Thomas Cavalier-Smith

Cavalier-Smith was a prolific taxonomist, drawing on a near-unparalleled wealth of information to suggest novel relationships. His suggestions were translated into taxonomic concepts and classifications with which he associated new names, or in some cases, reused old names. Smith did not follow or espouse an explicit taxonomic philosophy. He did not adopt the cladistic protocols that were bringing rigor to taxonomy in general; his approach was similar to that of many others' broad-based treatments of protists.[6][7]

The scope of Smith's taxonomic propositions was grand, but the number and composition of the components (taxa), and their relations were not stable. Propositions were often ambiguous and short-lived; he frequently amended taxa without any change in the name. Many of his assertions failed the expectation that taxonomic names should have an exact, stable relationship with a group of organisms, or branch of the evolutionary tree. His imprecise approach was not universal: Others attempted to underpin taxonomy of protists with a nested series of atomised, falsifiable propositions, following the philosophy of transformed cladistics.[8]

Smith's ideas that led to the taxonomic structures were usually first presented in the form of complex, annotated diagrams. When presented at scientific meetings, they were too rich, and often written too small, for the ideas to be grasped or criticized meaningfully. Some such diagrams made their way into publications, where careful scrutiny was possible, and where the conjectural nature of most assertions was evident. The richness of his ideas, their continuing evolution, and the transition into taxonomies that gave Smith's investigations into evolutionary paths (phylogeny) and the resulting classifications, its distinctive character.

First, was a residue of the ‘traditional’ approach that admitted speculation and which lacked any explicit rigor as to how a particular evolutionary insight should be translated into the arrangement and ranks of taxa. Inherent to this approach were narratives that were frequently dismissed as ‘just so’ statements, associated classifications which included paraphyletic and polyphyletic taxa, and in which subjective views rather than phylogenetic relationships would influence the rank assigned to taxa.

The second influence was the philosophy as to how scientific progress was made. It had been articulated by K. Popper[9][10] and had shifted the emphasis from verification of ideas to the falsification of hypotheses.

Popper saw that science progressed by a process that eliminated unsound hypotheses, so whittling down of the array of possible explanations leading towards the explanations which were more likely correct. To fit into this process, hypotheses needed to be falsifiable.

The third influence was ‘cladistics’ – an explicit way of presenting (and then falsifying) evolutionary hypotheses. This was initially articulated by Willi Hennig,[11] and was increasingly baked into how taxonomy should be done.[12][13]

Fourthly, technical advances in sequencing technology led to a massive growth of hypotheses about evolutionary relationships based on the similarities among sequences of compared organisms. Algorithms were used to analyse sequence data, with the results being usually presented in the form of dendrograms. These have a superficial similarity with the diagrams used to present evolutionary relationships (trees), and unfortunately gained the name of ‘phylogenies’.

The dendrograms of molecular phylogenetics differed, depending on the molecules chosen, the organisms included in an analysis, and the algorithms used to run comparisons. ‘Molecular phylogenies’ were probabilistic summaries that lacked the exactness that was required of the process of progressing through falsifiable hypotheses. The result of this ‘molecular phylogenetics’ was a plethora of hypotheses which had the ability to hide the signal, and were often uncertain in detail.

Cavalier-Smith's first major classification system was the division of all organisms into eight kingdoms. In 1981, he proposed that by completely revising Robert Whittaker's Five Kingdom system, there could be eight kingdoms: Bacteria, Eufungi, Ciliofungi, Animalia, Biliphyta, Viridiplantae, Cryptophyta, and Euglenozoa.[16]

In 1993, he revised his system particularly in the light of the general acceptance of Archaebacteria as separate group from Bacteria, to include an array of lineages that had been excluded from his 1981 treatment, to deal with issues of polyphyly, and to promote new ideas of relationships. In addition, some protists lacking mitochondria were discovered.[17] As mitochondria were known to be the result of the endosymbiosis of a proteobacterium, it was thought that these amitochondriate eukaryotes were primitively so, marking an important step in eukaryogenesis. As a result, these amitochondriate protists were separated from the protist kingdom, giving rise to the, at the same time, superkingdom and kingdom Archezoa. This was known as the Archezoa hypothesis. The eight kingdoms became: Eubacteria, Archaebacteria, Archezoa, Protozoa, Chromista, Plantae, Fungi, and Animalia.[18]

The kingdom Archezoa went through many compositional changes due to evidence of polyphyly and paraphyly before being abandoned.[19][20] He assigned some former members of the kingdom Archezoa to the phylum Amoebozoa.[21]

By 1998, Cavalier-Smith had reduced the total number of kingdoms from eight to six: Animalia, Protozoa, Fungi, Plantae (including Glaucophyte, red and green algae), Chromista, and Bacteria.[22] Nevertheless, he had already presented this simplified scheme for the first time on his 1981 paper[16] and endorsed it in 1983.[23]

Table 11 From Eukaryote kingdoms: seven or nine?

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

The kingdom Animalia was divided into four subkingdoms: Radiata (phyla Porifera, Cnidaria, Placozoa, and Ctenophora), Myxozoa, Mesozoa, and Bilateria (all other animal phyla).

He created three new animal phyla: Acanthognatha (rotifers, acanthocephalans, gastrotrichs, and gnathostomulids), Brachiozoa (brachiopods and phoronids), and Lobopoda (onychophorans and tardigrades) and recognised a total of 23 animal phyla.[22]

Cavalier-Smith's 2003 classification scheme:[24]

• 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)

Cavalier-Smith and his collaborators revised the classification in 2015, and published it in PLOS ONE. In this scheme they reintroduced the division of prokaryotes into two kingdoms, Bacteria (previously ‘Eubacteria’) and Archaea (previously ‘Archebacteria’). This is based on the consensus in the Taxonomic Outline of Bacteria and Archaea (TOBA) and the Catalogue of Life.[25]

In 2006, Cavalier-Smith proposed that the last universal common ancestor to all life was a non-flagellate Gram-negative bacterium ("negibacterium") with two membranes (also known as diderm bacterium).[26]