Thomas Cavalier-Smith, a world-famous evolutionist, cytologist and protistologist, one of the founders of eukaryotic megasystematics, passed away on March 19, 2021. We dedicated an essay to his life and scientific work, which was published in 2022 [1]. At the end of 2022, after the publication of this essay, the last paper by Cavalier-Smith was published posthumously, not being included in the obituaries published in 2021–2022. Article entitled “Ciliary transition zone evolution and the root of the eukaryote tree: implications for opisthokont origin and classification of kingdoms Protozoa, Plantae, and Fungi” [2] presents an extensive review published in “Protoplasma” journal which previously published reviews by Cavalier-Smith on the classification of Chromista [3], Rhizaria [4], and the origin of neomurans [5]. After Cavalier-Smith and his wife Ema Chao moved to Cornwall in 2016, Cavalier-Smith began taking stock of his activities and each of his reviews was thorough, exceeding 50 and sometimes 100 pages. Cavalier-Smith’s latest article is 106 pages long. Giving somewhat finality to the creative heritage of this scientist, the present essay prompted us to write an epilogue to our previous memorial paper. In addition, we set out to record some names of taxa and derived terms, introduced into use by Cavalier-Smith, but not usually used by his contemporaries. In the context of an intensifying information flow, these terms, which have deep content behind them, are at risk of oblivion every year, although they have not only heuristic, but also didactic value. To worry about these terms, at the end of this essay we present the “Cavalier-Smith Glossary” we compiled.
Ciliary transition zone evolution according to Cavalier-Smith
In his last paper, Cavalier-Smith discusses in detail the evolution of the eukaryotic ciliary transition zone, highlighting its evolutionary significant details previously overlooked.
The transition zone of the flagellum axoneme is located in the area where the flagellum (cilium) exits the cell (the outer part of the flagellum is called undulipodium). Inside the cell, the axoneme is attached to the kinetosome (basal body), located under the cell membrane. The kinetosome represents a hollow cylinder which wall consists of 9 triplets of microtubules, usually connected by fibrillar bridges. The triplet, in addition to the axonemal A- and B-microtubules, includes an additional C-microtubule adjacent to the B-microtubule. In the center of the proximal part of the kinetosome there is an axis with fibrillar connectives.
The details of the organization of the transition zone of the flagellar axoneme in different groups of eukaryotes have their own specificity. Typically, in the transition zone there are structures that help strengthen the flagellum at the site of its exit from the cell: a transverse plate, present from one to four in almost all groups of eukaryotes, a stellate formation characteristic of most green plants, a single and double helix characteristic of Heterokonta, a central filament characteristic of choanoflagellates.
All eukaryotes with a dense round transverse plate and the transition zone strengthened by doublets of microtubules at the extreme base Cavalier-Smith claims as discaria. Representatives of this group are characterized by the presence below the transverse plate 1) the so-called “acorn structure” and 2) V-shaped filament system. The “acorn structure” is a closed filament about 10 nm thick, attached to the A-microtubules of the first, second, seventh, eighth and ninth doublets and crossing the V-filament system connecting the A-microtubules of the fourth and fifth doublets in the central filament. According to Cavalier-Smith, all eukaryotes can be considered discaria except for malawimonads. The transition zone of the malawimonad flagellum differs sharply from that of discaria in that it is very short, lacks V-filaments, and has a segmented precursor to the “acorn structure”.
Therefore, Cavalier-Smith creates such a dichotomy as “malawimonads-discaria”, between which, according to the author, lies the “eukaryote root”. Malawimonas is a heterotrophic one-nucleate mitochondria-bearing flagellate with a developed glycocalyx and two long (about 1–1.5 times longer than the cell body) flagella. The anterior flagellum has a curved shape, while the posterior flagellum is pressed, but not attached to the ventral surface of the cell. Morphologically, this flagellate bears both the characteristics of Jakobida (Discoba) and representatives of the kingdom Crumalia, basal to amoebozoans and opisthokonts. Molecular data concerning the position of Malawimonas on the eukaryotic tree are contradictory, while the use of comparative data on the amino acid sequences of proteins of eubacterial origin shows the basal position of Malawimonas to Crumalia-Obazoa clade. [6].
