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Ксения Мироновна Суханова
(1919
2003)
Folia Cryptogamica Petropolitana
И.В. Змитрович,
В.В. Перелыгин,
М.В. Жариков
НОМЕНКЛАТУРА И
РАНГОВАЯ КОРРЕЛЯЦИЯ
ВЫСШИХ ТАКСОНОВ
ЭУКАРИОТ
Москва
«ИНФРА-М»
2022
УДК 574/578 : 576.1 + 58.001
ББК 28.09
З69
Змитрович И.В., Перелыгин В.В., Жариков М.В. Номенклату-
ра и ранговàÿ êîððåëÿöèÿ высших таксонов эукариот. —
Москва: ИНФРА-М, 2022. 184 с. (Folia Cryptogamica
Petropolitana. 2022. No 8. С. 1—184).
ISBN 978-5-16-018531-6
Монография посвящена обзору высших таксонов эукариот
и решению проблемы их ранговой корреляции. Затронуты су-
щественные вехи истории мегасистематики эукариот. Обсуж-
даются принципы и подходы к номенклатуре высших таксонов
эукариот. Проведена ревизия системы эукариотных организмов
с отсылками к первоописаниям соответствующих таксонов.
Рассматриваются тенденции трансформации системы и обсуж-
даются вопросы ее практического приложения. Описаны суб-
домен Obimoda, царство Crumalia, типы Mantamonadea,
Rigifilidea и Collodictyonidea. Приведены рестроспективный кон-
спект основных систем эукариот, опубликованных в период
19252022 гг. и обширный список работ по мегасистематике и
микробиологии эукариот.
Для биологов всех специальностей.
Библиогр. 356 назв. Табл. 3.
Ответственный редактор И.В. ЗМИТРОВИЧ
Рецензентû
В.Г. ЛУЖАНИН, канд. биол. наук, доцент, çàâåäóþùèé êàôåäðîé áîòàíèêè è ôàðìàöåâòè÷åñêîé áèîëîãè,
ðåêòîð Ïåðìñêîé ãîñóäàðñòâåííîé ôàðìàöåâòè÷åñêîé àêàäåìèè Ìèíèñòåðñòâà çäðàâîîõðàíåíèÿ Ðîññèéñêîé
Ôåäåðàöèè
Ì.Â.ÀÐÕÈÏÎÂ, ä-ð áèîë. íàóê, ïðîôåññîð, ãëàâíûé íàó÷íûé ñîòðóäíèê ñåêòîðà áèîôèçèêè ðàñòåíèé
ëàáîðàòîðèè ýêîëîãè÷åñêîé ôèçèîëîãèè è áèîôèçèêè ðàñòåíèé Àãðîôèçè÷åñêîãî íàó÷íî-èññëåäîâàòåëüñêîãî
èíñòèòóòà; ãëàâíûé íàó÷íûé ñîòðóäíèê îòäåëà ðàñòåíèåâîäñòâà è çåìëåäåëèÿ Ñåâåðî-Çàïàäíîãî Öåíòðà
ìåæäèñöèïëèíàðíûõ èññëåäîâàíèé ïðîáëåì ïðîäîâîëüñòâåííîãî îáåñïå÷åíèÿ – îáîñîáëåííîå ñòðóêòóðíîå
ïîäðàçäåëåíèå Ñàíêò-Ïåòåðáóðãñêîãî ôåäåðàëüíîãî èññëåäîâàòåëüñêîãî öåíòðà ÐÀÍ
Работа И.В. Змитровича выполнена в рамках госзадания
Ботанического института им. В.Л. Комарова РАН
(№ 122011900033-4)
© И.В. Змитрович, В.В. Перелыгин, М.В. Жариков
I.V. Zmitrovich,
V.V. Perelygin,
M.V. Zharikov
NOMENCLATURE AND
RANK CORRELATION
OF HIGHER TAXA
OF EUKARYOTES
Moscow
INFRA-M
2022
ISBN 978-5-16-018531-6
Zmitrovich I.V., Perelygin V.V., Zharikov M.V. Nomenclature and
rank correlation of higher taxa of eukaryotes. Мoscow: INFRA-M,
2022. 184 p. (Folia Cryptogamica Petropolitana. 2022. No 8. P. 1—
184).
The monograph is devoted to a review of the higher taxa of eu-
karyotes and the approaches to the problem of their rank correla-
tion. Significant milestones in the history of eukaryotic megasys-
tematics are touched upon. The principles and approaches to the
nomenclature of the higher taxa of eukaryotes are discussed. A revi-
sion of the system of eukaryotic organisms was carried out with re-
ference to the original descriptions. The tendencies of general sys-
tem transformation are considered and problems with some practical
applications of eukaryotic megasystematics are discussed. The
Obimoda subdomain, the Crumalia kingdom, the Mantamonadea,
Rigifilidea, and Collodictyonidea phyla are described. A retrospective
overview of basic systems of eukaryotes published in the period
1925—2022 and an extensive list of publications on megasystematics
and microbiology of eukaryotes are presented.
For biologists of all specialities.
Bibliography 356. Tab. 3.
Cover drawings after Ehrenberg (1838).
Responsible editor I.V. ZMITROVICH
Review by
V
.G. LUZHANIN, Cand. Sci. (Biol.), Associate Professor, Head of the Department of Botany and
Pharmaceutical Biology, Rector, Perm State Pharmaceutical Academy of the Ministry of Health of the
Russian Federation
M.V.ARKHIPOV, Dr. Sc. (Biol.), Professor, Chief Researcher of the Plant Biophysics Sector of the Laboratory of
Ecological Physiology and Plant Biophysics of the Agrophysical Research Institute; Chief Researcher of the Department
of Plant Growing and Agriculture of the Northwestern Center for Interdisciplinary Research of Food Supply Problems -
a separate structural unit of the St. Petersburg Federal Research Center of the Russian Academy of Sciences
The work by I.V. Zmitrovich was carried out within the
framework of the state task of Komarov Botanical Institute of
the Russian Academy of Sciences
(No 122011900033-4)
© I.V. Zmitrovich, V.V. Perelygin, M.V. Zharikov
7
PREFACE
Classification decisions at higher levels of the system of
eukaryotes have always had a fundamental sound, since it
reflects progress at the forefront of structural and evolu-
tionary biology, being a kind of overgeneralization of great
heuristic and didactic value. Widespread blowing of repro-
ducible procedures of molecular phylogenetics into classifi-
cation routines significantly stabilized the system at this
level as well, reducing a set of versions. However, a certain
subjectivism has not yet been overcome in the ranking of
well-recognized clades. The nomenclature of higher taxa of
eukaryotes is also an intricate matter, since the botanical
nomenclature code regulates the naming up to the phyla
(divisions) level, whereas the zoological code generally ap-
plies not higher than the family level, respectively, there
are no definite rules in naming the higher categories, and
any attempts to establish them tacitly have not hit the
mainstream.
It would be an immodest task to aim at eliminating the
aforementioned problems at the higher levels of the eukar-
yotic system, especially since such luminaries as Sta-
robogatov, Kusakin, and Drozdov tried to do at this field,
but the megaclassification, nevertheless, continued to go
its own, albeit roundabout, pathway. Our more modest
goal is overview a general system of eukaryotes with an
attempt at rank correlation, which would be important in
practical terms, e.g., to create practice-oriented Internet
classifiers. The relevance of this task is due to the fact that
in a course of studies of the biota as a whole, the promi-
nent splitting occurs at all levels of the taxonomic hierar-
chy, and its consequence is a tendency to inflation of high-
er ranks or, at least, no tendency to their downgrading in
metazoans, fungi, and embryophytes. In such a situation,
how to deal with unicellular lineages which, based on mo-
lecular phylogeny, are equal in their rank (or even are ba-
sal) to these large multicellular pools? Obviously, this
would lead to an over-raising of their rank, which would
8
have negative consequences (first of all, the confusion of
existing ideas concerning the domain structure of the or-
ganic world). There is also one didactic problem what
system should be followed in textbooks if the modern mega-
classification of eukaryotes is fundamentally non-stan-
dardized? The solution to this second problem is partly re-
lated to the first one and, in our opinion, it is possible to
advance in this area only by developing questions about
the rank correlation of the current system.
The present book consists of five sections, and in the in-
troductory one we highlight only the basic milestones in
the history of megaclassification thinking. The first chap-
ter generalizes the principles of the zoological and botani-
cal nomenclature codes relevant to the problem of mega-
classification. The second chapter provides a development
of the current hierarchical system of eukaryotes. The fourth
chapter analyzes current trends in the development of eu-
karyotic megaclassification, and in the final chapter it is
considered what terminological problems florists and fa-
unists face when working with intermediate groups of eu-
karyotes.
We don’t offer many nomenclatural novelties in this
book, although we point out the need to rank downgrade in
relation to some taxa. First of all, this applies to higher
taxa of fungi, metazoans, and embryophytes. The formal
lowering their ranks, from the point of view of entering the
mainstream, seems to be a rather counterproductive proce-
dure.
However, we believe that such a kind of generalization
alone is capable of casting doubt on what extent justifies a
modern classification trend to rank inflation, and whether
a global downgrading of higher taxa of multicellulars is
coming in the future.
St. Petersburg, November 7, 2022
9
INTRODUCTION
Eukaryotes are the most diverse group of living organ-
isms, dominating in most ecosystems, with the exception of
anaerobic zones. Representatives of this group are charac-
terized by: 1) the presence of a nucleus separated from the
cytoplasm by nuclear membrane; 2) DNA-based linear
(rarely circular) genome organized with the participation
of histones in the form of chromosomes; 3) cytoplasmic ri-
bosomes with a sedimentation coefficient ~80S; 4) presence
of cytoplasmic endomembrane complexes: endoplasmic re-
ticulum, Golgi apparatus, vacuoles, lysosomes, peroxiso-
mes, glyoxisomes, spherosomes. Most eukaryotes have mi-
tochondria and their absence is always secondary. Auto-
trophic eukaryotes are characterized by plastids of various
structures, acquired, like mitochondria, in the course of
symbiogenesis.
The total number of species of eukaryotic organisms
could be estimated at 8.7 million, and their real diversity
may be 1.52 times greater (Sweetlove, 2011). Eukaryotes
are the dominant and edificators of most of the Earth’s bi-
omes, the creators of reef germs in the ocean and multi-
layered vegetation on land, marine and freshwater sedi-
ment strata, and finally, the anthropogenic formations as
technosphere and urbanized environment. The technologi-
cal potential of these organisms cannot be overestimated.
Various eukaryote species represent a central object for
agricultural technology, food technology, and biotechnology
(including all industries related to biosynthesis and biore-
mediation). An increasing number of eukaryotes are beco-
ming in demand in such areas as biopharmacology and
bioengineering. Relevant in a practical respect is the crea-
tion of classification with the greatest predictive capabili-
ties for optimization a screening research.
Classification decisions adequately reflecting genealogi-
cal relationships between taxa, traditionally treated as na-
tural and declared by taxonomists as the main goal of their
work, is an issue of fundamental importance because it
leads to knowledge progression. Besides, in practice, the
heuristic power of classification approaching a natural one
10
is invaluable too, due to increasing its prognostic power,
i.e., the possibility of predicting certain properties in unex-
plored groups related in one or another aspect to the stud-
ied ones (Starobogatov, 1989). The predictive capabilities of
the phylogenetic system are associated with the idea that
the degree of divergence of groups is inversely related to
the preservation of their phenotypic features including
those that are in practical demand (Zmitrovich et al., 2007,
2022). At the large group level, a set of “prohibitions” for
the morphophysiological convergence of organisms is de-
veloped during evolution. An exact identification of such
groups opens some possibilities for predictive assessments
of varying degrees of certainty, concerning both the evolu-
tionary tendencies of organisms and some of their signifi-
cant properties in terms of applied research.
Fig. 1. A field of megasystematics and related issues with references
to work on overlapping areas: 1 Takhtadjan (1973); 2 Margulis
(1981); 3 Margulis (1983); 4 Cavalier-Smith (2002); 5 Leontyev,
Akulov (2004); 6 Zmitrovich (2010); 7 Doweld (2001); 8
Zmitrovich et al. (2021); 9 Seravin (1980); 10 Levine (1980); 11
Karpov (1990); 12 Adl et al. (2012); 13 Adl et al. (2018); 14
Wasser et al. (1989); 15 Karpov (2000); 16 Leontyev (2013); 17
Yakovlev et al. (2018).
The branch of biological classification that generalizes
knowledge about the largest subdivisions of the organic
world and, in particular, eukaryotes, was called mega-
systematics (Kusakin, Drozdov, 1994, 1997; Cavalier-Smith,
11
1997; Drozdov, 2017), although phylogenetic and classifica-
tion generalizations operating categories of phyla and
kingdoms, starting with Merezhkovsky (1910) and Chatton
(1925), was a privilege of some biologists. In the middle of
the 20th century, eukaryotic experimental systems com-
peted with each other in fundamental guides (Hall, 1953;
Chadefaud, 1960), whereas Whittaker (1969) proposed a
multi-kingdom eukaryotic system as a special object of
consideration.
The problem field of megasystematics is schematically
outlined in Fig. 1. This realm was elaborated by Russian
biologists (Kusakin, Starobogatov, 1973; Starobogatov,
1986, 1995; Kusakin, Drozdov, 1994, 1997). The heyday of
this direction falls in the period between the “ultra-
structural revolution” of the 1980s, when systematists be-
came aware of the peculiarities of the fine organization of
mitochondria, plastids, and a root system of cilium in vari-
ous groups of eukaryotes, and the “molecular revolution”
of the 2000s, when methods that make it possible to reveal
a groups divergence, and fierce disputes and extravagant
manifestations have been replaced by more or less congru-
ent molecular phylogenetic reconstructions. It was during
this period that the term “megasystematics” was gradual-
ly replaced by terms related to the problems of allocation
and ranking of “eukaryotic supergroups”.
Megasystematics Beginnings from a Historical Perspective
A trivial subdivision of the organic world into two
“pragmatic units” plants and animals goes back to
the mists of time. Linnaeus, the “father of systematics”,
legitimized this by dividing nature into the inorganic
kingdom of “stones” (Lapides) and the organic kingdoms of
plants (Vegetabilia) and animals (Animalia), “whose boun-
dary converges in zoophytes” (Linn, 1770). Fries (1821)
also proposed to distinguish the third living kingdom, the
fungi (Regnum Mycetoideum), whereas Bory de Saint-Vin-
cent (1825) singled out the coelenterates and sponges as a
separate kingdom, Regne Psychodiaire.
12
The Russian botanist Goryaninov (Horaninow, 1834,
1843), who can be designated as “first megasystematist”,I
felt a taste for the logical division of knowledge about the
characteristics of the main nature subdivisions, presented
to the public an alternative to Linnaean system, where he
distinguished two “worlds”: “Orbis elementaris, molecularis
seu anorganicus” and “Orbis organicus seu cellularis”. The
first “world” included four inorganic kingdoms (Regnum
Aethereum, Regnum Aqueum, Regnum Aereum, and Regnum
Minerale). The second world Goryaninov divided into four
kingdoms, too, namely Regnum Vegetabile (including an
expanded botanical system), Regnum Amphorganicum
Zoophyta et Phytozoa [including Fungi, Algae, Polypraii,
Ceratophyta (= Bryozoa), Creophyta (hydroid polyps)], Reg-
num Animale (rest metazoan groups), and Regnum Hominis.
Many of Goryaninov’s decisions concerning his Zoophyta
system, were, undoubtedly, influenced by the work of Ger-
man microscopist Ehrenberg (1838), who demonstrated the
beauty of the unicellular world, little known to zoologists
and botanists of his times.
In the middle of the 19th century, widely known among
naturalists were the works by Haeckel (1866, 1878, 1904),
in which organisms with mixed traits of plants and ani-
mals were proposed to be separated into a separate king-
dom, Protoctista or Protista. Moreover, if at first Haeckel
included in this new kingdom the sponges (Haeckel, 1866)
and the fungi (Haeckel, 1878), then in his last system
(Haeckel, 1904) he limited it only to unicellular and coloni-
al organisms.
At the end of the 19th century, within the plant world, it
was outlined to a separate group of pellet-like microorgan-
isms bacteria and blue-green algae in a division rank,
namely Schizophyta (Cohn, 1875), whereas Nmec (1929),
based on the nature of the cell structure of shizophytes,
opposed them as anuclear (Akaryonta),II or pre-nuclear
(Prokaryonta), vs all other nuclear (Karyonta) vegetable and
animal organisms.
Such a subdivision is accepted by most authors of the
mid-20th century, in particular Chadefaud (1960), who ac-
13
cepted these two large groups as the kingdoms of Pro-
tocaryota [with the subkingdoms of cyaneae (Cyanoschizo-
phyta) and bacteria (Bacterioschizophyta)] and Eucaryota
[with the subkingdoms of algae (Phycophyta), fungi (Myco-
phyta), shoot plants (Cormophyta), and animals (Animalia)].
Whittaker (1969) places prokaryotes in the kingdom Mo-
nera, in line with the four kingdoms of nuclear organisms:
protists (Protista), animals (Animalia), plants (Plantae), and
fungi (Fungi).
Takhtadjan (1973), on the contrary, displays prokaryotes
(Procaryota) and eukaryotes (Eucaryota) as superkingdoms,
limiting the first one to the kingdom of shizophytes (My-
chota) with the subkingdoms of bacteria (Bacteriobionta)
and cyaneae (Cyanobionta), and dividing the second one
into three kingdoms: animals (Animalia), fungi [Mycetalia,
with subkingdoms of lower fungi (Myxobionta) and higher
fungi (Mycobionta)] and plants [Vegetabilia, with subking-
doms of red algae (Rhodobionta), true algae (Phycobionta)
and higher plants (Embryobionta)].
For a more detailed overview of existing eukaryotic sys-
tems, see the Supplement section.
“Reductionist Gestures” and Experimental Systems
in Megasystematics
Since the late 1960s, using transmission and scanning
electron microscopy, a lot of new data on the structure of
eukaryotic cells have been accumulated, as well as bio-
chemical data on the composition of eukaryotic cell mem-
branes, on various biosynthetic pathways, and secondary
metabolites. A new set of characters was actively involved
in taxonomy and, in particular, megasystematics, but giv-
ing a certain taxonomic weight to one or another character
was still a subjective issue. The taxonomy of this period
was akin to art: the authors resorted to the manifestation
of new ideas and approaches, establishing of non-obvious
truths (associated with the reassessment of the taxonomic
weight of certain features) by means of certain violence
against consciousness.
14
Special attention should be paid to “reductionist ges-
tures” (reduction of a complex array of problems to simple
dichotomies), the possibility of which opens up as a result
of obtaining fundamentally new data. One of the first “re-
ductionist gestures” in megasystematics was the subdivi-
sion of eukaryotes into only two kingdoms according to the
shape of mitochondrial cristae: tubulicristata or dinobionts
(Tubulicristata = Dinobiota, mitochondrial cristae tubular)
and lamellicristates or bodonobionts (Lamellicristata =
Bodonobiota, mitochondrial cristae lamellate) (Taylor, 1978;
Stewart, Mattox, 1980). Both groups include eukaryotes of
different levels of organization, since tubular cristae are
characteristic of various groups of algae in the chromo-
phyte cycle, ciliates, several groups of heterotrophic flagel-
lates and fungus-like organisms, whereas lamellate (in the
understanding of the cited authors) cristae are characteris-
tic of higher plants, multicellular animals, euglenophytes
and a number of heterotrophic flagellates. Although later
the “lamellate” cristae of euglenoids and bodonids were
redescribed as discoid and a separate clade Discicristata
was identified (Cavalier-Smith, 2003), the variability of
lamellate and tubular cristae was established (Seravin,
1993) and heterogeneity in terms of the shape of cristae of
some monophyletic taxa was shown (Yakovlev et al., 2018),
at first, the new dichotomy attracted attention, provoked
cognitive interest, and stimulated exploratory research. In
particular, this concept was adopted by Seravin and
Starobogatov when they created their classification
schemes (Seravin, 1980; Starobogatov, 1986, 1995).
Another “reductionist dichotomy”, now already with-
standing the test of time, was the subdivision of eukaryotes
into groups of uniflagellates (Unikonts) and biflagellates
(Bikonts) (Cavalier-Smith, 2002). The former are characte-
rized by the fundamental absence of dikinetide and often
by a single-flagellated unicellular stage. Molecular evi-
dence supports this dichotomy, although both groups have
received less definite names, “shapeless” (Amorphea) in-
stead of uniflagellates and “diverse” (Diaphoretickes) in-
stead of biflagellates (Adl et al., 2012).
15
An example of a “reductionist gesture” not accepted by
the taxonomic community is the higher-rank taxon
Chrysoleucobionta described by Kusakin and Starobogatov,
uniting all groups of chlorophyll c containing algae,
oomycetes, ciliates as well as multicellular animals and
fungi (Kusakin, Starobogatov, 1973). In addition to reduc-
ing the basic subdivision of eukaryotes to the dichotomy of
“chlorobionts chrysobionts”, this forgotten taxon reflects
an idea of the easy loss of plastids in the “chrysophyte”
evolutionary line as well as the apochlorotic nature of ani-
mals and fungi (the latter idea hasn’t find further experi-
mental confirmation). However, the progressive signifi-
cance of the Kusakin Starobogatov scheme consisted in a
radical rejection of dominance within systematists in the
early 1970s, views of kingdoms as gross life forms, i.e.,
animals, plants, protists, and fungi.
A pride of place in megasystematics is taken by the
Cavalier-Smith’s experimental systems, the constant
change of which, followed by the search for preserved in-
variants, this scientist raised to the rank of a kind of cog-
nitive method. Working first at the University of British
Columbia, then at Oxford University, he liked to hold dis-
cussion sessions in the laboratories he headed. These ses-
sions also had a didactic value, since they taught students
to be critical of taxonomic constructions. The pace with
which Cavalier-Smith changed his evolutionary scenarios
was such that sometimes, over several summer conferences,
participants could observe the evolution of his ideas (Rog-
er, 2021). Cavalier-Smith’s work in the field of eukaryotic
megasystematics covers the period from 1978 to 2020, and
their analysis shows that his first systems were rather “ar-
tistic manifestations” [for example, in 1978 he derived all
eukaryotes from red algae (Cavalier-Smith, 1978),III or
from fungi (Cavalier-Smith, 1981)], wheras the latter ones
generally fit into the contours of the consensus system of
living beings (Cavalier-Smith, 1995b; 1998; Cavalier-
Smith, Chao, 2020).
16
Molecular Revolution
At the end of the 20th century, “a more pragmatic ap-
proach” (Karatygin, 1999) began to penetrate systematics,
associated with the study of taxon divergence, fixed by ex-
tracting phylogenetically significant information from a
comparative study of certain parts of the genome. The “au-
thor’s gestures” were replaced by reproducible procedures
for amplification, sequencing, alignment and comparison
of nucleotide sequences, as well as cladistic analysis. Pro-
ceeding from the obvious fact of the continuity of the DNA
flow in the generations of organisms, it became possible to
draw up a kind of “divergence protocol” for taxa through a
comparative study of the mutational saturation of compa-
rable loci of different organisms.
Starting with Woese and Fox (1977), the attention in
this regard was drawn to genes and spacers involved in
the formation of ribosomal RNA, since they are present in
all pro- and eukaryotes, determine one of the basic life-
supporting functions of the cell and are not directly related
to the functions of surface adaptive changes.
Not everyone morphosystematists, who during the entire
previous period were forced to turn to the “whole charac-
ters complex” in order to advance in understanding phy-
logeny, at first appreciated the “reductionist power” of this
new approach. Related to this, in particular, was the decla-
ration by many of them of the need for “polyphasic taxon-
omy,” i.e. using the phenotype in the broadest sense in ad-
dition to molecular evidence. Although, of course, an “addi-
tive effect” within a new to the morphosystematics seman-
tic field is conceivable only when “stories concerning di-
vergence” extracted from one locus are supplemented or
verified by “stories” extracted from another one (multi-
genetic analysis, phylogenomics).
The molecular revolution, which opened the possibility of
obtaining phylogenetically informative regions of the ge-
nome, the “divergence protocol” in the course of a compar-
ative study of nucleotide sequences, brings an objective
and more stable basis for classification. Of course, in the
area of ranking and correlating phylogenetic reconstruc-
17
tions with the Linnean hierarchy, the subjectivism still
persists. However, having data on basal and terminal ra-
diations in each reconstruction, the research community is
significantly closer to consensus on the rank and bounda-
ries of taxa. Since the 2000s, in connection with the intro-
duction of next-generation sequencing methods, eukaryotic
phylogenomics has started to progress. Moreover, as it tur-
ned out, many whole-genome phylogenetic trees turned out
to be congruent to trees built on the basis of ribosomal
cluster sequencing data.
As a result of whole-genome comparisons of representa-
tives of various eukaryotic supergroups (Cerón-Romero et
al., 2019; Strassert et al., 2021), a rather stable phylogene-
tic scheme was obtained (Fig. 2), reflecting the basic di-
chotomy (Amorphea Diaphoretickes) and including such
supergroups as Loukozoa, Amoebozoa, Opisthokonta, Dis-
coba, Cryptista, Plantae, Haptista, Rhizaria, Alveolata, and
Stramenopila (listed from basal to crown region of the phy-
logenetic tree).
Fig. 2. Phylogenetic relationships between eukaryote supergroups re-
vealed as a result of genome-wide comparisons of species samples.
The Loukozoa supergroup comprises anaerobic or micro-
aerophilic eukaryotes, some representatives with modified
nonrespiratory mitochondria (e.g. hydrogenosomes or mito-
somes), or without mitochondria. Cells are ciliated, ances-
trally with four kinetosomes per kinetid, though a great
18
variation exists; some free-living, many endobiotic, some
parasitic.
The Amoebozoa supergroup unites protozoans capable of
amoeboid locomotion with steady flow of the cytoplasm or
occasional eruptions in some groups or amoeboid locomo-
tion involving the extension and retraction of pseudopodia
or subpseudopodia with little coordinated movement of the
cytoplasm. Cells ± naked, often with well differentiated
glycocalyx. In several groups, cells are covered with a
tectum or a cuticle. Some groups are testate, i.e. enclosed
in a flexible or hard extracellular envelope with one to sev-
eral pores. Mitochondrial cristae tubular (ramicristate),
with few exceptions; mitochondria are secondarily reduced
to mitochondrion-related organelles (MRO) in archamo-
ebians. Most are only reported to be asexual, but sex and
life cycles consistent with sex have been reported in
Tubulinea, Evosea, and Discosea. Many taxa exhibit either
sporocarpic or sorocarpic sporulation. Biciliated, unicili-
ated or multiciliated stages in the life cycle of some taxa;
some taxa exhibit reduction of the bikont kinetid to a uni-
kont one.
