# 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.

► To cite this version:

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, 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. Ad¹,*, David Bassᵇ,c, Christopher E. Laneᵈ, Julius Lukes,e,f, Conrad L. Schochg, Alexey Smirnovh, Sabine Agatha¹, Cedric Berneyj, Matthew W. Brownk,l, Fabien Burkim, Paco Cárdenasn, Ivan Čepičkao, Lyudmila ChistyakovaP, Javier del Campoq, Micah Dunthornr,s, Bente Edvardsent, Yana Eglitu, Laure Guillouv, Vladimír Hamplw, Aaron A. Heissx, Mona HoppenrathY, Timothy Y. Jamesz, Anna Karnkowskaaa, 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, Guifré 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, České Budějovice, 37005, Czechia

f Faculty of Science, University of South Bohemia, České Budějovice, 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 Ecosystèmes Pélagiques, 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 Ciències del Mar, CSIC, Passeig Marítim 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, Universitätsstrasse 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 Université, Université Pierre et Marie Curie - Paris 6, CNRS, UMR 7144 (AD2M), Station Biologique de Roscoff, Place Georges Teissier, CS90074, Roscoff, 29688, France

w Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Prúmyslová 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 Neuchâtel, Rue Emile-Argand 11, Neuchâtel, 2000, Switzerland

ae Real Jardín Botánico, CSIC, Plaza de Murillo 2, Madrid, 28014, Spain

af Institut de Systématique, Évolution, Biodiversité, Muséum National d'Histoire Naturelle, Sorbonne Universités, 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 Ràpita, E-43540, Spain

ak Jardin Botanique de Neuchâtel, Chemin du Perthuis-du-Sault 58, Neuchâtel, 2000, Switzerland

al Department of Natural Sciences, National Museums Northern Ireland, 153 Bangor Road, Holywood, BT18 OEU, United Kingdom
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 Marítim 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 Systématique, Université 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**

Algae; amoebae; biodiversity; ciliate; ecol-
ogy; flagellate; fungus; microbiology; para-
site; plankton; protozoa; systematics;
taxonomy.

**Correspondence**

S.M. Adl, Department of Soil Sciences,
College of Agriculture and Bioresources,
University of Saskatchewan, 51 Campus
Drive, Saskatoon, SK, S7N 5A8 Canada
Telephone number: 306 966 6866
e-mail: sina.adl@usask.ca

Received: 2 September 2018; accepted
September 4, 2018.

doi:10.1111/jeu.12691

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.

THIS revision of the classification of eukaryotes updates that of the International Society of Protistologists (Adl et al. 2012). Since then, there has been a massive increase in DNA sequence information of phylogenetic relevance from environmental samples. We now have a much better sense of the undescribed biodiversity in our environment (De Vargas et al. 2015; Pawlowski et al. 2012). While significant, it still remains a partial estimation as several continents and soils in general are poorly sampled, and the deeper ocean is hard to reach. These new data clarified phylogenetic relationships and the new information is incorporated in this revision.

**Systematics**

We assembled the classification according to the princi-
ples outlined elsewhere, and we refer the reader to the
introductions of both Adl et al. 2005 and 2012 for

background information, and to Adl et al. 2007 for a dis-
cussion. Briefly, we adopted a hierarchical system with-
out formal rank designations. The hierarchy is
represented by indented paragraphs. The nomenclatural
priority is given to the oldest name (and its authority) that
correctly assembled genera or higher groups together
into a clade, except where its composition was substan-
tially modified. In these cases, we have used a newer
term and its appropriate authorship. In cases where ranks
were created to include a single lower rank, the higher
ranks were eliminated as superfluous. In this scheme,
monotypic taxa are represented by the genus only.
Nested clades represent monophyletic lineages as best
we know and para- or polyphyletic groups are so
indicated.

This system of hierarchical nameless ranks, that
ignores endings of clade names, has proved its utility in
providing name stability as we reconstructed a new
<figure><img src="image_2.png" /><figcaption>**Figure 1** Overview of the diversity of protists among eukaryotes. Amoebozoa, Nuclemyceae, and Holozoa together form the Amorphea; The Diaphoretickes includes Crypista, Chloroplastida and Embryophyta, Rhodophyceae, Haptista, Rhizaria, Alveolata (Apicomplexa, Dinoflagellata, Ciliata), Stramenopiles and Phaeophyta.</figcaption></figure>

phylogenetic classification during the past 20 years. Clade names in this system do not change when their rank or composition changes, and it is only the authority for the name that changes when each clade description is adjusted (Cantino, 1998; Pleijel and Rouse, 2003). Where a new term is introduced in this classification, it is identified with "Adl et al. 2019" as the authority, or by the submitting author (e.g. Mann in Adl et al., 2019), and they are to be cited as emended in this publication. The descriptions provided are not intended to substitute for formal diagnoses. They are provided primarily for the student and general users to identify common morphological features, such as synapomorphies and apomorphies, within monophyletic lineages.

There are two novel components in this revision. First, we have provided trophic assignments for most taxa. This will prove useful in interpreting communities from environmental samples. Second, we informally suggest a phylum rank and classes in most clades to provide a point of reference in the classification hierarchy for the nonspecialist. This became possible, as there has been some stability at this level in the molecular phylogenetic reconstructions. It should be obvious that genera grouped into a clade then represent a family, and families into an order.

## Nomenclature

This committee of the Society has had the responsibility of arbitrating nomenclature for protists in general. Historically, the task was simpler as most groups fell under one or the other of the two Codes of Nomenclature (algae 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 incompatible, some have proposed to provide parallel classifications in each Code, while others proposed to adopt a modern unified code of nomenclature. Since the rearrangement of the classification along monophyletic lineages 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 dictyostellid amoebae with the botanical Code (Sheikh et al. 2018) for genera that are unarguably in Amoebozoa governed 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 phylogenetic hypotheses, proposals for new names and name changes. Underlying these discussions are principles of nomenclatural priority in the spirit of the codes of nomenclature.

A classification is unlike a phylogenetic tree in a publication, where the discovery of new clades, branches, or robust nodes ultimately leads to proposing new names. Newly named clades and nodes have their utility in phylogenetic analysis and discussion, but do not need to be formalized in the classification immediately. An overwhelming number of spent names have thus accumulated, with an increasing frequency over the past four decades, most of which are no longer—or never were—in common use. Many of these names were ephemeral, as their monophyly did not stand the test of (time) statistical analysis. The proliferation of these names reflects a methodological error practiced by some. That is to formalize names prematurely and try to reorganize classifications single-handedly. As we argued before (Adl et al. 2012), this must be done with care, respecting nomenclatural priority, published as a proposal or a phylogenetic hypothesis first, to be verified by the community, and only eventually considered for change in the classification. The task of reëreeing and classifying falls on Society committees representing communities of professionals. The very formal and slow process of voting to conserve or reject names through the tradition of the botanical code takes years as it has to proceed through committees and then approved by vote on the floor of the congress at 6-year intervals. That is, however, too slow for the pace of changes today given the rate at which new information is becoming available.
In contrast to a phylogenetic tree, a classification system belongs to a community of users, and it is generated through discussions of the available evidence, for pragmatic purposes of teaching, curation, organizing data, archiving and communicating with a common language. It is a commonly agreed point of reference. It is not to be reimagined or re-done at will by one individual. The Linnaean system that we have inherited has detailed codes of nomenclature that guide and regulate how living organisms are named, names changed and classified. The elaborate rules arise from disputes and mistakes made in the past, in part out of respect for each other's work. Instead of providing a long list of rejected and invalid names, we can specify that those not selected in this classification were considered *nomina ambigua, nomina perplexa, nomina dubia, nomina nuda* or did not have nomenclatural priority and are declared *nomina rejicienda*.

Another proposed classification of prokaryotes and eukaryotes was published recently (Ruggiero et al. 2015). This effort may be reasonable in their classification of the prokaryotes, but the eukaryote section does not pass standards of modern biology. Specifically, it is their refusal to use monophyly as a guiding principle, but to argue to retain "ancestral (paraphyletic) taxa when it seemed beneficial to do so" instead, even where monophyletic clades are already established. Their insistence on using a hodge-podge of names that do not have nomenclatural priority, and that poorly describe the taxa included, further reduces its usefulness.

## Classification

The super-groups utilized since 2005 (Adl et al. 2005; Simpson and Roger 2004) are revised as follows (Fig. 1):

(1) Eukaryotes now form two Domains called Amorphea and Diaphoretickes, with several additional clades that do not group into a third Domain.

(2) In the Amorphea, the Opisthokonta, Breviatea and Apusomonadida now form a robust clade, as noted earlier (Adl et al. 2012), called Obazoa. Within the Opisthokonta, the Holozoa and Nuclemycea/(Holomycota) are robust clades with improved resolution of the basal sister lineages. In the Holozoa, the sponges and the other animals group together as the Metazoa (Porifera, Placozoa, Ctenophora, Cnidaria, Bilateria). In addition, a sister clade to the Amorphea comprising several genera was recently described as CRuMs (Brown et al. 2018).

(3) There are two sister clades in Opisthokonta, the Holozoa and the Nuclemycea (/Holomycota). They share several characters, including synthesis of extracellular chitin in an exoskeleton, cyst/spore wall or cell wall of filamentous growth and hyphae; the extracellular digestion of substrates with osmotrophic absorption of nutrients; and other cell biosynthetic and metabolic pathways. Genera at the base of each clade are amoeboid and phagotrophic.

(4) The Archaeplastida, Sar and several other clades remain a monophyletic clade under Diaphoretickes. The clade Cryptista comprising the cryptomonads, kathablepharids and *Palpitomonas* is well recognized and robust, although placement of its node within the Diaphoretickes

remains problematic. In some but not all analyses, the clade appears inside the Archaeplastida. This position has always occurred from time to time in some phylogenies with weak support, but there is now stronger support for this association. We are not committed to their inclusion within the Archaeplastida but do note its likelihood. The inclusion of the Cryptista in the Archaeplastida would expand that group without affecting its defining criteria. Questioning the single origin of a plastid within the Archaeplastida is a rare minority opinion. Yet, the possibility of more than one plastid origin must not be ruled-out until the cryptomonads are robustly positioned.

(5) The new robust support for the Cryptista clade is accompanied by a similarly robust support for a clade comprising the Centroplasthelida and Haptophyta as the Haptista within the Diaphoretickes.

(6) Nodes at the base of the Alveolata are better resolved with additional genera. The placeholder name Protalveolata is no longer required.

(7) The Excavata comprise three clades: the Metamonada, the Discoba, and the Malawimonada. Their mutual relationships, as well as their relationships to other clades of eukaryotes, remain uncertain. We have dropped the supergroup Excavata in favour of the informal Excavates when referring to the "Discoba, Metamonada, Malawimonada", as *Incertae sedis* in eukaryotes. The Excavates and several clades and genera fall outside of the two principal domains, but do not cluster together into a third domain.

This classification will serve as a primary starting reference for the taxonomic framework developed by UniEuk (unieuk.org; Berney et al. 2017), the Society supported, consensus-driven, community-based and expert-driven international initiative to maintain a universal taxonomy for, at least, microbial eukaryotes. A specific aim of the UniEuk project is to apply one taxonomic framework to all genetic data in the International Nucleotide Sequence Database Collaboration (INSDC) repositories, which includes DDBJ (ddbj.nig.ac.jp), GenBank (ncbi.nlm.nih.gov) and ENA (ebi.ac.uk/ena) databases. The system's broad use and preservation will be ensured by a direct implementation of the UniEuk taxonomic framework into the ENA (European Nucleotide Archive) at EMBL-EBI (http://www.ebi.ac.uk/ena). The project will capture our collective knowledge on eukaryotic diversity, evolution, and ecology via three main modules (EukRef, EukBank and EukMap). EukRef (eukref.org; del Campo et al. 2018) uses a standardized, open-source bioinformatics pipeline to generate homogenous, high-quality curation of sequences (primarily 18S rDNA) available in INSDC databases. EukRef is fully operational; outputs include (on a lineage-by-lineage basis) taxonomically curated sequences, sequence alignments, phylogenetic trees and metadata. EukBank is a public repository of (primarily V4 18S rDNA) high-throughput metabarcoding data sets, centralized at ENA, with standardized protocols for submitting data sets and metadata. EukMap (eukmap.unieuk.org) is an editable, user-friendly representation of the UniEuk taxonomy in the form of a publicly navigable tree, where each node/taxon is associated with contextual data (taxonomic and ecological information,
<table><caption>**Table 1.** Higher ranks of the eukaryotes suggesting the position of Linnaean ranks, and the number of known genera</caption><tbody><tr><td>AMORPHEA</td></tr><tr><td>CRuMs (O) 11</td></tr><tr><td>Collodictyonidae (F)</td></tr><tr><td>Rigifilida (F)</td></tr><tr><td>Mantamonas (G)</td></tr><tr><td>Amoebozoa 255</td></tr><tr><td>Incertae sedis 21</td></tr><tr><td>Tubulinea (P) 93</td></tr><tr><td>Corycida (C)</td></tr><tr><td>Echinamoebida (C)</td></tr><tr><td>Elardia (C) (Arcellinida 63)</td></tr><tr><td>Evosea (P) 106</td></tr><tr><td>Variosea (C)</td></tr><tr><td>Eumycetozoa (C)</td></tr><tr><td>Cutosea (C)</td></tr><tr><td>Archamoebea (C)</td></tr><tr><td>Discosea (P) 35</td></tr><tr><td>Flabellinia (C)</td></tr><tr><td>Stygamoebida (C)</td></tr><tr><td>Centramoebia (C)</td></tr><tr><td>Obazoa</td></tr><tr><td>Apusomonadida (F) 6</td></tr><tr><td>Breviatea (F) 4</td></tr><tr><td>Opisthokonta</td></tr><tr><td>Holozoa 25 (without Choanoflagellata, Porifera and Metazoa)</td></tr><tr><td>Incertae sedis Holozoa: <i>Corallochytrium, Syssomonas</i></td></tr><tr><td>Ichtyosporea (O)</td></tr><tr><td>Choanoflagellata (C) 57</td></tr><tr><td>Metazoa</td></tr><tr><td>Porifera (P) 742</td></tr><tr><td>Hexactinellida (C)</td></tr><tr><td>Homoscleromorpha (C)</td></tr><tr><td>Demospongiae (C)</td></tr><tr><td>Calcarea (C)</td></tr><tr><td><i>Trichoplax</i> (G/F?)</td></tr><tr><td>Cnidaria (P)</td></tr><tr><td>Ctenophora (P)</td></tr><tr><td>Bilateria (K, ~35 P)</td></tr><tr><td>Nuclemycea</td></tr><tr><td>Rotosphaerida (O) 9</td></tr><tr><td>(Fungi) ~8,600</td></tr><tr><td>Opisthosporidia (O)</td></tr><tr><td>Aphelidea (F) 4</td></tr><tr><td>Cryptomycota (F) 3</td></tr><tr><td>Microsporida (O?/F) >150</td></tr><tr><td>Blastocladiales (O) 14</td></tr><tr><td>Chytridiomycetes (C) 140</td></tr><tr><td>Dikarya ~8,000</td></tr><tr><td>Ascomycota (P) ~6,400</td></tr><tr><td>Basidiomycota (P) ~1,600</td></tr><tr><td>Mucoromycota (P) ~140</td></tr><tr><td>Neocallimastigaceae (F) 11</td></tr><tr><td><i>Olpidium</i> (G)</td></tr><tr><td>Zoopagomycota (P) ~200</td></tr><tr><td>DIAPHORETICKES</td></tr><tr><td>Incertae sedis: <i>Microhelliela maris, Ancoracysta twista, Rappemonads, Telonemia, Picozoa</i></td></tr></tbody></table>

(continued)

<table><caption>**Table 1 (continued)**</caption><tbody><tr><td>Cryptista (C) 21</td></tr><tr><td>Cryptophyceae (O)</td></tr><tr><td><i>Palpitomonas</i> (G)</td></tr><tr><td>Haptista (P)</td></tr><tr><td>Haptophyta (C) 80</td></tr><tr><td>Pavlovales (F)</td></tr><tr><td>Prymnesiophyceae (O)</td></tr><tr><td>Centroplasthelida (C) 16</td></tr><tr><td>Pterocystida (O)</td></tr><tr><td>Panacanthocystida (O)</td></tr><tr><td>Archaeplastida</td></tr><tr><td>Glaucophyta (F) 4</td></tr><tr><td>Rhodophyceae (P) 850</td></tr><tr><td>Cyanidiales (O)</td></tr><tr><td>Proteorhodophytina (O/C)</td></tr><tr><td>Eurhodophytina (C)</td></tr><tr><td>Chloroplastida (72,000 sp + Embryophyta)</td></tr><tr><td>Chlorophyta (P)</td></tr><tr><td>Ulvophyceae (C)</td></tr><tr><td>Trebouxiophyceae (C)</td></tr><tr><td>Chlorophyceae (C)</td></tr><tr><td>Chlorodendrophyceae (C)</td></tr><tr><td>Pedinophyceae (C)</td></tr><tr><td>Chloropicophyceae (C)</td></tr><tr><td>Picocystophyceae (C)</td></tr><tr><td>Pyramimonadales (C)</td></tr><tr><td>Mamiellophyceae (C)</td></tr><tr><td><i>Nephroselmis</i> (G)</td></tr><tr><td>Pycnococcaceae (C)</td></tr><tr><td>Palmophyllophyceae (C)</td></tr><tr><td>Streptophyta (P)</td></tr><tr><td><i>Chlorokybus atmophyticus</i></td></tr><tr><td><i>Mesostigma viridae</i></td></tr><tr><td>Klebsomidiophyceae (F)</td></tr><tr><td>Phragmoplastophyta (C)</td></tr><tr><td>Zygnemataceae (F)</td></tr><tr><td>Coleochaetophyceae (O)</td></tr><tr><td>Characeae (F)</td></tr><tr><td>Embryophyta (K)</td></tr><tr><td>Sar</td></tr><tr><td>Stramenopiles (P)</td></tr><tr><td>Bigyra (C) 49</td></tr><tr><td>Opalinata (O)</td></tr><tr><td>Placidida (F)</td></tr><tr><td>Bicosoecida (O/F)</td></tr><tr><td>Sagenista (C)</td></tr><tr><td>Labyrinthulomycetes (O)</td></tr><tr><td>Pseudophyllomitidae (F?)</td></tr><tr><td>Gyrista (C) 31 excluding Peronosporomycetes and Ochrophyta</td></tr><tr><td>Developea (F)</td></tr><tr><td>Hyphochytriales (O)</td></tr><tr><td>Peronosporomycetes (C/O) 46</td></tr><tr><td><i>Pirsonia</i> (G)</td></tr><tr><td>Actinophryidae (F)</td></tr><tr><td>Ochrophyta<sup>a</sup></td></tr><tr><td>Chrysista (C)<sup>a</sup></td></tr><tr><td>Chrysophyceae (O)</td></tr></tbody></table>

(continued)
<table><caption>**Table 1 (continued)**</caption><tr><td>Eustigmatales (O)</td></tr><tr><td>Phaeophyceae (O)</td></tr><tr><td>Raphidophyceae (O)</td></tr><tr><td>Schizocladia (O)</td></tr><tr><td>Xanthophyceae (O)</td></tr><tr><td>Diatomista</td></tr><tr><td>Bolidophyceae (F)</td></tr><tr><td>Diatomea (C) ~400</td></tr><tr><td>Alveolata, others 26</td></tr><tr><td>Colpodellida (O)</td></tr><tr><td>Perkinsidae (F)</td></tr><tr><td>Colponemidia (F)</td></tr><tr><td>Acavomonas (G)</td></tr><tr><td>Oxyrrhis marina</td></tr><tr><td>Dinoflagellata (P) 300</td></tr><tr><td>Syndiniales (O)</td></tr><tr><td>Noctilucales (O)</td></tr><tr><td>Dinophyceae (C)</td></tr><tr><td>Apicomplexa (P) ~350</td></tr><tr><td>Incertae sedis: Agamococcidiorida (F), Protococcidiorida (F)</td></tr><tr><td>Aconoidasida (C)</td></tr><tr><td>Conoidasida (C)</td></tr><tr><td>Ciliophora (P)</td></tr><tr><td>Karyorelictea (C) 18</td></tr><tr><td>Heterotrichida (O) 58</td></tr><tr><td>Spirotrichea (C) 139 (+Hypotrichia)</td></tr><tr><td>Hypotrichia 183</td></tr><tr><td>Armophorea (O) 41</td></tr><tr><td>Litostomatea (C) 263</td></tr><tr><td>Phyllopharyngea (C) 263</td></tr><tr><td>Colpodea (C) 73</td></tr><tr><td>Nassophorea (C) 23</td></tr><tr><td>Plagyopylea (C) 15</td></tr><tr><td>Oligomymenophorea (C) 433</td></tr><tr><td>Rhizaria</td></tr><tr><td>Cercozoa (P) >>204</td></tr><tr><td>Cercomonadida (F)</td></tr><tr><td>Paracercomonadida (F)</td></tr><tr><td>Glissomonadida (O)</td></tr><tr><td>Viridiraptoridae (F)</td></tr><tr><td>Pansomonadidae (F)</td></tr><tr><td>Sainouridae (F)</td></tr><tr><td>Thecofilosea (C)</td></tr><tr><td>Imbricatea (P) 89</td></tr><tr><td>Spongomonadida (F)</td></tr><tr><td>Marimonadida (F)</td></tr><tr><td>Variglissida (F)</td></tr><tr><td>Silicofilosea (C)</td></tr><tr><td>Metromonadea (F)</td></tr><tr><td>Granofilosea (O)</td></tr><tr><td>Chlorarachnea (F)</td></tr><tr><td>Endomyxa (P) >34</td></tr><tr><td>Vampyrellida (O)</td></tr><tr><td>Phytomypha (O)</td></tr><tr><td>Filoreta (G)</td></tr><tr><td>Gromia (G)</td></tr><tr><td>Ascetosporea (C)</td></tr></table>

(continued)

<table><caption>**Table 1 (continued)**</caption><tr><td>Retaria</td></tr><tr><td>Foraminifera (P) ~950</td></tr><tr><td>Monothalamea (C/O?)</td></tr><tr><td>Tubothalamea (C)</td></tr><tr><td>Globothalamea (C)</td></tr><tr><td>Radiolaria (P)</td></tr><tr><td>Acantharea (C) 50</td></tr><tr><td>Taxopodida (F) 1+environmental clades</td></tr><tr><td>Polycystinea (C) ~470</td></tr><tr><td>Aquavalon (G)</td></tr><tr><td>Tremula (G)</td></tr><tr><td>Incertae sedis Eukarya: Excavates</td></tr><tr><td>Metamonada 133</td></tr><tr><td>Fornicata (P)</td></tr><tr><td>Parabasalia (P)</td></tr><tr><td>Preaxostyla (P)</td></tr><tr><td>Discoba 94</td></tr><tr><td>Jakobida (P)</td></tr><tr><td>Tsukubamonas (G)</td></tr><tr><td>Heterolobosea (P)</td></tr><tr><td>Euglenozoa (P)</td></tr><tr><td>Euglenida (C)</td></tr><tr><td>Diplonemea (O)</td></tr><tr><td>Symbiontida (F)</td></tr><tr><td>Kinetoplastea (C)</td></tr><tr><td>Other incertae sedis Eukarya 158</td></tr></table>

G = genus; F = family; O = order; C = class; P = phylum; K = kingdom.

ªThe state of the classification in online databases are too poor to evaluate or work with this clade.

links to representative images, etc.). It will be operational by 2019 and will allow registered community members to directly interact with and inform the taxonomic framework, and to flag taxonomy issues requiring revision. As a whole, the UniEuk system will represent a community hub to centralize, standardize, and promote global knowledge on eukaryotic diversity, taxonomy and ecology.

