Cavalier-Smith's system of classification

The classification system of life introduced by British zoologist Thomas Cavalier-Smith involves systematic arrangements of all life forms on earth. Following and improving the classification systems introduced by Carl Linnaeus, Ernst Haeckel, Robert Whittaker, and Carl Woese, Cavalier-Smith's classification attempts to incorporate the latest developments in taxonomy. His classification has been a major foundation in modern taxonomy, particularly with revisions and reorgnisations of kingdoms and phyla.

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). Together with Chromalveolata, Amoebozoa (he amended their description in 1998), and Archaeplastida (which he called Plantae since 1981) the six form the basis of current taxonomy of eukaryotes. Prof. Cavalier-Smith 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)^[1] [and] Patterson (1999).^[2][3][4] Nevertheless, he deals with all of the relevant facts.^[5]

Eight kingdoms model

The first two kingdoms of life: Plantae and Animalia

The use of the word "kingdom" to describe the living world dates as far back as Linnaeus (1707–1778) who divided the natural world into three kingdoms: animal, vegetable, and mineral.^[6][7] The classifications "animal kingdom" (or kingdom Animalia) and "plant kingdom" (or kingdom Plantae) remain in use by modern evolutionary biologists.

By 1910 the animal kingdom had been subdivided into twelve phyla:

• protozoa,
• porifera (sponges),
• coelenterata (e.g. jellyfish),
• platyhelminthes (flat worms),
• nemathelminthes (e.g. nematodes),
• trochhelminthes (Rotifers and Gastrotricha),
• echinodermata (e.g. sea urchins, starfish),
• annulata (Polyzoa, Phoronida, and Brachiopoda),
• arthropoda (insects, arachnids and crustaceans),
• molluscoida,
• mollusca (e.g. octopus, clams), and
• chordata (e.g. vertebrates).

The protozoa were originally classified as members of the animal kingdom.^[8] Now they are classified as multiple separate groups.

Zoology is the study of animals while botany is the study of plants. While zoologists divided the animal kingdom into phyla, botanists carved the plant kingdom into "divisions". By 1940, five divisions were recognized:

• Thallophyta (algae, fungi, bacteria, and lichens),
• Charophyta (green algae),
• Bryophyta (Heptacae and Musci e.g. moss),
• Pteridophyta (ferns), and
• Spermatophyta (seed-bearing plants).

Fungi and bacteria were included within the plant division thallophyta.^[8] Today, bacteria are no longer classified as plants and fungi are known to be more closely related to animals than to plants.

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
• Bacteria (formerly regarded as plants).^[7]

In 1858, Richard Owen (1804–1892) proposed that the animal phylum Protozoa be elevated to the status of kingdom.^[9] In 1860, John Hogg (1800–1869) proposed that protozoa and protophyta be grouped together into a new kingdom which he called "Regnum Primigenum". 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 Primigenum kingdom and included bacteria in this third kingdom of life.^[7]

The fourth kingdom: Fungi

Fungi are more closely related to animals than to plants. By 1959, Robert Harding Whittaker (1920–1980) proposed that fungi, which were formerly classified as plants, be given their own kingdom. His four kingdoms of life were:

• the Protista, (or unicellular organisms);
• the Plantae, (or multicellular plants);
• the Fungi; and
• the Animalia (or multicellular animals).

Whittaker subdivided the Protista into two subkingdoms:

• Monera (bacteria) and
• Eunucleata (single celled eukaryotes).^[10]

The fifth kingdom: Bacteria

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

• plants,
• animals,
• protists (excluding bacteria),
• fungi, and
• Monera (the kingdom bacteria).^[11]

Note: the word "protist" is ambiguous.

Eunucleata = single celled eukaryotes

Before 1959: protist = prokaryotes + Eunucleata + sponges

From 1959 to 1969: protist = prokaryotes + Eunucleata

Since 1969: protist = Eunucleata

The sixth kingdom and the three domains of life

The kingdom Monera can be divided into two distinct groups: eubacteria and archaebacteria. In 1977 Carl Woese and George E. Fox proposed that eubacteria and archaebacteria both be elevated to the status of super-kingdom.^[13] In 1990, Woese further elevated the status of bacteria by dividing life into three domains:

• eubacteria (which he called "Bacteria"),
• archaebacteria (which he called "Archaea"), and
• eukaryotes (which he called "Eukaryota").^[12]

eukaryotes = plants + chromista + animals + fungi + Eunucleata

prokaryotes = Monera = eubacteria + archaebacteria

Note: the modern use of the word "bacteria" is ambiguous. It may refer either to eubacteria (as in the above phylogenetic tree) or prokaryotes (as in reference to the kingdom Monera).