The Opisthokonta supergroup is characterized by a sin-
gle posterior cilium without mastigonemes, present in at
least one life cycle stage or secondarily lost; a pair of kine-
tosomes or centrioles, sometimes modified; the flat (rarely
tubular) mitochondrial cristae in unicellular stage. Two
inclusive clades, Holozoa and Holomycota, comprise the li-
on’s share of euks’ species diversity. Breviatea and
Apusomonadida are sister/basal lineages (Obazoa clade =
Opisthokonta + Breviatea and Apusomonadida, see Brown et
al., 2013).
The cell body plan of the Discoba representatives is re-
duced to a dikinetid state (23 cilia or many pairs), while
usually three microtubule roots depart from a pair of
kinetosomes. Many taxa are characterized by trans-spli-
cing, i.e. the formation of a giant unsplitted transcript du-
ring RNA processing. Cells are usually large and, in dif-
ferent groups, are characterized by various particular
adaptations, such as paraxial road, kinetoplast, or undulat-
19
ing membrane. Mitochondria, if present, are with discoid,
rarely tubular cristae, but in some taxa they are reduced to
peroxisomes or mitosomes. Most species are phago-
heterotrophs, feeding on cytostomes or lobopodia, but there
are also osmotrophs and even autotrophic forms with chlo-
roplasts that have a 3-membrane envelope and chlorophylls
a and b (euglenoids). In many euglenoids, plastids are sec-
ondarily absent, but the ability to phagotrophy has also
been lost such forms feed osmotrophically (Rhabdo-
monadineae). However, some euglenoids (Peranematida) are
phagotrophs and are primarily devoid of plastids. The sex-
ual process is absent. Jakobea is a sister/basal lineage.
The Cryptista supergroup unites flagellates character-
ized by oval cells of constant shape, obliquely cut at the
anterior end, with a pronounced ventral groove, equipped
at the anterior end in the region of the pharynx with two
flagella long, bearing two rows of simple mastigonemes
and short, bearing one row of mastigonemes and two api-
cal filaments. Mitochondria having flat cristae. Plastids of
autotrophic forms contain a nucleomorph, chlorophylls a
and c, as well as a number of additional pigments
(phycoerythrin, phycocyanins). There are primary colorless
(Goniomonas) and secondarily colorless (Chilomonas) cryp-
tomonads. Katablepharids are heterotrophic flagellates, the
cell body plan of which comparable with that of
cryptomonads, but differs in a more developed digestive
apparatus, the nature of the flagellar membrane, and tubu-
lar mitochondrial cristae.
The Archaeplastida are basically biciliate (the number of
cilia varies from 0 to 16, sometimes cilia and centrioles
secondarily lost), predominantly autotrophic organisms,
the plastids of which are the result of the primary endo-
symbiosis with cyanobacteria. The root system in ciliate
forms characterized by cruciform lying of microtubular
roots. The cilia either smooth or scaly. The chloroplasts en-
velopes double membrane, photosynthetic pigments are
chlorophylls a and b, or in red algae, instead of chlorophyll
b, phycoerythrins/phycocyanins. Glaucophytes acquired cy-
anelles primarily or secondarily, but in the last case the
20
primary endosymbiont has a cyanobacterial nature too. Mi-
tochondrial cristae are predominantly flat, although some
rhodophytes have vesicular cristae. Among the arche-
plastids, all types of multicellular plant body organization
are observed, including the “crown” one, vascular plants.
The Haptista supergroup is charactirezed by microtu-
bule-based appendages (haptonema or axopodia) used for
feeding and complex mineralized (siliceous or calcareous)
scales in many species. Two major groups. Haptophytes:
autotrophic or heterotrophic flagellates have 2 (rarely 4)
smooth or rough unequal cilia at their anterior end. Be-
tween the cilia there is a filamentous structure the
haptonema which serves to attach to the substrate, move
and capture food. In contrast to the ciliar axoneme, a
transverse section of the haptoneme shows a bundle of 68
microtubules surrounded by cisterns of endoplasmic reticu-
lum. Plastids containing chlorophylls a and c as well as
fucoxanthin, are covered with a membrane of the endo-
plasmic reticulum. Mitochondria having tubular cristae.
Cells naked or covered with organic scales (Prymnesium
freshwater unicellular algae), in some marine forms with
large calcareous scales of complex structure (Coccolithus
marine unicellular algae). The life cycle alternates between
stationary and motile stages. The sexual process is not
known. Centrohelids: heterotrophic unicellular amoeboid
organisms with long radially arranged axopodia diverging
from a single center, the axoplast. The pellicle bearing
trichocysts and scale deposits of various shapes and com-
positions. Mitochondria having flat cristae. Predominantly
freshwater planktonic forms. The sexual process is not
known.
The Rhizaria supergroup unites mainly amoeboid hetero-
trophic (in some cases Chlorarachnion having an auto-
trophic eukaryotic symbiont) organisms capable of forming
the rhizopodia long, narrow and often branched pseudo-
podia. Amoeboid cells can fuse to form plasmodia. All rhi-
zarians are aerobes with mitochondria having tubular cris-
tae. In some groups, at certain stages of the life cycle, the
flagellated cells with two unequal smooth anterior cilia
21
may form. The cytostome is absent. The cell can form lo-
rica or skeletal structures penetrating the cytoplasm. In
parasitic forms, the cytoskeleton undergoes reduction, and
the plasmodia of such forms resemble the vegetative body
of some fungi. The sexual process is expressed in many
groups. Rhizaria include many soil amoebae as well as ra-
diolarians and foraminifera living in the Ocean. Of the
mycological objects related to rhizarians the group of
plasmodiophorids can be mentioned.
The Alveolata supergroup is characterized by a cortical
alveolae, sometimes secondarily lost; with ciliary pit or
micropore; mitochondrial cristae tubular or ampulliform. A
characteristic feature of many alveolate groups is cell co-
vers in the form of a pellicle with cortical alveolae and
subpellicular microtubules, or with large cisterns sur-
rounded by a membrane. Single-celled, rarely colonial,
mononucleate or multinucleate organisms, bearing, at least
at a certain stage of the life cycle, two or many cilia. The
nucleus of representatives of dinoflagellates is poor in his-
tones, in ciliates the nuclear dualism is observed. Mito-
chondria with tubular (very rarely flate or ampulliform)
cristae, in anaerobic ciliates can be replaced by hydro-
genosomes. Aquatic organisms that inhabit the Ocean and
fresh waters; a number of groups have adapted to the de-
velopment of arthropods and warm-blooded animals in the
internal environment. Endosymbiotic dinoflagellates take
part in the creation of reef biogerms.
Many representatives of diverse Stramenopila super-
group have a characteristic “visiting card” two cilia
that differ sharply from each other, and the motor one is
furnished with tripartite mastigonemes located in two
rows, while the backward cilium remains smooth. Some-
times the tail cilium is reduced (hyphochytrids) or the cell
is provided with many cilia (opalinates). In proteromonads,
both cilia are smooth, and mastigonemes are located in the
back of the cell and called somatonemata. In the transition
zone of the cilium, there are structures called single or
double helix, which are another unique feature of some
groups. Dikinetide have 4 microtubular roots. The
rhizoplast (a cross-striated cord connecting dikinetide with
22
the nucleus or mitochondria) is often expressed. The group
is represented by a variety of types of organization, i.e.
monades, amoeboid, coccoid, mycelial, filamentous,
heterotrichal, lamellar or parenchymatous; frequent coloni-
al forms. The tissue organization of brown algae has some-
thing in common with that of green and red algae con-
vergence in this case is based on the patterns of transfor-
mation of the multifilamentous thallus. The organization of
labyrinthulae is an ectoplasmic network with cells capable
of moving inside it has no convergent analogues in the
living world. Autotrophic forms contain plastids surround-
ed by a 4-membrane envelope, representing a derivative of
the red algal endosymbiont (the fourth membrane is an el-
ement of the endoplasmic reticulum that envelops the plas-
tid). The additional chlorophylls are c1 and c2, as well as
α-, β-, ε-carotenes. Opalinates and proteromonads do not
have any structures indicating a former autotrophic life
and, apparently, are primarily heterotrophic. Mitochondria
having tubular cristae. The sexual process is present or
absent.
The eukaryotic megasystem, built on the basis of
phylogenomic data, has stabilized substantially. Molecular
data also confirmed the symbiotic origin of the basic com-
ponents of the eukaryotic cell mitochondria, as well as
plastids of a number of plant phyla. It has been shown
that, despite known diversity, all mitochondria originate
from a common ancestral organelle that resulted from the
integration of an endosymbiotic alpha-proteobacterium into
a host cell from the Archaea domain. The transition from
an endosymbiotic bacterium to a permanent organelle en-
tailed a huge number of evolutionary changes, including
the emergence of hundreds of new genes and protein im-
port systems, the production of membrane transport com-
plexes, the integration of metabolism and reproduction, the
known reduction of the endosymbiont genome, and the im-
port of endosymbiont genes into the host nucleus (Roger et
al., 2017).
Among plastids, derivatives of both prokaryotes (name-
ly, cyaneae), which are associated with the primary act of
23
endosymiosis in ancestral forms of Archeplastida, and eu-
karyotes are observed. Within the latter ones, the plastids
derived from an endosymbiont close to Chlorophyta are ob-
served in Euglenoids (Discoba) as well as Chlorarachnion
(Rhizaria), whereas the plastids derived from an
endosymbiont close to Rhodophyta are characteristic of rep-
resentatives of Сryptista, Haptista, Alveolata, and
Stramenopila (Cavalier-Smith, 2002). At the same time,
there are monophyletic (Cavalier-Smith, 2002) and poly-
phyletic (Zmitrovich, 2003; Body et al., 2009) scenarios for
the origin of plastids of “red algal affinity”.
The rate of cyanelles transformation in different groups
of Archeplastida remains an unresolved problem. Thus, in
Glaucophyta, plastids are close to cyanella, while in Chlo-
rophyta they are significantly transformed. Possibly, Ar-
chaeplastida plastids are polyphyletic, too (Yakovlev et al.,
2018), and, therefore, the name of the taxon loses its mean-
ing (that is the reason why we apply the name Plantae to
this group in Fig. 2).
Where do the Kingdoms Disappear?
In the “pre-molecular period”, megasystematics was al-
so often called “a kingdoms history”, and the kingdom ca-
tegory was by no means avoided by researchers in their
constructions. However, in the modern period of a “more
pragmatic” classification, the term “kingdom” appears
more rarely. The large groups of eukaryotes, as a rule, are
currently referred to as “eukaryotic supergroups”, whereas
the rank of taxa is marked in the outline of the system with
a fixed indent number.
It must be said that the term “supergroup” was intro-
duced by Lipscomb (1989), whereas the concept of “super-
groups” took shape more or less by 2005, when Keeling
with his colleagues wrote: “Recent advances in resolving
the tree of eukaryotes are converging on a model composed
of a few large hypothetical ‘supergroups’, each comprising
a diversity of primarily microbial eukaryotes (protists, or
protozoa and algae). The process of resolving the tree in-
24
volves the synthesis of many kinds of data, including sin-
gle-gene trees, multigene analyses, and other kinds of mo-
lecular and structural characters” (Keeling et al., 2005).
The indication that “supergroups” in a certain respect are
hypotheses predetermined one of the interpretations of the
supergroup-reference as a purely new theoretical field,
fundamentally isolated from classification practice, and the
supergroups themselves should not be mixed with “tradi-
tional” taxa and, accordingly, they are fundamentally
should not have a rank. However, in practice, the super-
groups began to acquire the status of taxa, moving into
didactic and biodiversity classifiers. Taking into account
that all molecular taxa are, to some extent, hypotheses, too,
this idea is accustomed to in the classification routine.
This was facilitated by the studies of Cavalier-Smith, who
included the names of various supergroups in various edi-
tions of his systems, giving them a formal rank and some-
times changing it afterwards. The didactic literature also
did not encourage double minds regarding the eukaryotic
system and generally considered supergroups as
megataxa, for which there is no consensus in assessing the
rank.The described trend of “disappearance” of kingdoms
from the current system of eukaryotes has two main rea-
sons.
1. The first kingdoms described have united the multi-
cellular organisms, i.e. animals, plants, fungi. These are
widely diversified groups, whose subdivision on phyla (=
divisions) level occurred on grounds different from those on
which protozoologists did the same. The phylogenetic ap-
proach forces us to reconsider the rank of pools of multicel-
lular animals, plants and fungi, but tradition still does not
allow mycologists, zoologists, and taxonomists of higher
plants to downgrade their taxa lower than phylum level. In
the latest classifications, the number of phyla does not only
decrease, but often it extensively increases (Tedersoo et al.,
2018; Laumer et al., 2019). However, while maintaining the
unshakable kingdom rank on terminal branches of the eu-
karyotic tree, we inevitably come to inflation of the clades
ranks in its medial and basal parts. So, in the case of con-
sideration of Fungi in a kingdom rank, it would be neces-
25
sary to increase the rank of Opisthokonta and, that is more
importantly, the rank of such groupings as Discoba,
Cryptista, Alveolata, Stramenopila, which seems to be hardly
justified. The situation is no better with higher plants
(Embryophyta), whose phylogenetic status corresponds at
best to the class rank, and an increase in its rank inevita-
bly leads to a distortion of the entire phylogenetic radia-
tion of Archeplastida.
2. The second reason seems to be more universal. The
authors intuitively avoid rank designating, since the rank-
ing of even the lineages of molecular cladogram has not
yet been clearly formalized. The concept of rank itself re-
fers to the taxonomic hierarchy developed during the early
Linnaean period (Linnaeus, 1753; De Candolle, 1824). The
hierarchical subordination of categories is didactically
convenient and good for formal logical division, which is
the reason for the preservation of the “Linnean hierarchy”
to date.
The evolutionary understanding of biodiversity as a “re-
cent slice” of the phylogenetic tree in principle did not de-
prive an idea of subordination of Linnaean categories,
since the higher categories could be interpreted as a reflec-
tion of the relationship of basal branches, whereas the spe-
cies category could be interpreted as the terminal branch
of the phylogenetic tree. However, in contrast to molecular
taxonomy with its “objectivist” methodological arsenal,
which makes it possible to unambiguously interpret the
revealed order of branching of the phylogenetic tree, the
ranking of taxa remains a haven for subjective assess-
ments (Vasilyeva, 1999). There is no one-to-one correspond-
ence between the logical division of the “Linnean hierar-
chy” and the order of branching of the phylogenetic tree,
revealed by molecular methods, because a real phylogenet-
ic tree (by analogy with a woody plant) is the result of
random elimination of branches, therefore, the structure of
its crown region is not strictly dichotomous.
A comprehension by some taxonomists of this discrepan-
cy led them to call for the rejection of the “Linnean hierar-
chy” as a whole (Cantino, de Queiroz, 2003). But such a
26
refusal does not have sufficient distribution, both for
pragmatic and didactic reasons. Therefore, the taxonomic
community tries to work in the situation of the “Linnean
hierarchy” even after this hierarchy has revealed its pov-
erty (Ereshefsky, 2007).
The rank coordination by various authors is carried out
in one way or another, based on: 1) the nature of the taxa
set, and 2) the flexibility of the authors and their readiness
for use, along with the basic, also the intercalary taxonom-
ic categories. At the same time, the most common mistake
made in cladogram ranking is the postulation of the con-
gruence between the basic phylogram dichotomies and the
basic categories of a “Linnean hierarchy”. This error is a
consequence of the formal understanding of taxonomic ca-
tegories: both speciation and higher taxa formation are a
consequence of the elimination of a part of the spectrum of
ecotypic polymorphism, which is principally a stochastic
process.
In our opinion, it would be more justified to correlate
the basic categories of the “Linnean hierarchy” with large
phylogenetic radiations, i.e. with parts of the phylogram
with the highest concentration of nodes within one “zone”.
Wherein, the terminal radiation, obviously, would well cor-
respond to the taxon of a lower rank, whereas the basal
one, would well correspond to the taxon of a higher rank.
Concerning distant nodes, obviously, it would be more rea-
sonable its “apply up” to the nearest radiation, than as-
sign them a formally equal rank (e.g., Cryptista as a part
of Plantae rather than a sister group of Plantae). Basing on
these general considerations, we can say that further stabi-
lization of the eukaryotic system is impossible without a
development of formalized approaches to assessing the
rank of taxa.
Attempts to Clarify the Higher Rank Nomenclature
Seeing the rules of botanical nomenclature apply to taxa
not higher than the phylum (division) level (in zoological
nomenclature, not higher than a family), the botanical
27
megaclassifications of eukaryotes were more accurate in
terms of unifying the terminations of taxa names, that al-
lows the reader to make an assessment of their rank. The
botanist Zerov (1972) coordinated nomenclatural and taxo-
nomic considerations, believing that phyla are the highest
classification category that makes it possible to represent
the phylem of the organic world. Therefore, he did not fo-
cus on categories above the phylum (division), highlighting
three out-of-rank groups, Acytobionta (viruses), Procaryota
(phyla Cyanophyta and Bacteriophyta), and Eucaryota,
where he included two large animal phyla (Protozoa and
Metazoa) and 14 plant phyla (Myxomycota, Chytridiomycota,
Eumycota, Saprolegniomycota, Xanthophyta, Chrysophyta, Di-
atomophyta, Phaeophyta, Pyrrophyta, Cryptophyta, Eugleno-
phyta, Chloromonadophyta, Rhodophyta, and Chlorophyta
with subdivisions Chlorophycophytina, Anthocerotophytina,
Bryophytina, Psilophytina, Lepidophytina, Sphenophytina,
Pterospermophytina, Gymnospermophytina).
Zoologist Starobogatov (1991) proposed to unify the
terminations for the higher taxonomic categories in a
manner, continuing the unification of terminations that ex-
ists in the application to taxa of lower ranks in the Code of
Zoological Nomenclature. Of special interest to us are the
Starobogatov’s terminations applied to taxa above a class
rank:
classis: -iodes;
superclassis: -idees;
subphylum: -ozoines;
phylum: -ozoes;
superphylum: -ozoacei;
subregnum: -ionti;
regnum: -ontes.
In 1986, Starobogatov applied his classification with the
establishment of the kingdoms Rhodymeniontes, Mycota,
Cryptomonadontes, Euglenontes, Plantae, Animalia, Ellip-
soidiontes, Peridiniontes, Chromulinontes. The names of
practically all the kingdoms distinguished were unified at
their termination and typified (i.e., based on a certain ge-
nus, as it is recommended by the Code of Botanical No-
menclature for taxa up to division rank, however, the bo-
28
tanical code allows to keep also non-typified descriptive
names, such as Gymnospermae, Angiospermae, etc.).
Kusakin and Drozdov (1994) went even further and typi-
fied the names of almost all eukaryotic kingdoms. Their
terminations system has been modified. The unified termi-
nation at the kingdom level was -bionta, but they left the
terminations of taxa with a lower rank the way they devel-
oped historically. In total, Kusakin and Drozdov identified
11 eukaryotic kingdoms: Microsporobionta, Archemonado-
bionta, Rhodobionta, Cryptobionta, Euglenobionta, Dinobion-
ta, Chromobionta, Chlorobionta, Mycobionta, Inferiobionta (=
Parazoa), and Metazoa. Later (Kusakin, Drozdov, 1998), the
authors changed the terminations for kingdom-rank taxa to
-biontes, whereas the kingdom names Dinobionta and
Chromobionta were changed to Alveolates and Heterokontes,
respectively.
Another, rather consistent in its own way, approach was
proposed by Rotschild and Heywood (1988), who suggested
that all phyla of unicellular (and apparently related weakly
differentiated multicellular groups) eukaryotes be labeled with
the termination -protista. To date, when a polyphyletic group-
ing, Protista, was excluded from classification practice, this
approach has obviously lost its relevance.
The past two and a half decades have shown that typified
and unified names do not take root well in the taxonomy of
eukaryotes, and that higher taxa of eukaryotes are named
using “zoological” in spirit nomenclatural solutions. Basi-
cally, these are descriptive names with non-fixed termina-
tions, and, in order to avoid word creation, the earliest of
those described or the most famous is taken as a basis.
By no means do we aim to re-attempt the unification of
the names of the higher taxa of eukaryotes. Knowing how
unpredictable the mainstream is, we consider attempts of
this kind to be counterproductive. We just tried to reduce
the existing names into ranked (in accordance with current
taxonomic ideas) list, and for a number of taxa only re-
commend an increase or decrease in their rank, which
seems to have taxonomic and didactic significance.
29
CHAPTER 1
NOMENCLATURAL
PRINCIPLES
AND METHOD
OF PRESENTATION
30
31
Despite the ongoing talk about the transition to the phy-
locode (Cantino, de Queiroz, 2003), in practice, the clas-
sification of eukaryotes is based on the Zoological and Bo-
tanical codes of nomenclature, although only in part, since
these codes apply to the names of lower- and middle-rank
taxa (zoological code up to family level, botanical up
to division level). At the phylum (division) level, these rules
turn out to be useful (especially when lowering the rank of
phyla to subphyla, superclasses, classes), but for names
above the phylum-rank, taxonomists try to adhere to the
“zoological” principles names creation, using well-known
descriptive ones, not “spoiled with” invented unified ter-
mination.
The International Code of Zoological Nomenclature (Ri-
de et al., 2000) provides, in essence, very little information
of interest to us. First of all, this Code says that it regu-
lates the names of taxa in the family group, genus group
and species group, and only in some, the most general
form, can give extensions to the naming of higher taxa (Art
1.2). In particular, such names had to be published after
1757 (Art. 11.1), be printed in the obligatory use of the La-
tin alphabet (Art. 11.1), and hyphens, diacritics as well as
letters such as j, k, w, and y were allowed in the original
description (Art 11.2), however, the word itself may not be
purely Latin, but Greek, combined, and even an anagram,
the main thing is that it should be given a latinized form
by the Latin termination (Art. 11.3). This name must ini-
tially be accompanied by a description or differential diag-
nosis from which the described taxon can be distinguished
from others (Art. 13.1.1), followed by a bibliographic refer-
ence to the original source (Art. 13.1.2), or proposed as a
replacement name (Art. 13.1.3). Concerning the language
of the original description, the Code only recommends that
this language be widely known to zoologists (Rec. 13B).
The valid name of a taxon is the oldest available name ap-
plied to it, unless that name has been invalidated (Art.
23.1). Modern names (published after 1950) must not con-
tain diacritics and ligatures (Art. 27), and the supraspecies
name must always be uninomial and must always begin
with a capital letter (Art. 28). The authorship of the name
32
of a nominal taxon within a family group, genus group, or
species group is not affected by the rank in which it is
used (Art. 50.3.1). Strictly speaking, this rule applies to the
family group, but in practice, zoologists use the same
principle for higher taxa, which retain the authorship of
the original describer of the corresponding name, despite
its changed rank.
From these excerpts it can be understood that the Zoo-
logical Code doesn’t give any indication of the unification
of the terminations of the names of taxa with higher than a
family rank, nor the need for their typification. Only gen-
eral requirements remain for the names of the higher
ranks, e.g., to be typed in Latin without diacritics, to be
one word, a noun and a derivative of Latin or Greek (alt-
hough neologisms, anagrams are also possible if they meet
the aforementioned requirements). Of practical importance
are the provisions on the preservation of name authorship
regardless of its rank, as well as the possibility of typing
the names of taxa of higher ranks both in lowercase with
the first capital and in full capital letters.
It should be noted that the requirement for the language
of diagnosis in the Zoological Code is more flexible and
moved out of the article into a [non-binding] recommenda-
tion (13B), but even in this form does not indicate any one
language (“Authors should publish diagnoses of new taxa
in languages widely used internationally in zoology”). This
allows, for example, taxa that have appeared in the Rus-
sian-language literature not to be rejected for nomencla-
tural reasons.
More useful information for our purposes is provided by
the Botanical Code, or, in modern sound, the International
Code of Nomenclature for algae, fungi, and plants (Tur-
land et al., 2018).
The provisions of the Botanical Code apply to all organ-
isms traditionally considered to be algae, fungi or plants,
whether fossil or non-fossil, including blue-green algae
(cyanobacteria), chytrids, oomycetes, slime molds (but ex-
cluding microsporidia), and photosynthetic protozoans
(Preamble). The main ranks of “botanical” taxa in de-
scending order are: kingdom (regnum in Latin), division
33
(divisio, phylum), class (classis), order (ordo), family
(familia), genus (genus), and species (species) (Art. 3.1). If
more taxa ranks are desired, terms for them are created by
adding the prefix “sub-“ to terms denoting primary or sec-
ondary ranks. Thus, an organism can be assigned to taxa
in the following ranks (in descending order): kingdom
(regnum), subkingdom (subregnum), division or phylum
(divisio or phylum), supdivision or subphylum (subdivisio or
subphylum), class (classis), subclass (subclassis), order
(ordo), suborder (subordo), family (familia), subfamily
(subfamilia), tribe (tribus), subtribe (subtribus), genus (ge-
nus), subgenus (subgenus), section (sectio), subsection (sub-
section), series (series), subseries (subseries), species (spe-
cies), subspecies (subspecies), variety (varietas), subvariety
(subvarietas), form (forma) and subform (subforma) (Art.
4.2). Additional ranks may be added to aforementioned,
provided this does not lead to confusion or error (Art. 4.3).
The application of taxa names higher or lower to the
family rank is determined by nomenclatural types. The use
of taxa names of higher ranks is also determined by no-
menclatural type, when the names are derived from the
generic name. The principle of typification does not apply
to names of taxa above the rank of family, with the excep-
tion of names that are automatically typified, being de-
rived from generic names whose type is the same as that of
the generic name (Art. 7.1).
The valid name publication in various groups of plants
and fungi is treated as beginning at various “starting
points” [the main part of species names of algae, ferns,
sphagnum mosses and liverworts start from Linnaeus
(1753), whereas supra-generic names of ferns start from
Jussieu (1789), valid green mosses names start from Hed-
wig (1801), fossil plants (with the exception of diatoms)
start from Sternberg (1820)] (Art. 13.1) The names of non-
fossil fungi have a starting point from Linnaeus (1753)
(Art. F.1.1), although the hymenomycetes names sanctioned
by Fries (1821) and the gasteromycetes names sanctioned
by Persoon (1801) are conserved against earlier post-Lin-
naean names.