## Clarification of terms for trophic functional groups

Several terms were clarified to correct misuse of terminology in publications. In 2005, these were: eukaryote, prokaryote, algae, zoosporic fungi, protozoa, zooplankton, phytoplankton, cyst, spore and cilium. In 2012, they were related to the cytoskeleton and motility: lobopodia, lamellipodia, filopodia, granuloreticulopodia, reticulopodia, axopodia, centriole, centrosome, microtubular organizing centre (MTOC), basal body, kinetosome, kinetid and mastigont. In this revision, they pertain to trophic functional groups.

In addition to descriptions of morphology that accompany specimen, which is critical for understanding cell function and interpreting phylogenetic trees, improved descriptions of site and food preferences are required for an ecological interpretation of the role in the community and ecosystem. Often species lack sufficient description of the collection site or feeding habit.
To compare environmental DNA data sets, adequate metadata is necessary to select appropriate samples for comparison. The same issue exists when trying to re-isolate a species or to verify the type specimen. Therefore, it is important that the environment and habitat is sufficiently described. Merely stating marine, terrestrial or soil is grossly inadequate. The soil, for example, is heterogeneous horizontally at the sub-millimetre to regional scales. It is also stratified through the profile, and across the diameter of each ped. Whether a soil or aquatic sample, solution chemistry and site physical parameters contribute to define the niche space.

Because we care about nomenclature and the exact meaning of words and of names of things, especially species and their groupings into nodes and stems on phylogenetic trees, it is equally important to care for how we describe sampling sites and feeding habits. There are two parts to describing the feeding habit: what is eaten and how it is eaten.

Species that release enzymes extracellularly to digest substrates in their habitat, are generally called *saprotrophic* or *lysotrophic*, and contribute to the decomposition of organic matter. One incredible resource is Fun-Guild (Nguyen et al. 2016, (https://github.com/UMNFuN/FUNGuild) to determine substrate utilization for saprotrophic fungi. Probably all eukaryotes are capable of osmotrophy, the acquisition of soluble nutrients through the cell membrane. For example, plants obtain their carbon for photosynthesis from the air, as well as some oxygen—however, they rely on osmotrophy through the roots to obtain all the other elements they need. Osmotrophy occurs through the ciliary pit, by pinocytosis, by diffusion, and by various membrane transport proteins. Some species have no alternative form of acquiring energy, are very poor at decomposing substrates and are strict *osmotrophs* relying on dissolved nutrients. *Detritus* eaters ingest particles derived from cells and tissues, decomposing organic matter, starch granules, plant or animal debris, or wood (microchip) fragments.

Species that eat other species are called *consumers*, and there are a variety of terms to describe the functional groups. Some acquire suspended particles in the solution and accumulate the particles *by filtration* into an oral region or cytostome (not filter-feeders, as they do not feed on filters). The size of particles filtered out of the liquid depend on the current generated, and the structure of the feeding apparatus (Fenchel 1986), and it is a good idea to specify what size prey are ingested. The remaining consumers fall into two categories, the grazers and predators. *Grazers*, like a cow in a field of grasses, browse and ingest from surfaces covered with potential food items (e.g. an amoeba on a lawn of bacteria, or on soil particle surfaces). *Predators* pursue scarce prey according to optimal foraging theory, typically handle one prey at a time, and it is mathematically distinct (e.g. a *Jakoba* ingesting one bacterium). Species gather bacteria by filtration prior to phagocytosis, or directly by phagocytosis; it is best to specify "bacteria by filtration" or "bacteria by phagocytosis". A popular term bacterivore has the unintended implication of voraciously devouring (*voracitas* L.) which is a false description of how many bacteria

eaters acquire their prey, and an incomplete description. Use it, but be aware that some readers and reviewers will be more discriminating. In contrast, the more appropriate term –trophy (*trophe* Gr.), to eat for food and nourishment, sounds more awkward in English. For species that ingest unicellular protists by phagotrophy, the correct term is *cytotrophy*. Bacterium (Ehrenberg 1838) has been the word used to refer to a prokaryotic cell, while cell (Dutrochet 1824; Schleiden 1838; Schwann 1839) has been used since to refer to a eukaryotic cell. *Mixotrophy* refers to photosynthetic species that also ingest food by phagocytosis, and heterotrophs that retain prey plastids and symbionts.

There are two distinct mechanisms to feed on algal filaments (cellulosic cell wall) or fungal hyphae (chitinous cell wall). One mechanism is to slurp the filaments like nozzles and ingest them, and the other is to penetrate through the cell wall. Those that puncture through phagocytose cytoplasm, and some species even penetrate inside to ingest cytoplasm along the tube or in the spore. It is best to distinguish between the cell wall material to digest and the mechanism of ingestion. Thus, we have *mycotrophy* or *phycotrophy*, by either swallowing (*devo-ratis* L.) or by penetrating (*penetrando* L.).

In microbial food webs, there are also consumers of consumers, typically by predation, that are equivalent above-ground or in aquatic systems to carnivores (meat eaters), or other functional groups. Although 2° consumers, 3° consumers, and so on exist in microbial food webs, it is hardly correct to refer to carnivores in food webs where there is no meat.

Another poorly crafted term one encounters, albeit rarely, is eukaryovory. Although there are famous examples of eukaryovory (Saint-Exupéry 1943), eukaryotes eating eukaryotes can include *parasitism*, as intracellular or extracellular parasites, on hosts that are protists or multicellular, with various grades of host specificity, and it is a poor substitute for cytotrophy.

We have summarized the higher level classification of eukaryotes in Table 1, with an estimate of the known number of genera, and providing informal phylum and class designations to help orient the student and users along the hierarchy, or nodes on a phylogenetic tree. The revised classification of eukaryotes is presented in Table 2, and genera that have not been studied enough to place in the classification are listed in Table 3 as *incertae sedis* Eukarya. Table 4 provides recommended primers for analysing DNA from environmental samples, noting that the choice of primers and depth of sequencing are important sources of variation between studies. Appendix S1 provides additional supporting literature that we considered important to understand the changes. Appendix S2 provides more detail about the trophic functional assignments across protists, by noting exceptions at the genus level. Appendix S3 provides a standardized guide to East Asian users for the new terminology.

## ACKNOWLEDGMENTS

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 Fellow-
ship 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 informa-
tion 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.

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.
**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. Citations in the notes to this table can be found in the LITERATURE CITED. Named clades are monophyletic as best as we can determine; if parphyly 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).

* Apusomonadida* Karpov & Mylnikov 1989

Gliding cells (5–15 µm), with dorsal cell membrane underlain by thin theca extending laterally and ventrally as flanges that delimit a broad ventral region from which pseudopodia develop in most genera; with two heterodynamic cilia, the anterior enclosed by sleeve-like extension of flanges to form a proboscis, and the posterior cilium lying within the ventral region; tubular mitochondrial cristae; phagocytosis of bacteria. *Amastigomonas*, *Apusomonas*, *Chelonemonas*, *Manchomonas*, *Multimonas*, *Podomonas*, *Thecamonas*.

* Breviatea* Cavalier-Smith 2004

Amoeboid gliding cells (10–15 µm) with single anteriorly directed apical cilium and in some isolates a second posteriorly directed cilium; filopodia projecting unilaterally from cell, perpendicular to anteroposterior axis and direction of movement; filopodia forming at anterior end, moving posteriorly as cell moves forward (filopodia appearing attached to substrate), and resorbed at posterior; cell can also produce broad lamellopodia; anaerobic or microaerophilic, with large mitochondrion-like organelle; ingests bacteria; can form cysts. *Breviata*, *Lenisia*, *Pygsuia*, *Subulatomonas*.

**Amoebozoa Lühe 1913**, sensu Cavalier-Smith 1998

Organisms almost all demonstrating 'amoeboid activity'<fnref n="1" /> in all or in certain stage(s) of their life cycle. Amoeboid locomotion with steady flow of the cytoplasm or occasional eruptions in some groups; alternatively, amoeboid locomotion involving the extension and retraction of pseudopodia and/or subpseudopodia with little coordinated movement of the cytoplasm. Cells naked, often with well-developed, differentiated glycocalyx; in several groups cells are covered with a tectum<fnref n="2" /> or a cuticle<fnref n="3" />. Two groups are testate (enclosed in a flexible or hard extracellular envelope with one to several opening(s)). Mitochondrial cristae tubular (ramicristate), with few exceptions; mitochondria secondarily reduced to mitochondrion-related organelles (MRO) in archamoebians. Most only reported to be asexual, but sex and life cycles consistent with sex have been reported in all three major lineages—Tubulinea, Evosea and Discosea. Many taxa exhibit either sporocarpic<fnref n="4" /> or sorocarpic<fnref n="5" /> fruiting. Biciliated, uniciliated or multiciliated stages in the life cycle of some taxa; some taxa exhibit reduction of the bikont kinetid to a unikont kinetid.

(continued)

<footnote n="1">¹The ability of a unicellular organism or a cell type in a multicellular organism to actively change the conformation of the entire cell body by extending and retracting pseudopodia; pseudopodia are used for cell movement over the substratum and/or for feeding.</footnote>

<footnote n="2">²Monolayer of scales covering the cell adhering to the substratum from the dorsal surface; the ventral surface of the cell remains free. Known in amoebae of the genus *Cochliopodium*.</footnote>

<footnote n="3">³Layer of fibrous material covering the cell, adhering to the substratum from the dorsal surface; the ventral surface remains free. Known in amoebae of the genera *Gocevia*, *Paragocevia* and *Ovalopodium*.</footnote>

<footnote n="4">⁴Single amoeboid cell differentiates into a usually stalked, subaerial structure that supports one to many propagules termed spores. As defined here, this kind of sporocarp has only ever been observed in Amoebozoa and is potentially synapomorphic for Amoebozoa. Should this prove the case, non-sporocarpic amoebozoans are the products of reductive evolution.</footnote>

<footnote n="5">⁵Amoebae aggregate into a multicellular mass that develops into a multicellular, subaerial fruiting body consisting of either distinct stalk cells and spores or non-differentiated encysted cells (usually also called spores). Sorocarpic development is found in two lineages of amoebozoans, the Dictyostelia (Eumycetozoa) and in *Copromyxa* (Tubulinea).</footnote>
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

Incertae sedis Amoebozoa: Belonocystis*, Boveella*, Biomyxa, Corallomyxa, Gibbodiscus*, Hartmannia*, Malamoeba*, Malpighamoeba*, Microcorycia*, Microglomus*, Oscillosignum*, Parmulina*, Penardochlamys*, Pseudothecamoeba*, Rhabdamoeba*, Schoutedamoeba<fnref n="6" />, Stereomyxa*<fnref n="7" />, Subulamoeba*, Thecochaos*, Triaenamoeba*, Unda*<fnref n="8" />, Zonomyxa*

● Tubulinea Smirnov et al. 2005

Organisms producing lobose pseudopodia (lobopodia)<fnref n="9" />. The entire cell or individual pseudopodia (in polypodial cells) are tubular, cylindrical or subcylindrical, rounded in cross-section. If cells are flattened or branched they are capable of altering the locomotive form from a flattened, expanded one to monopodial or polypodial, with subcylindrical pseudopodia. Monoaxial flow of the cytoplasm in every pseudopodium or in the entire cell. No convincing evidence of ciliate stages<fnref n="10" />. Two groups are testate, and two sorocarpic taxa are known. No sporocarpy has been reported.

●● Corycida Kang et al. 2017

Cells covered with flexible, leather-like coating forming one or several openings used to protrude pseudopodia or are enclosed in hard test made of spicules with multiple apertures. The least inclusive clade containing *Amphizonella* sp.<fnref n="11" />, *Diplochlamys* sp.<fnref n="11" />, *Trichosphaerium* sp.<fnref n="11" />, *Amphizonella*, *Diplochlamys*, *Trichosphaerium*<fnref n="12" />.

●● Echinamoebida Cavalier-Smith 2004 (R)

Cells tubular, vermiform or flattened, with or without spine-like subpseudopodia; capable of adopting subcylindrical monopodial form under certain conditions. The least inclusive clade containing *Vermamoeba vermiformis*, *Echinamoeba silvestris* and *Micriamoeba testensis*. *Echinamoeba*, *Micriamoeba*, *Vermamoeba*.

●● Elardia Kang et al. 2017 (R)

Cells naked or covered with a hard test; tubular or produce tubular pseudopodia; if flattened or branched, capable of altering the locomotive form to monopodial or polypodial, with tubular pseudopodia. The least inclusive clade containing *Amoeba proteus*, *Arcella intermedia* and *Rhizamoeba saxonica*.

●●● Leptomyxida Pussard & Pons 1976, sensu Smirnov et al. 2017

Naked amoebae with locomotive form altering from a flattened expanded or reticulate one to a subcylindrical monopodial one when in rapid movement or under specific conditions; adhesive uoidal structures always present. *Flabellula*, *Gephyramoeba*, *Leptomyxa*, *Rhizamoeba*.

●●● Arcellinida Kent 1880

Cell covered with hard or highly rigid organic or mineral extracellular test consisting of either self-secreted elements (calcareous, siliceous or chitinoid), a sheet-like chitinoid structure, or recycled organic or mineral particles bound together, with a single main opening.

Incertae sedis Arcellinida: *Argynnia*, *Awerintzewia*, *Geamphorella*, *Jungia*, *Lagenodifflugia*, *Lamtoquadrula*, *Leptochlamys*, *Maghrebia*, *Microquadrula*, *Paraquadrula*, *Pentagonia*, *Pseudawerintzewia*, *Pomoriella*, *Pontigulasia*, *Physochila*, *Schoenbornia*, *Sexangularia*, *Zivkovicia*.

●●●● Sphaerothecina Kosakyan 2016

Test rigid or more or less flexible, either completely chitinoid or comprising recycled organic or mineral particles held together by an organic cement, or composed of self-secreted chitinoid or siliceous elements; always rounded in radial symmetry but varying in height from flattened saucer-shaped, hemispheric or more elongated to egg-shaped; pseudostome circular or lobed, surrounded by a collar; produce thick, digitate pseudopodia. *Antarcella*, *Arcella*, *Cornuapyxis*, *Cucurbitella*,

(continued)

<footnote n="6">⁶The species *Schoutedamoeba minuta* described by Van Vichelen et al. (2016) has a hartmannelid morphology (monopodial cells with pronounced frontal hyaline cap) but in SSU tree it shows affinities with Variosea, although with no support. More robust data are necessary to clarify its position among Amoebozoa.</footnote>

<footnote n="7">⁷The taxon name *Stereomyxa ramosa* is used in Tekle et al. (2016) and Tekle and Wood (2017) for an isolate that is a distinct genus named *Draacoamoeba* (see Tice et al. 2016). To date, no molecular data on a true *Stereomyxa* are available and thus it remains *incertae sedis*.</footnote>

<footnote n="8">⁸The name *Unda* is used in Tekle et al. (2016) as well as in Tekle and Wood (2017) for an isolate of *Vannella* as noted in Cavalier-Smith et al. (2016) and Kang et al. (2017).</footnote>

<footnote n="9">⁹Variable cell projections, smooth in outline, with rounded tips, which participate in the relocation of the main cytoplasmic mass of the cell and include both the granuloplasm and the hyaloplasm (sensu Smirnov 2008).</footnote>

<footnote n="10">¹⁰Schaudinn (1899) reported a complex life cycle in *Trichosphaerium* (Corycida) that included biciated stages, which undergo copulation; no further confirmation of this observation has been obtained.</footnote>

<footnote n="11">¹¹Strain numbers and source data for these isolates are provided by Kang et al. (2017).</footnote>

<footnote n="12">¹²The genus *Atrichosa* by Cavalier-Smith et al. 2016 is considered here a junior synonym of *Trichosphaerium* until the opposite is shown. The - position of the genera *Penardochlamys*, *Microcorycia*, *Zonomyxa* and *Parmulina*, which were listed by Meisterfeld (2002) under "Microcoryciidae" is not clear; by their morphological characters they may belong to this lineage as well but this requires demonstration by molecular data.</footnote>
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

Cyclopyxis*, Distomatopyxis*, Ellipsopyxella*, Ellipsopyxis*, Geopyxella*, Lamptopyxis*, Netzelia, Protocucurbitella*, Pseudocucurbitella*, Pyxidicula, Suiadifflugia*, Trigonopyxis*<fnref n="13" />.

●●●● Difflugina Meisterfeld 2002, sensu Kosakyan et al. 2016

Test either completely chitinoid or comprising organic or mineral particles, or recycled diatom frustules, scales or plates (often from Euglyphida), or composed of siliceous, calcite or chitinoid self-secreted plates (idiosomes) held together by an organic cement; may produce thick, digitate pseudopodia, or move using a flattened, disc-like hyaline projection. *Alocodera, Apodera, Bullinularia, Centropyxis, Certesella, Cornutheca, Difflugia, Geoplagiopyxis*, Gibbocarina, *Hyalosphenia, Hoogenraadia*, Lesquereusia, Longinebela, Mrabella, Nebela, Oopyxis*, Padaungiella, Paracentropyxis*, Plagiopyxis*, Planhoogenraadia*, Planocarina, Porosia, Proplagiopyxis*, Protoplagipyxis*, Quadrulella, Spumochlamys, probably Conicocassis*, Microchlamys*, Pseudonebela*.

●●●● Heleopera sphagni Leidy 1874¹⁴

Test reinforced with mineral particles, slit-like aperture, numerous small digitate pseudopodia; with symbiotic *Chlorella*.

●●●● Phryganellina Bovee 1985

Test proteinaceous, with calcified inner layer, or completely chitinoid with recycled mineral or organic particles; pseudopodia conical, pointed, consist solely of the hyaloplasm, sometimes branched and may anastomose. *Cryptodifflugia, Meisterfeldia*, *Phryganella, Wailesella*.

●●● Euamoebida Lepși 1960, sensu Smirnov et al. 2011

Naked amoebae with tubular, subcylindrical pseudopodia (or the entire cell is monopodial and subcylindrical); no alteration of the locomotive form; no adhesive uroidal structures; sorocarpic development in some species. *Amoeba, Cashia*, *Chaos, Copromyxa, Copromyxella*, *Deuteramoeba, Glaeseria, Hartmannella, Hydramoeba*, *Nolandella, Parachaos*⁸, *Polychaos, Ptolemeba, Saccamoeba, Trichamoeba*.

● Evosea Kang et al. 2017 (R)

Representatives of this clade can vary across almost the entire range of morphologies seen in Amoebozoa. Many members have complex life cycles<fnref n="15" /> that include amoeboid, ciliated and fruiting stages. Some species appear to be exclusively ciliated with no amoeboid features. Most taxa with only a subset of these life cycle stages. The least inclusive clade containing *Physarum polycephalum* (Eumycetozoa), *Protostelium nocturnum* (Variosea), *Squamamoeba japonica* (Cutosea), and *Entamoeba histolytica* (Archamoebea).

●● Variousa Cavalier-Smith et al. 2004 (R)<fnref n="16" />

Amoebae elongated or flabellate during locomotion and sometimes branched to reticulate, with long, pointed, often branching and occasionally anastomosing subpseudopodia; ciliated cells may be the sole state, or present as ciliated amoebaes, or be one state in a life cycle that also includes obligate amoebae; the kinetid of ciliates bikont or unikont, associated at least with one cone of microtubules; several taxa contain a sporocarp state. The least inclusive clade containing *Flamella balnearia, Protostelium nocturnum, Acramoeba dendroida and Phalansterium solitarium*.

●●● Flamellidae Cavalier-Smith 2016 (R)

Flattened amoebae capable of forming fan-shaped or semicircular locomotive form with numerous fine, tapering hyaline subpseudopodia, directed anteriorly; ciliated stages unknown. The least inclusive clade containing *Flamella aegyptia* and *Telaepolella tubasterens*. *Flamella, Telaepolella*.

(continued)

<footnote n="13">¹³The SSU rRNA sequence of *Trigonopyxis arcula* AY848967 is almost identical to *Bullinularia indica* AY848970, and represents probably a con- tamination.</footnote>

<footnote n="14">¹⁴This species typically positioned as sister clade of both Sphaerothecina and Difflugina in beta-tubulin (Lahr et al. 2011), SSU rRNA (Lara et al. 2008) and multigene phylogenies (Lahr et al. 2013), so it is listed here as a separate lineage.</footnote>

<footnote n="15">¹⁵In the most complete version spores from a sporocarp germinate as ciliated-amoebae, cells that are reversibly amoeboid or ciliated that then go on to develop into an obligate amoeboid stage that cannot produce cilia, with the obligate amoeba differentiating into one or more sporocarps. However, some members are always ciliated or obligate amoebae. The kinetid structures of swimming stages are diagrammed in Spiegel et al. (2017), Mikryukov and Mylnikov (1998), Hibberd (1983), and Pánek et al. (2016).</footnote>

<footnote n="16">¹⁶Recent papers with relatively broad taxon sampling, based on SSU phylogeny (Berney et al. 2015) and multigene phylogeny (Kang et al. 2017) suggest grouping of some variosean genera into higher rank clades. However, SSU phylogeny shows little or no statistical support for many of these groupings, while many important variosean taxa are not yet represented in the multigene trees. Therefore, we prefer to be cautious about including certain higher level taxa proposed in these studies at this time. Hence, we list most variosean clades under the similarly high level regardless of the traditional ranks until more robust groups are established.</footnote>
<table><caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption><tr><td>●●● Filamoeba Berney, Bass & Geisen 2015 (R) (M)</td><td>Flattened amoebae, fan-shaped, triangular or crescent-shaped in locomotion, with numerous spine-like hyaline subpseudopodia, directed anteriorly; ciliated stages unknown. The least inclusive clade containing <i>Filamoeba nolandi</i> and <i>F. sinensis</i>. <i>Filamoeba</i>.</td></tr><tr><td>●●● Heliamoeba Berney, Bass & Geisen 2015 (R) (M)</td><td>Binucleate amoebae with filose-like pseudopodia; with clearly distinct cell body always present, the pronounced pseudopodia making up most of the total cell dimension; cell body rarely branching; never reticulate; pseudopodia often branching and present mostly in the anterior and posterior parts of fully extended cells, or all around the cell body in more condensed forms; cell movement slow; ciliated stages unknown. <i>Heliamoeba mirabilis</i>.</td></tr><tr><td>●●● Protosteliida Olive & Stoianovitch 1966, sensu Shadwick et Spiegel in Adl et al. 2012;</td><td>Sporocarpic amoebae with acutely pointed subpseudopodia and usually orange pigmentation contained in lipid droplets visible in <i>masse</i>; one taxon ciliated amoebae with 1–9 unikont kinetids not associated with nucleus; taxa without cilia with ring-shaped component in a nucleus-associated MTOC; sporocarps of variable morphology, with long, delicate stalk supporting single spore. The least inclusive clade containing <i>Protostelium nocturnum</i> and <i>Protostelium mycophaga</i>. <i>Protostelium</i><sup>17</sup>.</td></tr><tr><td>●●● Fractovitellida Lahr et al. 2011, sensu Kang et al. 2017 (R)<sup>18</sup></td><td>Uninucleate, flabellate to branching amoebae; several members sporocarpic, one species with ciliated amoebae and obligate amoebae. The least inclusive clade containing <i>Soliformovum irregularis</i>, <i>Nematostelium gracile</i> and <i>Acramoeba dendroida</i>. <i>Acramoebidae</i>, <i>Schizoplasmodiidae</i>, <i>Soliformoviidae</i>.</td></tr></table>

●●●● Acramoebidae Smirnov, Nassonova & Cavalier-Smith 2008 (R) (M)
Uninucleate amoebae, flattened highly branched, with very slender, pointed, sometimes branched hyaline subpseudopodia never forming a network; ciliated stages unknown. *Acramoeba dendroida*.

