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A Revised Six-Kingdom System of Life

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A Revised Six-Kingdom System of Life Biol. Rev. (1998), 73, pp. 203–266 Printed in the United Kingdom # Cambridge Philosophical Society 203 A revised six-kingdom system of life T. CAVALIER-SMITH Evolutionary Biology Programme, Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4 (Received 27 March 1996; revised 15 December 1997; accepted 18 December 1997) ABSTRACT A revised six-kingdom system of life is presented, down to the level of infraphylum. As in my 1983 system Bacteria are treated as a single kingdom, and eukaryotes are divided into only five kingdoms: Protozoa, Animalia, Fungi, Plantae and Chromista. Intermediate high level categories (superkingdom, subkingdom, branch, infrakingdom, superphylum, subphylum and infraphylum) are extensively used to avoid splitting organisms into an excessive number of kingdoms and phyla (60 only being recognized). The two ‘zoological’ kingdoms, Protozoa and Animalia, are subject to the International Code of Zoological Nomenclature, the kingdom Bacteria to the International Code of Bacteriological Nomenclature, and the three ‘botanical’ kingdoms (Plantae, Fungi, Chromista) to the International Code of Botanical Nomenclature. Circumscrip- tions of the kingdoms Bacteria and Plantae remain unchanged since Cavalier-Smith (1981). The kingdom Fungi is expanded by adding Microsporidia, because of protein sequence evidence that these amitochondrial intracellular parasites are related to conventional Fungi, not Protozoa. Fungi are subdivided into four phyla and 20 classes; fungal classification at the rank of subclass and above is comprehensively revised. The kingdoms Protozoa and Animalia are modified in the light of molecular phylogenetic evidence that Myxozoa are actually Animalia, not Protozoa, and that mesozoans are related to bilaterian animals. Animalia are divided into four subkingdoms: Radiata (phyla Porifera, Cnidaria, Placozoa, Ctenophora), Myxozoa, Mesozoa and Bilateria (bilateral animals: all other phyla). Several new higher level groupings are made in the animal kingdom including three new phyla: Acanthognatha (rotifers, acanthocephalans, gastrotrichs, gnathostomulids), Brachiozoa (brachiopods and phoronids) and Lobopoda (onychophorans and tardi- grades), so only 23 animal phyla are recognized. Archezoa, here restricted to the phyla Metamonada and Trichozoa, are treated as a subkingdom within Protozoa, as in my 1983 six-kingdom system, not as a separate kingdom. The recently revised phylum Rhizopoda is modified further by adding more flagellates and removing some ‘rhizopods’ and is therefore renamed Cercozoa. The number of protozoan phyla is reduced by grouping Mycetozoa and Archamoebae (both now infraphyla) as a new subphylum Conosa within the phylum Amoebozoa alongside the subphylum Lobosa, which now includes both the traditional aerobic lobosean amoebae and Multicilia. Haplosporidia and the (formerly microsporidian) metchnikovellids are now both placed within the phylum Sporozoa. These changes make a total of only 13 currently recognized protozoan phyla, which are grouped into two subkingdoms: Archezoa and Neozoa; the latter is modified in circumscription by adding the Discicristata, a new infrakingdom comprising the phyla Percolozoa and Euglenozoa). These changes are discussed in relation to the principles of megasystematics, here defined as systematics that concentrates on the higher levels of classes, phyla, and kingdoms. These principles also make it desirable to rank Archaebacteria as an infrakingdom of the kingdom Bacteria, not as a separate kingdom. Archaebacteria are grouped with the infrakingdom Posibacteria to form a new subkingdom, Unibacteria, comprising all bacteria bounded by a single membrane. The bacterial subkingdom Negibacteria, with separate cytoplasmic and outer membranes, is subdivided into two infrakingdoms: Lipobacteria, which lack lipopolysaccharide and have only phospholipids in the outer membrane, and Glycobacteria, with lipopolysaccharides in the outer leaflet of the outer membrane and phospholipids in its inner leaflet. This primary grouping of the 10 bacterial phyla into subkingdoms is based on the number of cell-envelope membranes, whilst their subdivision into infrakingdoms emphasises their membrane chemistry; definition of the negibacterial phyla, five at least partly photosynthetic, relies chiefly on photosynthetic mechanism and cell-envelope structure and chemistry corroborated by ribosomal RNA phylogeny. The kingdoms Protozoa and Chromista are slightly changed in circumscription by transferring subphylum Opalinata (classes Opalinea, Proteromonadea, Blastocystea cl. nov.) from Protozoa into infrakingdom Heterokonta of the 204 T. Cavalier-Smith kingdom Chromista. Opalinata are grouped