis and discussion, but do not need to be for- rank or composition changes, and it is only the authority malized in the classification immediately. An for the name that changes when each clade description overwhelming number of spent names have thus accumu- is adjusted (Cantino, 1998; Pleijel and Rouse, 2003). lated, with an increasing frequency over the past four dec- Where a new term is introduced in this classification, it ades, most of which are no longer—or never were—in is identified with “Adl et al. 2019” as the authority, or common use. Many of these names were ephemeral, as by the submitting author (e.g. Mann in Adl et al., 2019), their monophyly did not stand the test of (time) statistical and they are to be cited as emended in this publication. analysis. The proliferation of these names reflects a The descriptions provided are not intended to substitute methodological error practiced by some. That is to formal- for formal diagnoses. They are provided primarily for the ize names prematurely and try to reorganize classifications student and general users to identify common morpho- single-handedly. As we argued before (Adl et al. 2012), logical features, such as synapomorphies and apomor- this must be done with care, respecting nomenclatural pri- phies, within monophyletic lineages. ority, published as a proposal or a phylogenetic hypothesis There are two novel components in this revision. First, first, to be verified by the community, and only eventually we have provided trophic assignments for most taxa. considered for change in the classification. The task of ref- This will prove useful in interpreting communities from ereeing and classifying falls on Society committees repre- environmental samples. Second, we informally suggest a senting communities of professionals. The very formal phylum rank and classes in most clades to provide a and slow process of voting to conserve or reject names point of reference in the classification hierarchy for the through the tradition of the botanical code takes years as nonspecialist. This became possible, as there has been it has to proceed through committees and then approved some stability at this level in the molecular phylogenetic by vote on the floor of the congress at 6-year intervals. reconstructions. It should be obvious that genera That is, however, too slow for the pace of changes today grouped into a clade then represent a family, and fami- given the rate at which new information is becoming lies into an order. available.
© 2018 The Authors Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists 6 Journal of Eukaryotic Microbiology 2019, 66, 4–119 Adl et al. Classification of Eukaryotes
In contrast to a phylogenetic tree, a classification sys- remains problematic. In some but not all analyses, the tem belongs to a community of users, and it is generated clade appears inside the Archaeplastida. This position has through discussions of the available evidence, for prag- always occurred from time to time in some phylogenies matic purposes of teaching, curation, organizing data, with weak support, but there is now stronger support for archiving and communicating with a common language. It this association. We are not committed to their inclusion is a commonly agreed point of reference. It is not to be within the Archaeplastida but do note its likelihood. The reimagined or re-done at will by one individual. The Lin- inclusion of the Cryptista in the Archaeplastida would naean system that we have inherited has detailed codes expand that group without affecting its defining criteria. of nomenclature that guide and regulate how living organ- Questioning the single origin of a plastid within the isms are named, names changed and classified. The elab- Archaeplastida is a rare minority opinion. Yet, the possibil- orate rules arise from disputes and mistakes made in the ity of more than one plastid origin must not be ruled-out past, in part out of respect for each other’s work. Instead until the cryptomonads are robustly positioned. of providing a long list of rejected and invalid names, we (5) The new robust support for the Cryptista clade is can specify that those not selected in this classification accompanied by a similarly robust support for a clade were considered nomina ambigua, nomina perplexa, nom- comprising the Centroplasthelida and Haptophyta as the ina dubia, nomina nuda or did not have nomenclatural pri- Haptista within the Diaphoretickes. ority and are declared nomina rejicienda. (6) Nodes at the base of the Alveolata are better resolved Another proposed classification of prokaryotes and eukary- with