34
The original spelling of the name or epithet must be
preserved, except for the correction of typographical or
spelling errors and standardization (letters and ligatures
alien to classical Latin, transposition between u/v, i/j or
eu/ev, diacritics, terminations, intentional latinization,
compound forms, hyphens, apostrophes and dots) (Art. 60).
The name of a taxon above family rank is represented as
a plural noun and is capitalized (Art. 16.1). Such names
may either be automatically typified names (Art. 10.10)
formed from a generic name in the same way as a sur-
name, by adding an appropriate rank termination preceded
by the connecting vowel o- if the termination begins with a
consonant. Or they are descriptive names, not formed in
such a way, which can be used without change at different
ranks (here we can see a certain echo in the Zoological
Code). For automatically typified names, the division or
subdivision name that includes the type name, as well as
the subclass name that includes the type of adopted class
name, as well as the suborder name that includes the type
name must be derived from the same generic name as its
corresponding higher name. The division (phylum) name
has a termination -phyta, unless it refers to fungi, in which
case the termination is -mycota; the subdivision (subphy-
lum) name has a termination -phytina, unless it refers to
fungi, in which case the termination is -mycotina. The
name of the class of algae has a termination -phyceae,
whereas in the subclass the termination is -phycidae. The
name of the class of fungi has a termination -mycetes,
whereas in the subclass the termination is -mycetidae. The
name of the class in embryophytes has a termination -op-
sida, whereas in the subclass the termination is -idae (but
not -viridae) (Art. 16). Automatically typified names that do
not follow this rule are subject to correction without chang-
ing the author or date of publication. However, if such
names are published with a non-latinized termination, they
will considered as not validly published. At the same time,
the terms “division” and “phylum” and their equivalents
in modern languages are interpreted as referring to the
same rank (Art. 3.1, note to Art. 17).
35
In higher-order taxa names, the word elements -clad-, -
cocc-, -cyst-, -monad-, -mycet-, -nemat-, or -phyt-, which are
the genitive singular of the stems of the second part of the
name of the included genus, may be omitted before the suf-
fix indicating rank. Such names are automatically typified
when their origin is obvious or specified in the protologue.
The principle of precedence does not apply above a family
rank (Art. 16).
In order to be officially published, the name of a new
taxon (excluding algae and fossils) published between Jan-
uary 1, 1935 and December 31, 2011 inclusive, must be ac-
companied by a description or diagnosis in Latin, or a ref-
erence to a previously and effectively published A Latin
description or diagnosis, while to be officially published,
the name of a new taxon published on or after January 1,
2012, must be accompanied by a Latin or English descrip-
tion or diagnosis, or a reference to a previously and effec-
tively published Latin or English description or diagnosis
(Art. 39).
Applications for recognition as nomenclatural reposito-
ries of organisms other than fungi must be addressed to
the General Committee, which will forward the application
to the Registration Committee and take action on his rec-
ommendation. Until such a recommendation is made, the
mechanisms and conditions for registration, as well as the
definition of scope, will be developed in consultation be-
tween the applicant, the Registration Committee and the
Permanent Nomenclature Committee for the relevant
group, and will be widely publicized in the taxonomic
community. Registration can be proactive and/or synchro-
nous and/or retrospective; that is, it may occur before
and/or simultaneously with and/or after the actual publica-
tion of a nomenclature novelty or the actual publication of
any nomenclature act (Art. 42). To be validly published,
nomenclatural innovations applying to organisms treated
as fungi (including fossil fungi and lichen-forming fungi)
published on or after January 1, 2013 must include a re-
ference in the protologue to an identifier issued for the
name by a recognized repository (Art. F.5.1).
36
Finally, if any taxon originally assigned to a group not
covered by the Botanical Code is considered to be an algae
or a fungus, any of its names need only satisfy the re-
quirements of the other relevant Code that the author has
used to obtain the status equivalent to a valid publication
under other than this Code. The Code used by the author is
determined by internal evidence, regardless of any claim
by the author about the group of organisms to which the
taxon belongs. However, a name created in zoological no-
menclature in accordance with the Coordination Principle
cannot be officially published under this Code until it ac-
tually appears in publication as an accepted name of a
taxon (Art. 45.1). The name of a taxon treated as a fungus
published on or after January 1, 2019 is invalid if it is a
later homonym of a prokaryotic or protozoan name (Art.
F.6.1). For the last article some minor revisions to the
wording were proposed with the addition of some examples
(May et al., 2019).
Thus, the Botanical Code gives us the opportunity to op-
erate with taxa at a level below the phylum and above the
class. Below the class lies an area of little interest for
megasystematics, whereas between the class and the phy-
lum of multicellular plants and fungi, a great deal of work
remains to be done for higher-rank taxonomists, given that
nowadays’s ranks of Chloroplastida subdivisions are unrea-
sonably raised. First of all, the Botanical Code clearly pre-
scribes taxonomic categories (phylum, class…), recommends
the formation of intercalary categories associated with
rank reduction, but also does not exclude other (non-
regulated) interstitial categories. In this regard, it seems
to us that the intercalary category of the superclass is very
promising at current state of our knowledge; the unifica-
tion of the terminations marking them for different groups
of botanical objects was proposed by Moore (1974):
fungi: -mycia;
algae: -phycia;
cormophytes: -itia.
Secondly, the Botanical Code allows untypified names
above the family level, which, however, are also subject to
37
terminations unification. This is an important circumstan-
ce that makes it possible not to typify such widely known
names as Ascomycota, Basidiomycota, Rhodophyta, Embryo-
phyta. That does not prevent giving them standardized
terminations when raising or lowering their rank. Chang-
ing the name to a typified one is thus optional and makes
sense only when the taxon strongly associated with a cer-
tain descriptive name has split into several taxa of the
same rank, as happened, for example, with the Zygomycota.
Thirdly, the Botanical Code gives clear references to
needed name features (in its basic provisions resembling
the Zoological Code). There are some specifics associated
with names of organisms treated as Fungi. So, Microspo-
ridia, despite the fact that they are often classified as part
of Fungi, are fundamentally declared to be not subject of
the Botanical Code. In addition, from January 1, 2013, all
newly described fungal taxa (including taxa of higher
rank) must be accompanied by a registration number,
which is not required for other taxa whose naming is regu-
lated by the Botanical Code.
Since the naming of taxa above the phylum level is not
covered by the Botanical Code, although the latter leads to
accuracy in rearrangements between phylum and class
levels, the naming of taxa having kingdom and supra-
kingdom rank seems to be closer in spirit to the decisions
of the Zoological Code first of all, an independent from
the rank association of taxon authorship with correspond-
ing name and an absence of requirement to terminations
unification. It is these principles that we propose to be
guided by in anyone revision of the eukaryotic
megasystem.
In the following outline of the eukaryotic system, we de-
note the rank of a taxon by a fixed number of indentations
filled with black circles (•). In addition, we recommend a
taxon rank with a representation of the Latin rank name
(dominium, subdominium, regnum, intraregnum, subregnum,
superphylum, phylum, subphylum, superclassis, classis, sub-
classis, ordo). The tilda symbol (~) indicates that the au-
thors do not insist on a clear binding of a taxon to a given
38
rank, but consider such an association to be the most justi-
fied. In most cases, we do not descend below the phylum
level in the system overview, but in some groups where an
explicit rank lowering of taxa is required, we descend to
the class level, and sometimes even lower (for example, to
show the “address” of plasmodiophorids in the modern
system; in fact, the rank of this group has been demoted
from the of phylum level to the subclass one). In the
Amoebozoa kingdom, to demonstrate the transfers of taxa
in recent decades, we reveal which orders each major class
contains.
For groups that were described with reference to both
nomenclatural codes (myxomycetes, phytomastigophorea),
we try to use the principles of the Botanical code to the
phylum level, the advantage of which in this case is that it
recommends standardized terminations up to the level in
question. Above the level of phyla, we, on the contrary, ad-
hered to the Zoological code, in particular, the principle of
fixed taxon authorship. In marginalia, we report the rank
of the first described taxon.
In the superscript, after the authorship of the taxon,
there is a footnote in Arabic numerals, unfolding in margi-
nalia. Typically, a footnote always contains a bibliographic
reference. Footnotes in Roman numerals refer to the
“Notes” section.
39
CHAPTER 2
AUTHORS’ OVERVIEW
OF THE CURRENT
EUKARYOTIC SYSTEM
40
41
In the following system, we give certain changes in
comparison with the current July Internet-version of our
system (Zmitrovich et al., 2022b). This is due to the funda-
mental discovery of the team Tikhonenkov et al. (2022),
who described a new Provora group basal to the TSAR. The
latter grouping thus became more knocked down within the
gross eukaryotic tree, like such multifurcations as
Amoebozoa, Obazoa, and Discoba. Accordingly, we here
equalize the mentioned groupings in their rank by picking
up such supergroups as Stramenopila, Alveolata, Rhizaria,
Haptista, Telonemia, Provora, and Hemimastigophora into
the TSAR supergroup and adapting the Cavalier-Smith’s
name Chromalveolata for the latter. In addition, we have
combined Cryptista and Archaeplastida into a single Plan-
tae supergroup. (Since both of these “gestures” are rather
experimental in the rank correlation field, we have left a
consensus range of supergroups in our Internet eukaryotes
overview). Besides, here we change the name of the
metagroup Opimoda to Obimoda (given that it includes the
entire grouping as Obazoa), and we changed the name of
the Diaphoretickes metagroup to Diphoda, since even in the
July system we included the Discoba into Diaphoretickes.
We designated the rank-estimating names in the Latin
spelling. The rank in which the names were first described
as a rule is given in marginalia.
Dominium EUKARYOTA R.T. Moore1
1 Moore (1974)
~Subdominium OBIMODA
subdom. nov.2
2 see Note IV for a formal diagnosis
~Regnum Loukozoa Caval.-Sm.3
3 corresponded to the phylum Loukozoa
(Cavalier-Smith, 1999)
~Phylum Malawimonadea
Caval.-Sm.4
4 corresponded to the class Malawimonadea
(Cavalier-Smith, 2003)
~Phylum Metamonadea
Corliss5
5 Corliss (1984)
~Classis Anaeromonadea
Caval.-Sm.6
6 Cavalier-Smith (1997)
~Classis Trichomonadea
Kirby7
7 Kirby (1947)
~Regnum Amoebozoa Corliss8
8 described at the phylum rank (Corliss, 1984)
~Phylum Lobosa Schultze9
9 described at the order rank (Schultze, 1854)
~Classis Tubulinea Smirnov
10 Smirnov et al. (2005)
42
et al.10
~Ordo Euamoebida Lepsi11
11 Lepi (1960)
~Ordo Arcellinida Kent12
12 Kent (1882)
~Ordo Leptomyxida
Pussard et Pons13
13 Pussard, Pons (1976)
~Ordo Nolandida Smirnov
et al.14
14 Smirnov et al. (2011)
~Ordo Echinamoebida
Caval.-Sm. et al.15
15 Cavalier-Smith et al. (2004)
~Classis Discosea Caval.-
Sm. et al.16
16 Cavalier-Smith et al. (2004)
~Ordo Flabellinia Smirnov
et al.17
17 Smirnov et al. (2005)
~Ordo Longamoebia
Smirnov et al.18
18 Smirnov et al. (2011)
~Phylum Conosa Caval.-Sm.19
19 described at the subphylum rank (Cavalier-
Smith, 1998)
~Subphylum Variosea
Caval.-Sm.20
20 Cavalier-Smith et al. (2004)
~Classis Varipodida
Caval.-Sm.21
21 Cavalier-Smith et al. (2004)
~Classis Phalansteriida
Hibberd22
22 described at the order rank (Hibberd, 1983)
~Classis Holomastigida
Lauterborn23
23 described at the order rank (Lauterborn,
1895)
~Subphylum Archamoebae
Caval.-Sm.24
24 described at the infraphylum rank (Cava-
lier-Smith, 1998)
~Classis Mastigamoebida
Caval.-Sm.25
25 Cavalier-Smith (2013)
~Classis Pelobiontida
Caval.-Sm.26
26 Cavalier-Smith (2013)
~Subphylum Mycetozoa de
By27 ex Rostaf.28
27 De Bary (1859); 28 Rostafinsky (1875)
~Superclassis Dictyostelio-
mycia ined.
~Classis Acytosteliomycetes
(Sheikh et al.) ined.29
29 described at the order rank (Sheikh et al.,
2018)
~Classis Dictyostelio-
mycetes Doweld30
30 Doweld (2001)
~Superlassis
Ceratiomyxomycia ined.
~Classis Protosporan-
giomycetes ined.31
31 Corresponded to the clade
Protosporangiida (Adl et al., 2012)
~Classis Ceratiomyxo-
mycetes D. Hawksw., B. Sutton et
Ainsw. in Leontyev et al.32
32 Leontyev et al. (2019)
~Superclassis Myxogaste-
romycia ined.33
33 Corresponded to Myxogastria (Cavalier-
Smith, 2013)
43
~Classis Liceomycetes
ined.34
34 Corresponded to subcl. Lucisporidia
(Leontyev et al., 2019)
~Classis Physaromycetes
Doweld35
35 Doweld (2001)
~Regnum Obazoa Brown et al.36
36 Brown et al. (2013) as unranked clade
~Intraregnum Opisthokonta
Copeland37
37 described at the phylum rank Copeland
(1956)
~Subregnum Holomycota Liu
et al.38
38 Liu et al. (2009) as unranked clade
~Superphylum Cristidiscoidea
Caval.-Sm.39
39 described at the class rank (Cavalier-
Smith, 1998)
~Phylum Fonticulida ined.
~Phylum Nucleariida ined.40
40 Tedersoo et al. (2018)
~Superphylum Zoosporia
ined.41
41 Torruella et al. (2018) as unranked clade
~Phylum Opisthosporidia
ined.42
42 Corresponded to superphylum
Opisthosporidia (Karpov et al., 2014)
~Phylum Eumycota Arx43
43 Arx (1967)
~Subphylum Chytridio-
mycotina Caval.-Sm.44
44 Cavalier-Smith (2013)
~Superclassis Chytridio-
mycia ined.
~Superclassis Monoble-
pharomycia ined.45
45 Corresponded to Monoblepharomycota
Doweld (2001)
~Superclassis Neocalli-
mastigomycia ined.46
46 Corresponded to Neocallimastigomycota
Hibbett et al. (2007)
~Subphylum Olpidiomycotina
ined.47
47 Corresponded to Olpidiomycota Doweld
(2013)
~Subphylum
Sanchytriomycotina ined.48
48 Corresponded to Sanchytriomycota Galin-
do et al. (2021)
~Subphylum
Blastocladiomycotina ined.49
49 Corresponded to Blastocladiomycota
James et al. (2021)
~Subphylum
Basidiobolomycotina ined.50
50 Corresponded to Basidiobolomycota
Doweld (2001)
~Subphylum
Zoopagomycotina ined.51
51 Corresponded to Zoopagomycota sensu
Spatafora et al. (2016)
~Superclassis Entomo-
phthoromycia ined.52
52 Corresponded to Entomophthoromycota
Humber (2012)
~Superclassis
Kickxellomycia ined.53
53 Corresponded to Kickxellomycota Tedersoo
et al. (2018)
~Subphylum Glomero-
mycotina ined.54
54 Corresponded to Glomeromycota Schuler
et al. (2001)
~Subphylum Phycomycotina
ined.55, V
55 Corresponded to Mucoromycota Doweld
(2001)
~Superclassis Phycomycia
ined.
~Superclassis Mortierel-
lomycia ined.56
56 Corresponded to Mortierellomycota
Tedersoo et al. (2018)
44
~Superclassis Calcarispori-
ellomycia ined.57
57 Corresponded to Calcarisporiellomycota
Tedersoo et al. (2018)
~Dikaryomycotina ined.58, VI
58 Corresponded to Dikarya (Hibbett et al.,
2007)
~Superclassis
Entorrhizomycia ined.59
59 Corresponded to Entorrhizomycota (Bauer
et al., 2015)
~Superclassis Basidiomycia
ined.60
60 Corresponded to Basidiomycota (Moore,
1980)
~Superclassis Ascomycia
ined.61
61 Corresponded to Ascomycota (Cavalier-
Smith, 1998)
~Subregnum Holozoa Lang62
62 as unranked clade (Lang et al., 2002)
~Superphylum Ichtyosporea
Caval.-Sm.63
63 at the class rank (Cavalier-Smith, 1998)
~Superphylum Pluriformea
Hehenberger et al.64
64 as unranked clade (Lang et al., 2002)
~Phylum Corallochytrea
Caval.-Sm.65
65 at the class rank (Cavalier-Smith, 1998)
~Phylum Syssomonadea
ined.66
66 as unranked and unnamed clade
(Tikhonenkov et al., 2020)
~Phylum Filozoa Shalchian-
Tabrizi et al.67
67 as unranked clade (Shalchian-Tabrizi et
al., 2008)
~Subphylum Filasterea
Shalchian-Tabrizi et al.68
68 as unranked clade (Shalchian-Tabrizi et
al., 2008)
~Subphylum Choanozoa
Caval.-Sm.69
69 corresponded to phylum Choanozoa (Cava-
lier-Smith, 1981)
~Superclassis
Choanoflagellatea Caval.-Sm.70
70 corresponded to class Choanflagellatea
(Cavalier-Smith, 1998)
~Superclassis Metazoa
Haeckel71
71 Corresponded to subkingdom Metazoa
(Haeckel, 1874)
[rank lowering needed]
Porifera Grant72
72 Corresponded to phylum Porifera (Grant,
1836)
[rank lowering needed]
Eumetazoa Btschli73, VII
73 Corresponded to superdivision Eumetazoa
(Btschli, 1910)
[basal clade intraregnum?]
Breviatea Caval.-Sm.74
74 Cavalier-Smith (2013)
[basal clade intraregnum?]
Apusomonadida Caval.-Sm.75
75 Cavalier-Smith (2013)
~Regnum Crumalia regnum
nov.76
76 see Note VIII for a formal diagnosis
~Phylum Mantamonadea77, IX
77 Corresponded to the order Mantamonadida
Glcksman et al. (2010)
~Phylum Rigifilidea78, X
78 Corresponded to the order Rigifilida
Yabuki et al. (2013)
~Phylum Collodictyonidea79, XI
79 Corresponded to the class Diphyllatea
Cavalier-Smith (2003)
~Subdominium DIPHODA De-
relle et al.80
80 as unranked clade (Derelle et al., 2015)
~Regnum Discoba Simpson in
81 as unranked clade (Hampl et al., 2009)
45
Hampl et al.81
~Superphylum Percolozoa
Caval.-Sm.82
82 at the phylum rank (Cavalier-Smith, 1991)
~Phylum Pharyngomonada
Caval.-Sm. et Nikolaev83
83 at the subphylum rank (Cavalier-Smith,
Nikolaev, 2008)
~Phylum Tetramitia Caval.-
Sm.84
84 at the subphylum rank (Cavalier-Smith,
1993)
~Classis Lyromonadea
Caval.-Sm.85
85 Cavalier-Smith (1993)
~Classis Heterolobosea
Page et Blanton86
86 Page, Blanton (1985)
~Superphylum Euglenozoa
Caval.-Sm.87
87 at the kingdom rank (Cavalier-Smith, 1981)
~Phylum Kinetoplastea
Honigberg88
88 at the class rank (Honigberg, 1963)
~Phylum Diplonemia Caval.-
Sm.89
89 at the superclass rank (Cavalier-Smith,
1993)
~Phylum Euglenophyta
Pascher90
90 Pascher (1931)
~Phylum Symbiontida ined.91
91 as unranked clade Yubuki, Leander (2018)
~Superphylum Jakobea
Caval.-Sm.92
92 at the class rank (Cavalier-Smith, 1997)
~Phylum Jakobida Leontyev93
93 Leontyev (2013)
~Phylum Tsukubea Caval.-
Sm.94
94 at the class rank (Cavalier-Smith, 2013)
~Regnum Plantae Haeckel95
95 Haeckel (1866)
~Subregnum Cryptista Adl et
al.96
96 as unranked clade (Adl et al., 2018)
~Superphylum Palpitomonada
ined.97
97 corresponded to the Palpitomonas lineage
(Yabuki et al., 2014)
~Superphylum Cryptomonada
ined.98
98 corresponded to the phylum Cryptophyta
(Silva, 1962)
~Phylum Cryptophyta Silva99
99 Silva (1962)
~Phylum Cyathophyta ined.100
100 corresponded to the family
Cyathomonadaceae (Pringsheim, 1944)
~Phylum Katablepharido-
phyta N. Okamoto et I. Inouye101
101 Okamoto, Inouye (2005)
~Subregnum Archaeplastida
Adl et al.102
102 as unranked clade (Adl et al., 2005)
~Superphylum Glaucophyta
Adl et al.103
103 as unranked clade (Adl et al., 2005)
~Phylum Glaucocystophyta104
104 Kies, Kremer (1986)
~Superphylum Rhodophyta
Karpov105
105 Karpov (1990)
~Phylum Rhodelphidiophyta
Gavryluk et al.106
106 Gawryluk et al. (2019)
~Phylum Cyanidiophyta107
107 Merola et al. (1981)
~Phylum Proteorhodophyta
108 corresponded to the subphylum
46
ined.108
Proteorhodophytina (Munoz-Gomez et al.,
2015)
~Phylum Eurhodophyta
ined.109
109 corresponded to the subphylum
Eurhodophytina (Saunders, Hommersand,
2004)
~Superphylum Chloroplastida
Adl et al.110
110 as unranked clade (Adl et al., 2005)
~Phylum Prasinodermophyta
Li et al.111
111 Li et al. (2020)
~Classis Prasinodermo-
phyceae Li et al.112
112 Li et al. (2020)
~Classis Palmophyllo-
phyceae Leliaert et al.113
113 Leliaert et al. (2016)
~Phylum Chlorophyta
Pascher114
114 Pascher (1914)
~Subphylum Chlorodendro-
phytina ined.115
115 corresponded to the class
Chlorodendrophyceae (Masyuk, 2006)
~Subphylum Pedinophytina
ined.116
116 corresponded to the class Pedinophyceae
(Moestrup, 1991)
~Subphylum Chloropico-
phytina ined.117
117 corresponded to the class
Chloropicophyceae (Lopes dos Santos et
al., 2017)
~Subphylum Picocysto-
phyceae ined.118
118 corresponded to the class
Picocystophyceae (Lopes dos Santos et al.,
2017)
~Classis Pyramimonado-
phyceae Moestrup et Daugbjerg119
119 Daugbjerg et al. (2019)
~Classis Mamiellophyceae
Marin, Melkonian120
120 Marin, Melkonian (2010)
~Classis Nephroselmido-
phyceae T. Nakayama, S. Suda, M.
Kawachi et I. Inouye121
121 Nakayama et al. (2007)
~Classis Pycnococcophyceae
ined.122
122 corresponded to the family
Pycnococcaceae (Guillard et al., 1991)
~Phylum Streptophyta
Bremer123
123 Bremer (1985)
~Subphylum Chlorokybo-
phytina ined.124
124 corresponded to the class
Chlorokybophyceae (Irisarri et al., 2021)
~Subphylum Mesostigmato-
phytina ined.125
125 corresponded to the class
Mesostigmatophyceae (Marin, Melkonian,
1999)
~Subphylum Klebsormidio-
phytina ined.126
126 corresponded to the class
Klebsormidiophyceae (van den Hoek et al.,
1995)
~Subphylum Zygnema-
tophytina ined.127
127 corresponded to the class
Zygnematophyceae (Guiry, 2013)
~Subphylum Coleochaeto-
phytina ined.128
128 corresponded to the class
Coleochaetophyceae (Jeffrey, 1982)
47
~Subphylum Charophytina
ined.129
129 corresponded to the phylum Charophyta
(Migula, 1889)
~Subphylum Embryophytina
ined.130, XII
130 corresponded to the superphylum
Embryophyta (Crane et al., 2004)
~Regnum Haptista Caval.-Sm.
et al.131
131 as unranked clade (Cavalier-Smith et al.,
2015)
~Phylum Haptophyta
Hibberd132
132 Hibberd (1976)
~Classis Pavlovaphyceae
Edvardsen et al.133
133 Edvardsen et al. (2000)
~Classis Prymnesiophyceae
Hibberd134
134 Hibberd (1976)
~Phylum Centroplasthelida
Febvre-Chevalier, Febvre135
135 at the order rank (Febvre-Chevalier,
Febvre, 1976)
~Classis Pterocystida
Caval.-Sm., von der Heyden136
136 at the order rank (Cavalier-Smith, von der
Heyden, 2007)
~Classis Panacanthocystida
Shishkin et Zlatogursky137
137 unranked taxon near to the class level
(Shishkin et al., 2018)
~Regnum Chromalveolata
Caval.-Sm.138
138 Cavalier-Smith (1998)
~informal unit Eochromista
ined.139
139 basal branches assemblage?