●●●●● Schizoplasmodiidae Shadwick & Spiegel in Adl et al. 2012
Exclusively sporocarpic group with multinucleate, highly branching and reticulate amoebae, or plasmodia; plasmodia without directional streaming and a beaded appearance during mitosis; prespore cells developing from multinucleate fragments of plasmodia; sporocarp stalk with cup-like apophysis that fits into annular hilum on spore; spores always multinucleate; one taxon (*Ceratiomyxella*) with scale-covered ciliated amoebae that can develop from zoocysts derived from the plasmodium that germinates from the spore or from a fragment of a feeding plasmodium; kinetids bikont. The least inclusive clade containing *Ceratiomyxella tahitiensis*, *Nematostelium ovatum*, *Schizoplasmodium cavostelioides*. *Ceratiomyxella*, *Nematostelium*, *Schizoplasmodium*.

●●●●● Soliformoviidae Lahr & Katz 2011 (R)
Uninucleate amoebae, thin, flabellate, fan-shaped to irregularly triangular with numerous finely pointed hyaline subpseudopodia often heavily concentrated at the leading edge during locomotion; lobed nucleoli present in at least one stage of the life cycle; multiple small contractile vacuoles; some species more branched than others; MTOC absent; ciliated stages unknown; two species sporocarpic; sporocarps deciduous in one species and ballistosporous in another. The least inclusive clade containing *Soliformovum irregularis* and *Grellamoeba robusta*. *Grellamoeba*, *Soliformovum*.

●●● Angulamoeba Berney, Bass & Geisen 2015 (R)
Uninucleate, branching amoebae with slender, pointed and/or filose-like, sometimes branched pseudopodia; trophozoites moving slowly; main cell body elongated, consisting of several main branches often with smaller lateral branches, never forming a network; numerous fine pseudopodia concentrated mostly at the extremities of the lateral and terminal branches, but can be formed anywhere around the cell body; multiple contractile vacuoles; some species with ciliated amoebae stages. The least inclusive clade containing *Angulamoeba microcystivorans* and *A. fungorum*. *Angulamoeba*.

●●● Cavosteliida Shadwick & Spiegel in Adl et al. 2012 (R)
Sporocarpic group with various types of amoebae, from uninucleate amoebae to multinucleate reticulate plasmodia, all characterized by producing long, filose, subspeudopodia, anastomosing in some taxa; one taxon with ciliated amoebae and obligate amoeba with possible sex in the life cycle; ciliated amoebae possesses one to several, reduced unikont kinetids per cell, not associated with the nucleus; species without ciliated amoebae have akinetid amoebae that germinate from spores; sporocarps in all species with single, nondeciduous spores; morphology variable and taxon specific; spores of all species displaying some type of sculpturing; cysts of some species displaying sculpturing as well. *Cavostelium*, *Schizoplasmodiopsis*, *Tychosporium*.

●●● Ischnamoeba Berney, Bass & Geisen 2015 (R)
Uninucleate, branching naked amoebae, cells usually thin, extended and flat, showing no well-defined cell body, except often a

(continued)

<footnote n="17"><sup>17</sup>The genus *Planoprotostelium* is subsumed into *Protostelium* (Shadwick et al. 2017).</footnote>

<footnote n="18"><sup>18</sup>This is the only group revealed in the paper by Lahr et al. (2011) which we suggest to apply because it is fully supported in a phylogenomic study by Kang et al. (2017) and combines several monotypic lineages; many of them group with each other in SSU trees as well.</footnote>
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

slight broadening in the area containing the nucleus; never reticulate, with whole cells often bent, but not extensively branched; branching more pronounced in condensed cells or in condensed parts of individual cells; very thin pseudopodia produced almost exclusively at distal parts of cells and more pronounced in condensed organisms, often branching; movement too slow to be directly observable; ciliated stages unknown. The least inclusive clade containing *Ischnamoeba montana* and *Ischnamoeba* sp. isolate F4 (Genbank: KP864094). *Ischnamoeba*.

●●● *Darbyshirella* Berney, Bass & Geisen 2015

Multinucleate, highly branching and reticulate amoebae with slender, pointed, sometimes branched and anastomosing pseudopodia; the whole cell body is strongly branching and narrow, especially in the most extended parts, while more condensed parts are wider; posterior end usually pointed with no or few pseudopodia and no branching; many contractile vacuoles present; movement very slow; ciliated stages unknown. The least inclusive clade containing *Darbyshirella terrestris* and *Darbyshirella* sp. (Genbank KP864088). *Darbyshirella*.

●●● Holomastigida Lauterborn 1895

Rounded cells with multiple radiating projections, which may be cilia arising from the solitary kinetosomes. *Artodiscus*, *Multicilia*.

●●● *Dictyamoeba* Berney, Bass & Geisen 2015 (M)

Multinucleate, highly branching and reticulate naked amoebae with slender, pointed, sometimes branched pseudopodia; movement of entire cells very slow; the main cell body is multiply branched and anastomosing, and can grow into giant networks (up to several mm) with intersecting segments of varying width and numerous terminal branching areas; abundant fine pseudopodia are concentrated mostly at the extremity of lateral and terminal branches, especially in complex networks, but can be formed anywhere around the cell body in simpler forms; ciliated stages unknown. *Dictyamoeba vorax*.

●●● *Arboramoeba* Berney, Bass & Geisen 2015 (M)

Multinucleate, highly branching and reticulate amoebae; cell body indistinct; nuclei and other cytoplasmic contents are distributed across the whole network, with network significantly more complex at the anterior front, forming a wide, very densely reticulate, non-permeable front where phagocytosis occurs; posterior part of the cells is much less reticulate and branching; branching, filose-like, pseudopodia are mostly present at the anterior front of the cell; very strong vacuolar activity across the whole network; movement very slow; ciliated stages unknown. *Arboramoeba reticulata*.

●●● *Phalansterium* Cienkowski 1870

Uniciliate sedentary cells, colonial or solitary; cilium arises from the apical part of the cell; one centriole per kinetid; ciliary pocket usually surrounded by a collar; some species form short tapering cytoplasmic projections and move over the substratum using the conformation of their body or producing cytoplasmic eruptions. The least inclusive clade containing *Phalansterium solitarium* and *P. filosum*. *Phalansterium*.

●● Eumycetozoa Zopf 1884 sensu Kang et al. 2017 (R)

All known members fruit, either sorocarpically (Dictyostelia), or sporocarpically (Myxogastria, Protosporangiida); with a life cycle having a single haploid amoeboid state (Dictyostelia); or a life cycle with a bikont ciliated amoebae state that gives rise to a non-ciliate obligate amoeboid state from which sporocarps develop (Myxogastria and Protosporangiida); ciliated amoebae of myxogastrids and protosporangiids and amoebae of dictyostelids flat and form wide pseudopodia with acutely pointed subpseudopodia and no pronounced streaming of the granular cytoplasm; where sex is well studied, the zygote cannibalizes haploid amoebae. The least inclusive clade containing *Dictyostelium discoideum*, *Physarum polycephalum* and *Ceratiomyxa fruticulosa*.

●●●*Dictyostelia* Lister 1909, sensu Sheikh et al. 2018 (R)

Sorocarpic amoebae, also known as cellular slime moulds or social amoebae, with stalked fruiting bodies developing from aggregation of amoebae; sorocarps consisting of stalks with terminal sori of haploid spores; stalks (sorophores) acellular (acytosteloid), cellular and unbranched or sparsely branched (dictyosteloid), or cellular and regularly branched with whorls of lateral branches (polysphondyloid); cells of stalks dead, consisting of walls, only, at maturity; spores usually ellipsoid, spherical in some species; cysts present in some species; sex, when present associated with a zygote that causes haploid amoebae to aggregate towards it such that the aggregate lays down a common cyst wall to form a macrocyst in which the haploid cells are ingested and digested by the zygote and meiosis occurring in the zygote prior to germination of the macrocyst; amoebae aciliate, haploid, with nucleus with peripheral reticulate nucleolus; upon starvation, amoebae aggregating, often in streams, towards an aggregation centre that signals with a chemical attractant (an acrasin) with aggregate developing into a slug-shaped, multicellular mass that can migrate then fruit or fruit directly; anterior cells becoming stalk cells in dictyosteloid and polyspondyloid species and bulk of the remaining cells becoming spores. *Acytostelium*, *Cavenderia*, *Coremiostelium*, *Dictyostelium*, *Hagiwaria*, *Heterostelium*, *Polysphodylium*, *Raperiostelium*, *Rostrostelium*, *Speliostelium*, *Synstelium*, *Tieghemostelium*, probably—*Coenonia*<fnref n="19" />.

(continued)

<footnote n="19">¹⁹*Coenonia* was seen only once by Van Tieghem (1884) who described but never illustrated it. On the basis of his description, it seems reasonable to conclude it was a dictyostelid.</footnote>
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

●●● Myxogastria Macbride 1899 [Myxomycetes Link 1833, sensu Haeckel 1866] (R)

Sporocarpic amoebae where a multinucleate obligate amoeba—the plasmodium—differentiates into one or more multinucleate spore-forming masses where the cell cleaves into individual, uninucleate spores that undergo meiosis after spore wall development in sexual species; sporocarps can be individual sporangia (with or without stalks), clustered sporangia, aethalia (massive fruiting derived from a whole plasmodium) or plasmodium-shaped plasmodiocarps; fruiting bodies initially covered by an extracellular peridium and may contain thread-like spore-suspending capillitium; spores germinating as bikont ciliated amoebae with rootlets as with Eumycetozoa with rootlet 3 consisting of a band of several microtubules; ciliated amoebae developing into plasmodia (involving plasmogamy and karyogamy of gametic ciliated amoebae in sexual species); plasmodia usually tubular in cross-section with streaming of central granular cytoplasm. One species known to lack plasmodial state and one species known to lack ciliated amoebae.

●●●● Lucisporidia Cavalier-Smith 2013 (R)

Containing taxa with light- or bright-coloured spores, in mass. *Alwisia*, *Arcyria*, *Calomyxa*, *Cornuvia*, *Cribraria*, *Dianema*, *Dictydiaethalium*, *Hemitrichia*, *Licea*, *Lindbladia*, *Lycogala*, *Metatrichia*, *Minakatella*\*, *Oligonema*, *Perichaena*, *Prototrichia*, *Reticularia*, *Trichia*, *Tubifera*.<fnref n="20" />

●●●●● Columellidia Cavalier-Smith 2015 (R)

Containing taxa predominantly with dark coloured spores, in mass. *Amaurochaete*, *Badhamia*, *Barbeyella*, *Brefeldia*, *Clastoderma*, *Collaria*, *Colloderma*, *Comatricha*, *Craterium*, *Diachaeopsis*, *Diachea*, *Diderma*, *Didymium*, *Echinosteliopsis*, *Echinos telium*, *Elaeomyxa*, *Enerthenema*, *Fuligo*, *Kelleromyxa*, *Lamproderma*, *Leocarpus*, *Lepidoderma*, *Leptoderma*, *Macbrideola*, *Meriderma*, *Mucilago*, *Paradiachea*\*, *Paradiachaeopsis*, *Physarella*, *Physarina*, *Physarum*, *Protophysarum*, *Stemonaria*, *Stemonitis*, *Stemonitopsis*, *Symphytocarpus*, *Willkommlangea*.<fnref n="20" />

●●● Protosporangiida Shadwick & Spiegel in Adl et al. 2012 (R)

Exclusively fruiting, with microscopic (protosteloid) sporocarps with a microscopic stalk with one to four, sometimes more, spores; life cycle with ciliated amoebae stage with rootlets as Eumycetozoa with rootlet 3 consisting of a band of only two microtubules; giving rise to a uninucleate to plurinucleate obligate amoeba that develops into one or more sporocarps; prespore cells site of meiotic prophase and meiosis completed in spore complement.

●●●● Protosporangiidae Spiegel in Adl et al. 2012

With ciliated amoebae as Protosporangiida; obligate amoeba uninucleate to plurinucleate, often resembling very early developmental stages of myxogastrid plasmodia; individually developing into a single two to four-spored sporocarp. *Clastostelium*, *Protosporangium*.

●●●●● Ceratiomyxa Schroeter 1889

With ciliated amoebae developing from cleavage of germling from a tetranucleate spore; obligate amoeba is multinucleate plasmodium secreting an extracellular slime mound or columns upon which it cleaves into single uninucleate prespore cells that individually develop into a stalked sporocarp bearing a single, tetranucleate spore. *Ceratiomyxa*.

●● Cutosea Cavalier-Smith et al. 2016

Amoebae bounded by a continuous thin, somewhat flexible, envelope separated from the plasma membrane and having oval scale-like substructure within a denser matrix; small pores penetrate the envelope, allowing subpseudopodia to protrude for very slow, occasional locomotion; locomotive cells flattened, oval, rounded or irregularly triangular. *Armaparvus*, *Sapocribrum*, *Squamamoeba*.

●● Archamoebea Cavalier-Smith 1983, sensu Cavalier-Smith et al. 2004

Amoebae or ciliated amoebae, anaerobic or microaerophilic, free-living or endobionts of different invertebrate or vertebrate hosts; ciliated amoebae usually with hyaline lateral pseudopodia; unikont, with single kinetosome at the base of cilia, connected to the microtubular cone, in some cases both the kinetosome and the axoneme have atypical complements of microtubules; without typical mitochondria, in several cases mitochondrial derivates, i.e. mitosomes, have been demonstrated.

●●● Mastigamoebida Frenzel 1897, sensu Cavalier-Smith 2013

Ciliated amoebae or amoeboid organisms without cilia. The single motile anterior cilium, when present, associated with microtubular cone connected to the nucleus. Ciliated amoebae with hyaline lateral pseudopodia. *Endamoeba*\*, *Endolimax*, *Iodamoeba*, *Mastigamoeba*, *Mastigina*\*.

●●●● Pelobiontida Page 1976, sensu Cavalier-Smith 2013

Anaerobic or microaerophilic ciliated amoebae with slow-beating monokinetid or immobile polykinetids; ciliated amoebae often with hyaline lateral pseudopodia. *Pelomyxa*, *Mastigella*.

(continued)

<footnote n="20">²⁰Many taxa in need of revision because of rampant paraphyly.</footnote>
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

●●● *Tricholimax* Frenzel 1897
Ciliated amoebae with single immobile cilium, microtubular cone associated with nucleus, when several nuclei present, each nucleus is connected to its own microtubular cone; with rhizostyle, derived from the lateral microtubular root. *Tricholimax*.

●●● *Entamoeba* Casagrandi & Barbagallo 1895
Cilia and kinetosomes absent; with mitosomes instead of classical mitochondria; peroxisomes absent; mitosis closed with endonuclear centrosome and spindle; reduced Golgi dictyosome. *Entamoeba*.

●●● *Rhizomastix* Alexeieff 1911
Ciliate ciliated, possessing a rhizostyle arising from the basal body of the cilium and probably derived from the microtubular cone. *Rhizomastix*.

● **Discosea** Cavalier-Smith et al. 2004, sensu Smirnov et al. 2011
Flattened naked amoebae, never producing tubular, subcylindrical pseudopodia and never altering the locomotive form to the tubular, subcylindrical one; cytoplasmic flow polyaxial or without a pronounced axis; ciliated stages unknown; several taxa sporocarpic.

●● Flabellinia Smirnov et al. 2005
Flattened generally fan-shaped, oblong or irregularly triangular cells, never with pointed subpseudopodia.

●●● *Thecamoebida* Schaeffer 1926, sensu Smirnov et al. 2011
Flattened amoebae, oblong, lingulate or irregularly triangular amoebae, usually with dorsal folds and/or ridges; anterior hyaloplasm often forms an anterolateral crescent and rarely occupies more than half of the body length; never produce discrete pseudopodia or subpseudopodia. *Sappinia*, *Stenamoeba*, *Stratorugosa*, *Thecamoeba*.

●●● *Dermamoebida* Cavalier-Smith 2004
Oblong, lancet-shaped or irregularly triangular cells; with a smooth cell surface or with few wide ridges, never wrinkled; short, wide triangular pseudopodia and, in some, subpseudopodia of dactylopodial type; thick cell coat, multilayered or consisting of tightly packed helical structures. *Dermamoeba*, *Mayorella*, *Paradermamoeba*.

●●● *Mycamoeba* Blandenier et al. 2017²¹ (M)
Flattened lingulate amoebae without differentiated glycocalyx; with complex life cycle where active cells transform into coccoid stages, which undergo subsequent buddings, eventually turning into ramified structures (pseudomycelia) with spherical cysts in a terminal position on the ramifications; these pseudomycelia disappear and cysts are released prior to germinating into active trophozoites. *Mycamoeba gemmipara*.

●●● *Dactylopodida* Smirnov et al. 2005, sensu Kang et al. 2017
Locomotive form mostly has a shape of an irregular triangle with basement directed forward; wide anterior hyaloplasm; fibrous axial cores both in dactylopodia and in the floating pseudopodia. *Cunea*, *Janickina*<fnref n="22" />, *Korotnevella*, *Neoparamoeba*, *Paramoeba*, *Pseudoparamoeba*, *Vexillifera*.

●●● *Vannellida* Smirnov et al. 2005
Locomotive form fan-shaped to spatulate; cells do not form discrete pseudopodia or subpseudopodia; wide anterior hyaloplasm up to a half of the cell; posterior granuloplasm concentrated in a "hump", often raised over the substratum; one species of *Vannella* (*V. fimicola*) with protosteloid sporocarps. *Clydonella*, *Lingulamoeba*, *Paravannella*, *Pessonella*<fnref n="23" />, *Ripella*, *Vannella*.

●● Stygamoebida Smirnov et al. 2011 (P)<fnref n="24" />
Flattened, elongate amoebae resembling tooth-picks or splinters, temporarily acquiring forked or branched form; elongate, expanded area of anterior hyaloplasm; mitochondrial cristae flattened, ribbon-like; MTOC known in one species. *Stygamoeba*, *Vermistella*.

(continued)

<footnote n="21">²¹The species *Mycamoeba gemmipara* in Blandenier et al. (2017) groups with *Dermamoeba*; however, the phylogenetic analysis in this paper uses a limited number of taxa and does not show *Dermamoebida* as a clade, so we list this genus as a separate branch until it position is better resolved.</footnote>

<footnote n="22">²²Two known species of this genus—*J. chaetognathi* (Grassi 1881) and *J. pigmentifera* (Grassi 1881) are not triangular but monopodial in locomotion which may be a consequence of their parasitic life style. No molecular data on this genus are available, so it is left among the *Dactylopodida* provisionally, basing on the presence of a kinetoplastid intracellular symbiont (PLO), which appears to have originated only once in the evolution of paramoebids (Sibbald et al. 2017).</footnote>

<footnote n="23">²³This genus may be a junior synonym of *Vannella*, being a life form of some *Vannella* species.</footnote>

<footnote n="24">²⁴These genera group together in some SSU phylogenetic trees, but usually they appear as separate branches in phylogenetic studies. In the phylogenomic study of Kang et al. (2017) they do not form a clade, but this is the only region of the tree that is not fully supported. Taking into account the superficial similarity of the ultrastructure, including the unique shape of the mitochondrial cristae, in these two genera we suggest keeping this assemblage as a potential branch in the tree unless the opposite is proven with increased taxon sampling.</footnote>
<table><caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>
  <tbody>
    <tr>
      <td>●● Centramoebia Cavalier-Smith et al. 2016 (R)</td>
    </tr>
    <tr>
      <td>MTOC located near the dictyosome; several taxa with protosteloid sporocarpy. The least inclusive clade containing <i>Pellita catalonica</i>, <i>Gocevia fonbrunei</i>, <i>Endostelium zonatum</i>, <i>Acanthamoeba castellanii</i>.</td>
    </tr>
    <tr>
      <td>●●● Acanthopodida Page 1976</td>
    </tr>
    <tr>
      <td>Flattened with prominent subpseudopodia, flexible and tapering to a fine tip and sometimes furcated near their base (acanthopodia); without adhesive uroid; trilaminate MTOC; some species in culture appear as a branched, flattened sheet; at least two taxa, <i>Acanthamoeba</i> and <i>Luapeleamoeba</i>, contain species with protosteloid sporocarpy. <i>Acanthamoeba</i>, <i>Balamuthia</i>, <i>Dra-coamoeba</i>, <i>Luapeleamoeba</i>, <i>Protacanthamoeba</i>, <i>Vacuolamoeba</i>.</td>
    </tr>
    <tr>
      <td>●●●● Pellitida Smirnov &amp; Cavalier-Smith 2011, sensu Kang et al. 2017</td>
    </tr>
    <tr>
      <td>Thick cell coat envelops the entire cell with the exception of subpseudopodial tips and is integrated with plasma membrane, or is located on the dorsal surface only, and is loosely attached to the plasma membrane; MTOC, when known, trilaminate. One genus, <i>Endostelium</i>, with several protosteloid sporocarpic species. <i>Endostelium</i>, <i>Gocevia</i>, <i>Paragocevia*</i>, <i>Pellita</i>.</td>
    </tr>
    <tr>
      <td>●●●● Himatismenida Page 1987</td>
    </tr>
    <tr>
      <td>Dorsal surface covered with a flexible coat without defined aperture; ventral surface entirely or partly naked; can form ventral flattened sheet of hyaloplasm used for adhesion to the substratum; MTOC, when known, bar-like. <i>Cochliopodium</i>, <i>Ovalopodium</i>, <i>Parvamoeba</i>.</td>
    </tr>
  </tbody>
</table>

**Opisthokonta Cavalier-Smith 1987**, emend. Adl et al. 2005

Single posterior cilium without mastigonemes, present in at least one life cycle stage or secondarily lost;
with a pair of kinetosomes or centrioles, sometimes modified; flat (rarely tubular) mitochondrial cristae in the uni-
cellular stage.

● Holozoa Lang et al. 2002 (R)

The most inclusive clade containing *Homo sapiens* Linnaeus 1758 (Metazoa), but not *Neurospora crassa* Shear and Dodge 1927 (Fungi). This is a branch-based definition in which all the specifiers are extant.

The apparent composition of Holozoa is Filasterea (Ministeria, Capsaspora, Pigoraptor), Ichthyosporea, Corallochytrium, Syssomonas, Choanoflagellata, and Metazoa. The primary reference phylogenies are Carr et al. (2017, Fig. 2), Hehenberger et al. (2017, Fig. 2), Tor-ruella et al. (2015, Fig. 1), Simion et al. (2017, Fig. 3), Whelan et al. (2017, Fig. 2).

*Incertae sedis* Holozoa:

Corallochytrium<sup>25</sup> limacisporum Raghu-Kumar 1987 (M)

Spherical single cells 4.5-20 µm in diameter; binary fissions releasing numerous elongated amoeboid cells; marine saprotrophic, usually recovered from coral reefs in the Indian Ocean; free-living cells grow as osmotrophic chitin cell-walled schizont as ichthyosporeans; a ciliary apparatus has been observed in culture conditions and further demonstrated by molecular means (conserved ciliary toolkit expressed in transcriptome).

Syssomonas<sup>25</sup> Tikhonenkov, Hehenberger, Mylnikov & Keeling 2017 (M)

Predominantly unicellular, roundish uniciated motile swimming cells; cilium emerges from the middle lateral point of the cell, ended by short acroneme and directs backward; cells naked; cells can form clusters of multiple cells; predatory phagotroph of heterotrophic chrysomonads and bodonids; life cycle includes unicilaited roundish motile swimming cells, ciliated amoeboid cells, amoeboid aciliated cells with filopodia and spherical cysts; known from freshwater. *Syssomonas multiforma*.

●● Ichthyosporea<sup>25</sup> Cavalier-Smith 1998 [Mesomycetozoea Mendoza et al. 2002]

Single-celled trophic organisms, *Ichthyophonus* with hyphal multinucleated filaments; flat mitochondrial cristae but some may have tubular mitochondrial cristae; if present, single cilium; without collar or cortical alveoli; some species form only elongate amoeboid cells; most animal parasites, some free-living and saprotrophic (*Sphaeroforma*, LKM51 isolate); chitin reported in cell wall (proven by staining with wheat germ agglutinin and molecular phylogeny of chitin synthases); both marine and freshwater.