additional genera. The placeholder name Protalveolata otes was published recently (Ruggiero et al. 2015). This is no longer required. effort may be reasonable in their classification of the prokary- (7) The Excavata comprise three clades: the Metamonada, otes, but the eukaryote section does not pass standards of the Discoba, and the Malawimonada. Their mutual relation- modern biology. Specifically, it is their refusal to use mono- ships, as well as their relationships to other clades of phyly as a guiding principle, but to argue to retain “ancestral eukaryotes, remain uncertain. We have dropped the super- (paraphyletic) taxa when it seemed beneficial to do so” group Excavata in favour of the informal Excavates when instead, even where monophyletic clades are already estab- referring to the “Discoba, Metamonada, Malawimonada”, lished. Their insistence on using a hodge-podge of names as Incertae sedis in eukaryotes. The Excavates and several that do not have nomenclatural priority, and that poorly clades and genera fall outside of the two principal domains, describe the taxa included, further reduces its usefulness. but do not cluster together into a third domain. This classification will serve as a primary starting refer- ence for the taxonomic framework developed by UniEuk Classification (unieuk.org; Berney et al. 2017), the Society supported, The super-groups utilized since 2005 (Adl et al. 2005; consensus-driven, community-based and expert-driven Simpson and Roger 2004) are revised as follows (Fig. 1): international initiative to maintain a universal taxonomy (1) Eukaryotes now form two Domains called Amorphea for, at least, microbial eukaryotes. A specific aim of the and Diaphoretickes, with several additional clades that do UniEuk project is to apply one taxonomic framework to all not group into a third Domain. genetic data in the International Nucleotide Sequence (2) In the Amorphea, the Opisthokonta, Breviatea and Database Collaboration (INSDC) repositories, which Apusomonadida now form a robust clade, as noted earlier includes DDBJ (ddbj.nig.ac.jp), GenBank (ncbi.nlm.nih.gov) (Adl et al. 2012), called Obazoa. Within the Opisthokonta, and ENA (ebi.ac.uk/ena) databases. The system’s broad the Holozoa and Nucletmycea(/Holomycota) are robust use and preservation will be ensured by a direct imple- clades with improved resolution of the basal sister lin- mentation of the UniEuk taxonomic framework into the eages. In the Holozoa, the sponges and the other animals ENA (European Nucleotide Archive) at EMBL-EBI (http:// group together as the Metazoa (Porifera, Placozoa, Cteno- www.ebi.ac.uk/ena). The project will capture our collective phora, Cnidaria, Bilateria). In addition, a sister clade to the knowledge on eukaryotic diversity, evolution, and ecology Amorphea comprising several genera was recently via three main modules (EukRef, EukBank and EukMap). described as CRuMs (Brown et al. 2018). EukRef (eukref.org; del Campo et al. 2018) uses a stan- (3) There are two sister clades in Opisthokonta, the Holo- dardized, open-source bioinformatics pipeline to generate zoa and the Nucletmycea (/Holomycota). They share sev- homogenous, high-quality curation of sequences (primarily eral characters, including synthesis of extracellular chitin in 18S rDNA) available in INSDC databases. EukRef is fully an exoskeleton, cyst/spore wall or cell wall of filamentous operational; outputs include (on a lineage-by-lineage basis) growth and hyphae; the extracellular digestion of sub- taxonomically curated sequences, sequence alignments, strates with osmotrophic absorption of nutrients; and phylogenetic trees and metadata. EukBank is a public other cell biosynthetic and metabolic pathways. Genera at repository of (primarily V4 18S rDNA) high-throughput the base of each clade are amoeboid and phagotrophic. metabarcoding data sets, centralized at ENA, with stan- (4) The Archaeplastida, Sar and several other clades dardized protocols for submitting data sets and metadata. remain a monophyletic clade under Diaphoretickes. The EukMap (eukmap.unieuk.org) is an editable, user-friendly clade Cryptista comprising the cryptomonads, kathable- representation of the UniEuk taxonomy in the form of a pharids and Palpitomonas is well recognized and robust, publicly navigable tree, where each node/taxon is associated although placement of its node within the Diaphoretickes with contextual data (taxonomic and ecological information,
© 2018 The Authors Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists Journal of Eukaryotic Microbiology 2019, 66, 4–119 7 Classification of Eukaryotes Adl et al.
