EMPIRE BIOTA
Summary
A phylogenetic classification system of bacteria is presented, based on a cladistic analysis of morphology, chemistry, physiology, and molecular biology for 23 taxons and 263 characters, and is the first comprehensive high level phylogeny of prokaryotes based on classical evidence. The results are in basic agreement with Gupta's protein phylogenies, i.e., Gram+s are primitive, Gram-s are advanced, and Mendosicutes (Metabacteria, Archeobacteria) evolved from G+s. G+s, G-s, and Metabacteria show up as monophyletic. Also presented is a phylogeny for eukaryotes. Both are designed to more accurately reflect evolutionary kinship. There are 4 bacterial kingdoms: Thermosiphia, Firmicutes, Mendosicutes, Gracilicutes. A cladistic analysis was done for eukaryotes, as well, based on 297 characters and 27 taxons. The final tree yields 9 kingdoms so 13 in all. The eukaryote-first hypothesis, the infallibility or superior reliability of genotypic evidence, and gradism as evolutionary or phylogenetic are rejected and a fusion origin for eukaryotes is proposed. A modified Farris system is used for rank prefixes. Also included are a utilitarian taxonomy, a tally table, and 4 new or standardized suffix systems. New taxons are Contobacteria, Cenobacteria, Aerobacteria, Deuterobacteria, Metasoma, Thermacidophilia, Eugracilicutes, Metakaryota, Neokaryota, Cellulosa, Tubulicristata, Ochrobiota, Dinobiota, Foramaxia, Metachrista, and Neochrista. The new names are Neosoma, Heterotropha, Autotropha, Chemoorganotropha, Chemolithotropha, Scotoautotropha, Rhodophyca, Euglenaria, Mycozoa, Neophyta, Apicophyta, Axopoda, Dinociliata, Chromophyca, and Chloroplasta.
Keywords: kingdoms, phylogeny, bacteria, phenotype, eukaryotes.
Introduction and Historical Overview
In the 1800s a reevaluation of the Linnean system (Linneus, 1735)(containing 24 plant classes, the 1st 23 for phanerogams and the 24th for algae, fungi, mosses, and ferns; and 6 animal classes: Vermes, Insecta, Pisces, Amphibia, Aves, and Quadripedia, in the 2 traditional kingdoms) produced several attempts at improved kingdom level taxonomies (Owen, 1859, 1861; Hogg, 1860; Wilson and Cassin, 1861; Haeckel, 1866, 1878, 1894). All introduced third kingdoms respectively named Protozoa (later Acrita), Primigenum (or Protoctista), Primalia, and Protista. Necker(1783) and Fries(1832) proposed kingdom status for Fungi and Enderlein (1925) for Bacteria. ) the former as Regnum Mesymale and the latter as regnum Mycetoideum. But these were not generally accepted and the 2-kingdom system persisted.
Protozoa was named by Goldfuss in 1817 as a class divided into 4 orders: Infusoria, Phytozoa, Lithozoa, and Medusinae. Infusoria had 4 families, Monades, Vorticellae, Brachioni, and Polypi. This was replaced by Butschli's familiar system (1880-82) containing classes Sarkodina, Mastigophora, Sporozoa, and Infusoria (ciliates and suctorians) which has survived well into the 1960s. There were then only 10 to 15 metazoan phylums. Previously, J-B de Monet (Lamarck), in Tableau du Regne Animal from 1806, distiguished between vertebrates and invertebrates recognizing 12 classes, adding Infusoires and separating out Cirripedes in 1807 and adding Tunicata in 1816. A year later Georges Cuvier established his 4 embranchements: Phytozoa, Articulata, Mollusca, Vertebrata, in Regne Animal. In ancient times, Aristotle, in his History of Animals, recognized Anaima (with white blood, invertebrates) and Enaima (with red blood, vertebrates). Doflein, in 1901, combined the 1st 3 of Butschli's classes as Plasmodroma. Lankester, in 1878, recognized Gymnomyxa and Corticata.