~Phylum Telonemia
Shalchian-Tabrizi et al.140
140 Shalchian-Tabrizi et al. (2006)
~Phylum Hemimastigophora
Foissner et al.141
141 Foissner et al. (1988)
~Phylum Provora
Tikhonenkov et al.142
142 as unranked “supergroup” (Tikhonenkov
et al., 2022)
~Subregnum Rhizaria Caval.-
Sm.143
143 Cavalier-Smith (2002)
~Phylum Gymnosphaerida
Poche144
144 described at the order rank (Poche, 1913)
~Phylum Cercozoa Caval.-
Sm.145
145 Cavalier-Smith (1998)
~Classis Cercomonadida
Poche146
146 described at the order rank (Poche, 1913)
~Classis
Paracercomonadida Caval.-Sm.147
147 described at the order rank (Cavalier-
Smith et al., 2018)
~Classis Glissomonadida
Howe et al.148
148 described at the order rank (Howe et al.,
2009)
~Classis Viridiraptoridae
Hess, Melkonian149
149 described at the family rank (Hess,
Melkonian, 2013)
~Classis Pansomonadidae
Vickerman et al.150
150 described at the family rank (Vickerman
et al., 2005)
~Classis Helkesea Caval.-
Sm.151
151 Cavalier-Smith et al. (2018)
~Classis Thecofilosea
Caval.-Sm.152
152 Cavalier-Smith, Chao (2003)
48
~Classis Cryomonadida
Caval.-Sm.153
153 described at the order rank (Cavalier-
Smith, 1993)
~Classis Ventricleftida
Howe et al.154
154 described at the order rank (Howe et al.,
2011)
~Classis Tectofilosida
Caval.-Sm.155
155 Cavalier-Smith, Chao (2003)
~Classis Ebriacea
Lemmermann156
156 described at the family rank
(Lemmermann, 1901)
~Classis Thaumatomas-
tigidae Patterson, Zlfell157
157 described at the family rank (Patterson,
Zlfell, 1991)
~Classis Euglyphida
Copeland158
158 described at the family rank (Copeland,
1956)
~Phylum Metromonadea
Howe et al.159
159 described at the order rank (Howe et al.,
2011)
~Phylum Granofilosea Howe
et al.160
160 described at the order rank (Howe et al.,
2011)
~Phylum Chlorarachnea
Hibberd, Norris161
161 Hibberd, Norris (2011)
~Phylum Endomyxa Caval.-
Sm.162
162 Cavalier-Smith (2002)
~Classis Vampyrellida Hess
et al.163
163 described at the order rank (Hess et al.,
2012)
~Classis Phytomyxea
Engler et Prantl164
164 described at the class rank (Engler,
Prantl, 1897)
~Subclassis
Plasmodiophorida Cook165
165 described at the order rank (Cook, 1928)
~Subclassis Phagomyxida
Caval.-Sm.166
166 Cavalier-Smith (1993)
~Classis Filoretidae Caval.-
Sm.167
167 at the family rank (Bass et al., 2009)
~Classis Gromiida Reuss168
168 at the family rank (Reuss, 1862)
~Phylum Ascetosporea
Caval.-Sm.169
169 at the family rank (Cavalier-Smith, 2002)
~Classis Haplosporida
Caullery et Mensil170
170 at the order rank (Caullery, Mensil, 1899)
~Classis Microcystida
Hartikainen et al.171
171 Hartikainen et al. (2013)
~Classis Paradiniidae
Schiller172
172 described at the family rank (Schiller,
1937)
~Phylum Retaria Caval.-
Sm.173
173 Cavalier-Smith (2002)
~Classis Foraminifera
d’Orbigny174
174 described at the order rank (D’Obrogny,
1826)
~Classis Acantharea Haec-
kel175
175 Haeckel (1881)
~Classis Taxopodida Fol176
176 described at the order rank (Fol, 1883)
~Classis Polycystinea Eh-
renberg177
177 Ehrenberg (1883)
49
~Phylum Aquavolonida Bass
et Berney178
178 as a clade (Bass et al., 2018)
~Classis Tremulida Howe
et al.179
179 at the order rank (Howe et al., 2011)
~Subregnum Alveolata Caval.-
Sm.180
180 at the superphylum rank (Cavalier-Smith,
1991)
~Superphylum Acavomonidia
Tikhonenkov et al.181
181 Tikhonenkov et al. (2018)
~Superphylum Colponemidia
Tikhonenkov et al.182
182 Tikhonenkov et al. (2018)
~Superphylum Myzozoa
Caval.-Sm. et Chao183
183 Cavalier-Smith, Chao (2004)
~Phylum Apicomplexa Levi-
ne184
184 Levine (1970)
~Classis Aconoidasida
Mehlhorn et al.185
185 Mehlhorn et al. (1980)
~Classis Coccidia
Leuckart186
186 at the subclass rank (Leuckart, 1879)
~Classis Gregarinasina
Dufour187
187 at the family rank (Dufour, 1828)
~Classis Blastogregarinea
Chatton et Villeneuve188
188 at the family rank (Chatton, Villenevue,
1936)
~Phylum Perkinsozoa Noren
et Moestrup189
189 Norén et al. (1999)
~Classis Perkinsida Lev-
ine190
190 Levine (1978)
~Classis Phagodiniida
Caval.-Sm.191
191 at the order rank (Cavalier-Smith, 1993)
~Classis Rastromonadida
Caval.-Sm. et Chao192
192 at the order rank (Cavalier-Smith, Chao,
2004)
~Phylum Dinophyta Jeffrey193
193 Jeffrey (1971)
~Classis Dinophyceae F.E.
Fritsch194
194 West, Fritsch (1927)
~Classis Blastodiniphyceae
Fensome et al.195
195 Fensome et al. (1993)
~Classis Syndiniophyceae
Loeblich196
196 Loeblich (1976)
~Classis Noctilucophyceae
Fensome et al.197
197 Fensome et al. (1993)
~Phylum Colpodellida Caval.-
Sm.198
198 described at the order rank (Cavalier-
Smith, 1993)
~Phylum Ciliophora Doflein199
199 Doflein (1901)
~Classis Prostomatea Sche-
wiakoff200
200 Schewiakoff (1896)
~Classis Colpodea Small et
Lynn201
201 Small, Lynn (1981)
~Classis Oligohymeno-
phorea de Puytorac et al.202
202 Puytorac et al. (1974)
50
~Classis Plagiopylea Small
et Lynn203
203 Small, Lynn (1985)
~Classis Nassophorea
Small et Lynn204
204 Small, Lynn (1981)
~Classis Phyllopharyngea
de Puytorac et al.205
205 Puytorac et al. (1974)
~Classis Spirotrichea
Btschli206
206 Btschli (1889)
~Subregnum Heterokonta
Caval.-Sm.207, XIII
207 at the superphylum rank (Cavalier-Smith,
1986a)
~Superphylum Gyrista Caval.-
Sm.208
208 Cavalier-Smith (1998)
~Phylum Bicosoecea Caval.-
Sm.209
209 at the class rank Cavalier-Smith (1989)
~Phylum Developea Aleoshin
et al.210
210 as a clade (Aleoshin et al., 2016)
~Phylum Ochrophyta Caval.-
Sm.211
211 Cavalier-Smith (1986)
~Classis Chrysophyceae
Pascher212
212 Pascher (1914)
~Classis Eustigmatophyceae
Hibberd et Leedale213
213 Hibberd, Leedale (1971)
~Classis Phaeophyceae
Hansgirg214
214 Hansgirg (1886)
~Classis Phaeothamnio-
phyceae Bailey et al.215
215 Bailey et al. (1998)
~Classis Raphidophyceae
Chadefaud216
216 Chadefaud (1950)
~Classis Schizocladiophy-
ceae Kawai et al.217
217 Kawai et al. (2003)
~Classis Xanthophyceae
Fritsch218
218 Fritsch (1935)
~Classis Bolidophyceae
Guillou et al.219
219 Guillou et al. (1999)
~Classis Bacillariophyceae
Hendey220
220 Hendey (1937)
~Classis Dictyochophyceae
Silva221
221 Silva (1980)
~Classis Pelagophyceae
Andersen et al.222
222 Andersen et al. (1993)
~Classis Pinguiophyceae
Kawachi et al.223
223 Kawachi et al. (2002)
~Classis Actinophryida
Hartmann224
224 Hartmann et al. (1913)
~Phylum Hyphochytriomycota
Whittaker225
225 Whittaker (1969)
~Phylum Peronosporomycota
Dick226, XV
226 Dick (2001)
51
~Classis
Saprolegniomycetes Hawksworth227
227 Hawksworth (1994)
~Classis Peronosporo-
mycetes Dick228
228 Dick (2001)
~Phylum Pirsonionea Caval.-
Sm.229
229 Cavalier-Smith (2017)
~Superphylum Bigyra Caval.-
Sm.230
230 at the phylum rank (Cavalier-Smith, 1998)
~Phylum Sagenista Caval.-
Sm.231
231 at the subphylum rank (Cavalier-Smith,
1995a)
~Classis Eogyrea Caval.-
Sm. et Scoble232
232 Cavalier-Smith, Scoble (2013)
~Classis Labyrinthulea Ol-
ive233
233 Olive (1975)
~Phylum Opalinata
Wenyon234
234 Wenyon (1926)
~Classis Proteromonadea
Grasse235
235 Grasse (1952)
~Classis Opalinatea
Wenyon236
236 Wenyon (1926)
~Phylum Placidozoa Caval.-
Sm.237
237 at the infraphylum rank (Cavalier-Smith,
Scoble, 2013)
~Phylum Platysulcea Caval.-
Sm.238
238 at the class rank (Cavalier-Smith, 2017)
52
53
CHAPTER 3
UNCERTAIN FUTURES
OF EUKARYOTIC
MEGASYSTEMATICS
54
55
Further progress in the megasystematics of eukaryotes
is conceivable, first of all, within the framework of impro-
ving molecular and bioinformatic techniques, which will
sooner or later involve all eukaryotic groups in a genome-
wide comparison, as well as discover new groups of
picoeukaryotes (as the Provora group was allocated in
2022) and identify all new environmental sequences.
Bioniformatic techniques may increase objectivism in esti-
mation the rank of taxa and may show a very fine lineage
pattern, rather difficult for rank standardization. The
progress in molecular and bioinformatic techniques could
be considered as a powerful factor for the convergence of
taxonomic reconstructions.
However, the competition of megasystems in the scien-
tific media will act in the opposite direction. Namely, iner-
tial trends of the mainstream will play a sufficient role
here, especially in the area of rank correlation. Therefore,
in the near future, there will not be any prerequisites for
eliminating the current parallelism between “protisto-
logical” megasystems with their “cell body plan-
centrated” principles of phylum identification and metazo-
ans/fungi/embryophytes systems, where the phyla based on
features of multicellular soma differentiation. Highly like-
ly, the multiauthor revisions of the eukaryotic tree will con-
tinue to bypass the rank issue, in the manner of the Adl
group (Adl et al., 2005, 2012, 2018). Also, it would be rather
unlikely if the Botanical and Zoological codes easily gave
way to the Phylocode with a corresponding “nomenclatural
revolution”. The preservation of the first ones is rather an
issue predetermined by practical and institutional consid-
erations. More likely, within a classical taxonomical tradi-
tion, two diverse schools will compete; 1) metaphyte and
metazoan taxonomists (joined with mycologists) tending to
phyla splitting/multiplication without interest in basal
rank estimation, and 2) protozoan taxonomists, which, most
likely, beyond necessarity will no multiply a supergroups
number, but will tend to filling of existing hard-to-
diagnose clades with “morphological contents”.
A certain order in the nomenclature of higher taxa of
eukaryotes would be brought into use by the introduction
56
of typified (non-descriptive) names of taxa with fixed rank-
associated terminations, recommended for taxa that go be-
yond the scope of the Zoological Code in their rank (Kluge,
1999).
Analyzing the systems of the last decade, we can see
some beautiful “reductionist compressions” of the system.
As an example, consider the reconstruction of Derelle et al.
(2015):
Opimoda
Opisthokonta
Amoebozoa
malawimonads and collodictyonids
Diphoda
Discoba
Jakobida
Heterolobosea
Euglenozoa
Diaphoretickes
Archaeplastida
Cryptomonadida
SAR
The name Opimoda was formed by authors from the let-
ters (shown in capitals) of OPIsthokonta and aMOebozoa,
whereas the name Diphoda was formed from the letters of
DIscoba and diaPHOretickes.
The mentioned system well correlates with the most re-
cent tree by Tikhonenkov et al. (2022), who managed to in-
tegrate into the Hemimastigophora and, newly described by
these authors, the Provora group. Both of these groups, as
well as Telonemia, were included as basal groups in the
SAR:
Diaphoretickes
SAR
Telonemia
Haptista
Provora
Nebulidia
Nibbleridia
Hemimastigophora
57
Cryptista
Archaeplastida
Discoba
Metamonada
Ancyromonadida
Malawimonadida
CRuMs
Amoebozoa
Obazoa,
where CRuMs is an acronym of the following constituent
groups: 1) collodictyonids also known as diphylleids, 2)
rigifilids, and 3) mantamonadids.
Apparently, some sister supergroups will merge one into
the other. Such a decision is ripe, e.g., for the Сryptista
Archaeplastida pair, especially after the intermediate clade
Microheliella was identified (Yazaki et al., 2022). Perhaps
the CAM-clade (Cryptista + Archeplastida + Microheliella)
will become a recognized and well-characterized morpho-
logically megataxon. That is, with the accumulation of ge-
nomic and additional morphological data on supergroups
and their agglomerations, we predict the fusion of some of
them into unusual for our perception unions, and some in-
variants are currently visible (Diaphoretickes Bikonta
Plantae sensu latissimo incl. CAM and TSAR; Opimoda
CRuMs + Amoebozoa + Obazoa).
Even 20 years ago, Bauldaf wrote about the obscure root
of the eukaryotic tree (Baldauf, 2003). Karpov (2005) comes
to the fair conclusion that the root of the common phyloge-
netic tree of eukaryotes is located between unikonts and
bikonts. In fact, little has changed since then and they are
looking for it either next to Discoba or the Louko-
zoa/Unikonta dichotomy. All currently existing representa-
tives of these groups are quite specialized organisms, so
morphological markers that would allow reconstructing the
eukaryotic archetype are unreliable. Perhaps, with the suc-
cessful reconstruction of the genome architecture of various
representatives of eukaryotes, it will be possible to move
forward in this matter.
A repercussion of these processes in manual and di-
dactic literature is difficult to predict, since this is the
58
most variegated canvas. Patterson (1999), to the exclusion
of any speculation, simply lists “eukaryotic taxa without
known sister groups” (see Supplement). Karpov, in his ac-
ademic manual “Protista” (2000), principally excludes all
kingdoms from the system, leaving phyla and classes in
rather modern circumscription. The system used in this
fundamental book hasn’t lost its relevance for decades, be-
cause questions of basal relationships between these phyla
were taken out of the focus of the presented system. On the
other hand, we can observe “ideologized” textbooks that try
to generalize everything new stated in recent years about
eukaryotes’ evolution (Leontyev, 2013; Yakovlev et al.,
2017). Today it is difficult to say which of these two
tendencies will prevail. Of course, the data that will not
change over time (i.e. phyla and classes in modern circum-
scription) seem to be preferable, but the trouble is that the
rank of both phyla and classes can be variegated quite a
bit. Recall, for example, such phyla as Xanthophyta, Chry-
sophyta, Phaeophyta (etc.) widely persisting in didactic lit-
erature on the one hand and still difficult for general en-
thusiastic recognition the phylum Ochrophyta, which actu-
ally must include all the listed phyla in a rank no higher
than the class on the other.
Here we return to the problem of rank correlation. It can
be assumed that in one form or another it will be solved
within the framework of large textbooks or global phyloge-
nies, but it is unlikely to become the subject of special con-
sideration. We pin some hope on the development of auxil-
iary services at the largest aggregators of genomic infor-
mation (such as GenBank), which would allow, at the us-
er’s request, to generate high-resolved trees that reflect the
structure of the eukaryotic domain. Ideally, such services
could completely replace the “author’s” phylogenies and
classifications competing in scientific media. But at the
current stage of development of molecular, genomic and
information technologies, this is a seemingly impossible
issue.
Here, we would like to acquaint the reader with our
modest contribution to the information support of the bio-
technological community with new information that has
59
been developed in the high-ranking classification of eukar-
yotes. In the authors’ view, the time has come to create a
taxonomic/biotechnological interface that allows the user-
biotechnologist to quickly select the classification solution
that is most adequate to modern data in order to optimize
the search for new nests of technologically significant or-
ganisms presumably bearing a certain properties of organ-
isms that have already been studied in a respect needed.
The creation of such a system implies a global coverage of
the users’ network on the one hand, and the possibility of
both periodically updating the classification part of the
catalogue with inclusion of all newly studied species on the
other. When creating a classification part, one should be
guided by consensus estimates of current phylogenomic
reconstructions, keeping in mind that periodic updating of
the classifier guarantees a gradual “alignment” of the
current imperfections, which undoubtedly do not pass by
the attention of the taxonomic community (Zmitrovich et
al., 2022a).
In July 2022, the authors created such a platform called
“Eukaryotic supergroups: Taxonomy/Biotechnology inter-
face” (Zmitrovich et al., 2022b). For each of the 10 super-
groups (Loukozoa, Amoebozoa, Opisthokonta, Discoba, Cryp-
tista, Archeplastida, Haptista, Rhizaria, Alveolata, and
Stramenopila), a current system was presented with a bib-
liography covering taxonomic primary sources and recent
advances in molecular phylogenetics as well as applied
significance of the group with reference to modern biotech-
nology research and sequenced genomes of key species. The
latter is outlined both as a list of classical biotechnology
fields (food technologies, biosynthesis and biomass produc-
tion, bioremediation, biopharmacology, agricultural tech-
nologies) as well as animal husbandry with crop produc-
tion, phytopathology, and clinical mycology and protozo-
ology. Separately, lists of works on the latest (current
year) systematic studies and, separately, works in the field
of biopharmacology are presented. The information on this
platform is expected to be updated annually (Zmitrovich et
al., 2022a, 2022b).
60
Far from all startups are successful in overcoming the
“thermal movement” of the Internet. Modern trends are
largely set by highly rated wide-ranging journals, because
such ratings are used by governments as indicators of the
effectiveness of investments in certain research institutes
and programs. The tradition of international cooperation in
the development of a consensus megaclassification of eu-
karyotes was established by high-rating journal work by
Levine et al. (1980) and this tradition was continued by
various teams led by Adl (Adl et al., 2005, 2012, 2018).
There is no reason to doubt that throughout the period un-
til the achievement of technical possibilities for approach-
ing a unified interpretation of the volume and boundaries
of higher eukaryotic taxa, such a consensus system will
remain almost the only landmark for fundamental and ap-
plied biology research.
61
CHAPTER 4
“FLORA”, “FAUNA”, “FUNGA”:
AN IMPACT OF DISCUSSION
IN MEGATAXONOMY
ON THE FLORISTIC
AND FAUNISTIC
TERMINOLOGY
62
63
The terminology used in the inventory of eukaryotic bio-
diversity, as well as in other fields divorced from phylo-
genetics, naturally turns out to be more conservative. So,
we still use the terms “floristics” and “faunistics” in eve-
ryday life, but still do not use, for example, such a term as
“fungistics”. The nomenclature of the entire diversity of
eukaryotes is also regulated by only two botanical and
zoological nomenclatural codes. However, the discussion
in megataxonomy has impacted everyday floristic-faunistic
terminology in some works. The rather aggressive promo-
tion of the idea of “mycological separatism” in floristic
field terminology forced us to highlight this problem
(Zmitrovich et al., 2021).
Two authors took part in the discussion started on IMA
Fungus pages with opening papers by Hawksworth (2010)
and Kuhar et al. (2018), who dedicated the proposal for
wide use of the term Funga. They did this in order to sub-
stitute the term Mycobiota for Funga in fields where the
term Flora (mycoflora) was previously used, i.e. in a
traditional field of biodiversity inventory and its bio-
geographic analysis as well as all the applied fields.
“Funga”: Pro et Contra
The main arguments in favor of the term Funga are
listed below:
1. Fungi are traditionally considered as a separate king-
dom of eukaryotes and require a separate general
biological and related terminological approach.
2. Fungi, plants, and animals are the most diverse
groups of multicellulars and, if the terms Flora and Fauna
traditionally correspond to species assemblages of the
former, then fungal species assemblages require some
equally short term that carries a conceptual significance.
3. The term Funga is consonant with the brevity, genus
and termination of the names Flora and Fauna, and to-
gether they form a good conceptual abbreviation (“FF&F”).
However, obviously, there are arguments against the
term Funga, among them the following should be
highlighted primarily:
64
1. Funga is a rather polysemantic word: in Portuguese
it means a “sniffing”, in Swahili “closer”, whereas in
urban USA language it means a bad man. This is not pu-
rely a Latin word and it is, in fact, also composite (the
termination is unified on the manner of Flora and Fauna).
2. Unlike such terms as Flora and Fauna, associated
with a centuries-old tradition and referring to corres-
ponding ancient deities, the term Funga is not rooted in
ancient mythology, even though in Kuhar’s paper it was
associated with goddess Diana. The term Diana seems to
be more consistent with this logic, although it does not
refer to any tradition, either.
3. A consequence of the rich history of the terms Flora
and Fauna was the emergence of two main derivative
terms, “floristic” and “faunistic” (including such subva-
riants as “algofloristic”, “mycofloristic”, “prostisto-
faunistic.”). Taking the term Mycobiota as an example, it
can be said that for almost 30 years of its existence, re-
searchers were embarrassed to design derivatives (“myco-
biotic”, “mycobiotistics”) and, apparently, a similar fate
threatens potential derivatives from the Funga term.
4. The tradition to associate the plant world with Flora,
and animal world with Fauna was a consequence of empi-
rical evidence: multicellular animals were characterized by
activity, whereas subjects of the plant world were charac-
terized by their inability to change location. A review of
the “plant world” polyphyly hasn’t yet led to development
of special biodiversity-analytical and biogeographic termi-
nology for each lineage, although many “plant” lineages
are diverged from each other deeper than fungi from
animals.
The last argument seems to be the most serious and de-
serves a more detailed consideration.
Kingdoms and Lineages
Recent advances in eukaryote phylogenomics have
yielded rather stable results, whereas against this
backdrop, fewer researchers are resorting to such a
category as “kingdom”. Usually, eukaryote groupings of
65
the highest rank are called supergroups (without
consideration how does this concept relate to the concept of
higher taxa), whereas the branches above traditionally
recognized phyla are considered as clades or lineages. The
term “kingdom” keeps in current use within zoologists and
mycologists, who don’t need to coordinate the rank of these
groups with a general eukaryote system, especially its
upper subdivisions. Also, these specialists avoid inevitable
ranks lowering of internal subdivisions in such large units
as Metazoa (Laumer et al., 2019) and Fungi (Tedersoo et
al., 2018). When mycologists keep Fungi on a kingdom
rank in mycological works, this doesn’t automatically lead
to the raising of the rank of such groupings as TSAR, or
Discoba, since this lies beyond their competence field. This
is reason for the two largest unions being firmly embedded
in the mainstream on a kingdom rank, whereas it is
difficult to imagine any changes to this doctrine. We are
too focused on kingdoms since such taxon status drives the
researchers and science organizers to a certain
“terminological separatism”.
Table 1 shows a distribution of “botanical” and
“mycological” ecomorphs across the main eukaryote
lineages. As it can be observed, a strict phylogenetic
approach makes some remnants of the “plant world”
orphans in the terminology field, although with in
practical florists vs. faunists each applies their own
terminology to some of these orphans. If the term Flora
were to be consistent with “terminological separatism”, it
would be associated with the Archaeplastida lineage only,
then territorial species assemblages in such supergroups
as TSAR, Haptista, or Discoba would require several new
terms, too.
Till now, literature avoids any terms for territorial
species assemblages of some heterotrophic protists, like
Rozella, Aphelideae, Rhodelphis.
Fungal ecomorphs lying outside groups such as
Opisthosporidia, DRIP and TSAR would not be covered
using such a “terminology separatism” approach. The
question also arises, how to name territorial species assem-
66
Table 1. Eukaryote supergroups in relation
Eukaryotic supergroups
Megalineages
“Botanical” taxa
Chromalveolata
Heterokonta
Ochrophyta
Alveolata
Dinophyta
Rhizaria
Chlorarachniophyta
Haptista
“ ”
Haptophyta
Cryptista
“ ”
Cryptophyta
Archaeplastida
glaucophytes
Glaucophyta
protist predators
red algae
Rhodophyta
green plants
Chlorophyta s.l.
Amorphea
Amoebozoa
Obazoa
Opisthokonta
Holozoa
Mesomycetozoea
Holomycota
Opisthosporidia
Fungi
Discoba
Euglenozoa
Euglenophyta
Heterolobosea
Only supergroups which contain traditionally botanical and mycological subjects are
listed here. The symbol “” means that the corresponding term has not been used in
known literature. The symbol “!” means that the corresponding term for the designa-
tion of territorial species assemblages when considering this group has so far been
avoided in use, but a separate term would be required in the case of orthodox “termi-
nological separatism”. The symbol “?” means that that the corresponding group does
not belong to the phylogenetic lineage known as “kingdom Fungi”, but has been
studied or is still being studied by mycological institutions and, in the case of avoid-
ing here the “Funga” term, does not have yet any special term. The numbers refer to
the works of the following authors: [1] Sukhanova (1984); [2] Yongnian (1998); [3]
Leander (2001); [4] Larkum et al. (2006); [5] Carty (1993); [6] Lewis, Dodge
(2002); [7] Sibewu et al. (2008); [8] Ab (1927); [9] Zamora, Schnetter (2002);
[10] Naumov (1954); [11] Gordon et al. (2012); [12] Preisig, 2002; [13]
Andruleit (1995); [14] Novarino (2002); [15] Whitton (2002); [16] Yu (2008a); [17]
Yu (2008b); [18] Carr (1939); [19] Garzoli et al. (2014); [20] Issi, Voronin
(2007); [21] Lakshmipathy et al. (2012); [22] Kubicek et al. (2019); [23]
Woowski (2002); [24] Farr (1976); [25] Smirnov, Brown (2004).
67
to floristic vs faunistic terminology
Fungal and
fungus-like taxa
Term applied to territorial species assemblages
Flora [author]
Fauna [author]
Funga [author]
current use
[1]
Oomycota
[2]
?
Labyrinthulomycota
[3]
[4]
?
[5], [6]
[7]
(Chytriodinium)
[8]
[9[
Plasmodiophoromycota
[10]
[11]
?
[12]
13
[14]
[1]
[15]
(Rhodelphis)
!
!
!
current use
(Holmsella etc.)
current use
[1]
(Prototheca)
Myxogastria
[16], [17]
[18]
?
(Amoebidium etc.)
[19]
?
Microsporidia
[20]
Aphelidea
!
!
!
Rozellomycota
!
!
!?
all taxa of the Fungi
widely used
[21], [22]
[2]
[23]
[1]
Acrasia
[24]
[25]
?
blage in other lineages of eukaryotes traditionally studied
by mycologists: Acrasia, Eumycetozoa, plasmodiophorids,
labyrinthulids, oomycetes, DRIP.
The discussion regarding the introduction of the term
Funga, therefore, should inevitably touch upon certain
terminological decisions affecting the lonely remnants of
“plant world” in the phylogenetic system of eukaryotes,
including fungus-like protists.
68
What’s the Alternative?