Table 1. Higher ranks of the eukaryotes suggesting the position of Table 1 (continued) Linnaean ranks, and the number of known genera Cryptista (C) 21 AMORPHEA Cryptophyceae (O) CRuMs (O) 11 Palpitomonas (G) Collodictyonidae (F) Haptista (P) Rigifilida (F) Haptophyta (C) 80 Mantamonas (G) Pavlovales (F) Amoebozoa 255 Prymnesiophyceae (O) Incertae sedis 21 Centroplasthelida (C) 16 Tubulinea (P) 93 Pterocystida (O) Corycida (C) Panacanthocystida (O) Echinamoebida (C) Archaeplastida Elardia (C) (Arcellinida 63) Glaucophyta (F) 4 Evosea (P) 106 Rhodophyceae (P) 850 Variosea (C) Cyanidiales (O) Eumycetozoa (C) Proteorhodophytina (O/C) Cutosea (C) Eurhodophytina (C) Archamoebea (C) Chloroplastida (72,000 sp + Embryophyta) Discosea (P) 35 Chlorophyta (P) Flabellinia (C) Ulvophyceae (C) Stygamoebida (C) Trebouxiophyceae (C) Centramoebia (C) Chlorophyceae (C) Obazoa Chlorodendrophyceae (C) Apusomonadida (F) 6 Pedinophyceae (C) Breviatea (F) 4 Chloropicophyceae (C) Opisthokonta Picocystophyceae (C) Holozoa 25 (without Choanoflagellata, Porifera and Metazoa) Pyramimonadales (C) Incertae sedis Holozoa: Corallochytrium, Syssomonas Mamiellophyceae (C) Ichtyosporea (O) Nephroselmis (G) Choanoflagellata (C) 57 Pycnococcaceae (C) Metazoa Palmophyllophyceae (C) Porifera (P) 742 Streptophyta (P) Hexactinellida (C) Chlorokybus atmophyticus Homoscleromorpha (C) Mesostigma viridae Demospongiae (C) Klebsomidiophyceae (F) Calcarea (C) Phragmoplastophyta (C) Trichoplax (G/F?) Zygnemataceae (F) Cnidaria (P) Coleochaetophyceae (O) Ctenophora (P) Characeae (F) Bilateria (K, ~35 P) Embryophyta (K) Nucletmycea Sar Rotosphaerida (O) 9 Stramenopiles (P) (Fungi) ~8,600 Bigyra (C) 49 Opisthosporidia (O) Opalinata (O) Aphelidea (F) 4 Placidida (F) Cryptomycota (F) 3 Bicosoecida (O/F) Microsporida (O?/F) >150 Sagenista (C) Blastocladiales (O) 14 Labyrinthulomycetes (O) Chytridiomycetes (C) 140 Pseudophyllomitidae (F?) Dikarya ~8,000 Gyrista (C) 31 excluding Peronosporomycetes and Ochro- Ascomycota (P) ~6,400 phyta Basidiomycota (P) ~1,600 Developea (F) Mucoromycota (P) ~140 Hyphochytriales (O) Neocallimastigaceae (F) 11 Peronosporomycetes (C/O) 46 Olpidium (G) Pirsonia (G) Zoopagomycota (P) ~200 Actinophryidae (F) DIAPHORETICKES Ochrophytaa Incertae sedis: Microhelliela maris, Ancoracysta twista, Chrysista (C)a Rappemonads, Telonemia, Picozoa Chrysophyceae (O)
(continued) (continued)
© 2018 The Authors Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists 8 Journal of Eukaryotic Microbiology 2019, 66, 4–119 Adl et al. Classification of Eukaryotes
Table 1 (continued) Table 1 (continued)