Cavalier-Smith’s review also touches on the crown region of the eukaryotic tree. He draws attention to recent discovery of the “basal red alga” Rhodelphis, a heterotrophic flagellate with reduced plastids [7], and considers the features of the flagellar transition zone of this protist which shows similarities with glaucophyte algae and heterotrophic flagellate Picomonas of uncertain relationship. The allocated similarities prompted Cavalier-Smith to revise the classification of the kingdom Plantae, namely to combine Picomonadea and Rhodelphea into the Pararhoda group (considered at the division). He united Pararhoda and Rhodophyta into the Rhodaria (subkingdom Biliphyta) characterized by similar structure of ciliary transition zone.
System and phylogeny of Eukaryotes
As in previous major reviews [8, 9], in his latest article, Cavalier-Smith adheres to the five-kingdom system of eukaryotes (kingdoms Protozoa, Animalia, Fungi, Chromista and Plantae). At the same time, the structure of the kingdoms Protozoa and Chromista undergoes dramatic changes from system to system, and Protozoa is recognized by the author himself as a polyphyletic group. In the latest Cavalier-Smith system, the taxonomic structure of the kingdom Protozoa was outlined as follows:
Subkingdom 1. Malawimonada
•••Тип Malawimonada (sole class and order)
Subkingdom 2. Natozoa
•Infrakingdom 1. Archezoa
•••Phylum Metamonada
••••Subphylum 1. Anaeromonada
••••••Class Anaeromonadea (orders Trimastigida, Paratrimastigida, Oxymonadida)
••••Subphylum 2. Trichozoa
•••••Infraphylum 1. Parabasalia
••••••Class Trichomonadea (sole order)
•••••Infraphylum 2. Fornicata
••••••Class Carpomonadea (sole order)
••••••Class Eopharyngea (orders Diplomonadida, Retortomonadida)
•Infrakingdom 2. Eozoa
•••Phylum 1. Eolouka
••••••Class Jakobea (sole order)
••••••Class Tsukubamonadea (sole order)
••Superphylum 2. Discicristata
•••Phylum 1. Euglenozoa
••••Subphylum 1. Euglenoida (further arrangement according to [10]).
••••Subphylum 2. Postgaardia (further arrangement according to [10])
••••Subphylum 3. Glycomonada
••••••Class Kinetoplastea (further arrangement according to [10])
••••••Class Diplonemea (further arrangement according to [10])
•••Phylum 2. Percolozoa
••••Subphylum 1. Orthozoa
••••••Class 1. Pharyngomonadea (sole order)
••••••Class 2. Lunosea (sole order Selenaionida)
••••Subphylum 2. Tetramitia
••••••Class Neovahlkampfea
•••••Infraphylum Eutetramitia
••••••Class 1. Heterolobosea (orders Acrasida, Schizophyenida)
••••••Class 2. Lyromonadea (sole order)
••••••Class 3. Percolatea (sole order)
•Infrakingdom 3. Hemimastigophora (sole phylum, class, order)
Subkingdom 3. Sarcomastigota
•Infrakingdom 1. Sulcozoa
•••Phylum 1. Sulcozoa
••••Subphylum 1. Planomonada
••••••Class Planomonadea (sole order)
••••Subphylum 2. Varisulca
••••••Class 1. Diphyllatea (sole order Diphylleida)
••••••Class 2. Glissodiscea (sole order Mantamonadida)
••••••Class 3. Hilomonadea (sole order Rigifilida)
•Infrakingdom 2. Diacentrida
•••Phylum 1. Apusozoa
••••••Class Thecomonadea (sole order Apusomonadida)
•••Phylum 2. Amoebozoa
••••Subphylum 1. Tevosa
•••••Infraphylum 1. Lobosa
••••••Class Tubulinea (sole order)
•••••Infraphylum 2. Conosa
••••••Class Archamoebea (sole order)
••••••Superclass Mycetozoa (listed in the rank of “large class”, uniting subordinate taxa well known to mycologists)
••••••Class Variosea (sole order)
••••••Class Cutosea (sole order)
••••Subphylum 2. Discosa
••••••Class Discosea (sole order)
Infrakingdom 3. Opizoa
•••Phylum 1. Choanozoa
••••Subphylum 1. Choanofila
••••••Class 1. Choanoflagellatea (sole order)
••••••Class 2. Filasterea (sole order)
••••••Class 3. Ichthyosporea (reference to traditionally accepted DRIP clade groups)
••••Subphylum 2. Paramycia
••••••Class Cristidiscoidea (orders Nucleariida, Fonticulida)
•••Phylum 2. Opisthosporidia
••••Subphylum 1. Rozellidia
••••••Class Rozellidea (sole order)
••••Subphylum 2. Aphelidia
••••••Class Aphelidea (sole order)
••••Subphylum 3. Microsporidia
••••••Class Microsporea (sole order)
••••••Class Metchnikovellea (sole order)
Cavalier-Smith contrasts the Malawimonada group with other eukaryotes (“discaria”), in which a typical transverse plate, V-filaments and so-called “acorn-shaped structure” have formed in the ciliary transition zone. At the same time, he classifies malawimonads along with some groups of discaria (sarcomastigotes, opizoans, diacentrids, sulcozoans, natozoans) in the Protozoa kingdom.