So, the aforementioned “terminological separatism” ap-
proach requires at least the naming of the territorial
species assemblages for the number of autotrophic and
fungal TSAR groups as well as the traditionally “algal”
representatives of Euglenozoa. As far as we know, such
attempts have not yet been made. If we don’t use this
option, then there are two alternatives for a mycologist:
continue to use terms derived from Flora, or adhere to a
faunistic terminology.
Flora-related terms applied to fungi corresponded most
with the evidence: the fungi are growing (Zmitrovich et al.,
2003). Historically, such a discourse has stayed in the
literature for a long time, since the majority of authors of
the 1720th centuries have associated the fungi with plant
organisms. For example, in Buxbaum’s “Plantarum minus
cognitarium centuria” (1728)”, we can find some species of
fungi among mosses and vascular plants.
The term “plant organism” represents a rather ab-
straction, an essential feature of which is the presence of a
rigid cell wall. The main lines of progressive multi-
cellularity from an ancestral non-motile cell with a rigid
wall are based on the superposition of linear aggregations
of such cells the filaments, whereas the parenchymatic
(autotrophs) and plectenchymatic (fungi) histoarchitecture
represents a limit of filaments evolution. Regarding this
aspect, the fungi seem to be more comparable with plants
than with epithelial-mesenchymal metazoans. Especially,
the flora-related terms have taken root in lichenology,
because due to their algal component, advanced lichenized
fungi have thallus with morphogenetic polarization
imitating those of autotrophic algae or mosses. Even in
recent years, when the term Mycobiota was recommended
for the fungi, the term Lichen Flora continued to persist in
mass lichenological literature (current “Nordic Lichen Flo-
ra” project see Arcadia, 2020).
The second alternative (the use of fauna-related terms to
fungi) seems to be not yet practically implemented (the
69
Google query for Mycofauna term yielded only 203 results),
although in some very old systems the fungi were
interpreted as closest relatives of the sponges (the term
Funga etymologically related just to Spongia) or other
“phytozoans”. For example, in the classification system by
Goryaninov (Horaninow, 1834, 1843), fungi and sponges
were regarded as neighboring subdivizions of the
“Phytozoa” division. Phylogenetically, there is a sound
basis for such juxtaposition: the opisthokontes clade
(holozoa + holomycota) together with the clades of
apusomonads and breviates form a single monophyletic
grouping Obazoa (Brown, 2003), all the basal lineages of
which are presented by amoeboid protozoans. In such a
hypothetical solution, the term Fauna of fungi (or
Mycofauna) would be understood by analogy with a real-
life concept of “sporozoan fauna”. In this connection, the
ascomycete Pneumocystis carinii represents an interesting
example, originally studied by parasitologists and
protozoologists (Delano, Delano, 2012).
What is the Internet Looking for?
Even though modern researchers avoiding a retrograde
brand try to reject the term Mycoflora, giving preference to
Mycobiota or Mycota, the term Mycoflora continues to be
most relevant in Google search queries (Table 2), which
can be interpreted as an inertial trend. The term Fauna,
paradoxical in this situation, currently is not particularly
accepted (203 results) and seems unlikely to be accepted in
the future, because the majority of mycologists are asso-
ciated with mycological or botanical, but not zoological
research institutions.
The terms Funga and Mycota are limited in our search
queries, since they have more than one meaning (for
example, in Portuguese texts the word “funga” is
mentioned 7,270,000 times, in Swahili texts 6,630,000
times, while the word “mycota”, if we don’t filter it with
an exclusion of cream name and kingdom name, is found in
the English segment of the Internet 297,000 times). With
70
an appropriate filtering, the term Mycota gives 145,000
results, whereas the term Funga only 68,000. Even these
results do not seem absolutely explicit, but it is vital to
understand the importance of a possible promotion of a
new term and obstacles in overcoming conservative
mainstream trends. A rather long transitional period
awaits, during which “Funga”, “Mycobiota”, “Mycoflora”
and, perhaps, the terms based on them, will compete. One
day, however, “Funga” may emerge as the basic term
covering fungi and fungal analogues, rather than Fungi,
for the broader historically rooted union. I would, however,
like to “Funga” increasingly adopted by mycologists for
treatments of the fungi in particular regions, especially for
major books and any new multi-volume series, where
“Flora” would otherwise have been used.
Table 2. Estimation of the relevance of key terms related to
territorial species assemblages of Fungi using a Google
queries (aсcessed 14.07.2020)
Term
Search results
number
Filters
Filtration
quality
estimation
Mycoflora
626 000
minus mycoflora@
medium
Mycobiota
189 000
minus journal; mycbiota@
medium
Mycota
145 000
minus -mycota; mycota@; Eu-; king-
dom; phylum; cream
low
Funga
68 000
English; minus -l; -funga; fanga;
alafia; funga@
low
Mycofauna
203
As we can see, the new term introduction, despite at-
tempts to promote it, didn’t lead to its dominance in every-
day use, although it cannot be said that such an insertion
remained unnoticed by the community and did not cause
certain “turbulence” in the literature. The same, we can
assume, awaits possible initiatives related to assessing the
biodiversity of other robust supergroups. Currently, one
can only guess what new terms might be born (a great
deal might depend on how multiple would be merging of
units described), however, anyway, the wide entry of new
71
terms into scientific use can taken place successfully only
if they would affect some derivative terms such as:
herbarium/collection;
floristics/faunistics;
floristic/faunistic;
floroanalytical/faunoanalytical;
florogenesis/faunagenesis;
paleoflora/paleofauna.
It is possible, however, that over time the “terminologi-
cal turbulence” in the literature, as well as attempts to di-
versify the terminology to the species composition of eu-
karyotes, will level out, and the scientific community will
appreciate the fundamental “flora/fauna” dichotomy, deep-
ly rooted in praxis and intellectual history.
72
CONCLUSION
1. Only a hundred years have passed since the taxonom-
ic paradigm was changed by Chatton’s studies and two
fundamentally different worlds prokaryotes and eukary-
otes stand before biologists. This basic generalization
gave the impulse to the development of protistology and,
more broadly, eukaryotic microbiology, megasystematics,
and the past century was marked by the search for the
most successful classification solutions in relation to the
upper levels of the biota subdivision.
2. Megasystematics of eukaryotes, which operate in ca-
tegories above the phylum level, which are not of interest
to monographs of narrow groups of plants and animals, in
the first steps developed mainly in didactic literature as a
kind of popularization of advances in morphology-based
(later molecular-based) systematics. Starting from the se-
cond half of the 20th century, when progress in the micro-
biology of eukaryotes brought significant results, the clas-
sification at the phylum level has attracted more and more
attention from systematists-monographs, whereas the
megasystematics from “mind games” has become a “con-
tinuation of classification” at the highest levels.
3. The transition of megasystematics from a purely the-
oretical field to the area of classification routine finds
practical expression in classifiers of general use, which
began to operate not only with taxa (described according to
the rules of both codes), but also with higher taxa of euka-
ryotes. Systems by Cavalier-Smith, who described a huge
variety of megataxa and time to time changed their rank,
served as a kind of catalyst for the process of such a tran-
sition.
4. During half a century of such active taxonomic work
on the upper levels of the eukaryotic system, many names
of taxa have accumulated and alternative interpretations of
some of them have appeared, as well as a number of prob-
lems associated with estimating their rank. Moreover, if, in
73
the new-generation sequencing era, the revealing of their
phylogenetic position has become easier, then the estab-
lishment of the taxon rank is still a haven for subjective
assessments. Therefore, the eukaryotic megasystem needs
to be revised precisely from the point of view of rank corre-
lation.
5. The main goal of our work was an overview of the
most significant sources related to the classification of eu-
karyotes, to reconstruct the system most appropriate to
known datasets, and to intercorrelate taxon ranks within
this system. We have proposed ranks based on a general
overview of the system, which is difficult to make centered
on one or another taxonomic group.
6. In the expanded version of our system, we gave a link
to the original source of the taxon and indicated its rank
both in the protologue as well as its recommended rank. To
represent the recommended rank, we used a system of fixed
indents, reflecting the taxa subordination, whereas the ref-
erence to bibliographic sources was given in marginalia.
7. In a compressed mode, the presented system has the
following structure:
OBIMODA
Loukozoa
Amoebozoa
Obazoa
Opisthokonta
Breviatea
Apusomonadida
Crumalia
DIPHODA
Discoba
Plantae
Cryptista
Archaeplastida
Haptista
Chromalveolata
Eochromista
Telonemia
Hemimastigophora
Provora
Rhizaria
74
Alveolata
Heterokonta
8. We also correlated ranks within the presented large
subdivisions, and we give out the recommended rank in the
summary (reflected in each record with a tilde symbol). For
the convenience of finding the required taxon, we provide
the Index, where this taxon has a basic reference to the
conspect, from which the user can extract information
about its status in the eukaryotic hierarchy.
9. Besides, we started work on filling in the updated In-
ternet-classifier (www.supergroups.ru), which is fundamen-
tally open to corrections in the light of new data.
10. In this paper, we also attempt to evaluate current
trends in the classification of eukaryotes and related ter-
minological problems in flora and fauna studies.
11. The practical point of application of the current de-
velopments in eukaryotic megasystematics is biotechnology
and related screening studies, since the knowledge of the
adequate taxonomic position of organisms allows the ra-
tional organization of exploratory research.
12. The authors hope that the first round of the revision
of the eukaryotic domain in terms of the rank structure
will cause a lively discussion among specialists and will
be an impulse for further improvement of the system of eu-
karyotes.
75
NOTES
76
77
I In the late 1940s, as part of the Soviet campaign
against cosmopolitism, the priority of Russians in the se-
emingly indisputable discoveries of West-associated tech-
nological progress was declared. For example, Kryakutny,
instead of the Montgolfier brothers, was recognized as the
pioneer of aeronautics, Mozhaisky was interpreted as the
first aviator, whereas the peasant Artamonov as the inven-
tor of the bicycle. Physician Polotebnov was also men-
tioned as the discoverer of penicillin, whereas botanist
Goryaninov (instead of Schwann and Schleiden) as the fa-
ther of the cell theory. Leaving aside the authorship of the
bicycle and the balloon, we would like to comment on the
situation with the discovery of penicillin and the develop-
ment of cell theory. Concerning penicillin, Botkin’s stu-
dents Manassein and Polotebnov elaborate an idea about
the benefits of molds. In a series of experiments with
Penicillium glaucum, they observed that bacteria didn’t
grow in a liquid medium containing molds. Polotebnov
draws a rather practical conclusion: Penicillium representa-
tives are capable of delaying the development of pathogens
of human skin diseases (Polotebnov, 1871). In 1928, similar
observations would be made by Scottish microbiologist
Fleming, who discovered the destruction of the culture of
Staphylococcus aureus by a mold fungus (Fleming, 1929).
Abrham and Chain (1940) isolated and named the active
substance of the fungus in question, penicillin. However,
only Robinson deciphered its chemical structure (Clarke et
al., 1949). Here we can see rather a convergence of scien-
tific thought. Strictly speaking, Russian scientists drew
attention to the bactericide properties of mold at the end of
the 19th century (which has priority vs Fleming’s observa-
tions), whereas actually penicillin was described by the
American Robinson. Regarding cell theory, Goryaninov’s
“Orbis organicus seu cellularis” (Horaninow, 1834), preced-
ed by Schwann’s (1837) and Ehrenberg’s (1838) works. On
the other hand, this theory has a solid background, begin-
ning with Hooke, Malpighi, Link, Brown and concluding
with Virchow’s works. Here, Goryaninov takes the role of
reviewer and generalizer. Summarizing, when we clarify
78
the priority issue, one cannot bypass the general discus-
sion context, woven by civilization polylogue. Paradoxical-
ly, innovations are sometimes produced in the depths of
“catching-up development”.
II From the end of the 19th century and until the 1970s,
in the latinized name applied to eukaryotes, the circulating
k/c symbols were varied. Classical Latin did not allow the
use the symbol k, so we see such names as Eucaryonta,
Eucaryota and Eucarya (to this would be added the French
version “Eucaryotes” used by Chatton in 1925, which,
strictly speaking, must be rejected by both nomenclature
codes insisting on a latinized stem and termination of
terms) seen in biological literature. German and English
elements of this name using symbol k referring to the
Greek stem (karyon) are not rejected by both codes
if they have latinized terminations. Accordingly, we refer
to the name dominium Eukaryota R.T. Moore (Moore, 1974)
as the most consistent with the recommendations of both
nomenclatural codes.
III At the beginning, and then in the 70s of the 20th cen-
tury, an idea of the origin of “higher fungi” (ascomycetes
and basidiomycetes) and red algae from the common an-
cestor (Florideae) was shared by a number of authors
(Zmitrovich, 2001). Initially the hypothesis was based on
similarity of their vegetative and generative structures
(Sachs, 1874; Dodge, 1914; Chadefaund, 1953, 1972, etc.),
but later it was confirmed by ultrastructural data (Demou-
lin, 1974; Kohlmeyer, 1975). It appears to be very useful for
the study of the development of terrestrial flora (Church,
1921; Kohlemeyer, Kohlmeyer, 1979; Atsatt, 1988) and regu-
larities in morphological evolution of higher fungi (Corner,
1964, 1970; Chadefaud, 1960, 1982, 1984). The description of
the order Spathulosporales (Kohlmeyer, 1973), combining
the characters of Ascomycetes and parasitic Florideae, was
one of the most important facts leading to the wide recog-
nition of the hypothesis in 197080s (Cavalier-Smith, 1978;
Taylor, 1978; Dodge, 1980; Hawksworth, 1982; Goff, 1983;
Goff, Coleman, 1985). Today, however, the Florideae hy-
pothesis is not confirmed by molecular data, but represents
79
an almost unique example of such a deep convergence.
Both groups independently lost cilia and cell motility, hav-
ing a basically filamentous structure, which predetermined
a number of morphogenetic analogies.
IV Subdominium OBIMODA Zmitr., Perelygin et Zharikov
subdom. nov.
Nom. descr., sine typus.
Etymology: anaphony playing on fragments such as
OBazoa, AMOebozoa, and MantaMOnadida. Substitute for
Opimoda (Opisthokonta plus Amoebozoa) by including
Obazoa as a whole (Opisthokonta plus Breviatea plus
Apusomonadida), collodictyonids, rigifilids, and mantamo-
nadids in this taxon.
Diagnosis: amoeboid (cellular or plasmodial) or flagel-
lated heterotrophic protozoans as well as multicellulars
(fungi, metazoans); as a rule without clearly formated
dikinetide in most groups. Mitochondrial cristae tubular,
flat, or mitochondria are reduced. Mitosis intranuclear to
open. Comprises Obazoa, Amoebozoa and CRuMs-clade.
V This name was mentioned by Cavalier-Smith (1981),
without specifying the diagnosis and type (nom. inval.).
VI The name Dicaryomycota was published by Kendrick
(1985), without specifying the diagnosis and type (nom.
inval.). The name Dicarya is invalid, too, because it is de-
scribed without a standardized termination (ICNAFP, Art.
16.2).
VII One of the authors in his work 20 years ago already
suggested lowering the rank of the metazoan internal sub-
divisions (Zmitrovich, 2003) and, even for experimental
purposes, showed what could happen. As expected, the re-
action to the attempt to change established perceptions
was rather negative. Here follows a citation from a forum
of paleontologists where this situation was briefly dis-
cussed (Megasystematics, 2006).
“Set O. Lopata : By the way, I’ve reached the letter “Z” in
your archive and I read the paper of Zmitrovich. To say that his
views seemed to me very extravagant is to say nothing. In a less
decent place, I would put it differently:
80
Regnum Animalia
Phylum Choanozoa
Classis Choanomonadea
Classis Corallochytrea
Phylum Porifera
Classis Hyalospongea
Classis Calcespongea
Classis Archaeocyathea
Phylum Enterozoa
Subphylum Cnidaria
Subphylum Placozoia
Subphylum Ctenophoria
Subphylum Mesozoia
Subphylum Myxozoia
Subphylum Scolecidia (supercl. Plathelminthes, Nemat-
helminthes, Nemertini)
Subphylum Coelomia (supercl. Mollusca, Sipunculida, Echinuri-
da, Annelida, Tardigrada, Pentastomida, Onychophora, Arthropoda,
Tentaculata, Chaetognatha, Brachiata, Echinodermata, Hemi-
chordata, Chordata) [shock].
Dilet a n t: I believe that then the Mammalia are a family...
Well, a maximum, a suborder [smile].
Plant a g o: Here is an example of a non-eclectic, consistent
approach [smile]”.
We can see that two arguments were, whether explicitly
or implicitly, voiced: 1) the rank lowering of higher taxa of
metazoans will inevitably lead to a lowering of the status
of taxa widely known in everyday life and persisting in di-
dactic literature, e.g., such as mammals; 2) the mega-
system should not be a continuation of those systems that
monograph-taxonomists are engaged in, but rather be an
autonomous and, in many respects, an experimental area.
The last argument is rather a good wish (even if it is
shared by all participants in the cited discussion), since all
known megasystems precisely claim to complete the gen-
eral system of organisms and are principally oriented on
integration of “partial systems”. As for the first thesis, it
has a rational grain, since without a previous adaptation
(e.g., the maximum possible use of interstitial categories
when approaching the order level) such a system would be
rejected by the mainstream. That is a reason why in this
81
state of discussion context we only indicate the problem,
but don’t propose to approach it.
VIII Regnum CRUMALIA Zmitr., Perelygin et Zharikov
regnum nov.
Nom. descr., sine typus.
Etymology: anaphony adapting the CRuMs-clade to lat-
inized record form.
Diagnosis: heterotrophic pelliculate amoebae or flagel-
lates. Cells more or less ventrally-flattened, with promi-
nent cytostome, 24-ciliate or devoid of cilia, but having
branching filopodia emanate from a ventral aperture. Mi-
tochondria having flat, tubular, or irregular cristae. Com-
prises collodictyonids, rigifilids, and mantamonadids.
IX Mantamonadea Zmitr., Perelygin et Zharikov phylum
nov. corresponded to the order Mantamonadida
Glcksman et al. (2010). Free-living heterotrophic flagel-
lates that move primarily by gliding on surfaces rather
than swimming. Cells around 5 m diam., asymmetric,
flattened, biciliate, rather plastic; the posterior gliding cil-
ium is long and highly acronematic; anterior cilium thin-
ner, shorter, and almost immobile points forward to the
cell’s left.
X Rigifilidea Zmitr., Perelygin et Zharikov phylum nov.
corresponded to the order Rigifilida Yabuki et al. (2013).
Free-living heterotrophic amoeboid organisms. Cells are
covered with either a single or a double-layered sub-
membrane pellicular lamina that makes them rigid in con-
sistence; slender branching filopodia emanate from a ven-
tral aperture of the cell and are employed to collect bacte-
ria upon which they feed and to attach the organism to the
substratum; around an aperture, the pellicle is reflexed
around forming a peristomial collar; mitocondrial cristae
flat or irregular shape, a nucleus single, dorsal; centrioles
and cilia none.
XI Collodictyonidea Zmitr., Perelygin et Zharikov phylum
nov. corresponded to the class Diphyllatea Cavalier-
Smith (2003). Simgle-celled omnivorous heterotrophic flag-
ellates; range in size from 30 to 50 µm in length, bear
82
broad pseudopodia, four flagella and a ventral feeding
groove which divides the organism longitudinally called
the sulcus; the lateral cell margins maybe somewhat angu-
lar leading to a broad, truncated rounded apex this pos-
terior margin narrows posteriorly and either bears 13
lobes or is simply broadly rounded, pseudopodiate; the nu-
cleus typically lies in the posterior half of the cell; the mi-
tochondria having tubular cristae.
XII This is the largest Chloroplastida subdivision (about
300,000 species), whose apomorphies are multicellular spo-
rophytes and gametangia, cuticle, embryo, plus molecular
apotypies showing the position “above” Coleochaetales
Charales lineage. This group combines such informal units
as bryophytes (liverworths, mosses, hornworths), pterido-
phytes (clubmosses, ferns, whiskferns, horsetails, cycads),
and seed plants (ginkgo, conifers, gnetophytes, flowering
plants). The subphylum status recommended for this divi-
sion suggests that such phyla as Marchantiophyta, Bryo-
phyta, Anthocerotophyta, Lycopodiophyta, Monilophyta,
Cycadophyta, Ginkgophyta, Gnetophyta, Pinophyta, and
Magnoliophyta could be less painfully lowered in rank to
superclasses. A recent review of angiosperm systems
(Geltman, 2019) states that the rank of this group is rather
apophasis, and also provides evidence that the latest APG
recommendations proposed to consider angiosperms at the
rank of subclass (Magnoliidae) with main clades of super-
order rank (Chase, Reveal, 2009). So, our proposal to treat
magnoliids at the superclass rank wouldn’t seem like a big
deal, but rather a conservative approach (e.g., there will be
space to operate with a possible integration of some new
sequences into the tree, etc.).
XIII This name was re-habilitated to replace the name
Chromista. The latter emphasized the color of plastids.
However, far from every representative of the subkingdom
is autotrophic. Besides, the name Straminipila (from Latin
straminis straw and pila villi) was also proposed, re-
ferring to tubular mastigonemes, which also was replicat-
ed in English pronunciation as Stramenopiles (strameno-
piles) (Patterson, 1989). However, it is not a very accurate
83
representation, since there are exceptions both in the mor-
phology of cilia and their number. Nevertheless, the name
Heterokonta(ae) has a longer history (Luther, 1899; Cava-
lier-Smith, 1986b), so we prefer it in the present compendi-
um.
XIV The name form Hyphochytriomycota (Whittaker, 1969)
is more correct than the subsequent form Hyphochytri-
diomycota (Leedale, 1974 and followers), since it is a typi-
fied name derived from the genus Hyphochytrium Zopf.
XV A typified name alternative to widely known
Oomycota (oomycetes). It is justified by the fact that the
phylogenetic system of the phylum includes two classes,
for which it is advisable to use typified names so that it is
clear which lineage is meant. This is an interesting group
of fungus-like protists. The similarity of the vegetative or-
gans of oomycetes with siphonal algae has long been con-
sidered as the main evidence of the apochlorotic nature of
this group (Brefeld, 1889; Lotsy, 1907; Bessey, 1942). Other,
albeit indirect, indications of the undoubted relationship of
oomycetes with some autotrophic groups of algae were the
morphologies of ciliate stages (Chadefaud, 1960; Zerov,
Zerova, 1968; Barr, 1981), the presence of cellulose in a cell
wall (Fuller, Barshad, 1960; Bartnicki-Garcia, 1970), a ly-
sine synthesis pathway similar to all autotrophic organ-
isms through ,-diaminopimelic acid (Vogel, 1965), a stor-
age product of -1,3-glucan mycolaminarin, similar in
structure to such substances of brown and diatom algae
(Zevenhuizen, Bartnicki-Garcia, 1970; Bacic et al., 2009).
According to the interpretation of some authors, the
kinetosome-associated microbodies found in zoospores of a
number of oomycetes (K-bodies) represent a reduced
leukoplast (Powell et al., 1985). Mentioned indications can-
not be unambiguous evidence in favor of the apochlorotic
nature of oomycetes. Therefore, in the literature of recent
decades, in addition to the view of oomycetes as
apoholorotic algae of the chromophyte cycle (Zerova,
Palamar-Mordvintseva, 1981; Zhukov, 1985; Zmitrovich,
2003), the opposite view was asserted on oomycetes as
primarily heterotrophic group associated with a protero-
84
monade ancestor (Liepe et al., 1994; Dyakov, 2003). In the
early 2000s it was shown that the nuclear genome of
oomycots contains genes of plastid origin (for example, the
gene for 6-phosphoglucanate dehydrogenase, gnd), similar
to those of diatoms and brown algae (Andersson, Roger,
2002), i.e., the ancestor of oomycetes might be an autotroph
(Cavalier-Smith, 2002). However, it quickly became clear
that plastid genes are found in all groups of chromal-
veolates, including those considered originally hetero-
trophic, e.g., in opalinates and proteromonads. This is a
good reason to assume that the acquisition and loss of
plastids in the evolution of chromalveolates occurred re-
peatedly, and in the evolutionary line leading to hetero-
trophic marine heterokonts and oomycetes, the loss of plas-
tids occurred at the single-celled (presumably amoeboid)
level, and at the same level, the secondary acquisition of
plastids was occurred, wereas the ancestors of ochrophyte
algae might be secondarly heterotrophic (Cavalier-Smith,
2002, 2018; Cavalier-Smith, Scoble, 2013). Thus, a cell wall
might develop in the evolution of oomycetets independently
of the cell wall of ochrophyte algae.
The use of SSU, LSU, β-tub, Cox1, Cox2 datasets and
genome-wide comparisons of economically important spe-
cies showed that together with ochrophytes and hypho-
chytryomycotes, Oomycota form a single clade HOOF, a
sister to clade BOL, which combines bicoseecids, opa-
linates, and labyrinthulids. Within the HOOF clade,
oomycetes cluster with sequences known as MAST (marine
stramenopiles) (Lin et al., 2012; Cavalier-Smith, Scoble,
2013; Cavalier-Smith, 2018). “Molecular clock” attributes
the origin of oomycetes to the Silurian (Matari, Blair,
2014). The oldest evidence for the presence of oomycete-like
structures dates back to the Devonian (Krings et al., 2011),
whereas phytopathogenic oomycetes are noted as early as
the Carbon (Strullu-Derrien et al., 2011). The “basal
oomycetes” (orders Eurychasmales, Haptoglossales, Olpidi-
opsidales, Rhipidiales) are represented by a number of
holocarpic predominantly marine genera, i.e. oomycetes are
presumably of marine origin. Of the taxa identified to date,
85
the genera Eurychasma and Haptoglossa are the most an-
cient. These are obligate parasites of brown algae (Eury-
chasma), rotifers, and nematodes (Haptoglossa), which
demonstrate a high degree of specialization of the extru-
sion apparatus, resembling that of some alveolates (Beakes
et al., 2006; Kpper et al., 2006; Hakariya et al., 2007;
Sekimoto et al., 2008). According to Dyakov (2012), the
parasitism of representatives of the Haptoglossales order on
nematodes opened two terrestrial adaptive zones for
oomycetes, 1) the living plants, and 2) the plant debris in
estuaries, freshwater reservoirs, and terrestrial ecosystems.