The seventh kingdom: Chromista

By 1981, Cavalier-Smith had divided the domain Eukaryota into nine kingdoms.^[14] By 1993, he reduced the total number of eukaryote kingdoms to six. He also classified the domains Eubacteria and Archaebacteria as kingdoms, adding up to a total of eight kingdoms of life:

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

Cavalier-Smith's new classification scheme retained the plant, animal and fungal kingdoms from the traditional five kingdom model. It also split the kingdom Monera into the two groups, eubacteria and archaebacteria, as proposed by Woese and Fox. In addition it split the kingdom protists into three new kingdoms: archezoa, protozoa, and chromista.

Most chromists are photosynthetic. This distinguishes them from most other protists. 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.^[9]

The eighth kingdom: Archezoa

Cavalier-Smith's eighth kingdom, Archezoa ^[15] is now defunct. He now assigns former members of the kingdom Archezoa to the phylum Amoebozoa.^[16]

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:^[9]

#	Phylum	Assigned to:	Characteristics	Fate
1	Percolozoa	subkingdom Adictyozoa	lacks Golgi dictyosomes
2	Parabasalia	subkingdom Dictyozoa branch Parabasalia	has Golgi dictyosomes lacks mitochondria
3	Euglenozoa	subkingdom Dictyozoa branch Bikonta infrakingdom Euglenozoa	has Golgi dictyosomes mostly with mitochondria with trans-splicing of miniexons
4	Opalozoa (flagellates)	subkingdom Dictyozoa branch Bikonta infrakingdom Neozoa parvkingdom Ciliomyxa superphylum Opalomyxa	has Golgi dictyosomes tubular mitochondrial cristae with cis-spliced introns predominantly ciliated, no cortical alveoli
5	Mycetozoa (slime molds)	subkingdom Dictyozoa branch Bikonta infrakingdom Neozoa parvkingdom Ciliomyxa superphylum Opalomyxa	has Golgi dictyosomes tubular mitochondrial cristae with cis-spliced introns predominantly ciliated, no cortical alveoli
6	Choanozoa (choanoflagellates)	subkingdom Dictyozoa branch Bikonta infrakingdom Neozoa parvkingdom Ciliomyxa superphylum Choanozoa	has Golgi dictyosomes flattened mitochondrial cristae with cis-spliced introns predominantly ciliated, no cortical alveoli
7	Dinozoa (Dinoflagellata and Protalveolata)	subkingdom Dictyozoa branch Bikonta infrakingdom Neozoa parvkingdom Alveolata superphylum Miozoa	has Golgi dictyosomes tubular mitochondrial cristae with cis-spliced introns with cortical alveoli	Reassigned to Miozoa in Alveolata.[17]
8	Apicomplexa	subkingdom Dictyozoa branch Bikonta infrakingdom Neozoa parvkingdom Alveolata superphylum Miozoa	has Golgi dictyosomes tubular mitochondrial cristae with cis-spliced introns with cortical alveoli	Reassigned to Miozoa in Alveolata.[17]
9	Ciliophora	subkingdom Dictyozoa branch Bikonta infrakingdom Neozoa parvkingdom Alveolata superphylum Heterokaryota	has Golgi dictyosomes tubular mitochondrial cristae with cis-spliced introns with cortical alveoli	Reassigned to Alveolata.[17]
10	Rhizopoda (lobose and filose amoebae)	subkingdom Dictyozoa branch Bikonta infrakingdom Neozoa parvkingdom Neosarcodina	has Golgi dictyosomes usually with tubular cristae with cis-spliced introns
11	Reticulosa (foraminifera; reticulopodial amoebae)	subkingdom Dictyozoa branch Bikonta infrakingdom Neozoa parvkingdom Neosarcodina	has Golgi dictyosomes usually with tubular cristae with cis-spliced introns
12	Heliozoa	subkingdom Dictyozoa branch Bikonta infrakingdom Neozoa parvkingdom Actinopoda	has Golgi dictyosomes mostly with mitochondria with cis-spliced introns has axopodia
13	Radiozoa	subkingdom Dictyozoa branch Bikonta infrakingdom Neozoa parvkingdom Actinopoda	has Golgi dictyosomes mostly with mitochondria with cis-spliced introns has axopodia
14	Entamoebia	subkingdom Dictyozoa branch Bikonta infrakingdom Neozoa parvkingdom Entamoebia	has Golgi dictyosomes with cis-spliced introns no mitochondria, peroxisomes, hydrogenosomes or cilia transient intranuclear centrosomes
15	Myxosporidia	subkingdom Dictyozoa branch Bikonta infrakingdom Neozoa parvkingdom Myxozoa	has Golgi dictyosomes with cis-spliced introns endoparasitic, multicellular spores, mitochondria, and no cilia	Reclassified as animals in 1998.[18]
16	Haplosporidia	subkingdom Dictyozoa branch Bikonta infrakingdom Neozoa parvkingdom Myxozoa	has Golgi dictyosomes with cis-spliced introns endoparasitic, multicellular spores, mitochondria, and no cilia	Reclassified as animals in 1998.[18]
17	Paramyxia	subkingdom Dictyozoa branch Bikonta infrakingdom Neozoa parvkingdom Myxozoa	has Golgi dictyosomes with cis-spliced introns endoparasitic, multicellular spores, mitochondria, and no cilia	Reclassified as animals in 1998.[18]
18	Mesozoa	subkingdom Dictyozoa branch Bikonta infrakingdom Neozoa parvkingdom Mesozoa	has Golgi dictyosomes with cis-spliced introns tubular mitochondrial cristae multicellular with no collagenous connective tissue	Reclassified as animals in 1998.[18]