There were previous 3rd kingdoms, however. Treviranus (1802-22), who coined the word “biology” in its current meaning and, like de Monet, was a proponent of species transmutation, recognized kingdoms Plantae, Amphorganicum (divided as animal-plants: zoophytes and infusorians(variously circumscribed by different authors and recognized as a kingdom by Nees Esenbeck); and plant-animals: fungi, confervae, fuci, bryophytes, ferns, and Najadales), and Animalia. Linneus (1767), aside from Animalia and Plantae, which were recognized since ancient times, the concept of the plant-animal dichotomy being introduced by Aristotle conceived the chaotic kingdom (Regnum Chaoticum) which had only 2 brief life-span. Bory de Saint-Vincent (1824) established the Regne Psychodiaire (2-souled) for zoophytes, vorticellids, and diatoms which contained 3 classes, Ichnozoaires, Phytozoaires, and Lithozoaires(corals). In his animal kingdom were included the Microscopiques comprising 4 orders: Gymnodes, Trichodes, Stomoblephardes, Rotiferes, Crustodes. It was the 1st order which contained bacteria, along with green algae, monads, amebas, ciliates, and cercaria. There was also a Regnum Neutrum (von Munchhausen, 1765-66) for polyps, corals, funguses, and lichens and a Regne des Némazoaires by Gaillon (1833).
Horaninoff (1834) proposed 2 kingdoms of nature, the inorganic and the organic, each with 4 unranked divisions, fire, water, air, and circulum corporum plus Vegetabilia (4 classes: Plantae sporophorae, Pseudospermae, Coccophorae, and Plantae spermophorae), Phytozoa (4 classes: Fungi, Algae, Polyparii(polyps), and Acelaphae(sponges and cnidarians)), Animalia (12 classes), and Homo sapiens. In 1843 he elevated his kingdoms to worlds or orbits (Orbis Anorganicum and Orbis Organicum), the 8 unranked groups becoming kingdoms (Ethereum, Aqueum, Aereum, and Minerale; Vegetabile, Amphorganicum, Animale, and Hominis). The various classes were arranged in concentric rings.
Even before this, Ammonius Hermiae, in the 400s AD, recognized animals, plants, and zoophytes and may have been the 1st to use the term "zoophytes"(if not, the honour would go to Sextus Empiricus or Iamblichus, both in the late 200s AD). The group was 1st formally established as part of Animalia by Edward Wotton in 1552.
In the 20th century, Haeckel's final version appeared in 1904, and included kingdom Histonia, but a major step occurred in 1925 (Chatton, 1925) with Chatton's recognition of the eukaryote prokaryote division classed as superkingdoms Akaryonta and Karyonta (viruses being named Aphanobionta) by Novak (1930) and named eucaryotique, procaryotique by Chatton himself (Chatton, 1937). it was Dougherty who formally named them (1957).
The 1st modern 4 kingdom system was by H.F Copeland with subsequent revisions (Copeland 1938, 1947, 1956) the final version being: Mychota (blue algae and bacteria), Protoctista (other eukarytic algae, fungi, slime molds, and protozoans), Plantae (including only embryophytes and green algae), and Animalia (including sponges). His father, E.B. Copeland had, in 1928 (Copeland, 1928) brought attention to the inadequacies of the 2 kingdom system and proposed the possible utility of multiple kingdoms. Other 4 kingdom schemes followed: Barkley (1939, 1949), Rothmaler (1948), Whittaker (1957, 1959), Takhtajan (1973), and Leedale's pteropod scheme (Leedale, 1974), all including a kingdom protista except the last.
Conard (1939), Vada (1952), and Whittaker (1957) proposed a 3- kingdom scheme, which were fungi-bacteria, plants (algae and cormophytes), and animals (protozoans and metazoans), corresponding to the 3 nutrional modes and the ecologist’s functional communities. The 1st author used the names Mycetalia, Phytalia, and Animalia, the 2nd did not use an explicit rank nor names, and the last only informally suggested them.