At the same time, the soil oomycetes also adapted to the
colonization of the vegetative organs of land plants. The
crown of phylogenetic tree of oomycetes includes so-called
“peronosporoid clades” (orders Rhipidiales, Pythiales, Pero-
nosporales) and “saprolegnioid clades” (orders Atkinsi-
ellales, Leptomitales, Saprolegniales), corresponded to the
widely recognized classes Peronosporomycetes and Sapro-
legniomycetes, while the rank of the basal groups has not
yet been determined (Beakes et al., 2012, 2014).
The evolution of oomycetes in the fungus-like direction
descends from the level of heterotrophic (lost plastids)
amoeboid chromalveolates and seems to be parallel to the
evolution of eumycota. The polar hyphal growth of
oomycetes could be realized according to the fixation
scheme of unidirectional outflow during the colonization of
the plant filaments and parenchymas. The Peronosporo-
mycetes represent an “extreme edge” in oomycote evolution,
reaching well developed mycelial coenocytic forms with a
reinforced cell wall that makes it possible to colonize ter-
restrial environments as destructive plant parasites. How-
ever, the features of cell wall composition and proliferation
did not allow these organisms to develop in the way of aer-
ial mycelium differentiation (Zmitrovich, 2010; Yakovlev et
al., 2017).
XVI In older literature one can often find the stereotyped
Latin notation “insertae sedis” (vs “incertae sedis”).
86
87
SUPPLEMENT
88
Here we provide a retrospective overview of eukaryotic
megasystems since 1925, when Chatton first introduced the
category of eukaryotes into everyday circulation. The ana-
lysis of the presented dataset could be the subject of a sep-
arate monograph, but for now we simply invite the reader
to take excursions along this canvas in various directions
and enjoy this intelligence symphony. Among the presented
systems one can see both progressive and conservative,
some ones containing amazing insights. There are systems
that are deliberately reductionist, or, conversely, deployed.
Some systems are deliberately deideologized and pragmat-
ic (in the form of an unranked set of monophyletic groups),
or, in contrast, over-ideologized. The reader, leafing
through this part of the book, will see different styles of
scientific thinking, and such an excursion will, undoubted-
ly, be able to prompt him to actual solutions to current
taxonomic problems.
Overview of main classification schemes for eukaryotes from a
historical perspective
Author
Higher rank system
of eukaryotes
Chatton (1925)
Eucaryotes
Mastigiae
Flagellata
Rhizopoda
Sporozoa
Ciliae
Cnidiae
Copeland (1956)
Kingdom Protoctista
Phylum Rhodophyta
Class Bangialea
Class Heterocarpea
Phylum Phaeophyta
Class Heterokontea
Class Bacillariacea
Class Oomycetes
Class Melanophycea
Phylum Pyrrophyta
89
Class Mastigophora
Phylum Opisthokonta
Class Archimycetes
Phylum Inophyta
Class Zygomycetes
Class Ascomycetes
Class Hyphomycetes
Class Basidiomycetes
Phylum Protoplasta
Class Zoomastigida
Class Mycetozoa
Class Rhizopoda
Class Heliozoa
Class Sarkodina (sic!)
Phylum Fungilli
Class Sporozoa
Class Neosporidia
Phylum Ciliophora
Class Infusoria
Class Tentaculifera
Chadefaud (1960)
Eucaryotes
•Algues Eucaryotes =
Phycophytes
Champignons = Mycophytes
Plantes a cormus (Plantes
suprieures, Cormophytes, ou
Archgoniates)
Animaux, ou Zoaires
Protozoaires
Mtazoaires
Jeffrey (1971)
Superkingdom Eucytota
Kingdom Rhodobiota
Kingdom Chromobiota
Kingdom Zoobiota
Kingdom Mycobiota
Kingdom Chlorobiota
Margulis (1971)
Eukaryotes
Kingdom Protista
90
Kingdom Fungi =
Amastigomycota (Zygomycota,
Ascomycota, Basidiomycota)
Kingdom Animalia (Metazoa)
Kingdom Plantae = Metaphyta
Bryophyta
Tracheophyta
Zerov (1972)
Eucaryota
Animal phyla
Protozoa
Metazoa
Plant phyla
Myxomycota
Chytridiomycota
Eumycota
Saprolegniomycota
Xanthophyta
Chrysophyta
Diatomophyta
Phaeophyta
Pyrrophyta
Cryptophyta
Euglenophyta
Chloromonadophyta
Rhodophyta
Chlorophyta
Chlorophycophytina
Anthocerotophytina
Bryophytina
Psilophytina
Lepidophytina
Sphenophytina
Pterophytina
Gymnospermophytina
Angiospermophytina
Kusakin, Starobogatov
(1973)
Eucaryota
Rhodobionta
Rhodophyta
Chlorobionta
91
Euglenophyta
Chlorophyta
Charophyta
Cormophyta
Chrysoleucobionta
Chloromonadophyceae
Cryptophyceae
Pyrrophyta
Xanthophyta
Bacillariophyta
Chrysophyta
Mycophyta
Myxomycophyta
Zoomastigina
Porifera
Phaeophyta
Metazoa
Ciliophora
Sarcodina
Sporozoa
Cnidosporidia
Leedale (1974)
Eukaryote
Plantae
Rhodophyta
[Oomycota, Bacillariophyta,
Xanthophyta, Chrysophyta,
Phaeophyta]
[Chlorophyta, Charophyta,
Bryophyta, Tracheophyta]
Cryptophyta
Haptophyta
Dinophyta
Euglenophyta
Fungi
Chytridiomycota
Hyphochytridiomycota (sic!)
[Zygomycota, Basidiomycota,
Ascomycota]
Myxomycota
92
Plasmodiophoromycota
Animalia
Zoomastigina
Sarcodina
Mesozoa
Ciliophora
[Coelenterata, Platyhelminthes,
Aschelminthes, Tentaculata, An-
nelida, Mollusca, Arthropoda,
Chaetognatha, Echinodermata,
Chordata, Hemichordata]
Sporozoa
Porifera
Cnidosporidia
Takhtadjan (1973)
Superkingdom Eukaryota
Kingdom Animalia
Kingdom Mycetalia
Subkingdom Myxobionta
Subkingdom Mycobionta
Kingdom Vegetabilia
Subkingdom Rhodobionta
Subkingdom Phycobionta
Subkingdom Embryobionta
Margulis (1974)
Superkingdom (chromosomal
organization) Eukaryota
Kingdom Protoctista
grade Amitotica
grade Mitotica
Kingdom Fungi
Kingdom Animalia
Kingdom Plantae
Edwards (1976)
Eucaryota
Erythrobionta = Rhodophyta
Chlorobionta
Tracheophyta
Bryophyta
Chlorophyta
Euglenophyta
Fungi 1
93
Basidiomycota
Ascomycota
Zygomycota
Chytridiomycota
Ochrobionta
Phaeophyta
Chrysophyta
Pyrrhophyta
Cryptophyta
Fungi 2
Hyphochytridiomycota (sic!)
Oomycota
Labyrinthulomycota
Myxobionta
Myxogastriomycota
Acrasiomycota
Dictyosteliomycota
Protosteliomycota
animals
Cavalier-Smith (1978)
Superkingdom Eukaryota
Kingdom Aconta
Rhodophyta
zygomycete fungi
ascomycete fungi
basidiomycete fungi
Acrasida
Kingdom Haptophyta
Kingdom Cryptophyta
Kingdom Heterokonta
Eustigmatophyta
chloromonads
Xanthophyta
biflagellate (= oomycete) fungi
Myxomycetes
hyphochytrid fungi
Phaeophyta
Chrysophyta
chytrid fungi
Actinopoda
94
Foraminifera
amoeboflagellates
diatoms
Kingdom Corticoflagellata
dinoflagellates
Metamonadina
Ciliata
Sporozoa
Choanoflagellata, sponges
opalinids, Mesozoa
eumetazoans
Kingdom Euglenoida
Euglenophyta
Kinetoplastida
Kingdom Chlorophyta
chlorophyte algae
Prasinophyta
Bryophyta
Tracheophyta
Stewart, Mattox (1980)
Eukaryotes
Kingdom Dinobiota (with tubu-
lar cristae)
Dinophyceae
Bacillariophyceae
Bicosoecida
Chloromonadophyceae
Chrysophyceae
Ciliophora
Eustigmatophyceae
Myxomycetes
Oomycetes
Opalinata
Phaeophyceae
Prymnesiophyceae
Xanthophyceae
Kingdom Bodonobiota [with flat-
tened (lamellar) cristae]
Ascomycetes
Basidiomycetes
95
Chlorophyta
Choanoflagellida
Chytridiomycetes
Cryptophyceae
Cyanophora
Euglenophyceae
higher animals
higher plants
kinetoplastida
Rhodophyceae
Krylov et al. (1980)
Subkingdom Protozoa
Phylum Mastigophora
Subphylum Lamellicristata
Superclass Cryptomastogonta
Superclass Chloromastigonta
Superclass Choanomastigonta
Superclass
Kinetoplastmastigonta
Subphylum Tubulicristata
Superclass Dinomastigonta
Superclass
Parachromomastigonta
Superclass Chromomastigonta
Superclass Parasitomastigonta
Superclass
Parachrysozoomastigonta
Phylum Opalinidomorpha
Phylum Sarcodina
Subphylum Lobosa
Subphylum Labyrinthomorpha
Subphylum Xenophiophora
Subphylum Filosa
Subphylum Foraminifera
Subphylum Granuloreticulosa
Subphylum Heliozoa
Subphylum Taxopoda
Subphylum Radiolaria
Class Polycystinea
Class Phaeodaria
96
Phylum Acantharia
Phylum Sporozoa
Phylum Microsporidia
Phylum Cnidosporidia
Phylum Ascetospora
Phylum Ciliophora
Cavalier-Smith (1981)
Superkingdom Eukaryota
Kingdom Eufungi
Kingdom Ciliofungi
Kingdom Animalia
Kingdom Biliphyta
Kingdom Viridiplantae
Kingdom Euglenozoa
Kingdom Protozoa
Kingdom Cryptophyta
Kingdom Chromophyta
Parker (1982)
Superkingdom Eukaryotae
Kingdom Plantae
Kingdom Protista
Kingdom Animalia
Cavalier-Smith (1983)
Eukaryota
Kingdom Protozoa
Archezoa
Sarcomastigota
Euglenozoa
Choanociliata
Kingdom Animalia
Parazoa
Metazoa
Kingdom Fungi
Ciliofungi
Eufungi
Kingdom Plantae
Biliphyta
Viridiplantae
Kingdom Chromista
Cryptophyta
Chromophyta
97
Mhn (1984)
Superkingdom Eukaryonta
Suprakingdom (sic!) Aconta
Kingdom Rhodocyanobionta
Phylum Cyanidiophyta
Kingdom Erythrobionta
Phylum Rhodophyta
Suprakingdom Contophora
Kingdom Chlorobionta
Phylum Prasinophyta
•••Phylum Charophyta
Phylum Ulvaphyta
Phylum Chlorophyta
Kingdom Flagelloopalinida
Phylum Protomonada (sic!)
Phylum Opalinidea
Kingdom Euglenophytobionta
Phylum Euglenophyta
Kingdom Eumycota
Phylum Opisthomastigomycota
Phylum Amastigomycota
Kingdom Dinophytobionta
Phylum Dinophyta
Phylum Granuloreticulosa
Phylum Acanthiolaria
Phylum Polannulifera
Phylum Ciliophora
Kingdom Crytophytobionta
Phylum Cryptophyta
Kingdom Colponemata
Phylum Colponemaria
Kingdom
Chloromonadophytobionta
Phylum Chloromonadophyta
Kingdom Chromophytobionta
○○○Subkingdom Chromobionta
Phylum Xanthophyta
Phylum Pantonemomycota
Phylum Proteomyxidea
Phylum Labyrinthomorpha
98
Phylum Chrysophyta
Phylum Hydraulea
Phylum Trichomycetea
Phylum Mycetozoidea
Phylum Pedinellaphyta
Phylum Bacillariophyta
Phylum Phaeophyta
○○○Subkingdom
Eustigmatobionta
Phylum Eustigmatophyta
○○○Subkingdom Choanobionta
Phylum Craspedophyta
○○○Subkingdom
Haptophytobionta
Phylum Haptophyta
Suprakingdom Animalia
○○Middle-Kingdom Parazoa
Kingdom Porifera
Kingdom Archeata
Kingdom Placozoomorpha
○○Middle-Kingdom Eumetazoa
Kingdom Radiata
Phylum Cnidaria
Phylum Ctenophora
Kingdom Bilateria
Lipscomb (1985)
Eukaryotes
Group 1
Cryptomonadida =
Cryptophyceae
Chloromonadida =
Chloromonadophyceae
Prymnesiida =
Prymnesiophyceae
Phaeophyceae
Chrysomonadida
Chrysophyceae
Xanthomonadida =
Xanthophyceae
Eustigmatomonadida =
99
Eustigmatophyceae
Group 2
Prasinomonadida =
Prasinophyceae
Phytomonadida = Chlorophyceae
Gameophyceae
Group 3
Ascomycetes
Zygomycetes
Group 4
Trypanosomatina
Bodonina
Euglenida = Euglenophyceae
Stephanopogonida
Group 5
Dinoflagellida = Dinophyceae
Ciliophora
Schizopyrenida
Opalinida
Group 6
Choanoflagellida
Porifera
Mesozoa
Cnidaria
Placozoa
Acoelomata
Group 7
Oomycetes
Chytridiomycetes
Group 8
Hypermastigida
Trichomonadida
Retortamonadida
Diplomonadida
Oxymonadida
Proteromonadida
Bicosoecia
Group 9
Rhodophyceae
100
Corliss (1986)
Superkingdom Eukaryota
Kingdom Animalia
Kingdom Plantae
Kingdom Fungi
Kingdom Protista
Starobogatov (1986)
Eukaryota
Superkingdom Akonta
Kingdom Rhodymeniontes
Kingdom Mycota
Superkingdom Lamellicristata
Kingdom Cryptomonadontes
Kingdom Euglenontes
Kingdom Plantae
Kingdom Animalia
Superkingdom Tubulicristata
Kingdoms Ellipsoidiontes
Kingdom Peridiniontes
Kingdom Chromulinontes
Lipscomb (1989)
Eukaryotes
Rhodophyca
Supergroup 1
Plantae
Supergroup 2
Cryptomonada
Supergroup 3
Amoebae
Oomycota
Chromobiota
Heliozoa
Supergroup 4
Polymastigota
Animalia, Choanozoa, Fungi
Opalinida, Dinociliata,
Euglenaria
Karpov (1990)
Kingdom Protista
Superphylum Rhodophyta
Phylum Rhodophytae
Superphylum Dinomorpha
101
Phylum Dinophyta
Dinomorpha insertae sedisXVI:
Ebriida, Syndinea, Ellobiopsida
Superphylum Cryptophyta
Phylum Cryptophytae
Superphylum Euglenozoa
Phylum Euglenophyta
Phylum Kinetoplastidae
Superphylum Choanomastigota
Phylum Choanomonada
Superphylum Polymastigota
Phylum Diplomonada
Class Retortamonadea
Class Diplomonadea
Phylum Oxymonada
Phylum Parabasalia
Class Trichomonadea
Class Hypermastiginea
Superphylum Sporozoa
Phylum Perkinsemorpha
Class Spiromonadea
Class Perkinsidea
Phylum Sporozoae
Superphylum Ciliophora
Phylum Ciliata
Superphylum Chromophyta
Phylum Chrysophyta
Class Chrysophyceae
Class Xanthophyceae
Class Synurophyceae
Class Pseudodendromonada
Phylum Phaeophyta
Phylum Bacillariophyta
Phylum Haptophyta
Phylum Raphidophyta
Phylum Eustigmatophyta
Phylum Saprolegnia
Subphylum Saprolegniea
Subphylum Labyrinthomorpha
102
Class Labyrinthulea
Class Thraustochytridea
Phylum Hyphochytrida
Phylum Slopalinata
Class Proteromonadea
Class Opalinatea
Phylum Pedinellomorpha
Class Pedinellidea
Class Actinophryidea
Class Desmothoracidea
Class Taxopodidea
Chromophyta insertae sedis:
Spongomonada
Superphylum Chytridia
Phylum Chytridea
Superphylum Plasmodiophora
Phylum Plasmodiophorea
Superphylum Mycetozoa
Phylum Eumycetozoa
Class Protostelea
Class Myxogastrea
Phylum Cercomonada
Superphylum Rhizopoda
Phylum Lobosea
Class Gymnamoebea
Class Tetaceolobosea
Lobosea insertae sedis: Pelomyxa
palustris, Mastigina hylae
Phylum Heterolobosea
Class Schizopyrenidae
Class Acrasidae
Phylum Filosea
Class Acotchulinea
Class Testaceafilosea
Filosea insertae sedis:
Dictyostelida
Phylum Granuloreticulosea
Class Athalamea
Class Monothalamea
103
Class Foraminiferea
Superphylum Actinopoda
Phylum Heliozoa
Class Axoplasthelidea
Class Centroplasthelidea
Phylum Radiolaria
Subphylum Acantharia
Subphylum Euradiolaria
Class Polycystinea
Class Phaeodarea
Superphylum Myxospora
Phylum Myxosporae
Class Myxosporidea
Class Actinomyxidea
Phylum Ascetosporae
Class Stellatosporea
Class Paramyxea
Superphylum Glaucophyta
Phylum Glaucophytae
Protista insertae sedis:
Apusomonadea,
Thaumatomonadea,
Xenophyophorea, Colponema
loxodes
Lipscomb (1991)
Eukaryotes
Rhodophyta
Chlorobionts
Cryptophytes
Chromobionts
Polymastigotes
Animals
Amoeboflagellates
Opalinids
Dinoflagellates
Ciliates
Euglenozoa
Cavalier-Smith (1993)
Empire Eukaryota
Superkingdom Archezoa
Kingdom Archezoa
104
Superkingdom Metakaryota
Kingdom Protozoa
Subkingdom Adictyozoa
Subkingdom Dictyozoa
Kingdom Plantae
Subkingdom Viridiplantae
Subkingdom Biliphyta
Kingdom Animalia
Subkingdom Radiata
Subkingdom Bilateria
Kingdom Fungi
Kingdom Chromista
Subkingdom Chlorarachnia
Subkingdom Euchromista
Corliss (1994)
Empire Eukaryota
Kingdom Archezoa
Kingdom Protozoa
Kingdom Chromista
Kingdom Plantae
Kingdom Fungi
Kingdom Animalia
Kusakin, Drozdov
(1994)
Dominion Eukaryota
Subdominion Archekaryota
Kingdom Microsporobionta
Kingdom Archemonadobionta
Subdominion Metakaryota
Kingdom Rhodobionta
Kingdom Cryptobionta
Kingdom Euglenobionta
Kingdom Dinobionta
Kingdom Chromobionta s. lato
Kingdom Chlorobionta =
Viridiplantae
Mycobionta = Fungi
Inferiobionta = Parazoa
Metazoa
Incertae sedis: Myxospora,
Chlorarachnida, Gyromitus,
Discocelis, Jacoba
105
Cavalier-Smith (1995)
Eukaryota
Kingdom Archezoa
Kingdom Protozoa
Kingdom Cryptista
Kingdom Chromista
Kingdom Plantae
Kingdom Animalia
Kingdom Fungi
Hausmann, Hlsmann
(1996)
Empire Eukaryota
Kingdom Microspora
Phylum Microspora
Kingdom Mastigota
○Subkingdom Archamoebaea
Phylum Karyoblasta
○Subkingdom Dimastigota
○○Superphylum Tetramastigota
Phylum Retortamonada
Phylum Axostylata
○○Superphylum Metakaryota
Phylum Euglenozoa
Phylum Heterolobosa
Phylum Dictyostela
Phylum Protostela
Phylum Myxogastra
Phylum Chromista
Phylum Alveolata
Phylum Choanoflagellata
Phylum Chlorophyta
Metakaryota incertae sedis:
Amoebozoa, Lobosea,
Gymnamoebia, Testacealobosia,
Acarpomyxea, Filosea,
Granuloreticulosa, Athalamea,
Monothalamea, Foraminiferea,
Actinopoda, Acantharea,
Polycystinea, Phaeodarea,
Heliozoea, Ascetospora,
Haplosporea, Paramyxea,
Myxozoa
106
Cavalier-Smith (1998)
Empire Eukaryota
Kingdom Protozoa
Subkingdom Archezoa
Subkingdom Neozoa
Infrakingdom Sarcomastigota
Infrakingdom Discicristata
Infrakingdom Alveolata
Infrakingdom Actinopoda
Kingdom Animalia
Subkingdom Radiata
Subkingdom Myxozoa
Subkingdom Bilateria
Kingdom Fungi
Subkingdom Eomycota
Subkingdom Neomycota
Kingdom Plantae
Subkingdom Biliphyta
Subkingdom Viridaeplantae
Kingdom Chromista
Subkingdom Cryptista
Subkingdom Chromobiota
Infrakingdom Heterokonta
Infrakingdom Haptophyta
Kusakin, Drozdov
(1998)
Dominion Eukaryota
Kindom Microsporobiontes
Phylum Microsporidiophyles
Kingdom Archemonadobiontes
Phylum Pelomyxophyles
Phylum Retortamonadophyles
Phylum Hexamitophyles
Phylum Oxymonadophyles
Phylum Trichomonadophyles
Kingdom Euglenobiontes
Subkingdom Percolobionti
Phylum Acrasiophyles
Subkingdom Euglenobionti
Phylum Stephanopogonophyles
Phylum Diplonemophyles
107
Phylum Bodonophyles
Phylum Euglenophyles
Kingdom Myxobiontes
Subkingdom Myxomycetobionti
Phylum Cercomonadophyles
Phylum Dictyosteliophyles
Phylum Physarophyles
Subkingdom Myxozoobionti
Phylum Entamoebophyles
Phylum Haplosporophyles
Phylum Paramyxophyles
Phylum Myxidiophyles
Kingdom Rhodobiontes
Phylum Bangiophyles
Kingdom Alveolates
Subkingdom Peridiniobionti
○Superphylum
Peridiniophylacei
Phylum Peridiniophyles
○Superphylum
Apicomplexophylacei
Phylum Perkinsophyles
Phylum Gregarinophyles
Subkingdom Parameciobionti
Phylum Hemimastigophyles
Parameciophyles
Kingdom Heterokontes
Phylum Bicosoecophyles
Phylum Labyrintulophyles
Phylum Saprolegniophyles
Phylum Hyphochytriophyles
Phylum Diatomophyles
Phylum Tribonematophyles
Phylum Fucophyles
Phylum Eustigmatophyles
Phylum Sinurophyles
Phylum Chrysococcophyles
Phylum Raphidomonadophyles
Phylum Dictyochophyles
108
Phylum Pedinellophyles
Class Pedinellodes
Class Actinophryiodes
Class Clathrulinodes
Class Pelagomonadiodes
Class Oikomonadiodes
Hampl et al. (2009)
Eukaryotic “supergroups”
“Unikonts”
Amoebozoa
Opisthokonta
[“Bikonts”]
Excavata
Malawimonas
Metamonada
Discoba
Jakoba
[Euglenozoa]
Archaeplastida
Rhizaria
“Chromalveolata” [paraphyletic]
Patterson (1999)
Eukaryotic taxa without known
sister groups
Acantharea
Actinophryids
Alveolates
Ancyromonas
apusomonads
Biomyxa
Caecitellus
Carpediemonas
Centroheliozoa
cercomonads
Chlorarachniophytes
Coelosporidium
Collodictyon
copromyxids
Cryothecomonas
cryptomonads
desmothoracids
109
dimorphids
Diphylleia
diplomonads
Discocelis
ebriids
ellobiopsids
Entamoebidae
Euglenozoa
Fonticula
Glaucophytes
Granuloreticulosa
Gymnophrea
Gymnosphaerida
haplosporids
haptophytes
Heterolobosea
Hyperamoeba
jakobids
kathablepharids
Komokiacea
Luffisphaera
Microsporidia
Ministeria
Multicilia
•nephridiophagids
Nucleariidae
opisthokonts
oxymonads
parabasalids
Paramyxea
pelobionts
Phaeodarea
Phagodinium
Phalansterium
plasmodiophorids
Polycystinea
pseudodendromonads
Pseudospora
ramicristates
110
red algae
Reticulomyxa
retortamonads
rosette agent
Spironemidae
spongomonads
Stephanopogon
Sticholonche
stramenopiles
Telonema
thaumatomonads
Trimastix
vampyrellids
Viridaeplantae
Xenophyophores
Protista without contemporary
identity
Karpov (2000)
[Protista]
Phylum Cryptophyta
Class Cryptophyceae
Phylum Euglenozoa
Class Euglenoidea
Class Kinetoplastidea
Phylum Chrysophyta
Class Chrysophyceae
Class Synurophyceae
Class Pelagophyceae
Phylum Haptophyta
Class Haptophyceae
Phylum Raphidophyta
Class Raphidophyceae
Phylum Saprolegnia
Class Saprolegnea (=
Oomycetes)
Class Labyrinthomorphea
Phylum Opalinata
Class Proteromonadea
Class Opalinatea
“Chromista” incertae sedis:
111
Spongomonada,
Pseudodendromonada
Phylum Choanomonada
Class Choanomonadea
Phylum Polymastigota
Class Diplomonadea
Class Oxymonadea
Class Parabasalea
Phylum Plasmodiophora
Phylum Mycetozoa
Class Cercomonadea
Class Eumycetozoea
Mycetozoa incertae sedis:
Hyperamoeba flagellata
Phylum Rhizopoda
Class Lobosea
Class Heterolobosea
Class Peloflagellatea =
Caryoblastea
Class Filosea
Class Xenophyophorea
Rhizopoda incertae sedis:
Komokiida, Athalamia,
Monothalamia
Phylum Foraminifera
Hausmann et al. (2003)
Empire Eukaryota = Eukarya
Phylum Tetramastigota
Phylum Discicristata
Phylum Hemimastigophora
Phylum Pseudociliata
Phylum Chromista
Phylum Alveolata
Phylum Cercozoa
Phylum Foraminifera =
Granuloreticulosa
Phylum Biliphyta
Phylum Viridiplantae =
Chlorobionta
Phylum Amoebozoa
112
Phylum Opisthokonta
Eukaryota incertae sedis:
Actinopoda, Paramyxea
Cavalier-Smith (2003)
Eukaryota
Kingdom Protozoa
clade unikonts
Phylum Amoebozoa
clade opisthokonts
Phylum Choanozoa
Kingdom Animalia
Kingdom Fungi
clade bikonts
○○Infrakingdom Rhizaria
Phylum Cercozoa
Phylum Retaria (Radiozoa,
Foraminifera)
○○Infrakingdom Excavata
Phylum Loukozoa
Phylum Metamonada
Phylum Euglenozoa
Phylum Percolozoa
Kingdom Plantae
Phylum Viridaeplantae
Phylum Rhodophyta
Phylum Glaucophyta
Kingdom Chromista
Phylum Cryptista
Phylum Heterokonta
Phylum Haptophyta
○○Infrakingdom Alveolata
Phylum Ciliophora
Phylum Miozoa
Protalveolata
Dinozoa
Apicomplexa
Phylum Apusozoa
Thecomonadea
Diphylleida
113
Zmitrovich (2003)
Supraregnum Discicristata
Regnum Euglenozoea
Phylum Diplonemea
Phylum Kinetoplastida
Phylum Euglenophyta
Phylum Percolozoa
Phylum Excavata
Supraregnum Lamellicristata
Regnum Plantae
○Subregnum Biliphytalia
Phylum Glaucocystophyta
Phylum Rhodophyta
○Subregnum Chimaerophytalia
Phylum Cryptophyta
Appendix Heliozoa
(Centrohelidea)
○Subregnum Mycetalia
Phylum Laboulbeniomycota
Phylum Eumycota
○Subregnum Prasinophytalia
Phylum Chlorophyta
Phylum Phragmophyta
Phylum Cormophyta
Phylum Phycomycota
Phylum Microsporidia
Regnum Animalia
Phylum Choanozoa
Phylum Porifera
Phylum Enterozoa
Supraregnum Tubulicristata
Regnum Dinozoea
○Subregnum Sarcodinia
Phylum Cercozoa
Phylum Entamoebia
Phylum Ebriida
Phylum Radiolaria
Phylum Haptophyta
Phylum Foraminifera
114
○Subregnum Alveodinia
Phylum Dinophyta
Phylum Apicomplexa
Phylum Ciliophora
Regnum Chromophyta
Phylum Ochrophyta
Phylum Sagenista
Phylum Opalinata
Cavalier-Smith (2004)
Empire Eukaryota
Kingdom Protozoa
Kingdom Animalia
Phylum Myxozoa and 21 other
phyla
Kingdom Fungi
Phylum Archemycota
Phylum Microsporidia
Phylum Ascomycota
Phylum Basidiomycota
Kingdom Plantae
○○Subkingdom Biliphyta
Phylum Glaucophyta
Phylum Rhodophyta
○○Subkingdom Viridaeplantae
Phylum Chlorophyta
Phylum Bryophyta
Phylum Tracheophyta
Kingdom Chromista
○○Subkingdom Cryptista
Phylum Cryptista
cryptophytes
goniomonads
katablepharids
○○Subkingdom Chromobiota
○○○Infrakingdom Heterokonta
Phylum Ochrophyta
Phylum Pseudofungi
Phylum Opalozoa (incl.
