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 reorganisations 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:

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:

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

The sea anemone is an animal that resembles a plant.

By mid-nineteenth century, microscopic organisms were generally classified into four groups:

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

Japanese popular mushrooms, clockwise from left, enokitake, buna-shimeji, bunapi-shimeji, king oyster mushroom and shiitake.

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:

Whittaker subdivided the Protista into two subkingdoms:

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:

  • Plantae,
  • Animalia,
  • Protista (excluding bacteria),
  • Fungi, and
  • Monera (the kingdom bacteria).[11]
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

Phylogenetic tree based on Woese et al. rRNA analysis in 1990 [12]

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:

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

The brown algae are a member of the 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:

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:

He created five new animal phyla:

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

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:

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

  1. ↑ Zrzavý, J (2001). "The interrelationships of metazoan parasites: A review of phylum-and higher-level hypotheses from recent morphological and molecular phylogenetic analyses". Folia parasitologica. 48 (2): 81–103. doi:10.14411/fp.2001.013. PMID 11437135.
  2. ↑ Patterson, David J. (1999). "The Diversity of Eukaryotes". The American Naturalist. 154 (S4): S96–S124. doi:10.1086/303287. PMID 10527921.
  3. ↑ Apusomonadida
  4. ↑ Eukarya.
  5. ↑ "Origins of the Eukarya". Archived from the original on December 20, 2010. Retrieved February 9, 2009.
  6. ↑ 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
  7. 1 2 3 Scamardella, JM (1999). "Not plants or animals: A brief history of the origin of Kingdoms Protozoa, Protista and Protoctista". International Microbiology. 2 (4): 207–16. PMID 10943416.
  8. 1 2 Penny, Douglas A.; Waern, Regina (1965). Biology. An Introduction to aspects of Modern Biological Science. Vancouver Calgary Toronto Montreal: Pitman Publishing. pp. 626–40.
  9. 1 2 3 4 Cavalier-Smith, T (1993). "Kingdom protozoa and its 18 phyla". Microbiological Reviews. 57 (4): 953–94. PMC 372943. PMID 8302218.
  10. ↑ Whittaker, R. H. (1959). "On the Broad Classification of Organisms". The Quarterly Review of Biology. 34 (3): 210–26. doi:10.1086/402733. JSTOR 2816520.
  11. ↑ Weeks, Benjamin S.; Alcamo, I. Edward (2008). Microbes and Society (2nd ed.). p. 32. ISBN 978-0-7637-4649-0.
  12. 1 2 Woese, Carl R.; Kandler, Otto; Wheelis, Mark L. (1990). "Towards a Natural System of Organisms: Proposal for the Domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences of the United States of America. 87 (12): 4576–9. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744.
  13. ↑ Gert Korthof, (2007). Carl Woese: from scientific dissident to textbook orthodoxy. Cited February 11, 2009.
  14. ↑ Cavalier-Smith, T (1981). "Eukaryote kingdoms: Seven or nine?". Bio Systems. 14 (3–4): 461–81. doi:10.1016/0303-2647(81)90050-2. PMID 7337818.
  15. ↑ Cavalier-Smith, T.; Chao, E. E. (1996). "Molecular phylogeny of the free-living archezoanTrepomonas agilis and the nature of the first eukaryote". Journal of Molecular Evolution. 43 (6): 551–62. doi:10.1007/BF02202103. PMID 8995052.
  16. ↑ Cavalier-Smith, T. (2004). "Only six kingdoms of life". Proceedings of the Royal Society B: Biological Sciences. 271 (1545): 1251–62. doi:10.1098/rspb.2004.2705. PMC 1691724. PMID 15306349.
  17. 1 2 3 4 5 Cavalier-Smith, Thomas (2003). "Protist phylogeny and the high-level classification of Protozoa". European Journal of Protistology. 39 (4): 338. doi:10.1078/0932-4739-00002.
  18. 1 2 3 4 5 6 Cavalier-Smith, T. (2007). "A revised six-kingdom system of life". Biological Reviews. 73 (3): 203–66. doi:10.1111/j.1469-185X.1998.tb00030.x. PMID 9809012.
  19. ↑ Cavalier-Smith, Thomas (1993). "The Protozoan Phylum Opalozoa". The Journal of Eukaryotic Microbiology. 40 (5): 609–15. doi:10.1111/j.1550-7408.1993.tb06117.x.
  20. ↑ Stechmann, Alexandra; Cavalier-Smith, Thomas (2003). "The root of the eukaryote tree pinpointed". Current Biology. 13 (17): R665–6. doi:10.1016/S0960-9822(03)00602-X. PMID 12956967.
  21. ↑ Cavalier-Smith, Thomas (2010). "Origin of the cell nucleus, mitosis and sex: Roles of intracellular coevolution". Biology Direct. 5: 7. doi:10.1186/1745-6150-5-7. PMC 2837639. PMID 20132544.
  22. ↑ Cavalier-Smith, Thomas (1987). "The origin of eukaryotic and archaebacterial cells". Annals of the New York Academy of Sciences. 503: 17–54. doi:10.1111/j.1749-6632.1987.tb40596.x. PMID 3113314.
  23. ↑ Ruggiero, Michael A.; Gordon, Dennis P.; Orrell, Thomas M.; Bailly, Nicolas; Bourgoin, Thierry; Brusca, Richard C.; Cavalier-Smith, Thomas; Guiry, Michael D.; Kirk, Paul M.; Thuesen, Erik V. (2015). "A higher level classification of all living organisms". PLoS ONE. 10 (4): e0119248. doi:10.1371/journal.pone.0119248. PMC 4418965. PMID 25923521.
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