Jahn and Jahn(1949) presented 6 kingdoms: Archetista (viruses), Monera (bacteria), Protista, Metaphyta, Metazoa, and Fungi. Verne Grant (1963)devised the 1st 5-kingdom system. This comprised Monera (blue algae, bacteria, and viruses), Protista (protozoans, diatoms, and phytoflagellates), Fungi, Plantae (embryophytes, red, green, and brown algae), and Animalia. Whittaker, 6 years later, published a 5 kingdom arrangement (Whittaker, 1969), inspired by Grant's with Monera (excluding viruses), Protista (comprising other eukaryotic algae, protozoans, chytrids, hvphochytrids, and plasmodiophorans). Fungi (including oomycotes, slime molds, and slirnes nets), Plantae (same as Grant), and Animalia, with Margulis (1971, 1974, 1998) in turn based on Whittaker's, these latter 2 authors teaming up for a 5 kingdom article in 1978 (Whittaker and Margulis, 1978).
Others have proposed alternative kingdom level arrangements. Walton (1930) and Dillon (1963) presented one kingdom systems, the former with 3 subkingdoms Protistodeae, Metaphytodeae (multicellular plants), and Zoodeae (multicellular animals) and called Bionta, the latter with 14 subkingdoms and called Plantae. Leedales (1974), as well as the pteropod sheme also proposed a 19 -kingdom fan scheme (red algae, Plantae, heterokonts, eustigs, haptophytes, cryptomonads, dinoflagellates, chytrids. Fungi, euglenoids, zooflagellates, myxomycetes, sarcodines, ciliates, sporozoans, sponges. Animalia, mesozoans. plus Monera) and Mohn's (1984) also had 19 kingdoms; these were distributed into the usual 2 superkingdoms with 6 suprakingdoms being Archeobacteria comprising the single kingdom Archeobacteriobionta; Neobacteria comprising kingdoms Bacteriobionta and Cyanobionta, and Aconta (with Erythrobionta and Rhodecyanobionta); Contophora (containing 8 kingdoms: Chlorobionta, Flagelloopalinida, Euglenophytobionta, Eumycota, Dinophytobionta, Cryptophytobionta, Colponemata, and Chloromonadaphytobionta); Cormobionta (with a single kingdom bearing the same name); Animalia, containing middle-kingdoms Parazoa (with kingdoms Porifera, Archeata, and Placozoomorpha), and Eumetazoa (with kingdoms Bilateria and Radiata).
Of note, as well, are Jeffrey's 7 kingdoms (1971) in 3 superkingdoms Acytota (viruses); Procytota with kingdoms Bacteriobiota and Cyanobiota; and Eucytota with Kingdoms Rhodobiota, Chromobiota (essentially Chromista but including dinoflagellates), Zoobiota, Mycobiota, Chlorobiota (embryophytes and green algae); and his 1982 5-kingdom system arranged as Prokaryota with kingdoms Bactericbiota and Arcbeobacteriobiota and superkingdom Eukaryota with kingdoms Phytobiota (comprising plants, red algae, protjstans, and sponges), Mycobiota (true fungi, including chytrids), and Zoobiota; Dodson's 3 kingdoms (1971), Mychota (blue algae, bacteria, and viruses), Plantae (including all eukaryotic algae plus all fungi), and Animaiia (including Protozoa); Edward's (1976) 9 kingdoms with Bacteria and Eucaryota containing Erythrobionta (red algae), Myxobionta (slime molds), Ochrobionta (Pheo-, Chryso-, Pyrrho-, and Cryptophyta), Chlorobionta (Tracheo-, Bryo-, Chloro-, and Euglenophyta), Fungi 1 and 2 (the latter comprising water molds and slime nets), and Animaiia; Stewart and Mattox's (198O) 2 eukaryotic kingdoms Bodonobiota (with flat cristae) and Dinobiota (with tubular cristae); Starobogatoff (1986) with 9 kingdoms in 3 eukaryotic superkingdoms: Aconta comprising Rhodymeniontes(red algae),Mychota(fungi including Microsporidia), Lamellicristata comprising Cryptomonadontes (cryptophytes, glaucophytes, centrohelians, and pseudociliates), Euglenontes, Plantae(including green algae), and Animalia(including choanoflagelates), and Tubulicristata made up of Ellipsoidiontes(vacuolarians, ellipsoids, sporozoans, trichomonads, entamebeans, opalinates, and ciliates), Peridiniontes(peridiniophytes, syndineans, ellobiophytes, spheriparaians, eberideans, sticholoncheans, and