Opalinata, Sagenista)
115
○○○Infrakingdom Haptista
Phylum Haptophyta
Adl et al. (2005)
Eukaryota
Amoebozoa
Opisthokonta
Rhizaria
Archaeplastida
Chromalveolata
Cryptophyceae
Haptophyta
Stramenopiles
Alveolata
Excavata
Incertae sedis Eukaryota
Lecointre, Le Guyader
(2006)
Eucaryotes
Bicontes
Ligne verte
Chromoalvols
Alvolobiontes
Stramnopiles
Cryptophytes
Haptophytes
Rhizariens
Excavobiontes
Unicontes
Amoebozoaires
Opisthocontes
Champignons
Choano-organismes
Choanoflagells
Mtazoaires
Cavalier-Smith (2009)
Eukaryota
Bikonta
Apusozoa
Excavata
Rhizaria
Corticata
Plantae = Archaeplastida
116
Chromalveolata
Chromista
Alveolata
Unikonta
Amoebozoa
Opisthokonta
Choanozoa
Animalia
Fungi
Cavalier-Smith (2010)
Eukaryota
Kingdom Protozoa
Subkingdom Sarcomastigota
Amoebozoa
Apusozoa
Choanozoa
Subkingdom Eozoa
○○Infrakingdom Excavata
○○Infrakingdom Euglenozoa
Kingdom Animalia
Kingdom Fungi
Kingdom Plantae (Glaucophyta,
Rhodophyta, Viridiplantae)
Kingdom Chromista
Subkingdom Hacrobia
Cryptista
centrohelid Heliozoa
Haptophyta
Subkingdom Harosa
Rhizaria
Halvaria
Alveolata
Heterokonta
Koonin (2010)
Eukaryotes
LEKA
excavates
diplomonads
oxymonads
parabasalids
117
jakobids
[kinetoplastids, Heterolobosea]
Rhizaria
[cercomonads, heteromitids]
Haplosporidia
Foraminifera
Acantharia
Unikonts
opisthokonts
Fungi [Microsporidia, Dikarya,
chytrids]
Metazoa
Amoebozoa
dictyostelids
Lobosea
Chromalveolates
[haptophytes, cryptomonads]
[diatoms, rapidophytes,
thraustochytrids, Oomycetes]
[Apicomplexa, dinoflagellates,
ciliates]
Plantae
glaucophytes
red algae
[green algae, land plants]
Korsun et al. (2011)
Eukaryota
Excavata
Discicristata
Heterolobosea
Acrasida
Schizopyrenida
Euglenoidea
Kinetoplastidea
Parabasalia
Trichomonadida
Hypermastigida
Diplomonadea
Oxymonadea
Amoebozoa
118
Pelobiontida
Gymnamoebia
Testaceolobosia
Myxomycetes
Protostelia
Dictyostelia
Myxogastria
Ancyromonas
Apusomonadida
?Hemimastigophora
Opisthokonta
Nucleariida
Rotosphaerida
Ichtyosporea
Choanoflagellata
Metazoa
Myxozoa
Fungi
”Chytridiomycetes”
”Zygomycetes”
Microsporidia
Ascomycetes
Basidiomycetes
Heterokonta
Actinophryida
Bicosoecida
Pseudodendromonadida
Blastocystida
Opalinata
Labyrinthomorpha
Oomycetes
Pedinellida
Chrysophyta
Raphidophyta
Phaeophyta
Bacillariophyta
Alveolata
Ciliophora
Sporozoa = Apicomplexa
119
Colpodellea
Dinoflagellata
Rhizaria
Cercozoa
Phaeodaria
Euglyphida
Thaumatomonadida
Spongomonadida
Cryomonadida
Pansomonadida
Cercomonadida
Desmothoracida
Dimorphida
Chlorarachnida
Paramyxea
Plasmodiophorea
Haplosporidia
Gromiida
Gymnosphaerida
Hacrobia
Haptophyta
Centrohelida
Katablepharida
Cryptophyta
Archaeplastida
Rhodophyta
Viridiplantae
Chlorophyta
Charophyta
Embryophyta
Luketa (2012)
Dominium Eukaryobiota
Subdominium Unikonta
Regnum Amoebozoida
Subregnum Amoebozoides
Subregnum Breviatides
Regnum Apusozoida
Regnum Breviatida
Subregnum Nucleariides
Subregnum Microsporides
120
Subregnum Fungides
Regnum Animalioida
Subregnum Mesomycetozoides
Subregnum Choanozoides
Subregnum Animalioides
Subdominium Bikonta
Regnum Excavatida
Regnum Corticatida
Subregnum Archaeplastides
Subregnum Cryptophytides
Subregnum Haptophytides
Subregnum Rhizarides
Subregnum Stramenopilides
Subregnum Alveolatides
Adl et al. (2012)
Eukaryota
Amorphea
Amoebozoa
Opisthokonta
Diaphoretickes
SAR
Stramenopiles
Alveolata
Rhizaria
Archaeplastida
Excavata
Incertae sedis Eukaryota
Cavalier-Smith (2013)
Eukaryota
Archezoa
Metamonada
mitozoa
neozoa
podiates (opisthokonts [= Fun-
gi, Animalia, Choanozoa] plus
Amoebozoa and Sulcozoa)
corticates (Plantae plus
Chromista)
Neolouka
Eolouka (Jakobea plus
Tsukubea)
121
Discicristata (Percolozoa plus
Euglenozoa)
Leontyev (2013)
Eukaryota
Subdomain Excavata
Superkingdom Excavata
Kingdom Metamonada
Phylum Fornicata
Phylum Parabasalia
Phylum Preaxostyla
Kingdom Discoba
Phylum Jakobida
Phylum Discicristata
Subdomain Diaphoretikes (sic!)
= Bikonta
Superkingdom Rhizaria
Kingdom Rhizaria
Phylum Cercozoa
Phylum Retaria
Superkingdom Chromalveolata
Kingdom Chromista =
Stramenopiles
Phylum Bicosoecida
Phylum Labyrinthulida
Phylum Opalinata
Phylum Actinophryidae
Phylum Oomycota =
Peronosporomycota
Phylum Hyphochytriomycota
Phylum Chromophyta =
Ochrophyta
Kingdom Alveolata
Phylum Dinoflagellata =
Dinophyta
Phylum Ciliata
Phylum Apicomplexa
Superkingdom Hacrobia
Kingdom Hacrobia
Phylum Haptophyta
Phylum Cryptophyta
122
Phylum Centrohelida
Superkingdom Archaeplastida
Kingdom Glaucophyta
Phylum Glaucophyta
Kingdom Rhodophyta
Kingdom Viridiplantae =
Chloroplastida
Phylum Chlorophyta
Phylum Streptophyta
Subdomain Amorphea =
Unikonta
Superkingdom Apusozoa
Kingdom Apusozoa
Phylum Apusomonadida
Phylum Ancyromonadida
Phylum Breviatea
Phylum Hemimastigophora
Superkingdom Amoebozoa
Kingdom Amoebozoa
Phylum Tubulinea
Phylum Discosea
Phylum Archamoebae
Phylum Mycetozoa
Superkingdom Opisthokonta
Kingdom Holomycota =
Nucleomycea
Subkingdom Nucleariida
Subkingdom Fonticulida
Subkingdom Rozellida
Subkingdom Fungi
Phylum Microsporomycota
Phylum
Neocallimastigomycota
Phylum Chytridiomycota
Phylum Blastocladiomycota
Phylum Zygomycota
Phylum Ascomycota
Phylum Basidiomycota
Kingdom Holozoa
123
Subkingdom Filasterea
Subkingdom Mesomycetozoea =
Ichtyosporea
Subkingdom Aphelidea
Subkingdom Choanozoa
Subkingdom Metazoa (35 phyla)
Paps et al. (2013)
Eukaryota
Bikonta
Unikonta
Amoebozoa
Apusozoa
Opisthokonta
Pawlowski (2013)
Eukaryotes
Opisthokonta
Amoebozoa (incl. Breviatea)
Apusomonadidae
Ancyromonadidae
Collodictyonidae
Rigidifilida
Excavata
Katablepharidae
Cryptophyta
Picobiliphyta
Archaeplastida (incl.
Glaucophyta)
Centrohelida
rappemonads
Haptophyta
Telonemia
SAR (Rhizaria, Stramenopiles,
Alveolata)
Boudouresque (2015)
Eukaryotes
Unikonts
Opisthokonta
Amoebobionta = Amoebozoa
Bikonts
Cryptobionta
Archaeplastida = Plantae;
Incertae sedis: Centrohelida
124
Rhizaria
Alveolata
Stramenopiles = Heterokonta
Haptobionta
Discicristates
Excavates
Ruggiero et al. (2015)
Superkingdom Eukaryota
Kingdom Protozoa
Subkingdom Eozoa
Infrakingdom Euglenozoa
Infrakingdom Excavata
Subkingdom Sarcomastigota
Phylum Amoebozoa
Phylum Choanozoa
Phylum Microsporidia
Phylum Sulcozoa
Kingdom Chromista
Infrakingdom Halvaria
○○Superphylum Alveolata
○○Superphylum Heterokonta
Infrakingdom Rhizaria
Kingdom Fungi
Subkingdom Dikarya =
Neomycota
Subkingdom Eomycota
Kingdom Plantae =
Archaeplastida
Subkingdom Biliphyta
Subkingdom Viridiplantae
Kingdom Animalia
Derelle et al. (2015)
Eukaryota
Opimoda
Opisthokonta
Amoebozoa
malawimonads and
collodictyonids
Diphoda
Discoba (Jakobida,
Heterolobosea, Euglenozoa)
125
Diaphoretickes
Archaeplastida
Cryptomonadida
SAR (Stramenopiles, Alveolata,
Rhizaria)
Speijer et al. (2015)
Eukaryotes
Opimoda
Obazoa
Opisthokonta (Metazoa,
Choanoflagellata, Filasterea,
Ichthyosporea, Opisthosporidia,
Fungi, Cristidiscoidea)
Apusomonadida
Breviatea
Amoebozoa
Collodictyonida =Diphyllatea
Rigifilida
Mantamonadida
Ancyromonadida =
Planomonadida
Malawimonadida
Metamonada (Fornicata,
Parabasalia, Preaxostyla)
Diphoda
Discoba (Heterolobosea,
Euglenozoa, Tsukubamonadida,
Jakobida)
Diaphoretickes
Archaeplastida (Rhodophyta,
Chloroplastida, Glaucophyta)
SAR (Stramenopiles, Alveolata,
Rhizaria)
Cryptista (Katablepharida,
Cryptomonadida,
Palpitomonadida)
Haptophyta (?incl.
rappemonads)
Picozoa
Telonemia
126
Centrohelida (incl.
?Microhelida)
Cavalier-Smith et al.
(2015)
Eukaryota
Corticata
Plantae
Chromista
Harosa
Rhizaria
Halvaria
Heterokonta
Alveolata
Hacrobia
Haptista
Cryptista
scotokaryotes
Metamonada
?Neolouka (Malawimonas)
Podiates
Sulcozoa (Varisulca, ?Neolouka,
Apusozoa)
opisthokonts (Animalia,
Choanozoa, Fungi)
Amoebozoa
Eozoa (similar to Discoba)
Eolouka
Jakobea
Tsukubamonadea
Percolozoa
Euglenozoa
Silar (2016)
Eukaryota
Amorphea
Sulcozoa
Opisthokonta
Amoebozoa
”Excavata”
Metamonada
Discoba
Diaphoretickes
Archaeplastida
127
“Hacrobia”
Heterokonta
Alveolata
Rhizaria
Tedersoo (2017)
Domain Eukaryota
Subdomain Archaeplastida
Kingdom Glaucocystoplantae
Kingdom Rhodoplantae
Kingdom Viridiplantae
Subdomain Excavata
Kingdom Euglenozoa
Kingdom Fornicata
Kingdom Heterolobosa
Kingdom Jakobida
Kingdom Malawimonada
Kingdom Oxymonada
Kingdom Parabasalia
Kingdom Tsukubamonada
Subdomain Harosa
Kingdom Alveolata
Kingdom Rhizaria
Kingdom Stramenopila
Subdomain Opisthokonta
Kingdom Apusozoa
Kingdom Breviatae
Kingdom Choanoflagellozoa
Kingdom Corallochytria
Kingdom Filasteriae
Kingdom Fungi
Kingdom Ichthyosporia
Kingdom Mantazoa
Kingdom Metazoa
Kingdom Nucleariae
Kingdom Planozoa
Kingdom Rigifilae
Subdomain Unikontamoebae
Kingdom Amoebozoa
subdomain unspecified
128
Kingdom Centroheliozoa
subdomain unspecified
Kingdom Cryptista
subdomain unspecified
Kingdom Haptista
subdomain unspecified
Kingdom Picozoa
subdomain unspecified
Kingdom Telonemae
subdomain unspecified
kingdom unspecified
Phylum Collodictyonida
subdomain unspecified
kingdom unspecified
Phylum Microheliellida
Yakovlev et al. (2017)
Subempire Eukaryota
Superkingdom Excavata
Kingdom Metamonada
Phylum Fornicata
Phylum Parabasalia
Phylum Preaxostyla
Kingdom Discoba
Phylum Jakobida
Phylum Kinetoplastida
Phylum Euglenophyta
Phylum Heterolobosea
Superkingdom Amoebozoa
Kingdom Archamoebae
Phylum Pelobiontida
Kingdom Euamoebae
Kingdom Myxobiontes
Phylum Protosteliomycota
(incl. Protosporangia)
Phylum Dictyosteliomycota
Phylum Myxomycota
(Myxogastria)
Superkingdom Opisthokonta
Kingdom Holozoa
129
Phylum Filasterea
Phylum Choanoflagellata
Series of phyla Metazoa
Kingdom Holomycota
Phylum Aphelidea
Phylum Cryptomycota
Phylum Microsporidia
Phylum Chytridiomycota
Phylum Blastocladiomycota
Phylum Zygomycota
Phylum Glomeromycota
Phylum Ascomycota
Phylum Basidiomycota
Superkingdom Heterokonta
Kingdom Opalobiontes
Phylum Opalinata
Kingdom Labyrinthulobiontes
Phylum Labyrinthulomycota
Kingdom Ochrophyta
Phylum Oomycota
Phylum Hyphochytriomycota
Series of phyla Ochrophyta
Superkingdom Alveolata
Kingdom Dinobionta
Phylum Dinophyta =
Dinoflagellata
Phylum Apicomplexa
Kingdom Ciliata
Phylum Ciliophora
Superkingdom Rhizaria
Kingdom Cercozoa
Phylum Cercomonada
Phylum Plasmodiophoromycota
Phylum Chlorarachnida
Phylum Monadofilosa
Kingdom Retaria
Phylum Foraminifera
Superkingdom Hacrobia
130
Kingdom Haptomonadontes
Phylum Haptophyta
Kingdom Centrohelidea
Phylum Centrohelida
Kingdom Cryptomonadontes
Phylum Сryptophyta
Phylum Katablepharida
Superkingdom Archaeplastida
Kingdom Glaucocystobiontes
Phylum Glaucocystophyta
Kingdom Rhodobiontes
Phylum Rhodophyta
Kingdom Chlorobiontes
Series of phyla
Chlorophycophyta
Kingdom Cormobiontes
Series of phyla Cormophyta
Adl et al. (2018)
Eukaryota
Amorphea
Amoebozoa
Tubulinea (phylum)
Evosea (phylum)
Discosea (phylum)
Obazoa
Apusomonadida
Breviatea
Opisthokonta
Diaphoretickes
Cryptista
Haptista (phylum)
Archaeplastida
Glaucophyta
Rhodophyta (phylum)
Chloroplastida
SAR
Stramenopiles (phylum)
Alveolata
Colpodellida
Perkinsozoa
131
Colponemidia
Dinoflagellata (phylum)
Apicomplexa (phylum)
Ciliophora (phylum)
•Rhizaria
Cercozoa (phylum)
Endomyxa (phylum)
Retaria
Foraminifera (phylum)
Radiolaria (phylum)
”Excavata”
Metamonada
Discoba
Heterolobosea
Euglenozoa (phylum)
Jakobida
Tsukubea
Malawimonas
CRuMs
Collodictyonidae
Rigifilida
Mantamonas
Ancyromonadida
Hemimastigophora
de Queiroz et al. (2020)
Eukarya
Metamonada
Discoba
Sar
[clades overview]
Amorphea
Fungi
[clades overview]
Animalia
[clades overview]
Archaeplastida
[clades overview]
Zmitrovich et al. (2022)
Eukaryota
Subdomain Amorphea
Kingdom Amoebozoa
132
○Subkingdom Lobosa
○○Parvkingdom Tubulinea
○○○Superphylum Euamoebida
○○○Superphylum Arcellinida
○○○Superphylum Leptomyxida
○○○Superphylum Nolandida
○○○Superphylum Echinamoebida
○○Parvkingdom Discosea
○○○Superphylum Flabellinia
Phylum Dactylopodida
Phylum Vannellida
Phylum Himatismenida
Phylum Stygamoebida
Phylum Pellitida
Phylum Trichosida
○○○Superphylum Longamoebia
Phylum Dermamoebida
Phylum Thecamoebida
○Subkingdom Conosa
○○Parvkingdom Variosea
Phylum Varipodida
Phylum Phalansteriida
Phylum Holomastigida
○○Parvkingdom Archamoebae
Phylum Mastigamoebida
Phylum Pelobiontida
○○Parvkingdom Mycetozoa
○○○Superphylum Dictyostelea
Phylum Acytostelia
Phylum Dictyostelia
○○○Superphylum
Ceratiomyxomycota
Phylum Protosporangia
Phylum Ceratiomyxida
○○○Superphylum Myxomycota
Phylum Lucisporidia
Phylum Columelliidia
unranked clade Obazoa
133
Kingdom Opisthokonta
○Infrakingdom Holomycota
○○○Superphylum Cristidiscoidea
Phylum Fonticulida
Phylum Nucleariida
○○○Superphylum Zoosporia
Phylum Opisthosporidia
Phylum Fungi = Eumycota
Subphylum Chytridiomycotina
Superclass Chytridiomycotera
Superclass
Monoblepharomycotera
Superclass
Neocallimastigomycotera
Subphylum Olpidiomycotina
Subphylum
Sanchytriomycotina
Subphylum
Blastocladiomycotina
Subphylum
Basidiobolomycotina
Subphylum Zoopagomycotina
Superclass
Enthomophthoromycotera
Superclass Kickxellomycotera
Superclass Zoopagomycotera
Subphylum Glomeromycotina
Subphylum Mucoromycotina
Superclass Mucoromycotera
Superclass
Mortierellomycotera
Superclass
Calcarisporiellomycotera
Subphylum Dikarya
Superclass
Entorrhizomycotera
Superclass Basidiomycotera
Superclass Ascomycotera
○Infrakingdom Holozoa
134
○○○Superphylum Ichtyosporea
○○○Superphylum Pluriformea
Phylum Corallochytrea
Phylum Syssomonadea
Phylum Filozoa
Subphylum Filasterea
Subphylum Choanozoa
Superclass Choanoflagellata
Superclass Metazoa
[rank lowering needed]
Porifera
[rank lowering needed]
Eumetazoa
unranked basal clade Breviatea
unranked basal clade
Apusomonadida
Subdomain Diaphoretickes
Kingdom Discoba
○Infrakingdom Percolozoa
Phylum Pharyngomonadea
Phylum Tetramitia
Subphylum Lyromonadea
Subphylum Heterolobosea
○Infrakingdom Euglenozoa
Phylum Kinetoplastida
Phylum Diplonemea
Phylum Euglenophyta
Phylum Symbiontida
○unranked basal clade Jakobea
Jakobida
Tsukubea
○unranked basal clade
Hemimastigophora
○unranked unit “CAM-clade”
(Cryptisa, Archeplastida,
Microheliella)
Kingdom Cryptista
○○○Superphylum Palpitomonada
○○○Superphylum Cryptomonada
135
Phylum Cryptophyta
Phylum Cyathomonadophyta
Phylum Kathablepharidophyta
Kingdom Archeplastida
○○○Superphylum Glaucophyta
Phylum Glaucocystophyta
○○○Superphylum Rhodophyta
Phylum Rhodelphidiophyta
Phylum Cyanidiophyta
Phylum Proteorhodophyta
Phylum Eurhodophyta
○○○Superphylum Chloroplastida
Phylum Prasinodermophyta
Class Prasinodermophyceae
Class Palmophyllophyceae
Phylum Chlorophyta
Subphylum
Chlorodendrophyceae
Subphylum Pedinophyceae
Subphylum Chloropicophyceae
Subphylum Picocystophyceae
Class Pyramimonadophyceae
Class Mamiellophyceae
Class Nephroselmidophyceae
Class Pycnococcophyceae
Phylum Streptophyta
Subphylum Chlorokybophytina
Subphylum
Mesostigmatophytina
Subphylum
Klebsormidiophytina
Subphylum Zygnematophytina
Subphylum
Coleochaetophytina
Subphylum Charophytina
Subphylum Embryophytina
Kingdom Haptista
Phylum Haptophyta
Class Pavlovaphyceae
136
Class Prymnesiophyceae
Phylum Centroplasthelida
Class Pterocystida
Class Panacanthocystida
unranked clade SAR
Kingdom Rhizaria
Phylum Gymnosphaerida
Phylum Cercozoa
Class Cercomonadida
Class Paracercomonadida
Class Glissomonadida
Class Viridiraptoridae
Class Pansomonadidae
Class Helkesida
Class Thecofilosea
Class Cryomonadida
Class Ventricleftida
Class Tectofilosida
Class Ebriacea
Class Thaumatomastigidae
Class Euglyphida
Phylum Metromonadea
Phylum Granofilosea
Phylum Chlorarachnea
Phylum Endomyxa
Class Vampyrellida
Class Phytomyxea
Subclass Plasmodiophorida
Subclass Phagomyxida
Class Filoreta
Class Gromiida
Phylum Ascetosporea
Class Haplosporida
Class Microcytida
Class Paradiniidae
Phylum Retaria
Class Foraminifera
Class Acantharea
137
Class Taxopodida
Class Polycystinea
Phylum Aquavolonida
Class Tremulida
Kingdom Alveolata
○○○Superphylum Acavomonidia
○○○Superphylum Colponemidia
○○○Superphylum Myzozoa
Phylum Apicomplexa
Class Aconoidasida
Class Coccidia
Class Gregarinasina
Class Blastogregarinea
Phylum Perkinsozoa
Class Perkinsida
Class Phagodiniida
Class Rastromonadida
Phylum Dinoflagellata
Class Dinophyceae
Class Gymnodiniophyceae
Class Syndiniophyceae
Phylum Alphamonada
Class Colpodellida
Class Chromerida s. stricto
○○○Superphylum Сiliata
Phylum Postciliodesmatophora
Phylum Intramacronucleata
Kingdom Stramenopila
○Subkingdom Gyrista
Phylum Bicosoecea
Phylum Developea
Phylum Ochrophyta
Class Chrysophyceae
Class Eustigmatophyceae
Class Phaeophyceae
Class Phaeothamniophyceae
Class Raphidophyceae
Class Schizocladia
138
Class Xanthophyceae
Class Bolidophyceae
Class Bacillariophyceae
Class Dictyochophyceae
Class Pelagophyceae
Class Pinguiophyceae
Class Actinophryida
Phylum Hyphochytrea
Phylum Peronosporomycota
Class Saprolegniomycetes
Class Peronosporomycetes
Phylum Pirsoniomycota
○Subkingdom Bigyra
Phylum Sagenista
Class Eogyrea
Class Labyrinthulea
Phylum Opalinata
Class Proteromonadea
Class Opalinatea
Phylum Placidozoa
Phylum Platysulcea
unranked basal clade
Telonemia
Incertae sedis [basal Discoba?