●●● Dermocystida Cavalier-Smith 1998 [Rhinosporidaceae Mendoza et al. 2001]

Zoospore with posterior cilium; flat mitochondrial cristae; when parasite of animals, spherical phenotypes with several 2-20 µm endospores that are eventually released and become mature cells with endospores to continue the parasitic cycle. *Amphibiocystidium ranae*, *Amphibiothecum penneri*, *Chromosphaera perkinsii*, *Dermocystidium, Rhinosporidium seeberi*, *Sphaerothecum destruens*.

(continued)

<footnote n="25"><sup>25</sup>Teretosporea Torruella et al. 2015 (R) is a monophyletic clade consisting of at least *Corallochytrium* and *Ichthyosporea*; Pluriformea Hehenberger et al. 2017 (R) is a monophyletic clade consisting of at least *Corallochytrium* and *Syssomonas*. These are two competing phylogenetic hypotheses.</footnote>
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

●●● Ichthyophonida Cavalier-Smith 1998 [Ichthyophonae Mendoza et al. 2001; Amoebidiidae Reeves 2003] (R)
Parasites of fish, arthropods and insects, or free-living and saprotrophic; usually with flat mitochondrial cristae but *Ichthyophonus* with tubular mitochondrial cristae; some characteristic amoeboid cells, but in others, amoeboid cells absent or unreported. *Abeoforma whis-leri*, *Amoebidium parasiticum*, *Anurofeca richardsi*, *Astreptonema*, *Caullerya mesnili*, *Creolimax fragrantissima*, *Eccrinimus flexilis*, *Enter-obryus oxidi*, *Enteropogon sexuale*, *Ichthyophonus*, *Palavascia patagonica*, *Pseudoperkinsus tapetis*, *Psorospermium haeckeli*, *Sphaeroforma arctica*; *S. tapetis*.

●● Filasterea Shalchian-Tabrizi et al. 2008
Trophic cells naked, unicellular; uninucleate; aerobic with flat mitochondrial cristae; long nontapering tentacles supported by microfilaments, unlike collar in choanoflagellates; phagotrophic. *Capsaspora*, filose amoeba with cystic and aggregative stages; *Ministeria* and *Pigoraptor* with cilium, *Ministeria* is not motile but uses a stalk attached to the substrate; *Pigoraptor*, ciliated amoeba and predator, as *Capsaspora* it can present pluricellular clusters. *Capsaspora*, *Ministeria*, *Pigoraptor*.

●● Choanoflagellata Kent 1880–1882 [Craspedomonadina Stein 1878; Craspedomonadaceae Senn 1900; Craspedophyceae Chade-faud 1960; Craspédomonadophycidées Bourrelly 1968; Craspedomonadophyceae Hibberd 1976; Choanomonadea Krylov et al. 1980; Choanoflagelliida Lee, Hutner, and Bovee 1985; Choanoflagellatea Cavalier-Smith 1997 emend. Cavalier-Smith 1998; Choanomonada<fnref n="26" /> Adl et al. 2005;]<fnref n="27" />

Phagotrophic with collar of actin-supported microvilli around a single cilium; radial symmetry; solitary or colonial; flat mitochondrial cristae; ciliated basal body associated with ring or multiple arcs of cytoskeletal (cortical) microtubules, with second aciliated basal body located at an angle; fibrillar root if present minor and without obvious banding; central filament in kinetosome transition zone.
This is a branch-based definition including the most recent common ancestor of animals and choanoflagellates (the Urchoanozoan), along with all of its descendants, including *Homo sapiens* Linnaeus 1758 and *Monosiga brevicollis* Ruinen 1938. The Greek root "choanê" (or funnel) refers to the collar, which in the current state of knowledge is a synapomorphy of the clade. Although "Choanozoa" was used previously to refer to an assemblage of protists that later proved paraphyletic, that usage was not adopted, and the name is more appropriately applied as defined here. The informal term "choanimal" and the formal term Apoikozoa have both been previously proposed for the clade containing choanoflagellates and animals, but neither has been formally described nor adopted. In particular, the term "Apoikozoa" is incorrect as the root "apoiko-" refers to colony formation, which is neither universally present in choanozoans, nor exclusive to them.

●●● Craspedida Cavalier-Smith 1997, emend. Nitsche et al. 2011
Extracellular glycocalyx or theca that is entirely organic and does not project above the anterior end of the extended feeding cell; vegetative stage usually sedentary and stalked; brief motile stage for dispersal.

●●●● Salpingoecidae Kent 1880–1882, emend. sensu Nitsche et al. 2011
Vegetative cells with glycocalyx or theca that is entirely organic; glycocalyx is flexible, nonrestrictive and fibrous; theca is rigid and microfibril-based; sedentary cells adhere to a surface by a peduncle extending from the base of the glycocalyx or theca; cell division with nonrestricting glycocalyx is longitudinal *in situ*, with restricting theca it is emergent and involves cell becoming amoeboid and dividing outside the theca; juvenile daughter cells disperse as naked; under certain conditions colonies of cells may develop. Type genus: *Salpingoeca* James-Clark 1867. Recognized genera: *Astrosiga*, *Aulomonas*, *Choanoeca*, *Cladospongia*, *Codonocladium*, *Codonosigopsis*, *Codosiga* (junior synonym *Codonosiga*), *Desmarella* (junior synonyms *Codonodesmus* and *Kentrosiga*), *Dicraspedella*, *Diploeca*, *Diplosiga*, *Diplosigopsis*, *Hartaetosiga*, *Kentia*, *Lagenoeca*, *Microstomoeca*, *Monosiga*, *Mylnosiga*, *Pachysoeca*, *Proterospongia*\*, *Salpingoeca*\*, *Salpingorhiza*, *Sphaeroeca*, *Stagondoeca*, *Stelexomonas*, *Stylochromonas*.

●●● Acanthoecida Cavalier-Smith 1997, emend. Nitsche et al. 2011
Cells surrounded by a basket-like lorica of siliceous costae comprising rod-shaped costal strips and a partial or entire organic matrix on inner surface.

●●●● Acanthoecidae Norris 1965, emend. sensu Nitsche et al. 2011
Lorica with costae arranged in two layers, outer longitudinal and inner helical; occasionally only one layer around cell body, in which case costae are helical; adult loricate cells sedentary; cell cycle, and lorica production accord to nudiform condition; cell division is diagonal resulting in both daughter cells facing forwards; upper daughter cell (juvenile) is naked with cilium for dispersal; juvenile attaches to surface, withdraws cilium and deposits costal strips in correct orientation; strips are accumulated in vertical bundles on the surface of the spindle-shaped cell body; costal strips destined for longitudinal costae are deposited first followed by those for the inner layer of costae; lorica assembly is achieved by a forwards and clockwise rotation which extends costal strips to form mature pattern of costae. Type genus: *Acanthoeca* Ellis 1929. Recognized genera: *Acanthoeca*, *Helgoeca*, *Polyoeca*, *Savillea*.

(continued)

<footnote n="26">²⁶Choanomonada was an unfortunate error in spelling that was corrected in an erratum, Journal of Eukaryotic Microbiology 60 (3): 321, published online March 11, 2013.</footnote>

<footnote n="27">²⁷The clade that comprises the Metazoa and Choanoflagellata is called Choanozoa Brunet and King 2017 [Choanozoa Cavalier-Smith et al. 1991].</footnote>
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

●●●●● **Stephanoecidae** Leadbeater 2011
Costae arranged in two layers with longitudinal costae outermost; internal costal layer is helical in posterior chamber of some species, but usually comprises transverse costae (rings) in the anterior chamber of lorica and some species only possess transverse rings; cell cycle and lorica production accords to tectiform condition; costal strips are deposited in inverted orientation; strips destined for the inner layer of costae are deposited first followed by those for the outer layer of longitudinal costae; costal strips are exocytosed through anterior end of cell and accumulated in bundles at the top of the inner surface of the collar; cell division is inverted with juvenile daughter cell being turned upside down and pushed into accumulated strips and emerging from parent lorica backwards; costal strips destined for longitudinal and helical costae are located vertically on juvenile cell, costal strips destined for transverse costae are located horizontally; once free of parent lorica, juvenile cell constructs new lorica immediately and there is no swimming dispersal stage. Type genus: *Stephanoeca* Ellis 1929. Recognized genera: *Acanthocorbis*, *Amoenoscopa*, *Apheloecion*, *Bicosta*, *Calliacantha*, *Calotheca*, *Campanoeca*, *Campyloacantha*, *Conion*, *Cosmoeca*, *Crinolina*, *Crucispina*, *Diaphanoeca*, *Didymoeca*, *Kakoeca*, *Monocosta*, *Nannoeca*, *Parvicorbicula*, *Platyleura*, *Pleurasiga*, *Polyfibula*, *Saepicula*, *Saroeca*, *Spinoeca*, *Spiraloecion*, *Stephanacantha*, *Stephanoeca*\*, *Syndetophyllum*.

●● Metazoa Haeckel 1874, emend. Adl et al. 2005 [Animalia Linnaeus 1758; Eumetazoa Bütschli 1910]
Reproduction sexual through an egg cell, fertilized usually by a monociliated sperm cell with acrosome; embryonic development with blastula followed by gastrulation that begins the differentiation into endoderm, ectoderm, mesoderm, and neuroderm; tissues organized into organs that share tasks for the individual, unless secondarily lost; some secondarily reduced to small number of cells (e.g. Myxozoa Grassé 1970); coordination of cells and tissues by membrane receptors that respond to ligands through elaborate signal transduction; characteristic cell-cell junctions with belt desmosomes or zonulae adherentes; basal lamina and extracellular matrix with collagen and other fibrous proteins (laminin, nidogen, perlecan); heterotrophic nutrition with secretion of digestive enzymes and osmotrophy through a digestive tract; without cell wall; ectoderm completely surrounding body, and endoderm surrounding a digestive tract; sensory cells in epithelium; nervous tissue in organized network; epithelial actin-myosin-based contractile cells between endoderm and ectoderm; some tissues with phagotrophic cells. Subdivisions beyond Porifera and *Trichoplax* not shown.

●●● Porifera<fnref n="28" /> Grant 1836 [Parazoa Sollas 1884]
Flat mitochondrial cristae; sexual species, zygotes forming larva (nine known larval types) or juveniles; asexual reproduction by gemmules, budding or fragmentation; sessile adult; differentiation of larva to a variety of cell types, including choanocytes, amoeboid cells and cells with granular inclusions; cell types transformable into other types as necessary; cells more or less independent; without mesoderm, nervous tissue, desmosomes, localized gonad or glandular digestive cells.

●●●●● **Hexactinellida** Schmidt 1870
Exclusively marine, and especially in the deep sea; siliceous spicules triaxonic, hexactinic; square axial proteinaceous filament in spicules, whole sponge formed by a single continuous multinucleate syncytium, with some differentiated cells; electrical conductance across body; reproduction when known is viviparous with a trichimella larvae.

●●●●●● **Amphidiscophora** Schulze 1886
*Amphidisc* spicules. *Amphidiscosida* Schrammen, 1924.

●●●●●●● **Hexasterophora** Schmidt 1870
*Hexaster* spicules. *Lychniscosida* Schrammen 1903; *Lyssacinosida* Zittel 1877; *Sceptrulophora* Mehl 1992; *Hexas-terophora* incertae sedis.

●●●●● **Demospongiae** Sollas 1885
Verongimorpha and Keratosa do not have (for the most part) siliceous spicules, Heteroscleromorpha have a high diversity of siliceous spicules; spicules differentiated in meglascleres and microscleres, triangular axial proteinaceous filament in spicules; larva with outer ciliated cells; one family (Cladorhizidae) with extracellular digestion, by amoeboid cell aggregation of captured crustacean prey; one order Spongillida living in freshwater.

●●●●●● Verongimorpha Erpenbeck, Sutcliffe, De Cook, Dietzel, Maldonado, van Soest, Hooper and Wörheide 2012
Mostly with spongin skeleton, otherwise with siliceous spicules (Chondrilla), or no skeleton at all. Synapomorphies include the following ultrastructure characters: orientation of accessory centriole, the nuclear apex, the Golgi apparatus and similarities in embryonic development. Chondrillida Redmond, Morrow, Thacker, Diaz, Boury-Esnault, Cárdenas, Hajdu, Lobo-Hajdu, Picton, Pomponi, Kayal and Collins 2013; Chondrosiida Boury-Esnault and Lopes 1985; Verongiida Bergquist 1978.

(continued)

<footnote n="28">²⁸The clade comprising the Porifera, *Trichoplax*, Cnidaria, Ctenophora, and Bilateria is called Metazoa, Metazoa Haeckel 1874.</footnote>
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

●●●●● Keratosa Grant 1861

Demospongiae with a skeleton made of spongin fibre; spongin fibres are either homogenous or pithed and strongly laminated with pith grading into bark. One genus has a hypercalcified basal skeleton (Vaceletia). Dendroceratida Minchin 1900; Dictyoceratida Minchin, 1900.

●●●●● Heteroscleromorpha Cárdenas, Pérez and Boury-Esnault 2012

Demospongiae with a skeleton composed of siliceous spicules which can be monaxones and/or tetraxones and when they are present, microscleres are highly diversified. Agelasida Hartman 1980; Axinellida Lévi 1953; Biemnida Morrow and Cárdenas 2015; Bubarida Morrow and Cárdenas 2015 Clionaida Morrow and Cárdenas 2015; Desmacellida Morrow and Cárdenas 2015; Haplosclerida Topsent 1928; Merliida Vacelet 1979; Poecilosclerida Topsent 1928; Polymastiida Morrow and Cárdenas 2015; Scopalinida Morrow and Cárdenas 2015; Sphaerocladina Schrammen 1924; Spongillida Manconi and Pronzato 2002; Suberitida Chombard and Boury-Esnault 1999; Tethyida Morrow and Cárdenas 2015; Tetractinellida Marshall 1876; Trachycladida Morrow and Cárdenas 2015.

●●●● Homoscleromorpha Bergquist 1978

Exclusively marine, from shallow depths to the deep sea; siliceous spicules or no spicules at all, tetraxonic, not differentiated between megascleres and microscleres, without defined axial proteinaceous filament in spicules (only observed in one species); true epithelium; hermaphroditic; viviparous cinctoblastula larva. Homosclerophorida Dendy, 1905.

●●●●●● Calcarea Bowerbank 1862 [Calcispongia Johnston 1842]

Exclusively marine, from shallow depths to the deep sea; calcium carbonate spicules; viviparous, hermaphrodites.

●●●●●●● Calcinea Bidder 1898

Unambiguous characters congruent with molecular phylogenies unclear. Larva amphiblastula. Clathrinida Hartman, 1958; Murrayonida Vacelet 1981.

●●●●●● Calcaronea Bidder 1898

Unambiguous characters congruent with molecular phylogenies unclear. Larva calciblastula; hermaphroditic. Leucosolenida Hartman 1958; Lithonida Vacelet 1981.

●●● *Trichoplax*<fnref n="29" /> von Schulze 1883 [Placozoa Grell 1971] (M)

Two layers of epithelial cells, with a middle layer of syncytial contractile fibrous cells, and undifferentiated cells; with digestive glandular cells; belt desmosomes or zonulae adherentes connecting adjacent cells; without extracellular matrix; collagen fibres absent; without endoderm, ectoderm, mesoderm or nerve cells; ventral cells having ated kinetosomes with two horizontal fibrillar rootlets and one vertical rootlet; egg cell and aciliate sperm in mid-layer; asexual binary division of body possible. *Trichoplax adhaerens*.

● **Nucletmycea** Brown et al. 2009 [syn. Holomycota Liu et al. 2009] (R)<fnref n="30" />,<fnref n="31" />

The most inclusive clade containing *Neurospora crassa* Shear and Dodge 1927 (Fungi) and not *Homo sapiens* Linnaeus 1758 (Metazoa). The composition of Nucletmycea is Fungi, Opisthosporidia, Nucleariida and *Fonticula*. The primary reference is Brown et al. (2009). Additional phylogenies are Brown et al. (2009, Fig. 3, 4). This is a branch-based definition in which all the specifiers are extant.

*Incertae sedis* Nucletmycea: Sanchytriaceae Karpov and Aleoshin 2017

Thallus monocentric, epibiotic, penetrates host wall with rhizoid in parasitic species; amoeboid zoospores with posterior pseudocilium; sporangia as in Rhizophydiales (Chytridiomycetes); sexual reproduction not observed. *Amoeboradix*.

●● Rotosphaerida Rainer 1968 [junior syn. Cristidiscoidida Page 1987, Cavalier-Smith 1993, 1998, Nucleariidae Patterson 1983, 1999]

Aciliate predominantly spherical or flattened amoebae from which elongated actin-based filopodia extend; with flat discoid mitochondrial cristae; uninucleate or polynucleate (with few nuclei); free-living phagotrophs that feed on bacteria, cyanobacteria and algae. Some sorocarpic, e.g. *F. alba*; some have symbionts, e.g. *N. thermophila*. *Fonticula*, *Nuclearia*, *Parvularia*.

*Incertae sedis* Rotosphaerida: *Pompholyxophrys*, *Lithocola*, *Vampyrellidium*, *Pinaciophora*, *Rabdiophrys*, *Rabdiaster*.

(continued)

<footnote n="29">²⁹Although monotypic, genetic diversity of isolates indicate there are probably multiple genera, and it is probably a sister clade to Cnidaria (Schierwater and DeSalle 2018; and Srivastava et al. 2008).</footnote>

<footnote n="30">³⁰Nucletmycea and Holomycota were proposed at about the same period and they are to be considered synonymous, but Nucletmycea has nomenclatural priority having been published first. Since, Holomycota has come into more usage in favour of the symmetry with Holozoa.</footnote>

<footnote n="31">³¹There is no agreement on the definition, thus placement, of a clade named Fungi. Variations differ from the historical understanding of Fungi that included social amoebae, now dispersed across protists, and several other clades also dispersed across protists.</footnote>
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

●● Fungi<sup>32</sup> R.T. Moore 1980
This is a minimum-crown clade definition: the smallest crown clade containing *Rozella allomycis* F.K. Faust 1937, *Batrachochytrium dendrobatidis* Longcore, Pessier and D.K. Nichols 1999, *Allomyces arbusculus* E.J. Butler 1911, *Entomophthora muscae* (Cohn) Frese 1856, *Coemansia reversa* Tiegh. and G. Le Monn 1873, *Rhizophagus intraradices* (N.C. Schenck and G.S. Sm.) C. Walker and A. Schüßler 2010, *Rhizopus oryzae* Went and Prins. Geerl. 1895, *Saccharomyces cerevisiae* Meyen 1838, and *Coprinopsis cinerea* (Schaeff.) Redhead, Vilgalys and Moncalvo 2001. The primary reference phylogeny is James et al. (2006: Fig. 1); see also James et al. (2013: Fig. 2), Karpov et al. (2013: Fig. 3), Paps et al. (2013: Fig. 1), Chang et al. (2015: Fig. 1), Torruella et al. (2015: Fig. 1) and Spatafora et al. (2016: Fig. 1). Its composition is *Rozella*, *Microsporidia*, *Aphelida*, *Chytridiomycota*, *Neocallimastigomycota*, *Blastocladiomycota*, *Mucoromycota*, *Zoopagomycota*, *Ascomycota* and *Basidiomycota* (Hibbett et al. 2007, Karpov et al. 2014, Spatafora et al. 2016). There are no unambiguous morphological, subcellular or biochemical synapomorphies of Fungi. Most Fungi are filamentous, have chitinous cell walls, lack cilia and have intranuclear mitosis with spindle pole bodies instead of centrioles.

●●● Opisthosporidia Karpov, Aleoshin & Mikhailov 2014
Opisthokont intracellular parasites/parasitoids with amoeboid vegetative stage. Invasive spores/cysts with chitin cell wall and specialized apparatus for penetration into host cell (penetration tube; posterior vacuole); if present, zoospores with filopodia and/or a posteriorly directed whiplash cilium (functional or rudimental); phagotrophic or osmotrophic.

●●●● Aphelidea Gromov 2000 [=Aphelida Karpov et al. 2014; =Aphelida Gromov 2000; =Aphelidiomycota Tedersoo et al. 2018; =Aphelidiomycota Tedersoo et al. 2018; =Aphelidiomycotina Tedersoo et al. 2018; =Aphelidiomycetes Tedersoo et al. 2018; =Aphelidiaceae Tedersoo et al. 2018]<sup>33</sup>
Intracellular parasitoids of algae with phagotrophic amoeboid vegetative stage and complex life cycle; invasive cyst with short infective tube of penetration apparatus; zoospore with filose pseudopodia and/or lamellipodium; zoospores attach to host cell wall and encyst, then cyst penetrates host wall with chitin tube, its contents migrates into the host becoming the phagotrophic amoeba which engulfs host cell contents; this results in a characteristic central food vacuole with red-brownish excretory body; parasite growth and subsequent nuclear divisions lead to multinucleate plasmodium which consequently produces either a resting spore rounded to oval with a thick smooth cell wall, or zoospores released from host wall; mitochondrial cristae from tubular to lamellar. *Amoeboaphelidium*, *Aphelidium*, *Pseudoaphelidium*, *Paraphelidium*.

●●●●● Rozellida Lara et al. 2010, emend Karpov and Aleoshin 2014 [Cryptomycota M. D. M. Jones & T. A. Richards 2011; Rozellomycota Doweld 2013; Rozellosporidia Karpov et al. 2017; Rozellomycotina Tedersoo et al. 2018) (R)
Unicellular, holocarpic, zoospores single-celled with a single posterior cilium; cysts with chitin cell wall; endobiotic (intracellular or intranuclear) parasites; known to be parasites on, at least, *Chytridiomycota*, *Blastocladiomycota*, *Peronosporomycetes*, *Basidiomycota* and the green alga *Coleochaete*. Related environmental DNA sequences are known, found widely in soil, marine, and fresh water. Related environmental DNA sequences are known, found widely in soil, marine, and fresh water. Chitin or cell wall may be secondarily lost due to parasitic habit. *Rozella*.