with the subphylum Pseudofungi and the zooflagellate Developayella elegans (in a new subphylum Bigyromonada) to form a new botanical phylum (Bigyra) of heterotrophs with a double ciliary transitional helix, making it necessary to abandon the phylum name Opalozoa, which formerly included Opalinata. The loss of ciliary retronemes in Opalinata is attributed to their evolution of gut commensalism. The nature of the ancestral chromist is discussed in the light of recent phylogenetic evidence. Key words: Megasystematics, Bacteria, Protozoa, Archezoa, Fungi, Animalia, Plantae, Chromista, Eomycota, Mycetozoa. CONTENTS I. Introduction ............................................................................................................................ 205 II. Philosophic preliminaries......................................................................................................... 210 (1) Darwinian evolutionary classification contrasted with Hennigian cladification................ 210 (2) Naming taxa and clades ................................................................................................... 213 (3) Principles of ranking taxa ................................................................................................. 214 (4) The need to weigh and integrate phylogenetic evidence from diverse sources ................. 215 III. In defence of Bacteria: the sole primary kingdom of life......................................................... 215 (1) The concept of a bacterium (synonym: prokaryote) ........................................................ 215 (2) Changing views on Archaebacteria................................................................................... 216 (3) The importance of cell structure in bacterial classification............................................... 217 (4) Characters important in the high-level classification of Bacteria...................................... 220 (5) Bacterial subkingdoms and infrakingdoms........................................................................ 222 IV. Protozoa, the basal eukaryotic kingdom.................................................................................. 226 (1) Status of Archezoa, early diverging amitochondrial eukaryotes ....................................... 226 (a) Changes in circumscription of the Archezoa .............................................................. 226 (2) The protozoan subkingdoms: Archezoa and Neozoa........................................................ 229 (3) Demarcation between the two zoological kingdoms: Protozoa and Animalia.................. 231 (4) Classification of the Neozoa .............................................................................................. 234 (a) The infrakingdom Sarcomastigota.............................................................................. 234 (b) The infrakingdom Alveolata....................................................................................... 238 (c) The infrakingdom Actinopoda.................................................................................... 238 V. The kingdom Animalia and its 23 phyla................................................................................. 239 (1) Radiata, the ancestral animal subkingdom....................................................................... 239 (2) The derived subkingdom Mesozoa.................................................................................... 239 (3) The number of animal phyla............................................................................................ 239 (4) A broadened phylum Annelida......................................................................................... 240 (5) The pseudocoelomate phyla Nemathelminthes and Acanthognatha phyl. nov. ............... 240 (6) The new phyla Brachiozoa and Lobopoda....................................................................... 241 (7) Phylogenetic assumptions behind the new bilaterian infrakingdoms and superphyla....... 241 (8) New animal subphyla and infraphyla............................................................................... 243 VI. The kingdom Fungi and its four phyla ................................................................................... 244 (1) Circumscription of the Fungi ............................................................................................ 244 (2) The trichomycete origin of microsporidia ......................................................................... 245 (3) Revision of higher fungal classification ............................................................................. 245 VII. The kingdom Plantae and its five phyla ................................................................................. 249 (1) New red algal
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