The next basal dichotomy of eukaryotes after “malawimonas/discaria”, according to Cavalier-Smith is “dorsata/natata”: the former (Crumalia, Obazoa) initially crawled along the substrate, have more pronounced dorsiventral symmetry and a frequently gliding flagellum; the latter (Discoba, SAR, Plantae) were originally free-swimming flagellates.
Among the natates, Cavalier-Smith contrasts metamonads which live in anaerobic environment with other groups, so-called photarians. Among the latter, he contrasts Discoba with “eucorts” (Hemimastogophora, SAR, Plantae) characterized by strengthening of the cell cortical layer.
Also, Cavalier-Smith contrasts planomonads with the rest dorsates characterized by phagocytosis or its secondary loss (Fungi).
Thus, in his last system, Cavalier-Smith abandoned the rapprochement of malawimonads with metamonads in the group of scotokaryotes, as he did earlier [11] and left his previous concept of the “euglenozoan root of eukaryotes”.
Cavalier-Smith and ranks
Even in the last system, Cavalier-Smith confirmed his credo “there should not be many kingdoms.” The polyphyly of the kingdom Protozoa as well as the distribution of clearly related fungi and animals into different kingdoms and different principles of distinguishing divisions in multicellular and unicellular organisms, received a very complex explanation in his works: according to Cavalier-Smith, the taxon has both gradistic and cladistic components, and this ratio is different for different taxa. However, the requirement of taxon monophyly, implicitly but definitely imposed by phylogenetic systematics, forces polyphyletic “unions,” “pragmatic” and “historical” classification units to be withdrawn from circulation. In addition, rank coordination is a requirement for any system, regardless of its scaling. Cavalier-Smith has long made extensive use of intercalary taxonomic categories (subkingdom, infrakingdom, superphylum, subphylum, infraphylum) in the case of the classification of Protozoa. Obviously, this practice can be extended to closely related groups located by Cavalier-Smith in other kingdoms.
For example, the phylum Opisthosporidia (with subphyla Rozellidia, Aphelidia, Microsporidia), considered by Cavalier-Smith in the infrakingdom Opizoa of the kingdom Protozoa, is a sister group of fungi (Fungi) [12], from the point of view of phylogenetic systematics, equal to them in rank. Fungi received the rank of the kingdom not even in the pre-molecular, but in the “pre-light-optical era”, and since then, consensus ideas about the rank of the kingdom have been supported for a variety of reasons (a large number of species of fungi, the description of many new divisions, the organizational isolation of mycologists), without, however, nothing to do with an objective assessment of the phylogenetic position of Fungi-group on the opisthokont tree (even if the polyphyletic kingdom Protozoa is abolished, the Fungi will have a rank equal to Opisthosporidia which more or less corresponding to the phylum/division level) [13].
Thus, the latest Cavalier-Smith system once again acutely poses the problem of ranking the Eukaryotes phylogenetic tree.
Cavalier-Smith’s Glossary
Being not only a brilliant thinker, but also a didactician, Cavalier-Smith avoided typified names of high-ranking taxa, preferring names that reflected a “phylogenetic essence” of the group. These names form an essential part of Cavalier-Smith’s theoretical heritage.
Alveolata, alveolates [14] – the clade of eukaryotes, more or less corresponding to superphylum the, uniting ciliates, dinoflagellates, apicomplexans and a number of other groups of protists having the cortical alveoli.
Apusozoa [15] – the phylum of heterotrophic flagellates (literally “legless animals”); a clade, basal to amoebozoans and opisthokonts.
Archezoa sensu Cavalier-Smith [16] – basal taxa of the eukaryotic tree, uniting protists lacking mitochondria; the scope of the concept changed due to the exclusion of pelobionts, entamoebas, and microsporidia from this group; in the last system, one of the Protozoa infrakingdom, including a sole phylum Metamonada.