Eustigmatales (O) Retaria Phaeophyceae (O) Foraminifera (P) ~950 Raphidophyceae (O) Monothalamea (C/O?) Schizocladia (O) Tubothalamea (C) Xanthophyceae (O) Globothalamea (C) Diatomista Radiolaria (P) Bolidophyceae (F) Acantharea (C) 50 Diatomea (C) ~400 Taxopodida (F) 1+environmental clades Alveolata, others 26 Polycystinea (C) ~470 Colpodellida (O) Aquavalon (G) Perkinsidae (F) Tremula (G) Colponemidia (F) Incertae sedis Eukarya: Excavates Acavomonas (G) Metamonada 133 Oxyrrhis marina Fornicata (P) Dinoflagellata (P) 300 Parabasalia (P) Syndiniales (O) Preaxostyla (P) Noctilucales (O) Discoba 94 Dinophyceae (C) Jakobida (P) Apicomplexa (P) ~350 Tsukubamonas (G) Incertae sedis: Agamococcidiorida (F), Heterolobosea (P) Protococcidiorida (F) Euglenozoa (P) Aconoidasida (C) Euglenida (C) Conoidasida (C) Diplonemea (O) Ciliophora (P) Symbiontida (F) Karyorelictea (C) 18 Kinetoplastea (C) Heterotrichida (O) 58 Other incertae sedis Eukarya 158 Spirotrichea (C) 139 (+Hypotrichia) ======Hypotrichia 183 G genus; F family; O order; C class; P phylum; K Armophorea (O) 41 kingdom. a Litostomatea (C) 263 The state of the classification in online databases are too poor to Phyllopharyngea (C) 263 evaluate or work with this clade. Colpodea (C) 73 Nassophorea (C) 23 links to representative images, etc.). It will be operational by Plagyopylea (C) 15 2019 and will allow registered community members to Oligomymenophorea (C) 433 directly interact with and inform the taxonomic framework, Rhizaria and to flag taxonomy issues requiring revision. As a whole, Cercozoa (P) >>204 the UniEuk system will represent a community hub to cen- Cercomonadida (F) tralize, standardize, and promote global knowledge on Paracercomonadida (F) eukaryotic diversity, taxonomy and ecology. Glissomonadida (O) Viridiraptoridae (F) Pansomonadidae (F) Clarification of terms for trophic functional groups Sainouridae (F) Thecofilosea (C) Several terms were clarified to correct misuse of terminol- Imbricatea (P) 89 ogy in publications. In 2005, these were: eukaryote, Spongomonadida (F) prokaryote, algae, zoosporic fungi, protozoa, zooplankton, Marimonadida (F) phytoplankton, cyst, spore and cilium. In 2012, they were Variglissida (F) related to the cytoskeleton and motility: lobopodia, lamel- Silicofilosea (C) lipodia, filopodia, granuloreticulopodia, reticulopodia, axopo- Metromonadea (F) dia, centriole, centrosome, microtubular organizing centre Granofilosea (O) (MTOC), basal body, kinetosome, kinetid and mastigont. In Chlorarachnea (F) this revision, they pertain to trophic functional groups. Endomyxa (P) >34 In addition to descriptions of morphology that accom- Vampyrellida (O) pany specimen, which is critical for understanding cell Phytomyxea (O) function and interpreting phylogenetic trees, improved Filoreta (G) descriptions of site and food preferences are required for Gromia (G) an ecological interpretation of the role in the community Ascetosporea (C) and ecosystem. Often species lack sufficient description (continued) of the collection site or feeding habit.
© 2018 The Authors Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists Journal of Eukaryotic Microbiology 2019, 66, 4–119 9 Classification of Eukaryotes Adl et al.