●●●● Microsporidia Balbiani 1882
Obligate intracellular parasites, usually of animals but also protists such as Amoebozoa, Ciliophora or Apicomplexa; without mitochondria and peroxisomes, with mitosomes; spores with inner chitin wall and outer proteinaceous wall; without

(continued)

<footnote n="32"><sup>32</sup>Holomycota is the sister lineage to Holozoa and is comprised of Fungi and the group Rotosphaerida containing nucleariids. In this classification, we include Opisthosporidia (Karpov et al. 2014), comprising the endoparasitic lineages Rozellida (Cryptomycota) Aphelida and Microsporidia, in the Fungi, noting that this is an ongoing point of contention. New genomic and transcriptomic data provide modest to poor support for the monophyly of an Opisthosporidia clade (Toruella et al. 2018), but multiple molecular studies nonetheless support the placement of all three lineages at the base of the Fungi (Torruella et al. 2019; Karpov et al. 2017a, 2017b; Letcher et al. 2017; Lopez-Escardo et al. 2018). A major point of contention has been the fact that Opisthosporidia all have a vegetative phase that is unbounded by a cell wall, unlike most Fungi, and that Aphelida and *Rozella* have an intracellular (parasitic) phagotrophic feeding mode (Karpov et al. 2014; Powell et al. 2017). On the other hand, all of the Opisthosporidia share with other Fungi a chitinous cell wall at some stage in their life cycle. Recent analysis of an aphelid transcriptome (the lineage that has most retained ancestral characters within opisthosporidians) suggests a genomic composition and metabolism more aligned with the free-living chytrid fungi with degradative enzymes, than other Opisthosporidia (Toruella et al. 2019). But an alternative interpretation places emphasis on Opisthosporida cell biology which is more similar to other Opisthokonta than to Fungi, because of the phagotrophic nature of their nutrition. Ultimately, additional cell biology and genomic sequencing is needed for these poorly known organisms. Because there is no synapomorphy for the Fungi regardless of whether the Opisthosporidia are included (Richards et al. 2017), determining the constituency of the Fungi will rely on which traits are deemed most relevant (presence of chitinous cell wall or osmoheterotrophy) as both traits have been convergently derived across the eukaryote tree. A similar debate is ongoing about the distinction between Rozellida (Cryptomycota) and Microsporidia (Bass et al. 2018) as some rozellids have a spore structure very similar to Microsporidia but a genomic content less reduced than core microsporidia, and more like other Fungi. The stance taken in this classification is to follow the majority opinion of the mycological community to include Opisthosporidia in the Fungi, noting that this consensus may change with the discovery of new taxa and improved phylogenies.</footnote>

<footnote n="33"><sup>33</sup>The placement of Aphelidea in the Opisthosporidia is unstable and may change.</footnote>
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

kinetosomes, centrioles or cilia; centrosomal plaque; extrusive specialized polar tube for host penetration; sexual, asexual or both. Contains numerous diverse lineages currently poorly defined by morphology, found ubiquitously in soil, marine and fresh water. Subdivisions uncertain. *Amblyospora*, *Amphiacantha*, *Buxtehudia*, *Caudospora*, *Chytridiopsis*, *Desportesia*, *Encephalitozoon*, *Enterocytozoon*, *Glugea*, *Hessea*, *Metchnikovella*, *Mitosporidium*, *Nosema*, *Nucleophaga*, *Paramicrosporidium*, *Spraguea*, *Vairimorpha*.

●●● Blastocladiales Petersen 1909 [= Blastocladiineae Petersen 1909, Blastocladiomycota T. Y. James 2007, Blastocladiomycetes T. Y. James 2007]

Thallus monocentric or polycentric; aerobic to facultatively anaerobic, found in aquatic and terrestrial environments, saprobic and/or parasitic; uniciliated motile cells with microtubules radiating anteriorly from the proximal end of the kinetosome and continuing on to wrap around a cone-shaped nucleus that also terminates near the kinetosome and is capped by a mass of membrane-bound ribosomes; no electron-opaque plug in kinetosome transition zone; one side-body complex (= microbody–lipid globule complex); reproduces asexually by unciated cells, while sexual reproduction occurs through fusion of planogametes with a sporic type of meiosis. *Allomyces*, *Blastocladia*, *Blastocladiella*, *Blastocladiopsis*, *Catenomyces*, *Catenophylyctis*, *Caternaria*, *Coelomomyces*, *Coelomomycidium*, *Paraphysoderma*, *Physoderma*, *Polycaryum*, *Sorochytrium*, *Urophlyctis*.

●●● Chytridiomycota Doweld 2001, emend. M. J. Powell in Adl et al. 2019

Thallus monocentric, polycentric or filamentous; unciated zoospores with a posteriorly directed cilium, nine ciliary props, micro-body-lipid globule complex (MLC) consisting of a cisterna which may be simple or fenestrated (=rumposome), microbodies and mitochondria associated with lipid globules; Golgi apparatus with stacked cisternae; nuclear envelope fenestrated at poles during mitosis; reproduction asexual by unciulated zoospores and where known sexually by zygotic meiosis; found in soil and water as saprotrophs but also parasitic on animals, plants, protists and other fungi.

●●●● Chytridiomycetes de Bary 1863, emend. Cavalier-Smith 1998, emend. M. J. Powell in Adl et al. 2019

Thallus monocentric or rhizomycelial polycentric, endobiotic or epibiotic; aerobic. Zoospore ciliary apparatus posterior and includes a non-ciliated centriole and a ciliated kinetosome, typically with kinetosome-associated structures; the MLC cisterna is adjacent to the lipid globule; asexual reproduction by posteriorly unciulated zoospores, sexual reproduction not oogamous. *Incertae sedis* Chytridiomycetes: *Blyttomyces*, *Dangeardia*.

●●●●●● Caulochytriales Doweld 2014

Thallus monocentric, eucarpic with endogenous development; parasitic, penetrating host with haustorium; sporangium inoperculate, sessile or aerial at tip of hollow-stalk. Zoospore with posteriorly directed, laterally inserted cilium; non-ciliated centriole at 45° angle to kinetosome and joined by uniformly dense material; pulsating vacuole; scattered ribosomes; striated rhizoplast joining kinetosome and nuclear envelope; MLC with one to numerous lipid globules, branched microbody, simple membrane cisternae and spherical mitochondria. *Caulochytrium*.

●●●●●● Chytridiales Cohn 1879, emend. Schröter 1892, emend. D. J. S. Barr 1980, emend. D. J. S. Barr 2001, emend. Letcher and Powell 2006, emend. Mozl.-Standr 2009, emend. Vélez et al. 2011

Thallus monocentric or polycentric rhizomycelial, sporangia operculate or inoperculate. Zoospores covered by cell coat over body; containing a MLC composed of microbodies, mitochondria and fenestrated or simple cisterna adjacent to lipid globules, paracrystalline inclusion, an electron-opaque plug at base of cilium; microtubule root when present a bundle of parallel microtubules extending from the side of kinetosome to MLC cisterna; kinetosome-associated structure a shield, saddle, globule, wing, stacked plates or combination; ribosomes aggregated around or near the nucleus; non-ciliated centriole parallel to ciliated kinetosome and connected to it by fibrous material; nucleus not associated with kinetosome; *Avachytrium*, *Chytridium*, *Chytriomyces*, *Delfinachytrium*, *Dendrochytrium*, *Dinochytrium*, *Fayochytromyces*, *Irineochytrium*, *Obelidium*, *Odontochytrium*, *Pendulichytrium*, *Physocladia*, *Podochytrium*, *Pseudorhizidium*, *Siphonaria*, *Rhizidium*, *Rhizoclosmatium*.

●●●●● Cladochytriales Mozl.-Standr 2009

Thallus epibiotic or endobiotic; eucarpic, monocentric or polycentric with intercalary swellings; sporangium operculate or inoperculate; rhizoidal axis apophysate or nonapophysate, and rhizoids can be catenulate, isodiametric or tapering; zoospores with ribosomal aggregation; MLC with fenestrated cisterna; non-ciliated centriole parallel to ciliated kinetosome and joined by fibrillar bridge, ciliary plug at base of cilium, up to 25 cross-linked microtubules in a cord-like microtubular root situated between the kinetosome and the fenestrated cisterna; lacking paracrystalline inclusions and kinetosome-associated structure. *Allochytridium*, *Catenochytridium*, *Cladochytrium*, *Cylindrochytridium*, *Endochytrium*, *Nephrochytrium*, *Nowakowskiella*, *Septochytrium*.

●●●●●● Gromochytriales Karpov & Aleoshin 2014

Thallus monocentric, eucarpic with endogenous development and inoperculate sporangium; parasite of green algae;

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<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

penetrates host with a single, weakly branched rhizoid. Zoospore spherical to oval; ribosomes clustered, posterior to the nucleus, covering anterior ends of kinetosome and centriole, and lacking associated endoplasmic reticulum; MLC anterior with fenestrated cisterna and microbody associated with lipid globule and microbody sandwiched between lipid globule and nucleus, mitochondria scattered; non-ciliated centriole at a 30° angle to kinetosome and connected by a dense band over their anterior ends; kinetosome-associated structure a short, straight spur. *Gromochytrium*.

●●●●● Lobulomycetales D. R. Simmons 2009, emend. D. R. Simmons 2012

Thallus monocentric, eucarpic with endogenous development; sporangium operculate or inoperculate; rhizoids isodiametric ranging from 0.5 to 1.5 µm wide. Zoospore contains a ribosomal aggregation surrounded by endoplasmic reticulum, an opaque ciliar plug with anterior or posterior plug extensions, non-ciliated centriole and kinetosome parallel and joined with a dense amorphous bridge, one to three lipid globules in the MLC; MLC cisterna absent, simple or irregularly fenestrated; microtubules, kinetosome-associated structures and Golgi apparatus absent. *Algomyces, Alogomyces, Cyclopsomyces, Clydaea, Lobulomyces, Maunachytrium*.

*Incertae sedis* Lobulomycetales: *Algochytops*.

●●●●● Mesochytriales Doweld 2013

Thallus monocentric, eucarpic with endogenous development and inoperculate sporangium; parasite of green algae; penetrates host with peg-like haustorium. Zoospore spherical to oval; ribosomes dispersed; MLC posterior to nucleus with a single lipid globule, large mitochondrion, lobed microbody, and fenestrated cisterna proximal to kinetosome; rough endoplasmic reticulum encircles MLC; non-ciliated centriole with a veil and at 30° angle to kinetosome and connected along their sides by a broad, dense fibrillar bridge; ciliar plug absent. *Mesochytrium*.

●●●●● Polychytriales Longcore & D.R. Simmons 2012

Thallus monocentric or polycentric lacking intercalary swellings; monocentric species with multiple rhizoidal axes; sporangia operculate or inoperculate. Zoospore with ribosomal aggregation; non-ciliated centriole parallel or at slight angle (14–24°) to kinetosome and connected by dense material throughout their lengths, length of non-ciliated centriole equal to or longer than its diameter; one to many lipid globules in MLC; may or may not possess each of the following: a ciliary plug, a kinetosome-associated structure as a spur, a fenestrated cisterna, and if present 1-3 microtubular roots. *Arkaya, Karlingiomyces, Lacustromyces, Neokarlingia, Polychytrium*.

●●●●● Polyphagales Doweld 2014

Thallus interbiotic with multiple rhizoids, functions as a prosporangium; Zoospore with posteriorly located MLC with fenestrated cisterna and single lipid globule; ribosomes aggregated with layers of endoplasmic reticulum; disc-like striated rootlet; resting spores sexually formed. *Polyphagus*.

●●●●● Rhizophydiales Letcher 2006, emend. Letcher 2008

Thallus monocentric, eucarpic, inoperculate or operculate. Zoospore with one or more of the following characters: microtubular root with one or more stacked microtubules extending from one side of the kinetosome to a MLC cisterna on the lipid globule; ribosomes aggregated with endoplasmic reticulum binding or ramifying through; mitochondria; microbodies, and fenestrated or simple cisterna associated with lipid globule (MLC); non-ciliated centriole either parallel or slightly angled to kinetosome and connected by a fibrillar bridge; fibrillar bridge either perpendicular to or diagonal between kinetosome and non-ciliated centriole; kinetosome-associated structure when present a solid spur, laminated spur or shield; no electron-dense ciliary plug. *Alphamyces, Angulomyces, Aquamyces, Batrachochytrium, Betamyces, Boothiomyces, Collimyces, Coralloidiomyces, Dinomyces, Gammamyces, Globomyces, Gorgonomyces, Halomyces, Kappamyces, Paranamyces, Operculomyces, Paranamyces, Pateramyces, Paludomyces, Protrudomyces, Staurastromyces, Terramyces, Rhizophydium, Uebelmesseromyces, Ulkenomyces, Urceomyces*.

*Incertae sedis* Rhizophydiales: *Homolaphyctis*.

●●●●● Rhizophlyctidales Letcher 2008

Thallus monocentric or polycentric, eucarpic; interbiotic sporangium that is either inoperculate or endo-operculate with one to several discharge short tubes; multiple rhizoidal axes. Zoospore possesses a non-ciliated centriole that is at an acute angle (<40°) to the kinetosome and attached by a fibrillar bridge along the length of the non-ciliated centriole; multiple mitochondria; ribosomes either dispersed or aggregated in the cytoplasm; MLC with one to many lipid globules, simple MLC cisterna when present; without microtubules. *Arizonaphyctis, Borealophyctis, Rhizophlyctis, Sonoraphlyctis*.

●●●●● Spizellomycetales D. J. S. Barr 1980, emend. D. J. S. Barr 1983

Thallus monocentric, sporangia epibiotic or interbiotic. Zoospore with nucleus either closely associated with the kinetosome or connected by its root; ribosomes dispersed in the cytoplasm; MLC cisterna simple; non-ciliated centriole typically at an angle to the ciliated kinetosome; without electron-opaque material in the kinetosome transition zone. *Barromyces, Brevicalcar, Bulbosomyces, Fimicolochytrium, Gaertneriomyces, Gallinipes, Geranomyces, Kochiomyces, Powellomyces, Spizellomyces, Thoreauomyces, Triparticalcar*.

*Incertae sedis* Polyphagales: *Endocoenobium*.

(continued)
<table><caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption><thead><tr><th></th><th></th></tr></thead><tbody><tr><td>●●●●● Synchytriales Doweld 2014, emend. Longcore, DR Simmons & Letcher 2016</td><td>The least inclusive clade of the Chytridiomycetes that includes <i>Synchytrium taraxaci</i> and <i>Synchytrium</i> species included in James et al. 2006, Smith et al. 2014, Longcore et al. 2016. <i>Synchytrium</i>.<br><i>Insertae sedis</i> Synchytriales: <i>Micromyces</i>.</td></tr><tr><td>●●● Dikarya Hibbett et al. 2007, emend. Hibbett et al. 2018</td><td>Unicellular or filamentous Fungi, lacking cilia, often with a dikaryotic state. The least inclusive clade that contains Ascomycota and Basidiomycota and Entorrhizomycete.</td></tr><tr><td>Insertae sedis Dikarya: Entorrhizomycetes Begerow et al., 2007 [=Entorrhizaceae R. Bauer and Oberw. 1997; =Entorrhizales R. Bauer and Oberwinkler 1997; =Entorrhizomycetes Begerow et al. 2007; =Entorrhizomycota R. Bauer et al. 2015; =Entorrhizomycotina Tedersoo et al. 2018] (M)</td><td>Phytoparasitic fungi infecting roots with regularly septate coiled hyphae; septal pores without Woronin bodies or membrane caps. Includes Entorrhizales (<i>Entorrhiza</i>), Talbotiomycetales.</td></tr><tr><td>●●●● Ascomycota Cavalier-Smith 1998</td><td>Sexual reproduction within asci (saccate structures); meiosis usually followed by mitosis to produce from one to over 1,000 ascospores, but usually eight; ascospore walls form inside ascus; mating types heterothallic, homothallic (selfing) or both; may reproduce sexually (teleomorph) or asexually (anamorph) only, or both sexually and asexually (holomorph); asci cylindrical, fusiform, clavate or globose, persistent or evanescent, with or without a fruiting structure (ascoma, -ata); asci developing directly from ascogenous hyphae, from a crozier or from a single cell; asexual reproduction by conidiospores (mitospores) formed by fragmentation of vegetative hyphae (thallic), blastically from single cells, hyphae or conidiophores; vegetative body of single cells or tubular, septate filaments (hyphae); septa with simple pores, except for those associated with ascogenous hyphae and asci; cell walls lamellate with a thin electron-dense outer layer and a relatively thick electrontransparent inner layer, consisting of varying proportions of chitin and glucans; saprobes, endophytes, parasites (especially on plants) or lichen forming.</td></tr><tr><td>●●●●● Taphrinomycotina O. E. Eriksson and Winka 1997</td><td>Mycelium present or absent; asci produced from binucleate cells; do not form croziers or interascal tissue.</td></tr><tr><td>●●●●●●● Archaeorhizomyces Rosling & T. James 2011 [=Archaeorhizomycetes Rosling and T. James 2011; =Archaeorhizomycetales Rosling and T. James 2011]</td><td>Phylogenetically placed among Taphrinomycotina, differing by mycelial growth on MMN agar together with an association with roots of living plants. Distinctive molecular characters (nuclear large subunit rRNA). Synonymous to "Soil Clone Group 1 (SCG1)". <i>Archaeorhizomyces finlayi</i>.</td></tr><tr><td>●●●●●●●● Neolecta Spegazzini 1881 [=Neolectomycetes Eriksson and Winka 1997; =Neolectales Landvik et al. 1997; =Neolectaceae Redhead 1977] (M)</td><td>Mycelium present, multinucleate; ascomata apothecial, stalked, fleshy; interascal tissue absent; cylindrical asci formed from binucleate cells undergo karyogamy, meiosis, and one mitotic division to produce eight cylindrical ascospores, thin-walled, walls blueing in iodine; ascus apex truncate, slightly thickened below ascus wall, with wide apical slit, persistent; ascospores ellipsoidal to globose, hyaline, aseptate; anamorph unknown; saprobic; found in wet mixed woodlands. <i>Neolecta flavovirescens</i>.</td></tr><tr><td>●●●●●●●●● Pneumocystis P. Delanoë & Delanoë 1912 [=Pneumocystidales O. E. Eriksson 1994; =Pneumocystidomycetes Eriksson and Winka 1997; =Pneumocystidaceae] (M)</td><td>Mycelium and ascomata absent; vegetative cells thin-walled, irregularly shaped, uninucleate, dividing by fission; sexual reproduction initiated by fusion of two vegetative cells followed by karyogamy, cyst wall formation, meiosis, and in some, one mitotic division, to produce 4-8 nuclei that are delimited by the cyst (ascus) vesicle; ascospore walls are deposited between the delimiting membranes; cyst walls rupture to release ascospores; extracellular parasite of mammalian lungs. <i>Pneumocystis carinii</i>.</td></tr><tr><td>●●●●●●●● Schizosaccharomyces Lindner 1893 [=Schizosaccharomycetaceae Beij. ex Klöcker 1905; Schizosaccharomycetales O. E. Eriksson et al. 1993; =Schizosaccharomycetes O. E. Eriksson and Winka 1997] (M)</td><td>Mycelium absent or poorly developed; ascomata absent; vegetative cells cylindrical, proliferating by mitosis followed by cell division to produce two daughter cells; cell wall composition differs from that of species of Saccharomycetes; sexual reproduction initiated by fusion of two vegetative cells to form an ascus; karyogamy and meiosis occur within the ascus to produce four nuclei, which may or may not divide once again mitotically; ascospores aseptate, delimited by enveloping membrane system (EMS), wall formed within bilayers of EMS, wall</td></tr></tbody></table>

(continued)
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

blueing in iodine, hyaline or pigmented; saprophytes in sugary plant exudates; fermentation positive. *Schizosaccharomyces pombe*.

●●●●●● Taphrinales Gäumann and C. W. Dodge 1928 [=Taphrinomycetes O. E. Eriksson and Winka 1997]
Vegetative mycelium mostly absent; ascomata absent; interascal tissue absent; dikaryotic mycelium infects host and proliferates through host tissue; dikaryotic cells or mycelium develop directly into asci, often forming a palisade layer on the host; asci globose or ellipsoidal, eight-spored; ascospores hyaline, aseptate; biotrophic on angiosperms forming galls or lesions; cells bud from ascospores to form a yeast-like, monokaryotic, saprobic anamorph. *Protomyces, Taphrina*.

●●●●● Saccharomycetales Kudryavtsev 1960 [=Saccharomycetes O.E. Eriksson and Winka 1997; =Saccharomycotina O.E. Eriksson and Winka 1997]

Mycelium mostly absent or poorly developed; hyphae, when present, septate, with septa having numerous pores rather than a single septal pore; vegetative cells proliferating by budding or fission; walls usually lacking chitin except around bud scars; ascomata absent; sexual reproduction by fusion of two vegetative haploid cells or fusion of two haploid nuclei in a single cell or within diploid cells, followed by meiosis and, in some cases, one mitotic division to produce either four or eight nuclei; cells undergoing meiosis become asci, ascospores delimited by an enveloping membrane system (EMS); ascospore wall formed within bilayers of EMS; ascospores aseptate, colourless or pigmented, often with wall thickenings of various types; most osmotrophic, some species parasitic on animals. *Ascoidea, Candida, Cephaloascus, Dipodascus, Endomyces, Lipomyces, Metschnikowia, Pichia, Saccharomyces, Scheffersomyces, Trichomonascus, Wickerhamomyces, Yarrowia*.

●●●●● Pezizomycotina O.E. Eriksson and Winka 1997

Mycelium present; hyphae filamentous, septate; septa with simple pores and Woronin bodies; life cycle haploid with a dikaryotic stage immediately prior to sexual reproduction; ascomata discoid, perithecial, cleistothecial or occasionally lacking; antheridium present or absent; ascogonium, ascogenous hyphae, and crosiers present; the penultimate cell of the crozier, in which meiosis and usually one mitotic division occur, becomes the ascus; asci fissitunicate or not fissitunicate, cylindrical, clavate or saccate; asci frequently with ascospore discharge mechanism; usually eight ascospores surrounded by enveloping membrane system; ascospore morphology and pigmentation varied; asexual state present or absent, produced from vegetative hyphae in a thallic or blastic manner; mitospores (conidiospores) varied in morphology and pigmentation.

●●●●●●● Arthoniales Henssen & Jahns ex D. Hawksw. and O. E. Eriksson 1986 [=Arthoniomycetes O. E. Eriksson and Winka 1997]

Ascomata usually apothecial, occasionally closed with an elongated poroid opening; peridium thin- or thick-walled; interascal tissue of branched paraphysoids in a gel matrix; asci thick-walled, fissitunicate, blueing in iodine, with or without a large apical dome; ascospores aseptate or septate, sometimes becoming brown and ornamented; anatomorphs pycnidial; forming crustose lichens with green algae, lichenicolous or saprobic on plants. *Arthonia, Chrysothrix, Melaspilea, Opegrapha, Roccella, Roccellographa*.

●●●●●●● Dothideomycetes O. E. Eriksson & Winka 1997

Ascomata variable (apothecial, perithecial, cleistothecial), formed lysigenously from stromatic tissue (ascolocular); interascal tissue present or absent, of branched paraphysoids or pseudoparaphyses; asci cylindrical to saccate, thick-walled, fissitunicate, rarely with apical structures; ascospores mostly septate or muriform, colourless to dark brown; anamorphs hyphomycetous or coelomycetous; saprobes, plant parasites, coprophilous or lichen forming. Note that this group partially includes loculoascomycetes. Containing Dothideomycetidae (Capnodiales, Dothideales, Myriangiales), Pleosporomycetidae (Hysteriales, Jahnulales, Mytilinidiales, Pleosporales).

*Incertae sedis* Dothideomycetes: Containing Abrothallales (*Abrothallus*), Acrospermales (*Acrospermum, Oomyces*), Asterinales (*Asterina*), Asterotexiales (*Asterotexis*), Botryosphaeriales (*Botryosphaeria, Guignardia, Saccharata*), Eremithallales (*Encephalographa*), Microthyriales (*Microthyrium*), Minutisphaerales (*Minutisphaera*), Monoblastiales (*Monoblastia, Anisomeridium*), Natipusillales (*Natipusilla*), Patellariales (*Baggea, Patellaria*), Phaeotrichales (*Phaeotrichum*), Stigmatodiscales (*Stigmatodiscus*), Strigulales (*Strigulales*), Superstratomycetales (*Superstratomyces*), Trypetheliales (*Laurera, Trypethelium*), Tubeviales (*Tubeufia, Bezeromyces, Wiesneriomyces*), Valsariales (*Valsaria*), Venturiales (*Apiosporina, Sympoventuria, Venturia*).

●●●●●●● Eurotiomycetes O. E. Eriksson & Winka 1997, emend. Geiser et al. 2006 (R)

Morphologically heterogeneous, circumscribed using phylogenetic re-delimitation to contain Chaetothyriomycetidae, Eurotiomycetidae, Mycocaliciomycetidae and Sclerococcomycetidae. Important industrially and medically; saprobic, pathogenic on animals and rarely on plants, some lineages lichenized. Chaetothyriomycetidae (Chaetothyriales, Pyrenulales, Verrucariales), Coryneliomycetidae (Coryneliales), Eurotiomycetidae (Eurotiales, Onygenales), Mycocaliciomycetidae (Mycocaliciales), Sclerococcomycetidae (Sclerococcales).