Bigyra [17] – described in phylum rank clade of Heterokonta uniting the Opalozoa and Sagenista gropus; the name refers to the double helix in the transition zone of the flagellum.
Bikonta, bikonts [18] – the superclade of eukaryotes, including Apusozoa, Excavata, Rhizaria, SAR, and opposed to the Unikonta superclade.
Biliphyta [19] – the paraphyletic group (originally a subkingdom) of Plantae, uniting red and glaucophyte algae containing additional photosynthetic pigments phycobilins; it should be noted that glaucophyte algae contain typical cyanelles, whereas the plastids of red algae have already lost a cell wall and morphology of free-living cyanophytes.
Breviatea [20] – the group originally described as an order of non-mitochondrial amoebas, is currently considered as a clade basal to amoebozoans; the name refers to the species name Breviata anathema.
Choanozoa [2] – the phylum of the Opizoa infrakingdom dividing into subphyla Choanofila (Choanoflagellatea, Filasterea, Ichtyosporea) and Paramycia (Cristidiscoidea).
Chromista, chromists [19] – the kingdom of eukaryotes, uniting SAR, Haptista and Cryptista; preserved by Cavalier-Smith to the widest extent possible [2, 3], although recently the closer relationships between Cryptista and Plantae have been estimated.
Corticata, corticates [21] – the group of eukaryotes uniting Plantae and Chromista; the name refers to the more strengthened (compared to discobs and amorpheas) outer layer of the corticate cell.
Cristidiscoidea [8] – the class of Protozoa that unites the amoebae Nucleariida and Fonticulida, characterized by discoid mitochondrial cristae.
Cryptista, cryptists [22] – the clade of eukaryotes, more or less corresponding to the rank of phylum (division), uniting heliozoan Endohelea and cryptophyte algae.
Diacentrida [2] – the infrakingdom of the Protozoa kingdom, uniting Apusozoa and Amoebozoa groups (see also Sarcomastigota).
Discicristata [23] – the superclade of protists, uniting the clades Euglenozoa and Percolozoa; the name refers to the disc-shaped mitochondrial cristae in both groups.
Dorsates, dorsates [2] – the protists that ancestrally gliding along the substrate, characterized by pronounced dorsiventral body flattening as well as by sliding flagellum in many cases.
Eolouka [24] – the paraphyletic phylum of protists uniting the monophyletic lineages of Jakobea and Tsukubea; the name refers to the presence of a ventral flagellar groove (louka) in flagellates and indicates the ancient age of the group.
Eozoa [17] – the subkingdom of Protozoa, positioned as the most ancient; in different Cavalier-Smith systems, the volume of this sub-kingdom sufficiently varied.
Eucorta, eucorts [2] – the eukaryotes characterized by a strengthened cytoskeleton as well as sometimes submembrane cell integument complications; the group includes Hemimastigophora, SAR, and Plantae.
Euglenozoa, euglenozoans [19] – the protistan kingdom (1981) or phylum (2022); a group that unites euglenophyte algae and kinetoplastids.
Gyrista [8] – the superphylum (superdivision) in the Heterokonta group, uniting Bicosoecea, Developea, Ochrophyta; the name refers to the double helix in ciliary transition zone.
Halvaria [18] – the clade of SAR, splitting into Heterokonta and Alveolata subclades.
Haptista, haptists [25] – the clade of eukaryotes, more or less corresponding to superphylum rank, uniting centrochelid heliozoans and haptophyte algae.
Harosa [26] – the clade of SAR, splitting into Halvaria and Rhizaria subclades; the name is derived from the first letters of the words Heterokonta, Alveolata, and Rhizaria.
Metamonada sensu Cavalier-Smith [16] – anaerobic flagellates with a complex flagellar apparatus; the phylum of infrakingdom Archezoa, combining anaeromonas and trichozoans.
Natates [2] – ancestrally free-swimming flagellates.
Natozoa [2] – the part of Protozoa kingdom uniting Archezoa, Eozoa and Hemimastigophora, i.e. neither dorsate nor corticate.
Neokaryotes [27] – the clade opposed to the “basal eukaryotes” (Percolozoa, Euglenozoa, Jakobea) in the 1993 Cavalier-Smith system.
Ochrophyta, ochrophytes [28] – the algal division of Heterokonta group uniting chrysophycean, xanthophycean, brown, raphidophyte algae and diatoms.
Opizoa [2] – the part of opisthokonts (Choanozoa and Opisthosporidia), remaining in the conservative five-kingdom system within the Protozoa kingdom.
