Cavalier-Smith's system of classification

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). Nevertheless, he deals with all of the relevant facts.

Eight kingdoms model

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. 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:

1. Protozoa (primitive animals),
2. Protophyta (primitive plants),
3. 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.)

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:

1. Protista, (or unicellular organisms);
2. Plantae, (or multicellular plants);
3. Fungi; and
4. Animalia (or multicellular animals).

Whittaker subdivided the Protista into two subkingdoms:

1. Monera (bacteria) and
2. 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:

1. Plantae,
2. Animalia,
3. Protista (Eunucleata),
4. Fungi, and
5. 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:

1. Eubacteria (all typical bacteria),
2. Archaebacteria (methanogens), and
3. Urkaryotes (all eukaryotes).

In 1990, Woese introduced domain above kingdom by creating three-domain system such as:

1. Bacteria,
2. Archaea, and
3. Eucarya.

But Cavalier-Smith considered Archaebacteria as a kingdom.

The seventh kingdom: Chromista

By 1981, Cavalier-Smith had divided all the eukaryotes into nine kingdoms. In it, he created Chromista for a separate kingdom of some protists.

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 suggested that even with his nine kingdoms of eukaryotes, "the best one for general scientific use is a system of seven kingdoms", which includes:

1. Plantae,
2. Animalia,
3. Protozoa,
4. Chromista
5. Fungi,
6. Eubacteria, and
7. Archaebacteria.

The eighth 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. He originally considered it as a subkingdom, but by 1989, with the establishment of Chromista as separate kingdom, he treated it as a kingdom.

Archezoa is now defunct. He now assigns former members of the kingdom Archezoa to the phylum Amoebozoa.

Kingdom Protozoa sensu Cavalier-Smith

Cavalier-Smith referred to what remained of the protist kingdom, after he removed the kingdoms Archezoa and Chromista, as the "kingdom Protozoa". In 1993, this kingdom contained 18 phyla as summarized in the following table. The first major division relied on the basis of presence or absence of dictyosomes, although a Gogli Apparatus was subsequently demonstrated in the 'Adictyozoa'.

The phylum Opalozoa was established by Cavalier-Smith in 1991.