To compare environmental DNA data sets, adequate meta- eaters acquire their prey, and an incomplete description. data is necessary to select appropriate samples for compari- Use it, but be aware that some readers and reviewers will son. The same issue exists when trying to re-isolate a species be more discriminating. In contrast, the more appropriate or to verify the type specimen. Therefore, it is important that term –trophy (trophe Gr.), to eat for food and nourishment, the environment and habitat is sufficiently described. Merely sounds more awkward in English. For species that ingest stating marine, terrestrial or soil is grossly inadequate. The unicellular protists by phagotrophy, the correct term is cy- soil, for example, is heterogeneous horizontally at the sub- totrophy. Bacterium (Ehrenberg 1838) has been the word millimetre to regional scales. It is also stratified through the used to refer to a prokaryotic cell, while cell (Dutrochet profile, and across the diameter of each ped. Whether a soil 1824; Schleiden 1838; Schwann 1839) has been used since or aquatic sample, solution chemistry and site physical param- to refer to a eukaryotic cell. Mixotrophy refers to photosyn- eters contribute to define the niche space. thetic species that also ingest food by phagocytosis, and Because we care about nomenclature and the exact heterotrophs that retain prey plastids and symbionts. meaning of words and of names of things, especially species There are two distinct mechanisms to feed on algal fila- and their groupings into nodes and stems on phylogenetic ments (cellulosic cell wall) or fungal hyphae (chitinous cell trees, it is equally important to care for how we describe wall). One mechanism is to slurp the filaments like noo- sampling sites and feeding habits. There are two parts to dles and ingest them, and the other is to penetrate describing the feeding habit: what is eaten and how it is through the cell wall. Those that puncture through phago- eaten. cytose cytoplasm, and some species even penetrate Species that release enzymes extracellularly to inside to ingest cytoplasm along the tube or in the spore. digest substrates in their habitat, are generally called It is best to distinguish between the cell wall material to saprotrophic or lysotrophic, and contribute to the decom- digest and the mechanism of ingestion. Thus, we have position of organic matter. One incredible resource is Fun- mycotrophy or phycotrophy, by either swallowing (devo- Guild (Nguyen et al. 2016, (https://github.com/UMNFuN/ ratis L.) or by penetrating (penetrando L.). FUNGuild) to determine substrate utilization for sapro- In microbial food webs, there are also consumers of trophic fungi. Probably all eukaryotes are capable of consumers, typically by predation, that are equivalent osmotrophy, the acquisition of soluble nutrients through above-ground or in aquatic systems to carnivores (meat the cell membrane. For example, plants obtain their car- eaters), or other functional groups. Although 2° con- bon for photosynthesis from the air, as well as some oxy- sumers, 3° consumers, and so on exist in microbial food gen—however, they rely on osmotrophy through the roots webs, it is hardly correct to refer to carnivores in food to obtain all the other elements they need. Osmotrophy webs where there is no meat. occurs through the ciliary pit, by pinocytosis, by diffusion, Another poorly crafted term one encounters, albeit and by various membrane transport proteins. Some spe- rarely, is eukaryovory. Although there are famous exam- cies have no alternative form of acquiring energy, are very ples of eukaryovory (Saint-Exupery 1943), eukaryotes eat- poor at decomposing substrates and are strict osmotrophs ing eukaryotes can include parasitism, as intracellular or relying on dissolved nutrients. Detritus eaters ingest parti- extracellular parasites, on hosts that are protists or multi- cles derived from cells and tissues, decomposing organic cellular, with various grades of host specificity, and it is a matter, starch granules, plant or animal debris, or wood poor substitute for cytotrophy. (microchip) fragments. We have summarized