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<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

●●●●●● Geoglossaceae Corda 1838, emend. Schoch et al. 2009 [=Geoglossales Zheng Wang et al. 2009; Geoglossomycetes Zheng Wang et al. 2009]
Ascomata scattered to gregarious, capitate, stipitate; stipe cylindrical, black, smooth to furfaceous; ascigerous portion capitate, club-shaped to pileate, indistinguishable from stipe; hymenium surface black, continues with stipe at early development stage; asci clavate, inoperculate, thin-walled, J+, usually eight-spored; ascospores elongate, dark-brown, blackish to hyaline, septate when mature; paraphyses filiform, blackish to hyaline; global distribution, terrestrial, habitat usually boggy and mossy. *Geoglossum, Trichoglossum*.

●●●●●● Laboulbeniomycetes Engler 1898
Mycelium absent except in Pyxidiophorales; cellular thallus hyaline to dark, with basal haustrium present; ascomata perithecial, surrounded by complex appendages, translucent, ovoid, thin-walled; interascal tissue absent; asci few and basal, not fissitunicate, clavate, thin-walled, evanescent, maturing sequentially, usually with four ascospores; ascospores two-celled, hyaline, elongate, one end modified as attachment to host; anamorphs hyphomyce tous, spermatial; ectoparasitic on insects, some may be coprophilous. Containing Laboulbeniales, Pyxidiophorales.

●●●●●● Lecanoromycetes O. E. Eriksson & Winka 2001
Ascomata apothecial, discoid, perithecial or elongated, sometimes stalked or immersed, occasionally evanescent; interascal tissue of simple or branched paraphyses swollen at the apices, often with a pigmented or iodine-staining epithecium; hymenial gel often present; asci not fissitunicate, but thick-walled, with a thickened, cap-like apex, often with an internal apical ocular chamber; ascus walls and thickened apex often stains blue with iodine; ascospores one to several septate, occasionally, multiseptate, rarely plurilocular, hyaline or pigmented; anamorphs pycnidial where known; mostly lichen forming with protococcoid algae, with thallus foliose, fruticose, crustose or occasionally absent; some lichenicolous, some saprobic. Containing Acarosporomycetidae (Acarosporales), Lecanoromycetidae (Caliciales, Lecanorales, Lecideales, Leprocaulales, Peltigerales, Rhizocarpales, Teloschistales), Ostropomycetidae (Arctomiales, Baeomycetales, Hymeneliales, Ostropales, Pertusariales, Sarrameanales), Umbilicariomycetidae (Umbilicariales).

*Incertae sedis* Lecanoromycetes: *Candelariales* (*Candelaria*, *Candelariella*)

●●●●●● Leotiomycetes O. E. Eriksson & Winka 1997
Ascomata apothecial, discoid, cleistothecial, elongated or rarely absent; apothecia stalked or sessile, frequently fleshy, sometimes hairy or with appendages, occasionally stromatic or sclerotiod; interascal tissue of simple paraphyses or absent; peridium thin-walled; asci typically inoperculate, cylindrical, thin-walled, not fissitunicate, occasionally with apical pore; apical apparatus variable; ascospores aseptate or transversely septate, hyaline or pigmented and longitudinally slightly asymmetrical; anamorphs occasionally present, hyphomycetous or coelomyce tous; saprobes or plant parasites, some lichenized or lichenicolous. Containing *Cyttariales* (*Cyttaria*), *Erysiphales* (*Blumeria*, *Erysiphe*, *Microsphaera*, *Oidium*, *Podosphaera*), *Helotiales* (*Botryotinia*, *Bulgaria*, *Dermea*, *Hyaloscypha*, *Lachnum*, *Leotia*, *Sclerotinia*, *Vibrissea*), *Rhytismatales* (*Ascodichaena*, *Cudonia*, *Rhytisma*) and *Thelebolales* (*Thele bolus*, *Antarctomyces*).

●●●●●● Lichinales Henssen & Büdel 1986 [=Lichinomycetes Reeb et al. 2004]
Ascomata apothecial, discoid, sometimes immersed, occasionally clavate, stalked, setose and fleshy; peridium often not well-defined; interascal tissue varied; hymenium often stains blue with iodine; asci thin-walled or apically thickened, not fissitunicate, without well-defined apical structures, usually with an iodine-staining outer gelatinized layer; ascospores one-septate or occasionally multiseptate, ellipsoidal to fusiform, hyaline or pigmented; anamorphs pycnidial; lichenized with cyanobacteria forming crustose, fruticose or foliose often gelatinized thalli. *Gloeoheppia*, *Heppia*, *Lichina*, *Peltula*.

●●●●●● Orbiliaceae Nannfeldt 1932 [=Orbiliales Baral et al. 2003; =Orbiliomycetes Eriksson and Baral 2003]
Ascomata apothecial, small, waxy, translucent or lightly pigmented; interascal tissue of simple paraphyses, usually with knob-like apices, united by a matrix; asci minute, not fissitunicate, apex truncate, with J apical rings, often forked at the base; ascospores minute, cylindrical, hyaline, often aseptate; anamorphs hyphomycetous where known; saprobic, often on wet wood. *Halorbilia, Orbilia*.

●●●●●● Pezizales J. Schröter 1894 [=Pezizomycetes O. E. Eriksson and Winka 1997]
Ascomata apothecial or cleistothecial, usually visible with unaided eye, leathery or fleshy; carotenoids as bright colours to dark, sometimes present; interascal tissue present (paraphyses); asci not fissitunicate, usually elongated, cylindrical but more or less globose in cleistothecial species, thin-walled, lacking obvious apical wall thickening or apical apparatus, with operculum or vertical slit except in cleistothecial species, forcibly discharging ascospores except in cleistothecial species; ascospores usually ellipsoidal or globose, aseptate, hyaline to darkly pigmented, smooth or ornamented; anamorphs hyphomycetous, where known; saprobes on soil, dead wood or dung; some

(continued)
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

species hypogeous and mycorrhizal. *Ascobolus*, *Ascodesmis*, *Caloscypha*, *Carpomyces*, *Chorioactis*, *Discina*, *Gla-ziella Helvella*, *Karstenella*, *Morchella*, *Peziza*, *Pyronema*, *Rhizina*, *Sarcoscypha*, *Sarcosoma*, *Tuber*.

●●●●●● Sordariomycetes O. E. Eriksson & Winka 1997 (R)

Defined using molecular phylogenetic methods, by a parsimony comparison of small subunit rRNA sequences, containing Boliniales (*Bolinia*, *Camarops*), Calosphaeriales (*Calosphaeria*, *Pleurostoma*), Chaetosphaeriales (*Chaeto-sphaeria*, *Melanochaeta*), Coniochaetales (*Barrina*, *Coniochaeta*), Diaporthales (*Cryphonectria*, *Diaporthe*, *Gnomonia*, *Melanconis*, *Phyllachorales* (*Phaeochora*, *Phyllachora*), Pseudovalsa, *Schizoparme*, *Sydowiella*, *Valsa*, *Vialaea*), Magnaporthales (*Gaeumannomyces*, *Magnaporthe*, *Ophioceras*), Ophiostomatales (*Kathistes*, *Ophiostoma*), Sordariales (*Annulatascus*, *Cephalotheca*, *Chaetomium*, *Lasiosphaeria*, *Neurospora*, *Sordaria*).

*Incertae sedis* Sordariomycetes: *Koralionastetales* (*Koralionastes*, *Pontogeneia*), *Lulworthiales* (*Lindra*, *Lulworthia*, *Spathulospora*), *Meliolales* (*Armatella*, *Meliola*), *Pisorisporiales* (*Pisorisporium*), *Trichosphaeriales* (*Trichosphaeria*).

●●●●●● Xanthopyreniaceae Zahlbr 1926 [=Collemopsidiales Pérez-Ortega et al. 2016; Collemopsidiomycetes Tedersoo et al. 2018]

Thallus comprised of fine hyphae loosely associated with Cyanobacteria and developing ascomata; ascomata perithecioid, solitary, unilocular, with a carbonized to hyaline exciple; branched and anastomosing, often irregularly thick, net-like physes; asci bitunicate, fissitunicate, with ocular chamber, ovoid to subcylindrical, usually stalked; ascospores hyaline (rarely brownish in mature specimens), oblong to ovoid-fusiform, one-septate, with gelatinous perispore usually present; conidiomata pycnidial; conidiogenous cells cylindrical; conidiogenesis phialidic; conidia bacilliform to ellipsoid; lichenized and lichenicolous fungi with crustose, epilithic or endolithic, or lichenicolous forms and Cyanobacteria as photobionts. *Collemopsidium*, *Xanthopyrenia*

●●●●●● Xylonomycetes R. Gazis & P. Chaverri 2012

Strongly supported as a separate class within the Pezizomycotina (BS: 100%; PP: 1) and contained by the super-class 'Leotiomyceta' (BS: 100%; PP: 1) sensu Schoch et al. (2009); based on six loci phylogeny (nucSSU, nucLSU, mitSSU, 5.8S, RBP1 and RPB2). *Xylona*. Contains *Symbiotaphrinales*, *Xylonales*.

●●●● Basidiomycota R. T. Moore 1980

Mycelium present, but some with a yeast state primarily in the Tremellomycetes; basidia produced in a fertile layer with or without fleshy sporocarp; basidia whole or divided longitudinally, typically with four spores per basidium but ranging from one to eight; fusion of compatible mycelia of opposite mating types results in a dikaryotic mycelium in which nuclei of the parent mycelia remain paired but not fused; karyogamy quickly followed by meiosis, one or more mitotic divisions and migration of the nuclei into the developing basidiospores; asexual reproduction may occur through production of conidiospores or via spores produced on basidia from nuclei that have not undergone karyogamy and meiosis (secondary homothallism); cell wall with xylose; septa with swelling near pore; septal pore caps (parentheses-multilayered endoplasmic reticulum) usually present, elaborate in Tremellomycetes; clamp connections present in hyphae or at base of basidia in some groups; mycelial or yeast states; karyogamy typically in probasidium or teliospore, followed by meiosis in a separate compartment (metabasidia), but in some it occurs in the same compartment (holobasidia); holobasidia remain whole or fragment at septation after meiosis (phragmobasidia); metabasidia typically transversely septate with basidiospore borne laterally; cell wall with xylose; paren-thesome pore caps absent but with microbodies at septal pores; septal pores occluded by a plug; centrosome multilayered; many are plant pathogens (rusts), animal pathogens, non-pathogenic endophytes and rhizosphere species.

●●●●● Agaricomycotina Doweld 2001

With a type B secondary structure of the 5S RNA; a cell wall carbohydrate composition with dominance of glucose and presence of xylose.

●●●●●●● Agaricomycetes Doweld 2001

Fruiting bodies hymenomycetous or gasteroid; basidia two- to eight-spored; parenthesesomes perforate or imperforate. The least inclusive clade containing *Agaricomycetidae* (*Agaricales*, *Amylocorticiales*, *Atheliales*, *Boletales*, *Jaapiales*, *Lepidostromatales*, *Phallomycetidae* (*Geastrales*, *Gomphales*, *Hysterangiales*, *Phallales*).

*Incertae sedis* Agaricomycetes: *Auriculariales* (*Auricularia*, *Exidia*, *Hyaloria*), *Cantharellales* (*Botryobasidium*, *Can-tharellus*, *Ceratobasidium*, *Clavulina*, *Hydnum*, *Tulasnella*), *Corticiales* (*Corticium*, *Punctularia*), *Gloeophyllales* (*Gloeo-phyllum*), *Hymenochaetales* (*Hymenochaete*), *Polyporales* (*Antrodia*, *Coriolopsis*, *Donkiopora*, *Ganoderma*, *Lentinus*, *Phanerochaete*, *Phlebia*, *Polyporus*, *Sparassis*, *Trametes*), *Russulales* (*Heterobasidion*, *Lactarius*, *Peniophora*, *Rus-sula*), *Sebacinales* (*Piriformospora*, *Sebacina*), *Thelephorales* (*Hydnellum*, *Sarcodon*), *Trechisporales* (*Trechispora*) and *Tremellodendropsidales* (*Tremellodendropsis*).

●●●●●●● Dacrymycetales Hennings 1898 [=Dacrymycetes Doweld 2001]

Fruiting bodies gelatinous; basidia furcate, rarely unisporous; parenthesesomes imperforate. *Cerinomyces*, *Dacrymyces*.

(continued)
<table><caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption><thead><tr><th></th><th></th></tr></thead><tbody><tr><td>●●●●●●● Tremellomycetes Doweld 2001</td><td>Dimorphic fungi; fruiting bodies gelatinous or absent; basidia septate or nonseptate; parenthesomes sacculate or absent. Containing Cystofilobasidiales (<i>Cystofilobasidium</i>, <i>Mrakia</i>), Filobasidiales (<i>Filobasidium</i>), Holtermanniales (<i>Holtermannia</i>) and Tremellales (<i>Sirobasidium</i>, <i>Syzygospora</i>, <i>Tremella</i>).</td></tr><tr><td>●●●●●●●● Pucciniomycotina R. Bauer et al. 2006 [=Urediniomycetes Swann and Taylor 1995]</td><td>Mycelial or yeast states; karyogamy typically in probasidium or teliospore, followed by meiosis in a separate compartment (metabasidia), but in some it occurs in the same compartment (holobasidia); holobasidia remain whole or fragment at septation after meiosis (phragmobasidia); metabasidia typically transversely septate with basidiospore borne laterally; cell wall with xylose; parenthesome pore caps absent but with microbodies at septal pores; septal pores occluded by a plug; centrosome multilayered; many are plant pathogens (rusts), animal pathogens, non-pathogenic endophytes and rhizosphere species.</td></tr><tr><td>●●●●●●●●● Agaricostilbomycetes R. Bauer et al. 2006</td><td>Dimorphic, nonphytoparasitic, with fucose as cell wall carbohydrate component, septal pores without associated microbodies, aseptate basidiospores during germination and no colacosomes, teliospores, curved holobasidia and radiate conidia; septal pores without microbodies, nucleoplasmic spindle pole body (SPB) separation, metaphasic SPB intranuclear. Containing Agaricostilbales (<i>Agaricostilbum</i>, <i>Chionosphaera</i>) and Spiculogloeales (<i>Mycogloea</i>, <i>Spiculogloea</i>).</td></tr><tr><td>●●●●●●●● Atractiellales Oberwinkler & Bandoni 1982 [=Atractiellomycetes R. Bauer et al. 2006]</td><td>With symplechosomes. <i>Atractiella</i>, <i>Phleogena</i>, <i>Saccoblastia</i>.</td></tr><tr><td>●●●●●●●●● Classicales R. Bauer et al. 2003 [=Classiculomycetes R. Bauer et al. 2006]</td><td>With septal pores associated with microbodies and tremelloid haustorial cells. <i>Classicula</i>, <i>Jaculispora</i>.</td></tr><tr><td>●●●●●●●●● Cryptomycocolax Oberwinkler & R. Bauer 1990 [=Cryptomycocolacaceae Oberw. and R. Bauer 1990; =Cryptomycocolacales Oberwinkler and R. Bauer 1990; =Cryptomycocolacomycetes R. Bauer et al. 2006] (M)</td><td>With microbodies. <i>Cryptomycocolax abnormis</i>.</td></tr><tr><td>●●●●●●●● Cystobasidiomycetes R. Bauer et al. 2006</td><td>With cell wall carbohydrate composition without fucose; cytoplasmic SPB separation; metaphasic SPBs intranuclear. Containing Cystobasidiales (<i>Cystobasidium</i>), <i>Erythrobasidiales</i> (<i>Bannoa</i>, <i>Erythrobasidium</i>) and <i>Naohideales</i> (<i>Naohidea</i>).</td></tr><tr><td>●●●●●●●●● Microbotryomycetes R. Bauer et al. 2006</td><td>With colacosomes and septal pores without microbodies; with colacosomes and taxa derived from colacosome fungi; metaphasic SPBs intranuclear. Containing Heterogastridiales (<i>Heterogastridium</i>), Leucosporidiales (<i>Leucosporidiella</i>, <i>Mastigobasidium</i>), Microbotryales (<i>Microbotryum</i>, <i>Ustilentyloma</i>) and Sporidiobolales (<i>Rhodosporidium</i>, <i>Sporidiobolus</i>).</td></tr><tr><td>●●●●●●●● Mixia Kramer 1959 [=Mixiaceae C.L. Kramer 1987; =Mixiales R. Bauer et al. 2006; Mixiomycetes R. Bauer et al. 2006] (M)</td><td>With multinucleate hyphae and multiple spores produced simultaneously on sporogenous cells. <i>Mixia osmundae</i>.</td></tr><tr><td>●●●●●●●●● Pucciniomycetes R. Bauer et al. 2006</td><td>With a metaphasic intermeiotic SPB duplication. Containing Helicobasidiales (<i>Helicobasidium</i>), Pachnocybales (<i>Pachnocybe</i>), Platygloeales (<i>Eocronartium</i>, <i>Platygloea</i>), Pucciniales (<i>Coleosporium</i>, <i>Cronartium</i>, <i>Dasyspora</i>, <i>Diorchidium</i>, <i>Melampsora</i>, <i>Mikronegeria</i>, <i>Nyssopsora</i>, <i>Ochropsora</i>, <i>Phakopsora</i>, <i>Phragmidium</i>, <i>Pileolaria</i>, <i>Puccinia</i>, <i>Pucciniastrum</i>, <i>Pucciniosira</i>) and Septobasidiales (<i>Auriculoscypha</i>, <i>Septobasidium</i>).</td></tr><tr><td>●●●●●●●● Spiculogloeaceae Denchev 2009 [=Spiculogloeales R. Bauer et al. 2006; =Spiculogloeomycetes Q.M. Wang et al. 2015]</td><td>Characterized by teleomorphic members that may form tremelloid haustorial cells (nanometre-fusion mycoparasitism). <i>Spiculogloea</i>.</td></tr><tr><td>●●●●●●●●● Tritirachium Limber 1940 [=Tritirachiaceae Aime and Schell 2011; =Tritirachiales Aime and Schell 2011; =Tritirachiomycetes Aime and Schell 2011] (M)</td><td>With multinucleate hyphae, simple pore septa, conidiophores that are subhyaline to dematiaceous and subhyaline to dematiaceous sympodial conidiogenous cells that occur in whorls and bear conidia on an elongated rachis; teleomorph not known. <i>Tritirachium dependens</i></td></tr><tr><td>●●●●●●●● Ustilaginomycotina R. Bauer et al. 2006</td><td>Mycelial in the parasitic phase, and many with saprobic yeast or ballisticonidial states; plant parasites causing rusts and</td></tr></tbody></table>

(continued)
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

smuts; meiospores produced on septate or aseptate basidia; cell wall carbohydrates dominated by glucose; xylose absent; parenthesomes absent at septal pores; swellings absent at septal pores except in *Tilletia*; centrosomes globose, unlayered.

●●●●●●● Exobasidiomycetes Begerow et al. 2007

With local interaction zones and no intracellular hyphal coils. Containing Ceraceosorales (Ceraceosorus), Doassansiales (Doassansia, Melaniella, Rhamphospora), Entylomatales (Entyloma), Exobasidiales (Kordyana, Laurobasidium, Exobasidium, Graphiola), Georgefischeriales (Eballistra, Georgefischereria, Gjaerumia, Tilletiaria), Golubeviales (Golubevia), Microstromatales (Microstroma, Quambalaria, Volvocisporium) Robbauerales (Robbauera), Tilletiales (Tilletia).

●●●●●●● Malassezia Baill 1889 [=Malasseziales R.T. Moore 1980; =Malasseziaceae Denchev and R.T. Moore 2009; =Malasseziomycetes Boekhout et al. 2014] (M)

Cells globose, ovoid or cylindrical; budding typically monopolar on a more or less broad base, enteroblastic and percurrent; cell wall multilamellate, and the inner layer of the cell wall corrugated with a groove spiralling from the bud site; lipid dependent or lipophilic; sugars are not fermented, urease and diazonium blue B (DBB) reactions are positive; coenzyme Q-9 is formed; xylose absent in whole-cell hydrolysates; sexual morph unknown. *Malassezia furfur*.

●●●●●●● Moniliella Stolk & Dakin 1966 [=Moniliellaceae Q.M. Wang et al. 2014; =Moniliellales Q.M. Wang et al. 2014; =Monilielliomycetes Q.M. Wang et al. 2014] (M)

Colonies are smooth or velvety, greyish to olivaceous black; budding cells are ellipsoidal and form terminally on true hyphae that disarticulate with artroconidia; pseudohyphae and chlamydospores may be present; cell walls are multilamellar; hyphal septa typically possess dolipores with an arch of endoplasmic reticulum, but 'micropore'-like structures may also be present; sugars are fermented by most species; nitrate is assimilated; urease and diazonium blue B (DBB) reactions are positive; coenzyme Q-9 is present; xylose and fucose absent from whole-cell hydrolysates; sexual morph unknown. *Moniliella acetoabutans*.

●●●●●●● Ustilaginomycetes R. Bauer et al. 1997

With enlarged interaction zones. Containing Urocystales (Doassansiopsis, Floromyces, Thecaphora, Melanotae-nium, Urocystis) and Ustilaginales (Anthracoidea, Ustanciosporium, Sporisorium, Ustilago).

●●●●● Wallemiomycotina Doweld 2014

Conidia arthros pore-like, verruculose, short cylindrical, becoming spherical; conidiophores unbranched or sympodially proliferating, continuous with conidiogenous cells, smooth; conidiogenesis basauxic; hyphal septa with a single pore, flaring out near the periphery of the pore, barrel-shaped, dolipore-like.

●●●●●●● Wallemia Johan-Olsen 1887 [=Wallemiaceae R.T. Moore 1996; =Wallemiales Zalar et al. 2005; =Wallemiomycetes Zalar et al. 2005] (M)

Xerophilic; produce basauxic anamorphs and do not produce basidiomata in culture; with dolipore septa with adseptal tubular extensions that arise from sheets of endoplasmic reticulum that form the septal pore cap; septal pore cap sometimes absent; septal pore has an electron-dense non-membranous septal pore occlusion and stria-tions that are oriented vertically. *Wallemia ichthyophaga*.

●●●●●●● Geminibasiidiaceae H.D.T. Nguyen et al. 2013 [=Geminibasidiales H.D.T. Nguyen et al. 2013; =Gemini basidiomycetes H.D.T. Nguyen and Seifert 2015]

Xerotolerant; basidiomata not produced in culture; basidia arising from somatic hyphae or from swollen basidium-bearing cells (primary cells) with a basal lateral projection occurring either on the basidium or the swollen primary cell; basidiospores symmetrical on sterigma, not forcibly discharged, and brown at maturity; arthroconidial and/or yeast-like asexual morphs sometimes produced; species have a dolipore septum that is electron-dense at the pore swelling with an electron-dense membranous septal pore occlusion; some species are heat resistant. *Gemi-nibasidium*.

●●● Monoblepharidomycetes J.H. Schaffn. 1909

Thallus epibiotic, filamentous (hyphal or rhizomycelial), either extensive or a simple unbranched thallus, often with a basal holdfast. Zoospores oval possessing a non-ciliated centriole parallel to the ciliated kinetosome with a striated disc partially extending around the kinetosome; microtubules radiating anteriorly from the striated disc; ribosomal aggregation around the nucleus; fenestrated cisterna (=rumposome) adjacent to the microbody in the MLC; Golgi apparatus with stacked cisternae; nuclear envelope fenestrated at poles during mitosis; aerobic and anaerobic; asexual reproduction occurs via production of posteriorly uniciliated cells or autospores while sexual reproduction is oogamous via fusion of uniciliated antherozoids produced in antheridia and non-ciliated female gametes produced within oogonia. *Gonapodya, Harpochytrium, Hyaloraphidium, Monoblepharella, Monoblepharis, Oedogoniomyces, Telasphaerula*.