Photaria, photarians [2] – all the aerobic natates, opposed to anaerobic scotokaryotes (metamonads).
Planomonada [2] – the subphylum of Sulkozoa phylum; the name refers to the dorsiventrally flattened body of these flagellates.
Podiata, podiates, podiates [24] – the superclade splitting into the clades Amorphea and Crumalia, which representatives are capable of forming pseudopodia.
Sarcomastigota [18] – the subkingdom of Protozoa, uniting Apusozoa and Amoebozoa; this group combines the characteristics of amoebae and flagellates.
Scotokaryotes [24] – the basal clade of Neokaryotes; in addition to metamonads, it also included Malawimonas (in the latter system, Cavalier-Smith contrasted Malawimonas with all other eukaryotes); in terms of logical division it is opposed to the Photaria grouping.
Torcids [2] – a synonym of Amorphea; the name refers to Latin torcides, i.e. twisted.
Unikonta, unikonts [18] – the superclade of eukaryotes uniting Amoebozoa, Opisthokonta and some other groups.
Varisulca [29] – the clade basal to podiata, synonymous with Crumalia [13], the name refers to the presence of a ventral groove.
Viridiplantae [19] – the subkingdom of Plantae originally opposed to Biliphyta, uniting green algae and higher plants (containing the chlorophylls a, b and don’t contain the phycobilins).
The history of eukaryotic megataxonomy remembers several attempts to reveal the “basic dichotomy”. All such attempts had important heuristic significance, but during the accumulation of new knowledge, the general concept became more complicated. The “tubulicristates/lamellicristates” dichotomy became unobvious when the variability in the shape of mitochondrial cristae was shown, e.g., in red algae. In cryptophyte algae, a special type of lamellate cristae (rib-shaped) was identified, whereas the Euglenozoa and Percolozoa cristae began to be called discoid and, on this basis were even created higher Discoba group which does not fit into a previous “dichotomy”. Later, the discoid cristae were identified in naked filose amoebae nuclearia and cellular slime molds of fonticulids. Therefore, the “dichotomy” became the subject of history. The “bikont/unikont” dichotomy was initially complicated by the presence of a group of metamonads. The morphological data did not allow this group to be classified as unikonts. Therefore, so that the dichotomy didn't look like a trichotomy, metamonads were brought together with the basal group of bikonts, Discoba. However, using archaebacterial/eukaryotic protein sequences was confirmed previously obtained on the SSU datasets the concept of metamonads as a basal eukaryotes [30].
Thus, the historical background makes us wary of new “basic dichotomies,” including the “Malawimonas/discaria” dichotomy presented in the analyzed article. Simplification of the structures of the transition zone of the flagellum may well be the result of morpho-functional reduction. According to the amino acid sequences of eubacterial proteins, Malawinonas fall into the Crumalia clade, i.e. “basal Obazoa” [6].
On the other hand, testing Cavalier-Smith’s theses will undoubtedly shed light on the finer structure of the “basal unikonts” tree.
A few months earlier of the last paper by Cavalier-Smith, the work devoted to solving one of the problems in the crown region of the eukaryotic tree was published by Japanese researchers [31]. However, basing on multigene tree (GlobE analysis), the root eukaryote clade combined Nutomonas longa (Planomonadida, basal Obazoa) and Paratrimastix pyriforme (Preaxostyla, metamonads), i.e. lower the malawimonads and Crumalia. Another important conclusion from the Japanese work is the confirmation of the position of the Cryptista basal to Plantae, the Glaucophyta basal to “Viridiplantae”, and the Picozoa basal to Rhodophyta. These data can be considered as step towards leveling the “Plantae/Chromista”, another Cavalier-Smith dichotomy, and the unexpected entry of Cavalier-Smith’s Corticata into the forefront of eukaryote megataxonomy.
It should be noted that, as a thinker, Cavalier-Smith was formed before the “molecular revolution” in taxonomy and had a rich experience and culture of “morphological spectaculations”. He was interested in group genealogy in connection with revealing of possible ways of body plan transformation in various evolutionary lines. In his last paper, Cavalier-Smith presents 28 theses concerning the evolution of cytoskeleton and organization of ciliary transition zone in various groups of eukaryotes. However, in addition to the carefully elaborated morphological part, the last paper of Cavalier-Smith because valuable questions concerning the rank structure of eukaryote system and an universal eukaryote ancestor and provides an example of profound evolutionary synthesis.