The phylum Opalozoa was established by Cavalier-Smith in 1991.^[19]

Six kingdoms models

By 1998, Cavalier-Smith had reduced the total number of kingdoms from eight to six: Animalia, Protozoa, Fungi, Plantae (including red and green algae), Chromista and Bacteria.^[18]

Five of Cavalier-Smith's kingdoms are classified as eukaryotes as shown in the following scheme:

• Eubacteria
• Neomura
  • Archaebacteria
  • Eukaryotes
    • Kingdom Protozoa
    • Unikonts (heterotrophs)
      • Kingdom Animalia
      • Kingdom Fungi
    • Bikonts (primarily photosynthetic)
      • Kingdom Plantae (including red and green algae)
      • Kingdom Chromista

Eukaryotes are divided into two major groups: unikonts and bikonts. Uniciliates are cells with only one flagellum and unikonts are descended from uniciliates. Unikont cells often have only one centriole as well. Biciliate cells have two flagella and bikonts are descended from biciliates. Biciliates undergo ciliary transformation by converting a younger anterior flagellum into a dissimilar older posterior flagellum. Animals and fungi are unikonts while plants and chromista are bikonts. Some protozoa are unikonts while others are bikonts.

The Bacteria (= prokaryotes) are subdivided into Eubacteria and Archaebacteria. According to Cavalier-Smith, eubacteria is the oldest group of terrestrial organisms still living. He classifies the groups which he believes are younger (archaebacteria and eukaryotes) as neomura.

The 1998 model

Kingdom Animalia

In 1993, Cavalier-Smith classified Myxozoa as a protozoan parvkingdom. By 1998, he had reclassified it as an animal subkingdom. Myxozoa contains three phyla, Myxosporidia, Haplosporidia, and Paramyxia, which were reclassified as animals along with Myxozoa. Likewise, Cavalier-Smith reclassified the protozoan phylum Mesozoa as an animal subkingdom.

In his 1998 scheme, the animal kingdom was divided into four subkingdoms:

• Radiata (phyla Porifera, Cnidaria, Placozoa, and Ctenophora),
• Myxozoa,
• Mesozoa, and
• Bilateria (all other animal phyla).

He created five new animal phyla:

• Acanthognatha (rotifers, acanthocephalans, gastrotrichs, and gnathostomulids),
• Brachiozoa (brachiopods and phoronids),
• Lobopoda (onychophorans and tardigrades),
• Kamptozoa (Entoprocta and Symbion), and
• Nemathelminthes (Nematoda, Nematomorpha, Loricifera, Priapulida, and Kinorhyncha)

and recognized a total of 23 animal phyla, as shown here:

• Kingdom Animalia
  • Subkingdom Radiata
    • Infrakingdom Spongiaria
      • Phylum Porifera
    • Infrakingdom Coelenterata
      • Phylum Cnidaria
      • Phylum Ctenophora
    • Infrakingdom Placozoa
      • Phylum Placozoa
  • Subkingdom Myxozoa
    • Phylum Myxosporidia
  • Subkingdom Bilateria
    • Branch Protostomia
      • Infrakingdom Lophozoa
        • Superphylum Polyzoa
          • Phylum Bryozoa
          • Phylum Kamptozoa
        • Superphylum Conchozoa
          • Phylum Mollusca
          • Phylum Brachiozoa
        • Superphylum Sipuncula
          • Phylum Sipuncula
        • Superphylum Vermizoa
          • Phylum Nemertina
          • Phylum Annelida
      • Infrakingdom Chaetognathi
        • Phylum Chaetognatha
      • Infrakingdom Ecdysozoa
        • Superphylum Nemathelminthes
          • Phylum Nemathelminthes
        • Superphylum Haemopoda
          • Phylum Lobopoda
          • Phylum Arthropoda
      • Infrakingdom Platyzoa
        • Phylum Platyhelminthes (Incl. Xenacoelomorpha)
        • Phylum Acanthognatha
    • Branch Deuterostomia
      • Infrakingdom Coelomopora
        • Phylum Echinodermata
        • Phylum Hemichordata
      • Infrakingdom Chordonia
        • Phylum Urochorda
        • Phylum Chordata
  • Subkingdom Mesozoa
    • Phylum Mesozoa^[18]