(continued)
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

●●● Mucoromycota Doweld 2001, emend. Spatafora and Stajich 2016 [Zygomycota F. Moreau 1954, pro parte] (R)
The least inclusive clade containing Mucoromycotina, Mortierellomycotina, and Glomeromycotina. Characters associated with sexual reproductive states, where known, include zygospor e production by gametangial conjugation. Asexual reproductive states can involve chlamydospores and spores produced in sporangia and sporangioles.

●●●●● Glomeromycotina C. Walker & A. Schüßler 2016
Filamentous; primarily endomycorrhizal, forming arbuscules in roots, sometimes with vesicles; without cilium; presumed asexual spores outside or within roots of host; some complex spores with multiple wall groupings, others simple (blastic chlamydospores); without centrioles, conidia, and airborne spores.

●●●●●● Archaeosporales C. Walker & A. Schüßler 2001 [=Archaeosporomycetes Sieverding et al. 2011]
Known to form symbiosis with plant roots or thalli, or with cyanobacteria; if symbiosis occurs between plants and fungi, fungal spores may have two morphs, but often only one is known; species form vesicular-arbuscular or arbuscular mycorrhiza. *Archaeospora, Ambispora, Geosiphon*.

●●●●●●● Glomeromycetes Cavalier-Smith 1998, emend. Oehl et al. 2011
Glomoid chlamydospores formed terminally, subterminally or intercalarily in hyphae, either in or on the surface of soils or sometimes in roots, either singly, in spore clusters or multiple-spored loose to compact sporocarps, on subtending hyphae: complex multiwalled spores on sporogenous structures, or laterally or centrally within a sporiferous saccule or intrahyphally in the stalk of sporiferous saccules, forming arbuscular or vesicular-arbuscular mycorrhiza.

●●●●●●●● Diversisporales C. Walker & A. Schüßler 2001
Spore formation by blastic expansion of hypha (chlamydosporic), or sometimes with complex spores with up to three walls or wall groups: multiple layered outer wall, and hyaline middle and inner walls that may be of several components or layers; spores with subtending hyphae, sometimes with a conspicuous colour change distant to the septum most proximal to the spore base; spores with 1-3 wall layers; pore rarely open. *Acaulospora, Diversispora, Gigaspora, Pacispora, Racocetra, Scutellospora*.

●●●●●●● Glomerales J. B. Morton & Benny 1990
Spores by blastic expansion of the hyphal tip or intercalarily formed in hyphae, either in soils or occasionally in roots, or other subterranean structures such as rhizomes, either singly, in spore clusters or multiple-spored; sporocarps loose to compact, with a mono- to multiple-layered spore wall; wall of subtending hyphae continuous with the spore wall and coloured the same as or slightly lighter than it or hyaline to subhyaline; subtending hyphae funnel-shaped, cylindrical or constricted; forming arbuscular mycorrhiza. *Claroideoglomus, Funneliformis, Glomus, Rhi-zophagus, Sclerocystis, Septoglomus*.

●●●●●●●● Paraglomus J.B. Morton & D. Redecker 2001 [=Paraglomeraceae J. B. Morton and D. Redecker 2001; =Paraglomerales C. Walker and A. Schüßler 2001; =Paraglomeromycetes Oehl et al. 2011] (M)
Endomycorrhizal, forming arbuscular mycorrhiza; asexual spores (chlamydospores) usually formed in soil, sometimes within roots or other host tissue, sometimes with vesicles; without cilium; without centrioles, conidia and aerial spores. *Paraglomus occultum*.

●●●●● Mortierellaceae A. Fischer 1892 [Mortierellales Cavalier-Smith 1998; =Mortierellomycotina Kerst et al. 2011; =Mortierellomycetes Doweld 2014; =Mortierellomycota Tedersoo et al. 2018]
Mycelium with anastomosing hyphae, dichotomously branching, bearing stylospores; hyphae sporangiferous, sporangio-phores basally inflated and elongating towards the sporangiophore apex, erect, coenocytic initially, but irregularly septated at maturity; asexual reproduction via sporangia and sporangiola; sporangia spherical, multispored; columella absent; ramifications gracilous, primarily horizontally expanding, erecting hyphae sometimes terminate with sporangiola; spores globose to ellipsoid or irregular, smooth or ornamented; rhizoids only occasional; giant cells absent; zygospores naked. *Mortierella*.

●●●●● Mucoromycotina Benny 2007
Saprobes, or rarely gall-forming, non-haustorial, facultative mycoparasites or forming ectomycorrhiza; mycelium branched, coenocytic when young, sometimes producing septa that contain micropores at maturity; asexual reproduction by sporangia, sporangiola or merosporangia, or rarely by chlamydospores, arthrospores or blastospores; sexual reproduction by more or less globose zygospores formed on opposed or apposed suspensors.

●●●●●● Endogonales Moreau ex R. K. Benjamin 1979 [=Endogonomycetes Doweld 2014]
Filamentous, hyphae coenocytic; saprobic and ectomycorrhizal; zygospores with apposed suspensors produced in a subterranean sporocarp. *Endogone, Sphaerocreas*.

(continued)
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

●●●●● Mucorales Fritz 1832, emend. Schröter 1897 [=Mucoromycetes Doweld 2014] (P)
Filamentous, generally saprotrophic, with exceptions; septa absent except in older hyphae; with plasmodesmata at septal pores; asexual reproduction with one to many spores in merosporangia, sporangiola or sporangium; reproduction by zygospore, typically with opposed suspensors. Traditional subdivisions artificial. *Backusella*, *Chaetocladium*, *Choanephora*, *Cunninghamella*, *Lentamyces*, *Lichtheimia*, *Mucor*, *Mycotypha*, *Phycomyces*, *Pilobolus*, *Radiomyces*, *Saksenaea*, *Syncephalestrum*.

●●●●● Umbelopsidales Spatafora, Stajich and Bonito 2016 [=Umbelopsidomycetes Tedersoo et al. 2018]
The least inclusive clade containing the genus *Umbelopsis*. Asexual reproduction by sporangia and chlamydospores. Sporangiophores may be branched in a cymose or verticillate fashion. Sporangia are typically pigmented red or ochre, multi- or single-spored and with or without conspicuous columella. Sporangiospores are globose, ellipsoidal or polyhedral and pigmented like sporangia. Chlamydospores are filled with oil globules and often abundant in culture. Sexual reproduction is unknown. *Umbelopsis*.

●●● Neocallimastigaceae Heath 1983, emend. Barr 1989 [:=Neocallimastigales J. L. Li et al. 1993, =Neocallimastigomycetes M. J. Powell 2007, = Neocallimastigomycota M. J. Powell 2007]

Thallus monocentric or polycentric; anaerobic fermentative, found in digestive system of larger herbivorous mammals and possibly in other terrestrial and aquatic anaerobic environments; asexual reproduction; mitochondria absent; hydrogenosomes of mitochondrial origin; uni- and multiciliated zoospores with a kinetosome-associated complex that includes a skirt, strut, spur and circulatory ring, microtubules stretching from the spur and radiating around the nucleus, forming a posterior fan; unikont kinetid and without props; nuclear envelope is retained during mitosis. *Anaeromyces*, *Buwchfawromyces*, *Caecomyces*, *Cyllamyces*, *Feramyces*, *Neocallimastix*, *Oontomyces*, *Orpinomyces*, *Pecoramyces*, *Piromyces*.

●●● Olpidium (A. Braun) Rabenh. 1868 [=Olpidiaceae J. Schröt 1889; =Olpidiales Cavalier-Smith 2013; Olpidiomycota Doweld 2013; =Olpidiomycotina Doweld 2013; =Olpidiomycota Tedersoo et al. 2018] (M)

Thallus monocentric, holocarpic or eucarpic, with no hyphae; zoospores posterior, uniciliate, generally with a single globule, cone-shaped striated rhizoplast fused to both the functional and vestigial kinetosomes, gamma-like particles and rough endoplasmic reticulum; sporangium single, endobiotic; nucleus associated with the basal body, no nuclear cap; two parallel centrioles linked to nucleus by shared, tapering, striated rhizoplast; no root microtubules or dictyosome; side-body complex lacking; pathogens of terrestrial plants. *Olpidium brassicae*.

●●● Zoopagomycota Gryganskyi, M.E. Smith, Spatafora & Stajich 2016 [Zygomycota F. Moreau 1954, pro parte]
The least inclusive clade containing Entomophthoromycotina, Kickxellomycotina and Zoopagales. Sexual reproduction, where known, involves the production of zygospores by gametangial conjugation. Morphologies associated with asexual reproductive states include sporangia, merosporangia, conidia and chlamydospores.

●●●● Entomophthoromycotina Humber 2007
Obligate pathogens of animals (primarily arthropods), cryptogamic plants, or saprobes; occasionally facultative parasites of vertebrates. Somatic state consisting of a well-defined mycelium, coenocytic or septate, walled or protoplastic, which may fragment to form multinucleate hyphal bodies; protoplasts either hyphoid or amoeboid and changeable in shape; cystidia or rhizoids formed by some taxa. Conidiophores branched or unbranched. Primary spores true conidia, uni-, pluri- or multinucleate, forcibly discharged by diverse possible means or passively dispersed; secondary conidia often produced. Resting spores with thick bilayered walls form as zygospores after conjugations of undifferentiated gametangia from different or the same hyphal bodies or hypha or as azygospores arising without prior gametangial conjugations.

●●●●● Basidiobolus Eidam 1886 [=Basidiobolomycetes Doweld 2001 emend. Humber 2012] (M)
Differs from Entomophthoromycetes and Neozygitomycetes by unusually large nuclei (often ≥10 µm long) with a large central nucleolus that is the major feature of uninucleate cells. Mitoses involve barrel-shaped spindles, mitotic organelles incorporating microtubules (but not centrioles) but not always located at the spindle poles, and the nuclear content isolated from the cytoplasm by a layer of nuclear and cytoplasmic membrane fragments. *Basidiobolus ranarum*.

●●●●● Entomophthorales G. Winter 1880 [=Entomophthoromycetes Humber 2012]
Filamentous, primarily without septa; mostly parasites of insects, mites, and spiders; sexual reproduction by thick-walled zygospore, strictly homothallic, where known; asexual reproduction by conidia formed by blastosporogenesis; conidia forcibly discharged and often form secondary conidia. *Ancylistes*, *Completoria*, *Entomophthora*, *Meristacrum*.

●●●●● Neozygitaceae Ben-Ze'ev, R.G. Kenneth and Uziel 1987 [=Neozygitomycetes Humber 2012; = Neozygitales Humber 2012]

(continued)
<table><caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption><thead><tr><th></th><th></th></tr></thead><tbody><tr><td>Differs from Basidiobolomycetes and Entomophthoromycetes by vermiform, moderately sized chromosomes that con-dense during mitosis on a central metaphase plate but uncoil during interphase. Nuclear numbers in vegetative cells and conidia are low and apparently controlled at (3)-4-(5). <i>Neozygites</i>.</td><td></td></tr><tr><td>●●●● Zoopagales Bessey ex R.K. Benjamin 1979 [=Zoopagomycotina Benny 2007]<br>Filamentous, hyphae coenocytic or septate; parasites of soil fungi, invertebrates, and amoebae; asexual reproduction by conidia or merosporangia; sexual reproduction by globose zygospores with apposed suspensions. <i>Amoebophilus, Piptocephalis, Rhopalomyces, Sigmoideomyces, Stylopage.</i></td><td></td></tr><tr><td>●●●● Kickxellomycotina Benny 2007<br>Saprobes, mycoparasites or obligate symbionts; thallus arising from a holdfast on other fungi as a haustorial parasite, or branched, septate, subaerial hyphae; mycelium branched or unbranched, regularly septate; septa with median, disciform cavities containing plugs; asexual production by one- or two-spored merosporangia, trichospores or arthrospores; sexual reproduction by zygospores that are globose, biconical or allantoid and coiled.</td><td></td></tr><tr><td>●●●●● Asellariales Manier ex Manier & Lichtwardt 1978 [=Asellariaceae Manier ex Manier and Lichtw 1968]<br>Kickxellomycotina with filamentous, branched thalli; asexual reproduction by arthrospore-like cells that disarticulate from the corresponding thallus; in the digestive tracts of terrestrial, aquatic and marine isopods, as well as springtails. <i>Asellaria, Baltomyces, Orchesellaria.</i></td><td></td></tr><tr><td>●●●●●● Dimargaritaceae R.K. Benjamin 1959 [=Dimargaritales R. K. Benjamin 1979]<br>Hyphae regularly septate; septa containing a lenticular cavity; asexual reproduction by bisporous merosporangia; sexual reproduction by a zygospore, often ornamented; obligate haustorial parasites of fungi, especially Mucorales. <i>Dimargaris, Dispira, Spinalia, Tieghemiomyces.</i></td><td></td></tr><tr><td>●●●●●●● Harpellales Lichtwardt & Manier 1978<br>Endosymbionts of freshwater arthropods with basal cell attached to the host, from which a filamentous thallus develops; hyphae septate, with or without branching; septa contain a lenticular cavity; asexual reproduction occurs by lateral elongate monosporous trichospores; sexual reproduction by conical or biconical zygospores. Note that this group includes taxa previously referred to as trichomycetes. <i>Harpella, Orphella, Smittium, Zygopolaris.</i></td><td></td></tr><tr><td>●●●●●●●● Kickxellaceae Linder 1943 [=Kickxellales Kreisel ex R. K. Benjamin 1979]<br>Filamentous; hyphae possessing septa with a lenticular cavity; asexual reproduction by unispored sporangiola (merosporangia) produced on a sporocladium; saprobic or mycoparasitic, isolated from soil and dung. <i>Coemansia, Dipsacomyes, Kickxella, Linderina, Martensella, Martensiomyces, Spirodactylon, Spiomyces.</i></td><td></td></tr><tr><td colspan="2"><strong>DIAPHORETICKES Adl et al. 2012;</strong><br><em>Incertae sedis</em> Diaphoretickes:</td></tr><tr><td><em>Microheliella</em> Cavalier-Smith 2012 (M)<br>Aciliated, central centrosome with two concentric shells of dense material and a dense central core;<br>axopodia supported by triads of microtubules, bearing ellipsoid extrusomes; single nucleus eccentric, with internal channels where microtubular triads pass; mitochondrial cristae tubular; cortical filogranular network. <em>Microheliella maris</em>.</td><td></td></tr><tr><td><em>Ancoracysta</em> Janouskovec et al. 2017 (M)<br>Small ovoid marine cytotrophic predators on small protists; cell covered by a theca and dense glycocalyx; one pair of heterodynamic cilia; anterior cilium with mastigonemes at its anterior; posterior cilium with short vane, and traverses cell along a groove; mitochondria with lamellar cristae; characteristic extrusome (ancoracyst). <em>Ancoracysta twista</em>.</td><td></td></tr><tr><td>Rappemonads Kim et al. 2011<br>Marine and fresh water 5-7 µm cells with 2-4 plastids containing chlorophyll a. Poorly characterized, rare low abundance organisms, known only from environmental samples, and no species or genera described.</td><td></td></tr><tr><td>Telonemia Shalchian-Tabrizi 2006<br>Biciliated cells with a proboscis-like structure located at the ciliary pole and a complex cytoskeleton composed of layers of microtubules and microfilaments; tripartite tubular hairs on the long cilium; mitochondria with tubular cristae; peripheral vacuoles located just beneath the cell membrane; chloroplasts not observed. <em>Telonema</em> Griessmann 1913, may consist of several genera.</td><td></td></tr><tr><td>Picozoa Seenivasan et al. 2013 [Picobiliphytes Not et al. 2007] (M)</td><td></td></tr></tbody></table>

(continued)
<table><caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>
  <tr>
    <td>Cell oblong separated in two by a cleft; of picoplanktonic size; marine; without plastid; cytotrophic; two cilia inserted laterally; mito-chondrion with tubular cristate; heterotrophic, possibly feeding on small viruses or colloidal particles. <i>Picomonas judraskeda</i>.</td>
  </tr>
  <tr>
    <td><strong>Archaeplastida Adl et al. 2005</strong><br>Photosynthetic plastid with chlorophyll type-a from an ancestral primary endosymbiosis with a cyanobacterium; plastid with two mem-branes without periplastid endoplasmic reticulum; plastid reduced in some; usually with cell wall or other extracellular covering; flat mitochondrial cristae; starch storage product.</td>
  </tr>
  <tr>
    <td><strong>● Glaucophyta Skuja 1954</strong> [Glaucocystaceae West 1904 Glaucocystophyta Kies and Kremer 1986]<br>Unicellular or colonial algae; plastid in the form of a cyanelle, which is distinct from the chloroplasts of other organisms in that, like cyanobacteria, it has a conspicuous peptidoglycan wall between its two membranes; chlorophyll type-a only, with phycobiliproteins and other pigments; ciliated and non-ciliated species or life cycle stages; without cellulosic cell wall except <i>Glaucocystis</i>. Reported only in freshwater. <i>Cyanophora</i>, <i>Cyanoptyche</i>, <i>Glaucocystis</i>, <i>Gloechaete</i>.</td>
  </tr>
  <tr>
    <td><strong>● Rhodophyceae Thuret 1855</strong>, emend. Rabenhorst 1863 [Rhodophyta Wettstein 1901, Rhodoplantae Saunders and Hommersand 2004] emend. Adl et al. 2005<br>Red algae without ciliated stages, and without centrioles, or basal bodies, or other 9 + 2 microtubular structures—presence of polar rings instead; two-membraned simple chloroplasts, unstacked thylakoids with phycobilisomes, and chlorophyll a only, lacking external endoplasmic reticulum; cytoplasmic carbohydrate reserve floridean starch; chromosomal and interzonal microtubules not converging towards polar rings, so spindle poles very broad; telophase spindle and nuclear envelope persisting with closed mitosis surrounded by perinuclear endoplasmic reticulum; cell wall of cellulose; cells in filamentous forms linked by pit plugs, formed between cells after incomplete cell division; sexual reproduction typically oogamous; triphasic life history common.</td>
  </tr>
  <tr>
    <td>●● Cyanidiales T. Christensen 1962 [Cyanidiophyceae Merola et al. 1981, Cyanidiophyta Moehn ex Doweld 2001]<br>Unicellular, spherical or elliptical in shape; thick cell wall or lack of cell wall; facultative heterotrophs or obligate photoautotrophs; cell division or endospore formation; inhabiting acidic and high temperature environments. <i>Cyanidioschyzon</i>, <i>Cyanidium</i>, <i>Galdieria</i>.</td>
  </tr>
  <tr>
    <td>●● Proteorhodophytina Muñoz-Gómez et al. 2017 (R)<br>Clade consisting of Compsopogonales, Porphyridiophyceae, Rhodellophyceae, Stylonematales, based on phylogenetic analysis.</td>
  </tr>
  <tr>
    <td>●●● Compsopogonales Skuja 1939 [Compsopogonophyceae G. W. Saunders and Hommersand 2004]<br>Pluricellular with monosporangia and spermatangia usually cut out by curved walls from ordinary vegetative cells; Golgi-ER associ-ation; encircling thylakoids in the plastid; life history biphasic if known; inhabiting freshwater or marine environment. <i>Boldia</i>, <i>Comp-sopogon</i>, <i>Erythrotrichia</i>, <i>Rhodochaete</i>.</td>
  </tr>
  <tr>
    <td>●●●● Porphyridiophyceae H. S. Yoon et al. 2006<br>Unicellular with a single branched or stellate plastid, with or without pyrenoid; Golgi association with mitochondria and ER; cells with floridoside as a low molecular-weight carbohydrate; reproduction by cell division; inhabiting marine, freshwater and even moist terrestrial areas. <i>Erythrolobus</i>, <i>Flintiella</i>, <i>Porphyridium</i>.</td>
  </tr>
  <tr>
    <td>●●●●● Rhodellophyceae Cavalier-Smith 1998 [Rhodellophytina Cavalier-Smith 1998]<br>Unicellular; single highly lobed plastid with eccentric or centric pyrenoid; Golgi association with nucleus and ER; contains mannitol; reproduction by cell division; inhabiting marine and freshwater habitats. <i>Dixoniella</i>, <i>Glaucosphaera</i>, <i>Rhodella</i>.</td>
  </tr>
  <tr>
    <td>●●●● Stylonematales K. Drew 1956 [Stylonematophyceae H.S. Yoon et al. 2006]<br>Unicellular or pseudofilamentous or filamentous; various plastid morphologies with or without pyrenoid; Golgi association with mitochondria and ER; reproduction by cell division or monospores; inhabiting freshwater, brackish and marine environment. <i>Ban-giopsis</i>, <i>Chroodactylon</i>, <i>Chroothece</i>, <i>Purpureofilum</i>, <i>Rhodosorus</i>, <i>Rhodospora</i>, <i>Rufusia</i>, <i>Stylonema</i>.</td>
  </tr>
  <tr>
    <td>●● Eurhodophytina G.W Saunders & Hommersand 2004 (R)<br>Clade containing Bangiales and Florideophycidae, based on phylogenetic analysis.</td>
  </tr>
  <tr>
    <td>●●● Bangiales Nägeli 1847 [Bangiophyceae A. Wettstein 1901]<br>Pluricellular with Golgi-ER/mitochondrion association; life history biphasic, heteromorphic, gametophyte macroscopic, initially unis-eriate, becoming pluriseriate or foliose by diffuse growth; carposporangia and spermatangia produced in packets by successive perpendicular divisions; sporophyte filamentous, with pit plugs with a single cap layer, but lacking membranes; typically forming conchospores in fertile cell rows; inhabiting mostly marine environment. <i>Bangia</i>, <i>Bangiomorpha</i>, <i>Boreophyllum</i>, <i>Dione</i>, <i>Minerva</i>, <i>Porphyra</i>, <i>Pyropia</i>, <i>Pseudobangia</i>.</td>
  </tr>
  <tr>
    <td>●●●● Florideophycidae Cronquist 1960<br>Pluricellular with Golgi-ER/mitochondrion; growth by means of apical cells and lateral initials forming branched filaments in which</td>
  </tr>
</table>

(continued)
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

the cells are linked throughout by pit connections; life history fundamentally triphasic consisting of gametophytic, carposporophytic and tetrasporophytic phases; reproductive cells (monosporangia, spermatangia, carposporangia, tetrasporangia) generally terminal or lateral on the filaments; carpogonia terminal or lateral, bearing an apical extension, the trichogyne, to which the spermatangia attach; carposporophyte developing directly from the carpogonium or its derivative; inhabiting mostly marine environment.

●●●● Hildenbrandiaceae Rabenhorst 1868 [Hildenbrandiophycidae G. W. Saunders and Hommersand 2004]
Pluricellular that are crustose and smooth to tubercular or with erect branches; composed of a basal layer of laterally adhering branched filaments and laterally adhering simple or branched erect filaments; pit plugs with a single cap layer and membrane; tetrasporangia zonately or irregularly divided, apomeiotic, borne in ostiolate conceptacles; sexual reproduction unknown. *Apophloea*, *Hildenbrandia*.

●●●●● Nemaliophycidae Christensen 1978
Pluricellular; pit plugs characterized by two cap layers. *Acrochaetium*, *Balbiania*, *Ballia*, *Batrachospermum*, *Colaconema*, *Entwisleia*, *Nemalion*, *Palmaria*, *Rhodychlya*, *Thorea*.

●●●●● Corallinophycidae L. Le Gall & G. W. Saunders 2007
Pluricellular; carpogonial branches two-celled; tetrasporangia zonate or cruciate in division; pit plug with two cap layers at cytoplasmic faces, outer dome shaped, membrane absent; calcification in the form of calcite. *Corallina*, *Harveylithon*, *Hydroli-thon*, *Lithophyllum*, *Mastophora*, *Melobesia*, *Metagoniolithon*, *Neogoniolithon*, *Porolithon*, *Rhodogorgon*, *Sporolithon*.

