The initial version of a classification system of life by British zoologist Thomas Cavalier-Smith appeared in 1978.Cavalier-Smith, T. 1978. The evolutionary origin and phylogeny of microtubules, mitotic spindles and eucaryotic flagella. BioSystems 10: 93-114.C. Jeffrey. 1982. Kingdoms, Codes and Classification. Kew Bulletin: 37: 403-416 This initial system continued to be modified in subsequent versions that were published until he died in 2021. As with classifications of others, such as Carl Linnaeus, Ernst Haeckel, Robert Whittaker, and Carl Woese, Cavalier-Smith's classification attempts to incorporate the latest developments in taxonomy. Cavalier-Smith used his classifications to convey his opinions about the evolutionary relationships among various organisms, principally microbial. His classifications complemented his ideas communicated in scientific publications, talks, and diagrams. Different iterations might have a wider or narrow scope, include different groupings, provide greater or lesser detail, and place groups in different arrangements as his thinking changed. His classifications has been a major influence in the modern taxonomy, particularly of protists.

Cavalier-Smith has published extensively on the classification of protists. One of his major contributions to biology was his proposal of a new kingdom of life: the Chromista, although the usefulness of the grouping is questionable given that it is generally agreed to be an arbitrary (polyphyletic) grouping of taxa. He also proposed that all chromista and alveolata share the same common ancestor, a claim later refuted by studies of morphological and molecular evidence by other labs. He named this new group the Chromalveolates. He also proposed and named many other high-rank taxa, like Opisthokonta (1987), Rhizaria (2002), and Excavata (2002), though he himself consistently does not include Opisthonkonta as a formal taxon in his schemes. Together with Chromalveolata, Amoebozoa (he amended their description in 1998), and Archaeplastida (which he called Plantae since 1981) the six formed the basis of the taxonomy of eukaryotes in the middle 2000s. He has also published prodigiously on issues such as the origin of various cellular organelles (including the nucleus, mitochondria), genome size evolution, and endosymbiosis. Though fairly well known, many of his claims have been controversial and have not gained widespread acceptance in the scientific community to date. Most recently, he has published a paper citing the paraphyly of his bacterial kingdom, the origin of Neomura from Actinobacteria and taxonomy of prokaryotes.

According to Palaeos.com: Prof. Cavalier-Smith of Oxford University has produced a large body of work which is well regarded. Still, he is controversial in a way that is a bit difficult to describe. The issue may be one of writing style. Cavalier-Smith has a tendency to make pronouncements where others would use declarative sentences, to use declarative sentences where others would express an opinion, and to express opinions where angels would fear to tread. In addition, he can sound arrogant, reactionary, and even perverse. On the other [hand], he has a long history of being right when everyone else was wrong. To our way of thinking, all of this is overshadowed by one incomparable virtue: the fact that he will grapple with the details. This makes for very long, very complex papers and causes all manner of dark murmuring, tearing of hair, and gnashing of teeth among those tasked with trying to explain his views of early life. See, [for example], Zrzavý (2001) [and] Patterson (1999).Eukarya . Nevertheless, he deals with all of the relevant facts.

Background

The first two kingdoms of life: Plantae and Animalia

The use of the word "kingdom" to describe a major branch of the living world dates as far back as Linnaeus (1707–1778) who divided the natural world into three kingdoms: animal, vegetable, and mineral.Dan H. Nicolson. Animal, Vegetable or Mineral?. Proceedings of a Mini-Symposium on Biological Nomenclature in the 21st Century held at the University of Maryland on 4 November 1996. Edited by James L. Reveal The taxa "animal kingdom" (or kingdom Animalia) and "plant kingdom" (or kingdom Plantae) remain in use by some modern evolutionary biologists. The initial targets of Cavalier-Smith's classification, the protozoa were classified as members of the animal kingdom, and many algae were regarded as part of the plant kingdom. With growing awareness that the animals and plants embraced unrelated taxa, the use of the two kingdom system was rejected by specialists. It remains in use in less critical circles.

The third kingdom: Protista

By mid-nineteenth century, microscopic organisms were generally classified into four groups: Protozoa (primitive animals), Protophyta (primitive plants), Phytozoa (animal-like plants & plant-like animals), and In 1858, Richard Owen (1804–1892) proposed that the animal phylum Protozoa be elevated to the status of kingdom. In 1860, John Hogg (1800–1869) proposed that protozoa and protophyta be grouped together into a new kingdom which he called "Regnum Primigenum" (kingdom primitive). According to Hogg, this new classification scheme prevented "the unnecessary trouble of contending about their supposed natures, and of uselessly trying to distinguish the Protozoa from the Protophyta". In 1866, Ernst Haeckel (1834–1919) proposed the name "Protista" for the primigenial kingdom and included bacteria in this third kingdom of life.Kutschera, U. Haeckel's 1866 tree of life and the origin of eukaryotes. Nat Microbiol 1, 16114 (2016). https://doi.org/10.1038/nmicrobiol.2016.114)

The fourth kingdom: Fungi

By 1959, Robert Whittaker proposed that fungi, which were formerly classified as plants, be given their own kingdom. Therefore, he divided life into four kingdoms such as: Protista, (or unicellular organisms); Plantae, (or multicellular plants); Fungi; and Animalia (or multicellular animals). Whittaker subdivided the Protista into two subkingdoms: Monera (bacteria) and Eunucleata (single celled eukaryotes).