Kingdom Protozoa

Under Cavalier-Smith's proposed classification system, protozoa share the following traits:

• they have or are descended from organisms with mitochondria
• they have or are descended from organisms with peroxisomes
• they lack collagenous connective tissue
• they lack epiciliary retronemes (rigid thrust-reversing tubular ciliary hairs)
• they lack two additional membranes outside their chloroplast envelope

Organisms that do not meet these criteria were reassigned to other kingdoms by Cavalier-Smith.

The 2003 model

Kingdom Protozoa

In 1993, Cavalier-Smith divided the kingdom Protozoa into two subkingdoms and 18 phyla.^[9] By 2003 he used phylogenic evidence to revise the total number of proposed phyla down to 11: Amoebozoa, Choanozoa, Cercozoa, Retaria, Loukozoa, Metamonada, Euglenozoa, Percolozoa, Apusozoa, Alveolata, Ciliophora, and Miozoa. ^[17]

Unikonts and bikonts

Amoebozoa do not have flagella and are difficult to classify as unikont or bikont based on morphology. In his 1993 classification scheme, Cavalier-Smith incorrectly classified amoebas as bikonts. Gene fusion research later revealed that the clade Amoebozoa, was ancestrally uniciliate. In his 2003 classification scheme, Cavalier-Smith reassigned Amoebozoa to the unikont clade along with animals, fungi, and the protozoan phylum Choanozoa. Plants and all other protists where assigned to the clade Bikont by Cavalier-Smith.^[17]

Cavalier-Smith's 2003 classification scheme:

• Unikonts
  • protozoan phylum Amoebozoa (ancestrally uniciliate)
  • opisthokonts
    • uniciliate protozoan phylum Choanozoa
    • kingdom Fungi
    • kingdom Animalia
• Bikonts
  • protozoan infrakingdom Rhizaria
    • phylum Cercozoa
    • phylum Retaria (Radiozoa and Foraminifera)
  • protozoan infrakingdom Excavata
    • phylum Loukozoa
    • phylum Metamonada
    • phylum Euglenozoa
    • phylum Percolozoa
  • protozoan phylum Apusozoa (Thecomonadea and Diphylleida)
  • the chromalveolate clade
    • kingdom Chromista (Cryptista, Heterokonta, and Haptophyta)
    • protozoan infrakingdom Alveolata
      • phylum Ciliophora
      • phylum Miozoa (Protalveolata, Dinozoa, and Apicomplexa)
  • kingdom Plantae (Viridaeplantae, Rhodophyta and Glaucophyta)

Cladogram of life

By September 2003, Cavalier-Smith's tree of life looked like this:^[20]

	Eubacteria Neomura Archaebacteria Eukarya Bikonts Apusozoa Cabozoa Excavata Rhizaria Retaria Cercozoa Kingdom Plantae Chromalveolata Kingdom Chromista Alveolata Unikonts Amoebozoa Opisthokonts Choanozoa Kingdom Animalia Kingdom Fungi

In the above tree, the traditional plant, animal, and fungal kingdoms, as well as Cavalier-Smith's proposed Chromista kingdom, are shown as leaves. The leaves Eubacteria and Archaebacteria together make up the Bacteria kingdom. All remaining leaves together make up the protozoa kingdom.

By 2010 new data emerged that showed that Unikonts and Bikonts, originally considered to be separate because of an apparently different organization of cilia and cytoskeleton, are in reality more similar than previously thought. As a consequence, Cavalier-Smith revised the above tree and proposed to move its root to reside in between the Excavata and Euglenozoa kingdoms.^[21]

Seven kingdoms model

In 1987, Cavalier-Smith introduced a classification divided into two superkingdoms (Prokaryota and Eukaryota) and seven kingdoms, two prokaryotic kingdoms (Eubacteria and Archaebacteria) and five eukaryotic kingdoms (Protozoa, Chromista, Fungi, Plantae and Animalia).^[22]

Cavalier-Smith and his collaborators revised the classification in 2015, and published it in PLOS ONE. In this scheme they reintroduced the classification with the division of prokaryotes superkingdom into two kingdoms, Bacteria (=Eubacteria) and Archaea (=Archaebacteria). This is based on the consensus in the Taxonomic Outline of Bacteria and Archaea (TOBA) and the Catalogue of Life.^[23]

References