Basal Amorphea? Basal Eukary-
otes?]
Kingdom Loukozoa
Phylum Malawimonadea
Phylum Metamonada
Class Anaeromonada
Class Trichozoa
unranked basal clade
Ancyromonadida
unranked basal clade
Collodictyon
unranked basal clade
Mantamonadidae
unranked basal clade
Rigifilida
139
Tikhonenkov et al.
(2022)
Eucaryotic supergroups
Diaphoretickes
SAR
Telonemia
Haptista
Provora
Nebulidia
Nibbleridia
Hemimastigophora
Cryptista
Archaeplastida
Discoba
Metamonada
Ancyromonadida
Malawimonadida
CRuMs
Amoebozoa
Obazoa
140
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170
Person Index
Adl S.M. 55, 60, 115, 120, 130
Baldauf S.L. 57
Bory de Saint-Vincent J.B. 11
Boudouresque C.F. 123
Buxbaum J.C. 68
Cavalier-Smith T. 15, 24, 72,
93, 96, 103, 105, 106, 112, 114–
116, 120, 126
Chadefaud M. 12, 89
Chatton E. 11, 78, 88
Cohn F. 12
Copeland H.F. 88
Corliss J.O. 100, 104
De Queiroz K. 131
Derelle R. 56, 124
Drozdov A.L. 7, 28, 104, 106
Edwards P. 92
Ehrenberg C.G. 12, 77
Fleming A. 77
Fox G. 16
Fries E.M. 33
Goryaninov P.F. 12, 69, 77
Haeckel E. 12
Hampl V. 108
Hausmann K. 105, 111
Hawksworth D. 63
Hedwig J. 33
Heywood P. 28
Hlsmann N. 105
Jeffrey C. 89
Jussieu A.L. 33
Karpov S.A. 57, 58, 100, 110
Keeling P.G. 23
Koonin E.V. 116
Korsun S.A. 117
Krylov M.V. 95
Kuhar F. 63
Kusakin O.G. 7, 15, 28, 90, 104,
106
Lecointre G. 115
Le Guyader H. 115
Leedale G.F. 91
Leontyev D.V. 121
Levine N.D. 60
Linnaeus C. 11, 33
Lipscomb D. 23, 98, 100, 103
Luketa S. 119
Margulis L. 89, 92
Mattox K.R. 94
Merezhkovsky K.S. 11
Mhn E. 97
Moore R.T. 36, 78
Nmec B. 12
Paps J. 123
Parker S.P. 96
Patterson D.J. 58, 108
Pawlowski J. 123
Persoon C. 33
Polotebnov A.G. 77
Rotschild L.J. 28
Ruggiero M.A. 124
Schleiden M. 77
Schwann T. 77
Silar P. 126
Speijer D. 125
Starobogatov Ya.I. 15, 27, 90,
100
Stewart K.D. 94
Takhtadjan A.L. 13, 92
Taylor F.G.R. 14
Tedersoo L. 127
Tikhonenkov D.V. 41, 56, 139
Whittaker R.H. 11, 13
Woese C.R. 16
Yakovlev G.P. 128
Zerov D.K. 27, 90
Zmitrovich I.V. 79, 113, 131
171
Taxonomy Index
Acantharea 48
Acantharia 103
Acanthiolaria 97
Acavomonidia 49
Acoelomata 99
Aconoidasida 49
Aconta 93
Acrasia 67
Acrasiomycota 93
Actinomyxidea 103
Actinophryida 50
Actinophryids 108
Acytobionta 27
Acytosteliomycetes 42
Adictyozoa 104
Akaryonta 12
Akonta 100
Algae 12
Alveodinia 114
Alveolata 17, 21, 49, 59, 66,
74
Alveolates 28, 106
Amastigomycota 97
Amitotica 92
Amoebae 100
Amoebidium 67
Amoeboflagellates 103
Amoebozoa 17, 18, 41, 56,
57, 59, 66, 73
Amoebozoida 119
Amoebozoides 119
Amorphea 14, 66
Anaeromonadea 41
Ancyromonadida 57
Ancyromonadidae 123
Ancyromonas 108
Angiospermae 28
Animalia 11, 27, 80, 100
Animalioida 120
Animalioides 120
Animals 103
Annelida 80
Anthocerotophyta 82
Anthocerotophytina 27, 90
Aphelidea 122
Aphelidea 67
Apicomplexa 49
Apusomonadida 17, 18, 44,
73, 79
Apusomonadidae 123
Apusozoa 115, 121
Apusozoida 120
Aquavolonida 49
Arcellinida 42
Archaea 22
Archaeocyathea 80
Archaeplastida 19, 45, 56,
57, 66, 73
Archamoebae 42
Archamoebaea 105
Archeata 98
Archekaryota 104
Archemonadobionta 28, 104
Archemonadobiontes 106
Archemycota 114
Archeplastida 17, 23, 59
Archezoa 104
Archimycetes 89
Arthropoda 80
Ascetosporae 103
Ascetosporea 48
Ascomycetes 78
Ascomycia 44
Ascomycota 37, 44
172
Ascomycotera 134
Athalamea 103
Atkinsiellales 85
Axoplasthelidea 103
Axostylata 105
Bacillariacea 88
Bacillariophyceae 50
Bacteriophyta 27
Bacterioschizophyta 13
Bangialea 88
Basidiobolomycota 43
Basidiobolomycotina 43
Basidiomycetes 118
Basidiomycia 44
Basidiomycota 37, 44
Basidiomycotera 134
Bicosoecea 50
Bicosoecia 99
Bicosoecida 118
Bigyra 51
Bikonta 115
Bikonta 57
Bikonts 14
Biliphyta 96
Biomyxa 108
Blastocladiomycota 43
Blastocladiomycotina 43
Blastocystida 118
Blastodiniphyceae 49
Blastogregarinea 49
Bodonina 99
Bodonobiota 14
Bolidophyceae 50
Brachiata 80
Breviatea 17, 18, 44, 73
Breviatida 120
Breviatides 119
Bryophyta 82
Bryophytina 27, 90
Bryozoa 12
Caecitellus 108
Calcarisporiellomycia 44
Calcarisporiellomycota 44
Calcarisporiellomycotera 133
Calcespongea 80
Carpediemonas 108
Centroheliozoa 108
Centroplasthelida 47
Centroplasthelidea 103
Ceratiomyxomycetes 42
Ceratiomyxomycia 42
Ceratophyta 12
Cercomonada 102
Cercomonadida 47
Cercozoa 47
Chaetognatha 80
Charales 82
Charophyta 47
Charophytina 47
Chilomonas 19
Chimaerophytalia 113
Chlorarachnea 48
Chlorarachnia 104
Chlorarachnion 20
Chlorarachniophyta 66
Chlorarachniophytes 108
Chlorobionta 28, 104
Chlorobionts 103
Chlorobiota 89
Chlorodendrophyceae 46
Chlorodendrophytina 46
Chlorokybophyceae 46
Chlorokybophytina 46
Chloromastigonta 95
Chloromonadophyceae 89
Chloromonadophyta 27, 90
Chloromonadophytobionta
97
Chlorophycophytina 27, 90
Chlorophyta 23, 27, 90, 46,
66
Chloropicophyceae 46
173
Chloropicophytina 46
Chloroplastida 36, 46, 82
Choanobionta 98
Choanociliata 96
Choanoflagellatea 44
Choanoflagellozoa 127
Choanomastigonta 95
Choanomastigota 101
Choanomonadea 80
Choanozoa 44, 80
Choanozoides 120
Chordata 80
Chromalveolata 41, 47, 66,
73
Chromista 82
Chromobionta 28, 104
Chromobionts 103
Chromomastigonta 95
Chromophyta 101
Chromophytobionta 97
Chromulinontes 27, 100
Chrysoleucobionta 15
Chrysophyceae 50
Chrysophyta 27, 90, 58
Chytridea 102
Chytridia 102
Chytridiomycetes 43
Chytridiomycia 43
Chytridiomycota 27, 90
Chytridiomycotera 133
Chytridiomycotina 43
Chytriodinium 67
Ciliae 88
Ciliates 103
Ciliofungi 96
Ciliophora 49
Cnidaria 80
Cnidiae 88
Coccidia 49
Coccolithus 20
Coelomia 80
Coelosporidium 108
Coleochaetales 82
Coleochaetophyceae 46
Coleochaetophytina 46
Collodictyon 108
Collodictyonidae 123
Collodictyonidea 44, 81
Colpodea 49
Colpodellida 49
Colponema loxodes 103
Colponemaria 97
Colponemata 97
Colponemidia 49
Conosa 42
Contophora 97
Corallochytrea 44, 80
Cormophyta 13
Corticata 116
Corticatida 120
Corticoflagellata 94
Craspedophyta 98
Cristidiscoidea 43
Crumalia 44, 73, 81
Cryomonadida 48
Cryothecomonas 109
Cryptista 19, 45, 57, 59, 66,
73
Cryptobionta 28, 104
Cryptomastogonta 95
Cryptomonada 100
Cryptomonada 45
Cryptomonadida 56
Cryptomonadontes 27, 100
Cryptophyceae 91
Cryptophyta 27, 90, 45, 66
Cryptophytes 103
Crytophytobionta 97
Ctenophoria 80
Cyanidiophyta 45
Cyanidiophyta 97
Cyanobionta 13
174
Cyanophyta 27
Cyanoschizophyta 13
Cyathophyta 45
Cycadophyta 82
Desmothoracidea 102
Developea 50
Diaphoretickes 14, 56
Diaphoretikes 121
Diatomophyta 27, 90
Dicarya 79
Dicaryomycota 79
Dictyochophyceae 50
Dictyosteliomycetes 42
Dictyosteliomycia 42
Dictyozoa 104
Dikarya 44
Dikaryomycotina 44
Dimastigota 105
Dinobionta 28, 104
Dinobiota 14
Dinoflagellates 103
Dinomastigonta 95
Dinomorpha 101
Dinophyceae 49
Dinophyta 49
Dinophytobionta 97
Dinozoa 112
Diphoda 44, 56, 73
Diphyllatea 81
Diplomonadida 99
Diplonemia 45
Discicristata 111
Discicristata 14
Discicristates 124
Discoba 17, 18, 44, 56, 57,
59, 66, 73
Discocelis 109
Discosea 18, 42
Ebriacea 48
Echinamoebida 42
Echinodermata 80
Echinurida 80
Ellipsoidiontes 27, 100
Embryobionta 13
Embryophyta 37, 47
Embryophytina 47
Endomyxa 48
Enterozoa 80
Enthomophthoromycotera
133
Entomophthoromycia 43
Entomophthoromycota 43
Entorrhizomycia 44
Entorrhizomycota 44
Eochromista 47, 73
Eogyrea 51
Eozoa 116
Erythrobionta 92
Euamoebida 42
Eucarya 78
Eucaryonta 78
Eucaryota 13, 27, 78
Eucaryotes 78
Euchromista 104
Eucytota 89
Eufungi 96
Euglenobionta 28, 104
Euglenobiontes 106
Euglenoida 94
Euglenoidea 110
Euglenoids 23
Euglenontes 27, 100
Euglenophyta 27, 90, 45, 66
Euglenophytobionta 97
Euglenozoa 45, 56, 66, 68
Euglenozoa 96
Euglenozoea 113
Euglyphida 48
Eukaryonta 12
Eukaryonta 97
Eukaryota 41, 78, 88–139
Eumetazoa 44
175
Eumycota 27, 90, 43
Euradiolaria 103
Eurhodophyta 46
Eurhodophytina 46
Eurychasma 85
Eurychasmales 84
Eustigmatobionta 98
Eustigmatomonadida
Eustigmatophyceae 50
Evosea 18
Excavata 114
Excavates 124
Excavatida 120
Filasterea 44
Filoretidae 48
Filozoa 44
Flabellinia 42
Flagellata 88
Flagelloopalinida 97
Florideae 78
Fonticula 109
Fonticulida 43
Foraminifera 48
Fornicata 121
Fungi 12, 37, 65, 66
Fungi 1 92
Fungi 2 93
Fungides 120
Fungilli 89
Gameophyceae 99
Ginkgophyta 82
Glaucocystophyta 45
Glaucophyta 23, 45, 66
Glaucophytae 103
Glissomonadida 47
Glomeromycota 43
Glomeromycotina 43
Gnetophyta 82
Goniomonas 19
Granofilosea 48
Granuloreticulosa 97
Gregarinasina 49
Gromiida 48
Gymnamoebea 102
Gymnophrea 109
Gymnospermae 28
Gymnospermophytina 27,
90
Gymnosphaerida 47
Gyrista 50
Hacrobia 116
Halvaria 116
Haplosporida 48
Haptista 17, 20, 47, 56, 59,
66, 73
Haptobionta 124
Haptoglossa 85
Haptoglossales 84, 85
Haptophyta 47, 66
Haptophytobionta 98
Heliozoa 100
Heliozoa 89
Helkesea 47
Hemichordata 80
Hemimastigophora 41, 47,
56, 73
Heterocarpea 88
Heterokonta 50, 65, 74, 83
Heterokontae 83
Heterokontea 88
Heterokontes 28, 106
Heterolobosea 45, 56, 66
Holmsella 67
Holomastigida 42
Holomycota 18, 43, 66
Holozoa 18, 44, 66
Hyalospongea 80
Hydraulea 98
Hyperamoeba 109
Hypermastigida 99
Hypermastiginea 101
Hyphochytrida 102
176
Hyphochytridiomycota 83
Hyphochytridiomycota 91
Hyphochytriomycota 50, 83
Hyphochytrium 83
Hyphomycetes 89
Ichthyosporia 127
Ichtyosporea 44
Inferiobionta 28, 104
Infusoria 89
Inophyta 89
Jakoba 108
Jakobea 19, 45
Jakobida 45, 56
Karyoblasta 105
Katablepharidophyta 45
Kickxellomycia 43
Kickxellomycota 43
Kinetoplastea 45
Kinetoplastidae 101
Kinetoplastmastigonta 95
Klebsormidiophyceae 46
Klebsormidiophytina 46
Komokiacea 109
Laboulbeniomycota 113
Labyrinthomorpha 98
Labyrinthulea 102
Labyrinthulea 51
Labyrinthulomycota 67
Lamellicristata 14
Lepidophytina 27, 90
Leptomitales 85
Leptomyxida 42
Liceomycetes 43
Lobosa 41
Longamoebia 42
Loukozoa 17, 41, 57, 59, 73
Luffisphaera 109
Lycopodiophyta 82
Lyromonadea 45
Magnoliidae 82
Magnoliophyta 82
Malawimonadea 41
Malawimonadida 57
Mammalia 80
Mantamonada 81
Mantamonadea 44, 81
Mantamonadida 78
Mantamonas 131
Mantazoa 127
Marchantiophyta 82
Mastigamoebida 42
Mastigiae 88
Mastigina hylae 102
Mastigophora 89
Mastigota 105
Melanophycea 88
Mesostigmatophyceae 46
Mesostigmatophytina 46
Mesozoia 80
Metakaryota 104
Metamonada 57
Metamonadea 41
Metazoa 27, 90, 28, 44, 65,
104
Metromonadea 48
Microcystida 48
Microheliella 57
Microspora 105
Microsporidia 37, 67
Microsporobionta 28, 104
Ministeria 109
Miozoa 112
Mitotica 92
Mollusca 80
Monera 13
Monilophyta 82
Monoblepharomycia 43
Monoblepharomycotera 133
Monothalamea 103
Mortierellomycia 43
Mortierellomycota 43
Mortierellomycotera 133
177
Mucoromycotera 133
Multicilia 109
Mycetalia 13
Mycetozoa 42
Mycetozoidea 98
Mychota 13
Mycobionta 13, 28, 104
Mycobiota 89
Mycophyta 13
Mycophyta 91
Mycota 27, 100
Myxobionta 13
Myxogasteromycia 42
Myxogastrea 102
Myxogastria 67
Myxogastriomycota 93
Myxomycophyta 91
Myxomycota 27, 90
Myxospora 103
Myxosporae 103
Myxosporidea 103
Myxozoa 21
Myxozoia 80
Myzozoa 49
Nassophorea 50
Nebulidia 56
Nemathelminthes 80
Nemertini 80
Neocallimastigomycia 43
Neocallimastigomycotera
Neocallimastigomycotera
133
Neomycota 124
Neosporidia 89
Neozoa 106
Nibbleridia 56
Noctilucophyceae 49
Nolandida 42
Nucleariae 127
Nucleariida 43
Nucleariidae 109
Obazoa 18, 43, 57, 66, 73
Obimoda 41, 73, 79
Ochrobionta 93
Ochrophyta 50, 58, 66
Oligohymenophorea 49
Olpidiomycota 43
Olpidiomycotina 43
Olpidiopsidales 84
Onychophora 80
Oomycetes 88
Oomycota 67, 83, 84
Opalinata 51
Opalinatea 51
Opalinida 99
Opalinidea 97
Opalinidomorpha 95
Opalinids 103
Opimoda 41, 56, 57, 79
Opisthokonta 17, 18, 43, 56,
59, 66, 79
Opisthomastigomycota 97
Opisthosporidia 43, 66
Oxymonadida 99
Palmophyllophyceae 46
Palpitomonada 45
Panacanthocystida 47
Pansomonadidae 47
Pantonemomycota 97
Parabasalia 101
Paracercomonadida 47
Parachromomastigonta 95
Parachrysozoomastigonta
95
Paradiniidae 48
Paramyxea 109
Parasitomastigonta 95
Parazoa 28, 104
Pavlovaphyceae 47
Pedinellaphyta 98
Pedinophyceae 46
Pedinophytina 46
178
Pelagomonadiodes
Pelagophyceae 50
Pelobiontida 42
Pelomyxa palustris 102
Penicillium 77
Penicillium glaucum 77
Pentastomida 80
Peranematida 19
Percolozoa 45
Peridiniobionti
Peridiniontes 27, 100
Perkinsemorpha 101
Perkinsida 49
Perkinsidea 101
Perkinsozoa 49
Peronosporales 85
Peronosporomycetes 51, 85
Peronosporomycota 50
Phaeophyceae 50
Phaeophyta 27, 90, 58
Phaeothamniophyceae 50
Phagodiniida 49
Phagodinium 109
Phagomyxida 48
Phalansteriida 42
Phalansterium 109
Pharyngomonada 45
Phragmophyta 113
Phycobionta 13
Phycomycia 43
Phycomycotina 43
Phycophyta 13
Phyllopharyngea 50
Physaromycetes 43
Phytomyxea 48
Phytozoa 12, 69
Picocystophyceae 46
Picozoa 128
Pinguiophyceae 50
Pinophyta 82
Pirsonionea 51
Placidozoa 51
Placozoia 80
Placozoomorpha 98
Plagiopylea 50
Plantae 13, 17, 23, 27, 92,
100, 45, 57, 73
Plasmodiophora 102
Plasmodiophorea 102
Plasmodiophorida 48
Plasmodiophoromycota 67
Plathelminthes 80
Platysulcea 51
Pluriformea 44
Polannulifera 97
Polycystinea 48
Polymastigota 100
Polymastigotes 103
Porifera 44, 80
Prasinodermophyceae 46
Prasinodermophyta 46
Prasinophyta 94
Prasinophytalia 113
Prokaryonta 12
Prostomatea 49
Proteomyxidea 98
Proteorhodophyta 45
Proteorhodophytina 45
Proteromonadea 51
Proteromonadida 99
Protista 12
Protocaryota 13
Protoctista 12
Protomonada 97
Protoplasta 89
Protosporangiomycetes 42
Protostelea 102
Prototheca 67
Protozoa 103, 105, 106, 112,
114, 116, 124
Provora 17, 41, 47, 55, 56,
73
179
Prymnesiophyceae 46
Prymnesium 20
Pseudociliata 111
Pseudodendromonada 101
Pseudofungi 114
Pseudospora 110
Psilophytina 27, 90
Pterocystida 46
Pterosperophytina 27, 90
Pycnococcaceae 46
Pycnococcophyceae 46
Pyramimonadophyceae 46
Pyrrhophyta 27, 90
Pythiales 85
Radiolaria 95
Raphidophyceae 50
Raphidophyta 101
Rastromonadida 49
Retaria 48
Retaria 112
Retortamonada 105
Retortamonadida 99
Rhabdomonadineae 19
Rhipidiales 82, 85
Rhizaria 17, 20, 47, 59, 66,
73
Rhizopoda 88
Rhizopoda 89
Rhodelphidiophyta 45
Rhodelphis 67
Rhodobionta 13, 28, 104
Rhodobiota 89
Rhodocyanobionta 97
Rhodophyca 100
Rhodophyceae 99
Rhodophyta 27, 37, 90, 45,
66
Rhodophytae 101
Rhodymeniontes 27, 100
Rigifilae 128
Rigifilida 81
Rigifilidea 44, 81
Rozellomycota 67
Sagenista 51
Sanchytriomycota 43
Sanchytriomycotina 43
Saprolegnia 101
Saprolegniales 85
Saprolegniea 102
Saprolegniomycetes 51, 85
Saprolegniomycota 27, 90
Sarcomastigota 96
Sarkodina 89
Schizocladiophyceae 50
Schizophyta 12
Schizopyrenida 99
Scolecidia 80
Sipunculida 80
Slopalinata 102
Spathulosporales 78
Sphenophytina 27, 90
Spiromonadea 101
Spirotrichea 50
Spongia 69
Spongomonadida 119
Sporozoa 88
Sporozoae 101
Staphylococcus aureus 77
Stellatosporea 103
Stephanopogon 110
Stephanopogonida 99
Sticholonche 110
Stramenopila 17, 21, 59
Stramenopiles 82
Straminipila 82
Streptophyta 46
Sulcozoa 126
Symbiontida 45
Syndiniophyceae 49
Synurophyceae 101
Syssomonadea 44
Tardigrada 80
180
Taxopodida 48
Taxopodidea 102
Tectofilosida 48
Telonema 110
Telonemia 17, 41, 47, 56, 73
Tentaculata 80
Tentaculifera 89
Tetaceolobosea 102
Tetramastigota 105
Tetramitia 45
Thaumatomastigidae 48
Thaumatomonadida 119
Thecofilosea 47
Thraustochytridea 102
Tracheophyta 89
Tremulida 49
Trichomonadea 101
Trichomonadea 41
Trichomycetea 98
Trimastix 110
Trypanosomatina 99
Tsukubea 45
Tubulicristata 14
Tubulinea 18, 41
Unikonta 116
Unikonta 57
Unikontamoebae 128
Unikonts 14
Vampyrellida 48
Variosea 42
Varipodida 42
Vegetabilia 11
Ventricleftida 48
Viridiplantae 96
Viridiraptoridae 47
Xanthophyceae 50
Xanthophyta 27, 90, 58
Xenophyophores 110
Zoobiota 89
Zoomastigida 89
Zoopagomycota 43
Zoopagomycotina 43
Zoophyta 12
Zoosporia 43
Zygnematophyceae 46
Zygnematophytina 46
Zygomycetes 89
Zygomycota 37
181
Abbreviations
Amst. Amsterdam
APG Angiosperm phylogeny group
Bibltheca bibliotheca (syneresis)
BOL Bicosoecida, Opalinata, Labyrhintulida
CAM Cryptophyta, Archaeplastida, Microheliella
Caval.-Sm. T. Cavalier-Smith
Cox1 cytochrome C oxidase subunit I gene
Cox2 cytochrome C oxidase subunit II gene
CRuMs collodictyonids, rigifilids, mantamonadids
DNA deoxyribonucleic acid
DRIP Dermocystidium, rosette agent, Ichtyophonus, Psorospermium
ed. editor
eds editors (syneresis)
et al. and others (et alia)
etc. and so on (et cetera)
HOOF Hyphochytriomycota, Oomycota, Ochrophyta
incl. includenda (lat.), including
L. London
LEKA the last eukaryotic common ancestor
LSU — large subunit ribosomal ribonucleic acid gene
MAST marine stramenopiles
MRO mitochondrion-related organelle
N.J. New Jersey
N.Y. New York
RNA ribonucleic acid
s. lato sensu lato
s. strict sensu stricto
SAR Stramenopiles, Alveolata, Rhizaria
SSU small subunit ribosomal ribonucleic acid
TSAR Telonemia, Stramenopiles, Alveolata, Rhizaria
vs versus (syneresis)
β-tub -tubulin gene
182
CONTENTS
Preface ………………...
7
Introduction .………………
9
Megasystematics beginnings from a historical perspective ..
11
“Reductionist gestures” and experimental systems in
megasystematics
13
Molecular revolution ...
16
Where do the kingdoms disappear? .
23
Attempts to clarify the higher rank nomenclature …………………
26
Chapter 1. Nomenclatural principles and method of presentation ...
29
Chapter 2. Authors’ overview of the current eukaryotic system
39
Chapter 3. Uncertain futures of eukaryotic megasystematics
53
Chapter 4. “Flora”, “Fauna”, Funga”: An impact of discussion in
megataxonomy on the floristic and faunistic terminology ..
61
“Funga”: pro et contra ...
63
…Kingdoms and lineages ...
64
…What’s the alternative?
68
…What the Internet looking for? .
69
Conclusion
72
Notes .
75
Supplement ..
85
References
140
Person Index
170
Taxonomy Index .
171
Abbreviations
181
Contents
182
183
184
Иван Викторович Змитрович,
Владимир Вениаминович Перелыгин,
Михаил Владимирович Жариков
НОМЕНКЛАТУРА
И РАНГОВАЯ КОРРЕЛЯЦИЯ
ВЫСШИХ ТАКСОНОВ
ЭУКАРИОТ
Научное издание
Технический редактор
И.В. Змитрович
Сдано в набор 17.12.2022 г. Подписано к печати
25.12.2022 г. Формат 60 90 1/16. Гарнитура «Лите-
ратурная». Уч.-издат. листов. 10,4. Тираж 300 экз.
Научно-издательский центр
«ИНФРА-М»
г. Москва,
127214, Москва, Полярная ул.,
д. 31В, стр.1, эт. 3, пом. 1, к. 9Б.
Тел. 8 (495) 859-48-60
books@infra-m.ru