The fifth kingdom: Bacteria (Monera)

Bacteria are fundamentally different from the eukaryotes (plants, animals, fungi, amebas, protozoa, and chromista). Eukaryotes have cell nuclei, bacteria do not. In 1969, Whittaker elevated the bacteria to the status of kingdom. His new classification system divided the living world into five kingdoms: Plantae, Animalia, Protista (Eunucleata), Fungi, and Monera (the kingdom bacteria).

The sixth kingdom: Archaebacteria

The kingdom Monera can be divided into two distinct groups: eubacteria (true bacteria) and archaebacteria (archaea). In 1977 Carl Woese and George E. Fox established that archaebacteria (methanogens in their case) were genetically different (based on their ribosomal RNA genes) from bacteria so that life could be divided into three principle lineages, namely: Eubacteria (all typical bacteria), Archaebacteria (methanogens), and Urkaryotes (all eukaryotes). In 1990, Woese introduced domain above kingdom by creating three-domain system such as: Bacteria, Archaea, and Eucarya. Cavalier-Smith considered Archaebacteria as a kingdom in 1989, but later abandoned this view.

Kingdom Chromista

By 1981, Cavalier-Smith had divided all the eukaryotes into as many as nine kingdoms, with kingdoms Cryptophyta and Chromophyta being alternatively grouped as a single kingdom: Chromista.

Most chromists are photosynthetic. This distinguishes them from most other protists which lack photosynthesis. In both plants and chromists photosynthesis takes place in chloroplasts. In plants, however, the chloroplasts are located in the cytosol while in chromists the chloroplasts are located in the lumen of their rough endoplasmic reticulum. This distinguishes chromists from plants.

Based on the addition of Chromista as a kingdom, he stated "the best one for general scientific use is a system of seven kingdoms", which includes: Viridiplantae, Biliphyta, Animalia, Euglenozoa, Protozoa, Chromista, Fungi. An even more compact classification is proposed in the article: Euglenozoa and Protozoa can be united as kingdom Protista, and Viridiplantae and Biliphyta can be united as kingdom Plantae. All prokaryotes were included in kingdom Bacteria at this point.

Kingdom Archezoa In 1983, Cavalier-Smith adapted the term Archezoa, previously used by Haeckel, Perty, and for protists that lack mitochondria. Initially, the taxon included the quite unrelated metamonads and microscopridia, and expanded to include other unrelated taxa such that the term referred to many different groupings of protists.Cavalier Smith, T. 1983. A six-kingdom classification and a unified phylogeny. Endocytobiology 2:1027–1034.Cavalier Smith, T. 1987. Eukaryotes with no mitochondria. Nature (London) 326:332–333.Cavalier Smith, T. 1987 The origin of eukaryote and archaebacterial cells. Annals of the New York Academy of Sciences 503:17–54.Cavalier Smith, T. 1989. Archaebacteria and Archezoa. Nature (London) 339:100–101.Cavalier Smith, T. 1990. Microorganism megaevolution: integrating the fossil and living evidence. Revue de Micropalêontologie 33:145–154.Cavalier Smith, T. 1991. Archamoebae: the ancestral eukaryotes? Biosystems 25:25–38.Cavalier Smith, T. . The evolution of cells. pp 271–304 in S. Osawa and T. Honjo, eds. Evolution of life. Springer, Berlin.Cavalier Smith, T. 1992. Percolozoa and the symbiotic origin of the metakaryote cell. Endocytobiology 5:399–406.Cavalier Smith, T. Kingdom Protozoa and its 18 Phyla. Microbiological Reviews 57:953–994.Cavalier Smith, T. 1995. Zooflagellate phylogeny and classification. Cytology 37:1010–1029.Cavalier Smith, T. 1997. Amoeboflagellates and mitochondrial cristae in eukaryote evolution: megasystematics of the new protozoan subkingdoms Eozoa and Neozoa. Archiv für Protistenkunde 147:237–258.Cavalier Smith, T. 1997. Zooflagellate phylogeny and the evolution and classification of protozoa. Page 65 in Programme and abstracts, Tenth International Congress of Protozoology, Sydney.Cavalier Smith, T. 1998. A revised six–kingdom system of life. Biological Reviews of the Cambridge Philosophical Society 73:203–266.Cavalier Smith, T. 1999. Zooflagellate phylogeny and the systematics of protozoa. Biological Bulletin (Woods Hole) 196: 393–395.Cavalier-Smith, T.and Chao, E. 1995. The opalozoan Apusomonas is related to the common ancestor of animals, fungi and choanoflagellates. Proceedings of the Royal Society of London B, Biological Sciences 261:1–6.Cavalier-Smith, T.and Chao, E. 1996. Molecular diversity of the free-living archezoan Trepomonas agilis and the nature of the first eukaryote. Journal of Molecular Evolution 43:551–563. He originally considered it as a subkingdom, but by 1989, with the establishment of Chromista as separate kingdom, he treated it as a kingdom.

+ Composition of Archezoa Patterson, D. J. 1999. The diversity of eukaryotes. American Naturalist, Supplement 65: 96-124. 1983a1983b1987198919901991199319951996199719981999Diplomonads + + + + + + + + + + + + Retortamonads + + + + + + + + + + + + Oxymonads + + + + + + + + + + + + Microspora + + + + + + + + + Hypermastigids + + + Trichomonads + + + Mastigamoebids + + + + + + Pelomyxa + + + + + Entamoeba + + + + + Phreatamoeba + + Trimastix +

Archezoa is now defunct. He assigned former members of the kingdom Archezoa to the phylum Amoebozoa. Today, its former members belong to the Metamonada (e. g. Trimastix), fungi (Microsporidia), Amoebozoa (e. g. Pelomyxa).

Kingdom Protozoa sensu Cavalier-Smith