the higher level classification of Species that eat other species are called consumers, and eukaryotes in Table 1, with an estimate of the known num- there are a variety of terms to describe the functional ber of genera, and providing informal phylum and class desig- groups. Some acquire suspended particles in the solution nations to help orient the student and users along the and accumulate the particles by filtration into an oral region hierarchy, or nodes on a phylogenetic tree. The revised clas- or cytostome (not filter-feeders, as they do not feed on fil- sification of eukaryotes is presented in Table 2, and genera ters). The size of particles filtered out of the liquid depend that have not been studied enough to place in the classifica- on the current generated, and the structure of the feeding tion are listed in Table 3 as incertae sedis Eukarya. Table 4 apparatus (Fenchel 1986), and it is a good idea to specify provides recommended primers for analysing DNA from what size prey are ingested. The remaining consumers fall environmental samples, noting that the choice of primers into two categories, the grazers and predators. Grazers, like and depth of sequencing are important sources of variation a cow in a field of grasses, browse and ingest from surfaces between studies. Appendix S1 provides additional support- covered with potential food items (e.g. an amoeba on a lawn ing literature that we considered important to understand of bacteria, or on soil particle surfaces). Predators pursue the changes. Appendix S2 provides more detail about the scarce prey according to optimal foraging theory, typically trophic functional assignments across protists, by noting handle one prey at a time, and it is mathematically distinct exceptions at the genus level. Appendix S3 provides a stan- (e.g. a Jakoba ingesting one bacterium). Species gather bac- dardized guide to East Asian users for the new terminology. teria by filtration prior to phagocytosis, or directly by phago- cytosis; it is best to specify “bacteria by filtration” or ACKNOWLEDGMENTS “bacteria by phagocytosis”. A popular term bacterivore has the unintended implication of voraciously devouring (voraci- After the first author, D. Bass, C.E Lane, J. Lukes, C. L. tas L.) which is a false description of how many bacteria Schoch and A. Smirnov have contributed equally and are
© 2018 The Authors Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists 10 Journal of Eukaryotic Microbiology 2019, 66, 4–119 Adl et al. Classification of Eukaryotes to be considered second authors; subsequent authors 1557102; VZ by RFBR 16-34-60102 mol-a-dk; UniEuk and are listed alphabetically and are to be considered third EukRef by the Gordon and Betty Moore Foundation. authors. We thank numerous colleagues who were consulted ad We were saddened and hurt by the untimely loss of hoc throughout this process. In addition, we specifically two dear colleagues, D.H. Lynn and J. Clamp, both thank Alexander Ereskovsky (CNRS, Station marine ciliatologists. d’Endoume, Marseille, France) for help with the sponges; Research support was provided as follows: SMA by and Inaki~ Ruiz-Trillo (ICREA - Institut de Biologia Evolutiva, NSERC 249889-2007; DB by NERC NE/H009426/1 and CSIC-Universitat Pompeu Fabra, Barcelona, Catalonia, NE/H000887/1; MWB by NSF 1456054; FB by a Fellow- Spain) with the Holozoa; David S. Hibbett (Biology Depart- ship from Science for Life Laboratory and VR/2017-04563; ment, Clark University, Worcester, MA USA, and Radcliffe PC by EU-Horizon 2020 research and innovation program Institute for Advanced Study, Harvard University, Cam- through the SponGES project 679849 (This document bridge, MA) with the Holomycota; Isabelle Florent (Institut reflects only the authors’ view and the Executive Agency de Systematique, Evolution, Biodiversite, Museum for Small and Medium-sized Enterprises (EASME) is not National d’Histoire Naturelle, Sorbonne Universites, Paris, responsible for any use that may be made of the informa- France) with Apicomplexa; Shauna Murray (Climate tion it contains); IC by CSF 18-18699S; BE by RCN Tax- Change Cluster, University of Technology