●●●●● Ahnfeltiophycidae G. W. Saunders & Hommersand 2004
Pluricellular; carpogonia terminal and sessile; carposporophyte developing outward; pit plugs naked, lacking caps and mem-branes. *Ahnfeltia*, *Pihiella*.

●●●●● Rhodymeniophycidae G. W. Saunders & Hommersand 2004
Pluricellular with sexual life histories generally triphasic; carposporophyte developing directly from the carpogonium or car-pogonial fusion cell, or indirectly from an auxiliary cell that has received the postfertilization diploid nucleus; pit plugs with membranes only (single inner cap in Gelidiales). *Acrosymphytum*, *Bonnemaisonia*, *Ceramium*, *Gelidium*, *Gigartina*, *Gracilaria*, *Halymenia*, *Nemastoma*, *Peyssonnelia*, *Plocamium*, *Rhodymenia*, *Sebdenia*.

● Chloroplastida Adl et al. 2005 [Viridiplantae Cavalier-Smith 1981; Chlorobionta Jeffrey 1982, emend. Bremer 1985, emend. Lewis and McCourt 2004; Chlorobiota Kendrick and Crane 1997]

Plastid with two membranes without periplastid endoplasmic reticulum; plastid with chlorophyll *a* and *b*; starch inside plastid; cell wall often with cellulose, or scaly extracellular covering; swimming cells with cilia in multiples of two, or rarely single cilium, with stellate structure linking nine pairs of microtubules at basal body transition zone; with centrioles; Rubisco small subunits encoded in the nuclear genome.

●● Chlorophyta Pascher 1914, emend. Lewis & McCourt 2004

Plastid thylakoids single or stacked; glycolate dehydrogenase present; cell division without phragmoplast.

●●● Ulvophyceae Mattox & Stewart 1984 (P)
Swimming cells with one or two pairs of cilia, without mastigonemes; basal bodies with four microtubular rootlets in cruciate arrangement, and smaller roots of two sizes, alternating between two and more microtubules; cilia with scales and rhizoplasts; cell wall more or less calcified; cell division by furrowing with mitotic spindle closed, centric and persistent; phycoplast absent; thallus can be branched or unbranched, mono- or distromatic sheet (phyllose), or cushiony forms of compacted tubes; thallus often multinucleate and siphonous; free-living diplobionic life cycle, iso- or heteromorphic. *Acetabularia*, *Caulerpa*, *Chladophora*, *Codium*, *Pithophora*, *Pseudonochloris*, *Rhizoclonium*. Note: The inclusion of *Oltmannsiellopsis* in Ulvophyceae causes instability in phylogenies, and the monophyly is questioned.

●●●● Trebouxiophyceae Friedl 1995 [Pleurastrophyceae Mattox et al. 1984, Microthamniales Melkonian 1990] (P?)
Swimming cells with one or two pairs of cilia, without mastigonemes; basal bodies with four microtubular rootlets in cruciate arrangement, including a multilayered structure, and as smaller root, alternating between two and more microtubules; basal bodies with prominentrhizoplast, cruciate, displaced counterclockwise and counterclockwise basal body orientation; closed mitosis with metacentric spindle, semi-closed mitosis; cytokinesis with phycoplast; asexual reproduction by autospores or zoospores; sexual reproduction reported but not observed; lichenose and free-living forms; most with cell walls; osmotrophy and autotrophy. *Botryococcus*, *Chlorella*, *Choricystis*, *Coccomyxa*, *Microthamnion*, *Nannochloris*, *Oocystis*, *Pabia*, *Prasiola*, *Prototheca*, *Trebouxia* (P).

●●● Chlorophyceae Christensen 1994
Swimming cells with one to hundreds of cilia, without mastigonemes; when two or four cilia, basal bodies with four microtubular rootlets in cruciate arrangement, alternating between two and more microtubules; basal bodies displaced clockwise or directly opposed; rhizoplast connects basal bodies and extends to nucleus; in colonial forms, basal bodies reoriented to face outside of

(continued)
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

colony; closed mitosis; cytokinesis has phycoplast with microtubules, sometimes with furrowing, with formation of plasmodesmata cell-cell connections; haplobiontic life cycle; sexual reproduction by isogamy, anisogamy, or oogamy; asexual reproduction by aplanospores, akinetes, or autosporic; osmotrophy and autotrophy. *Bracteacoccus, Chlamydomonas (P), Desmodesmus, Floydiella, Hydrodictyon, Oedegonium, Pediastrum, Scenedesmus, Volvox*.

Incertae sedis Chlorophyceae: *Carteria, Cylindrocapsa, Hafniomonas, Mychanastes, Treubaria, Trochiscia*.

●●● Chlorodendrophyceae Fritsch 1917

Cells with a pair of cilia, inserted in a ciliary pit; cilia beat in breast-stroke pattern; basal body rootlets structure in X2X2 configuration; with organic extracellular scales, outer layer of scales fused to form a theca; metacentric spindle collapses at telophase; nutrition by autotrophy and osmotrophy. Treated as prasinophyte clade IV (Nakayama et al. 1998). *Scherffelia, Tetraselmis*.

●●●● Pedinophyceae Moestrup 1991, emend. Fawley et al. in Adl et al. 2012

Unicellular, with single cilium; closed mitosis with persistent spindle; phycoplast absent; counterclockwise basal body orientation; cilia covered with rigid or thin, hair-like appendages; single parietal chloroplast. *Marsupiomonas, Pedinomonas*.

●●● Chloropicophyceae Lopes dos Santos & Eikrem 2017

Small coccoid cells with a diameter of 1.5–4 µm; pyrenoid absent; without cilium; with layered cell wall; marine. Treated as prasinophyte clade VII A & B (Lopes dos Santos et al. 2017). *Chloroparvula, Chloropicon*.

●●●● Picocystophyceae Lopes dos Santos & Eikrem 2017

Coccoid, but ovoid or tri-lobed forms observed in old cultures; layered cell wall containing polyarabinose, mannose, galactose and glucose. Treated as prasinophyte clade VII C (Lopes dos Santos et al. 2017). *Picocystis*.

●●● Pyramimonadales Chadefaud 1950

Swimming cells with 4–16 cilia; helical structure in the ciliary transitional region; trailing cells bearing a single cillum observed in some, which may represent gametes; chloroplast cup-shaped; pyrenoid present; some with eyespot(s); several layers of body and ciliary scales; some producing conspicuous cyst (called phycoma); with one or more large vacuoles and associated duct system; phagotrophy in some. Treated as prasinophyte clade I (Nakayama et al. 1998). *Cymbomonas, Halosphaera, Pterosperma, Pyramimonas*.

●●●● Mamiellophyceae Marin & Melkonian 2010

Cells typically solitary, with single chloroplast, sometimes two; prasinoxanthin commonly present; two cilia, single or no cilium present; cilia equal or unequal in length; eye spot posterior if present; cells and/or cilia with 1–2 layers of flattened, rounded or elliptical scales, or scales absent; scales ornamented with spider web-like or uniformly reticulate pattern; mostly marine, some freshwater. Treated as prasinophyte clade II (Nakayama et al. 1998). *Bathycoccus, Crustomastix, Dolichomastix, Mamiella, Monomastix, Mantoniella*.

●●●● Nephroselmis [Nephroselmidophyceae Cavalier-Smith 1993, emend. Yamaguchi 2011]

Cells laterally compressed; two cilia inserted laterally; square- or diamond-shaped scales cover cell body and cilia, except in at least one species—*Nephroselmis pyriformis*; single, cup-shaped chloroplast with pyrenoid and eyespot; contractile vacuole near ciliary bases in freshwater species; sexual reproduction by hologamy; mostly marine, some freshwater. Treated as prasinophyte clade III (Nakayama et al. 1998). *Nephroselmis*.

●●●●● Pycnococcaceae Guillard 1991, emend. Fawley 1999 [Pseudoscourfieldiales and Pseudoscourfieldiaceae Melkonian 1990]

Plastid with prasinoxanthin; with or without scaly covering; vegetative cells with two cilia or no cilia; trailing cells bearing a single cilium rarely observed in *Pycnococcus* culture; pyrenoid in the plastid; intrusion of mitochondrial membranes into the pyrenoid. Treated as prasinophyte clade V (Fawley et al. 2000). *Pycnococcus, Pseudoscourfieldia*.

●●● Palmophyllophyceae Leliaert et al. 2016

Marine; solitary, in loose colonies, or cells grouped in gelatinous matrix; strongly supported in plastid multigene and nuclear ribosomal DNA phylogenies.

●●●●● Palmophyllales Zechman et al. 2010

Thallus macroscopic, crustose or erect; subspherical cells in gelatinous matrix make up thallus; cell diameter 6–10 µm; each cell with single cup-shaped chloroplast lacking pyrenoids; benthic marine. *Palmophyllum, Palmoclathrus, Verdigellas*.

●●●●●● Prasinococcales Guillou et al. 2004, as in Leliaert et al. 2016

Marine; planktonic; solitary or forming loose colonies; no cilium; without scaly covering; with cell wall; chloroplast cup-shaped and with pyrenoid; cell division by unequal binary fission in which one of the daughter cells retains the parent wall, while the other is released with a newly produced cell wall. Treated as prasinophyte clade VI (Fawley et al. 2000). *Prasinococcus, Prasinoderma*.

(continued)
<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

Streptophyta Bremer & Wanntorp 1981 [Charophyta Migula 1897, emend. Karol et al. 2009; Charophyceae Smith 1938; Jeffrey 1967; Streptophyta, Mattox and Stewart 1984]

Asymmetric motile cells, when present, with pair of cilia without mastigonemes; basal bodies with distinctive multilayered structure of microtubular rootlet and cytoskeletal anchor; thylakoids stacked; open mitosis; usually with phycoplast, but some with phragmoplast and cell plate; with primary plasmodesmata between adjacent cells in filamentous forms; filaments branching or nonbranching; with non-motile vegetative phase; some with multinucleate cells; with or without sexual reproduction; sexual species with haplobiontic life cycle; with desiccation-resistant cysts (zygospores); glycolate oxidase in peroxisomes; Cu/Zn superoxide dismutase; ciliary peroxisome.

Chlorokybus Geitler 1942 [Chlorokybophyceae Lewis and McCourt 2004] (M)

Sarcinoid packets of cells; subaerial; biciliated zoospores; cilia with hairs; multilayered structure (MLS) at ciliary root. *Chlorokybus atmophyticus*.

Mesostigma Lauterborn 1894 [Mesostigmatophyceae Marin and Melkonian 1999, emend. Lewis and McCourt 2004; Mesostigmata Turmel et al. 2002] (M)

Asymmetrical cell with pair of lateral cilia without mastigonemes, emerging from a pit; presence of multilayered structures adjacent to the ciliary basal bodies; with glycolateoxidase; ciliary peroxisome present; cell wall of cellulose; organic scales cover cell wall and cilia. *Mesostigma viride*.

Klebsormidiophyceae van den Hoek et al. 1995

Coccoid or unbranched filaments; one or two chloroplasts with one pyrenoid; most chloroplasts parietal; cleavage furrow during cell division but no cell plate or phragmoplast; sexual reproduction unknown. *Entransia, Interfilum, Klebsormidium*.

Phragmoplastophyta Lecointre & Guyander 2006

Cell division by way of some form of phragmoplast; some oogamous, others anisogamous with nonmotile female gamete and motile male gamete.

Zygnematophyceae van den Hoek et al. 1995, emend. Hall et al. 2009

Without ciliated stages; sexual reproduction via conjugation; thalli unicellular or filamentous; no centrioles. *Spirogyra, Staurastrum*.

Coleochaetophyceae Jeffrey 1982

Thalli discs of cells or branched filaments; sheathed hairs as extensions of the cell wall. *Coleochaete, Chaetosphaeridium*.

Charophyceae Smith 1938, emend. Karol et al. 2009 [Charales Lindley 1836; Charophytae Engler 1887]

Thallus attached to substrate with rhizoids; thallus a central axis of multinucleate internodal cells, with whorls of branchlets radiating from mononucleate cells at nodes; calcium carbonate accumulates in cell wall of many species; haplobiontic life cycle; sexual reproduction oogamous with sperm cells; differentiated sperm and egg producing organs; antheridium with several shield cells and a manubrium that gives rise to spermatogenous filaments; primarily in fresh water. *Chara, Nitella, Tolypella*.

Embryophyta Engler 1886, emend. Lewis and McCourt 2004 [Cormophyta Endlicher 1836; Plantae Haeckel 1866]

Ciliated basal bodies, when present, with distinctive multilayered structure of microtubules and cytoskeletal anchor; open mitosis with phragmoplast at cytokinesis; plasmodesmata and other characteristic cell-cell junctions; diplobiontic life cycle, with vegetative propagation possible in many; alternation of generations with fertilization of egg by sperm inside protective test; embryology with tissue differentiation coordinated by hormones; differentiated sperm and egg cells, may be on different sexual individuals, on different organs of the same individual or in the same organ. Subdivisions not shown.

Sar Burki et al. 2008, emend. Adl et al. 2012

The least inclusive clade containing *Bigelowiella natans* Moestrup and Sengco 2001 (Rhizaria), *Tetrahymena thermophila* Nanney and McCoy 1976 (Alveolata), and *Thalassiosira pseudonana* Cleve 1873 (Stramenopiles). 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—*Homo sapiens* Linnaeus 1758 (Opisthokonta), *Dictyostelium discoideum* Raper 1935 (Amoebozoa), *Arabidopsis thaliana* (Linnaeus) Heynhold 1842 (Archaeoplastida), *Euglena gracilis* Klebs 1883 (Excavata), *Emiliania huxleyi* (Lohmann) Hay and Mohler in Hay et al. 1967 (Haptophyta). The name is derived from the acronym of the three groups united in this clade. The apparent composition of Sar is: Alveolata, Rhizaria and Stramenopiles, as defined in Adl et al. 2012. The primary reference phylogeny is Burki et al. (2008, Fig. 1).

Stramenopiles Patterson 1989, emend. Adl et al. 2005

Motile cells typically biciulate, typically with heterokont ciliation—anterior cilium with tripartite mastigonemes in two opposite rows and a posterior usually smooth cilium; tubular mitochondrial cristae; typically, four microtubular kinetosomal roots.

*Incertae sedis* Stramenopiles: Environmental lineages MAST-21, MAST-25 Massana et al. 2014

Uncultured groups detected in molecular marine surveys amplifying directly 18S rDNA genes. These clades are mostly detected in the

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<caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption>

analysis of small size fractions (pico- and nanoeukaryotes).
*Incertae sedis* Stramenopiles: *Platysulcus*. Marine bacterivorous heterokont cell with short anterior cilium and long posterior cilium; cell with wide, shallow ventral furrow.

●● Bigyra Cavalier-Smith 1998, emend. 2006 (R)

Heterotrophs, mostly phagotrophs, without vegetative cell walls.

●●● Opalozoa Cavalier Smith 1991, emend. 2006

Cilia without tubular hairs or absent; without plastids, typically without vegetative cell walls; most of them phagotrophic but often osmotrophic saprotrophs in vertebrate guts.

*Incertae sedis* Opalozoa: Spherical or D-shaped cells with two heterokont cilia; microaerophilic, in marine sediments. *Cantina, Rictus*.

*Incerta sedis* Opalozoa: Environmental lineages MAST-12, MAST-16, MAST-22 and MAST-24. Massana et al. 2014 (R)

Uncultured groups detected in molecular marine surveys amplifying directly 18S rDNA genes, detected mostly in the analysis of small size fractions (pico and nanoeukaryotes).

●●●● Nanomonadea Cavalier-Smith 2012 (clade MAST-3)

Phagotrophic and non-photosynthetic free-living ciliated cells. Includes the uniciilated *Solenicola* and *Incisomonas*, and their related environmental 18S rDNA sequences. *Incisomonas*, *Solenicola*.

●●●●● Opalinata Wenyon 1926, emend. Cavalier-Smith 1997 [Slopalinida Patterson 1985]

Pluriciliated with double-stranded transitional helix at the transitional region between kinetosome and cilium; cilia without tubular hairs evenly spaced cortical ridges underlain by microtubules, ranging from singlets to ribbons; cyst-forming; many are osmotrophic in vertebrate guts.

●●●●●● Proteromonadea Grasse 1952 (P?)

One or two anterior pairs of anisokont cilia; uninucleate; endobionts in intestinal tract of amphibians, reptiles and mammals. *Karotomorpha*, *Proteromonas*.

●●●●●● Opalinea Wenyon 1926

Multiciliated with cilia originating from an anterior morphogenetic centre, the falx, and forming oblique longitudinal rows or files; microtubular ribbons supporting longitudinal pellicular ridges between ciliary rows; two to many monomorphic nuclei; endobionts in amphibians and some fish; life cycle complex, with sexual processes induced by hormones of host and linked to the host's life cycle. *Cepedea*, *Opalina*, *Protoopalina*, *Protozelleriella*, *Zelleriella*.

●●●●●●● Blastocystis Alexieieff 1911

Rounded aciliated yeast-like cells, anaerobic commensals/parasites of intestinal tracts; cilia secondarily lost. Environmental samples and from mammalian, avian, and reptile hosts, many without specific host. *Blastocystis*.

●●●● Placidida Moriya et al. 2002

Biciliate cells without plastids; described species have mastigonemes on anterior cilium, attach to substrates by posterior cilium during feeding; double-stranded transitional helix. *Placidia*, *Suigetsumonas*, *Wobblia*.

●●●● Bicosoecida Grasse 1926, emend. Karpov 1998

Biciliate with or without tripartite mastigonemes, typically lacking transitional helix; without plastids; phagotrophic with cytosome, supported by broad microtubular rootlet No. 2 of posterior cilium; predominantly sedentary, often attach to substrate with posterior cilium; with or without lorica; solitary and colonial. *Adriamonas*, *Anoeca*, *Bicosoeca*, *Caecitellus*, *Cafeteria*, *Cyathobodo*, *Filos*, *Halocafeteria*, *Nanum*, *Paramonas*, *Pseudobodo*, *Pseudodendromonas*.

●●● Sagenista Cavalier-Smith 1995

Heterotrophic phagotrophs and in some cases osmotrophs, biciliated cells present in some stages of their life cycle in most species.

*Incertae sedis* Sagenista environmental lineages MAST-4, MAST-7, MAST-8, MAST-9, MAST-10, MAST-11, MAST-20 Massana et al. 2014 (R).

Uncultured groups detected in molecular marine surveys amplifying directly 18S rDNA genes. These clades are mostly detected in the analysis of small size fractions (pico and nanoeukaryotes). The majority of these clades form a sister group to Labyrinthulomycetes.

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<table><caption>**Table 2** Classification of the higher ranks of the protists and multicellular organisms.</caption><thead><tr><th></th><th></th></tr></thead><tbody><tr><td>●●●● Labyrinthulomycetes Dick 2001</td><td>Producing an ectoplasmic network of anastomosing branched wall-less filaments with an organelle called both chromosome; Golgi-derived scales; bicipile zoospores with lateral insertion in many species.</td></tr><tr><td>●●●●● Amphitremida Poche 1913, emend. Gomaa et al. 2003</td><td>Phagotrophs or mixotrophs; planktonic or benthic; aerobic, freshwater and marine, and anaerobic/microaerophilic environments. Amphitrema, Archerella, Diplophrys, Paramphitrema.</td></tr><tr><td>●●●●●● Amphifilida Cavalier-Smith 2012</td><td>Pseudostomes instead of true bothrosomes, ectoplasmic elements in the form of pseudopodia. Amphifila, Fibrophrys, Sorodiplophrys.</td></tr><tr><td>●●●●●●● Oblongichytrida Bennett et al. 2017</td><td>Slender oblong zoospores. Oblongichytrium</td></tr><tr><td>●●●●●● Labyrinthulida Doffein 1901</td><td>Spindle-shaped vegetative cells distributed in an extensive ectoplasmic net; zoospores with eyespots; sexual reproduction. Aplanochytrium, Labyrinthula Stellarchytrium.</td></tr><tr><td>●●●●●●● Thraustochytrida Sparrow 1943</td><td>Cells producing a small ectoplasmic net; presence of interphase centrioles in vegetative cells; no eyespots; no sexual reproduction. Althornia, Aurantiochytrium, Botryochytrium, Japanochytrium, Monorhizochytrium, Parietichytrium, Schizochytrium, Sicyoidochytrium Thraustochytrium, Ulkenia.</td></tr><tr><td>●●●● Pseudophyllomitidae Shiratori et al. 2016 (MAST-6)</td><td>Free-living phagotrophic biciliates, anterior cilium with tubular mastigonemes; mitochondria with tubular cristae; ciliary transitional region with transitional helix. Pseudophyllomitus (P).</td></tr><tr><td>●● Gyrista Cavalier-Smith 1998</td><td>Cells with helical or double helix/ring system ciliary transition zone.</td></tr><tr><td colspan="2"><i>Incertae sedis</i> Gyrista: Environmental lineages MAST-1, MAST-2, MAST-23 Massana et al. 2014</td></tr><tr><td colspan="2">Uncultured groups detected in molecular marine surveys amplifying directly 18S rDNA genes. These clades are mostly detected in the analysis of small size fractions (pico and nanoeukaryotes).</td></tr><tr><td>●●● Developea Karpov et Aleoshin 2016</td><td>Free-swimming, naked, heterotrophic, bearing two cilia, anterior cilium with mastigonemes. Developayella, Develorapax.</td></tr><tr><td>●●●● Hyphochytriales Sparrow 1960</td><td>Single anteriorly directed cilium.</td></tr><tr><td>●●●●● Anisolpidiaceae Karling 1943, emend. Dick 2001</td><td>Thallus holocarpic. Anisolpidium, Canteriomyces.</td></tr><tr><td>●●●●●● Hyphochytrium Karling 1939 [Hyphochytridiomycetaceae Fischer 1892, emend. Karling 1939]</td><td>Thallus eucarpic and polycentric. Hyphochytrium.</td></tr><tr><td>●●●●● Rhizidiomycetaceae Karling 1943</td><td>Thallus eucarpic and monocentric. Latrostium, Rhizidiomyces, Rhizidiomycopsis.</td></tr><tr><td>●●●● Peronosporomycetes Dick 2001 [Oomycetes Winter 1897, emend. Dick 1976]</td><td>Thallus mainly aseptate; cell wall of glucan-cellulose, may have minor amount of chitin; haplomictic-B nuclear cycle; lysine synthesized via the diaminopimelate (DAP) pathway; lanosterol directly from squalene oxide; zoospores bicipile and heterokont but rarely unicipile; cilia anteriorly inserted; anteriorly directed cilium shorter; transitional plate of kinetosome sitting above the plasma membrane with a central bead; kinetid base structure with six parts, including four roots; oogamous reproduction that results in the formation of thick-walled sexual spores known as oospores, due to contact between male and female gametangia in the most derived groups.</td></tr><tr><td colspan="2"><i>Incertae sedis</i> Peronosporomycetes: Atkinsella, Ciliomyces, Crypticola, Ectrogella, Eurychasma, Halodaphnea, Haliphthoros, Haptoglossa, Lagena, Lagenisma, Olpidiopsis, Pontisma, Pythiella, Rozellopsis, Sirolpidium.</td></tr><tr><td>●●●●● Saprolegnialean lineage Lara in Adl et al. 2019</td><td>Obligate biotrophs and facultative parasites. Oogamous sexual reproduction. Two, often morphologically different generations of zoospores, which may have lost cilia secondarily. Complex kinetosome-associated "K-bodies". Achlya, Aphanomyces,</td></tr></tbody></table>

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