Sydney, Aus- MArc 268286/GMR; LG by ANR HAPAR (ANR-14-CE02- tralia), Albert Ren~e (Dept. Biologia Marina i Oceanografia, 0007); VH MK JL by ERDF; MEYS with ERC 771592 CZ Institut de Ciencies del Mar, CMIMA (CSIC), Barcelona, 1.05/1.1.00/02.0109 BIOCEV; SK by RSF 16-14-10302; MK Spain) and Nicolas Chomerat (IFREMER, ODE/UL/LER by CSF GA18-28103S; CEL by NSF 1541510 and NIH- Bretagne Occidentale, Concarneau, France) for dinoflagel- AI124092; EL by CAM: 2017-T1/AMB-5210; and by grant late primers and barcoding; Urban Tillmann (Alfred Wege- 2017-T1/AMB-5210 from the program "Atraccio´ n de talen- ner Institut, Helmholz-Zentrum fur€ Polar- und tos" from the Consejerı´a de Educacio´ n, Juventud y Meeresforschung, Bremerhaven, Germany) and Per Juel Deporte, Comunidad de Madrid; JL by ERC CZ LL1601 Hansen (Marine Biological Section, Dept. of Biology, and OPVVV 16_019/0000759; MP by NSF DEB-1455611; University of Copenhagen, Denmark) for the dinoflagellate DJR by the Beatriu de Pinos postdoctoral programme of literature and functional assignments; William Bourland the Government of Catalonia’s Secretariat for Universities (Biology, Boise State University) for discussions on cili- and Research of the Ministry of Economy and Knowledge; ates; Alastair Simpson (Dalhousie University) for discus- CLS by the intramural research program of the National sions on higher level ranking and structure; Angela Mele Library of Medicine, National Institutes of Health; AS by (Philadelphia) for the cover art. RSF 17-14-01391 and RFBR 16-04-01454 NY by NSF DEB
© 2018 The Authors Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists Journal of Eukaryotic Microbiology 2019, 66, 4–119 11 Classification of Eukaryotes Adl et al.
Table 2. Classification of the higher ranks of the protists and multicellular organisms. The authority to whom the taxon name is attributed appears immediately after the taxon name. For purposes of nomenclature and stability of names in the classification, we have tried to retain the oldest term that correctly described the grouping, emended if necessary; in the square bracket following are inappropriate and incorrect names used in the literature, or that do not have nomenclatural priority. If the taxon name has been emended herein, the authority is indicated and the reference is to this manuscript (“emend. Adl et al. 2019”). Selected references to the literature since 2012 can be found in Appendix S1. Cita- tions in the notes to this table can be found in the LITERATURE CITED. Named clades are monophyletic as best as we can determine; if para- phyly or polyphyly is suspected, it is indicated by P; robust clades recovered in phylogenetic analysis that do not have morphological diagnosis are indicated by R (ribo-group); monotypic genera with only one described species are indicated by M; MTOC, microtubular organizing centre. * Denotes genera lacking DNA sequence information or known to require taxonomic revision.
AMORPHEA Adl et al. 2012 The least inclusive clade containing Homo sapiens Linnaeus 1758, Neurospora crassa Shear and Dodge 1927 (both Opisthokonta), and Dictyostelium discoideum Raper 1935 (Amoebozoa). This is a node-based definition in which all of the specifiers are extant; it is intended to apply to a crown clade; qualifying clause—the name does not apply if any of the following fall within the specified clade—Arabidopsis thaliana (Linnaeus) Heynhold 1842 (Archaeplastida), Tetrahymena thermophila Nanney and McCoy 1976 (Alveolata), Thalassiosira pseudonana Hasle and Hiemdal 1970 (Stramenopiles), Bigelowiella natans Moestrup and Sengco 2001 (Rhizaria), Euglena gracilis Klebs 1883 (Excavata) and Emiliania huxleyi (Lohmann) Hay and Mohler 1967 (Haptophyta).
Incertae sedis Amorphea: Obazoa Brown et al. 2013 (R) Obazoa is a clade that is robustly recovered in phylogenetic trees and consists of the Opisthokonta and two other clades, Apusomonadida and Breviatea. It is the least inclusive clade containing Homo sapiens Linnaeus 1758 (Opisthokonta), Neurospora crassa Shear & Dodge 1927 (Opisthokonta), Pygsuia biforma Brown et al. 2013 (Breviatea) and Thecamonas trahens Larsen & Patterson 1990 (Apusomonadida).