radiolarians), Chromulinontes(heterokonts, haptophytes, heliozoans, haplo- and myxosporidians, myxomycetes, forams, acantharians, and archeocyathans); Mayr's system (1990) comprising Domain Prokaryota with subdomains Eubacteria (with a single kingdom) with a subsequent version the following year (1991), and Archeobacteria (containing kingdoms Euryarcheota and Crenarcheota); Domain Eukaryota with subdomains Protista (with a single kingdom) and Metabionta (containing Kingdoms Metaphyta, Fungi and Metazoa); Cavalier-Smith's taxonomies (1978, 1981, 1983, 1986) his first being a eukaryote scheme consisting of 7 kingdoms: Aconta (red algae and fungi), Haptophyta, Cryptophyta, Heterokonta, Corticoflagellata(most protozoans plus animals), Euglenoida, and Chlorophyta, with his 8 kingdoms (l991) comprising Empire Prokaryota composed of Archeobacteria and Eubacteria, and Empire Eukaryota with superkingdom Archeozoa including a single kingdom by the same name plus, and superkingdom Metakaryota made up of Protozoa, Plantae, Animalia, Fungi and Chromista, and Corliss's 6 eukaryotic kingdoms (Corliss, 1994, 1995) similar to Cavalier-Smith's, whose last taxonomy(I998) comprised 6 kingdoms which were Bacteria(including Archeobacteria) in Prokaryota, and Protozoa, Animalia, Fungi, Plantae, and Chromista in Eukaryota, with which he comes full circle having presented the same kingdoms in a general system 17 years earlier, presented also in 1983 and 1986.
Lipscomb's eukaryotic system (1985, 1989, 1991), was the 1st based on cladistic analysis of classical evidence and contained 9 major groups and is discussed later. Molecular phylogenies were published by Woese, Kandler, and Wheelis (1990) which was a 3 primary kingdom set up (Archea, Bacteria, Eucarya) and by Lake (1988) which was a 2 primary kingdom set up (Parkaryotae + eukaryotes and eocytes + Karyotae). This latter author (Lake. 1986; Lake et al., 1986) has also suggested a 5 primary kingdom scheme (Eukaryola, Eocyta, Methanobacteria. Halobacteria, and Eubactcria) based on ribosomal structure and a 4 primary kingdom scheme (Eukaryota, Eocyta, Methanobacteria, and Photocyta), bacteria being classified according to 3 major biochemical innovations: photosynthesis (Photocyta), methanogenesis (Methanobacteria), and sulfur respiration (Eocyta). Baldauf and Palmer (2000) presented a 7-kingdom taxonomy for eukaryotes based on a synthesis of molecular phylogenies. These were Polymastigota, Tubulicristata(excavates, alveolates+ heterokonts), Plantaria (Plantae, red algae, glaucophycans), Lobosa-Myxomonada, Animalia, and Fungi. And Jack Holt and Carlos Iudica (Taxa of Life website, 2007) presented an arrangement which comprises 22 kingdoms in 3 domains: Eubacteria(Proteobacteriae, Spirochetae, Oxyphotobacteriae, Saprospirae, Chloroflexae, Chlorosulfatae, Pirellae, Firmicutae, and Thermotogae), Archeota(Euryarcheota, Crenarcheota), Eukaryota(Rhodophytae and Viridiplantae in supergroup Planta; Cercozoae in supergroup Rhizaria; Alveolatae, Heterokontae, Eukaryomonadae in supergroup Chromalveolata; Discicristatae and Euexcavatae in supergroup Excavata; and Amebozoae, Fungi, and Animalia in supergroup Unikonta.
The classification of bacteria has had a checkered and relatively short past. They were “invented” by Leewenhoek (1683) who considered them animalcules and in the Linnean system(1735) they were placed as specia dubia in Vermes and regarded as infusorians by Ehrenberg (1838) who first named them “Bakterien” (the English cognate was coined in 1847) but were switched to Plantae by Cohn (1872) who realized that blue algae were related to bacteria and set up the order Schizosporeae to accommodate both groups with the latter as family Bacteriaceae and later integrated as Schizophyta (1875) and were placed in Fungi in Eichler’s Thallophyta(1883) as Schizomycetes. In the first taxonomic tree (Haeckel, 1871) they were in Moneres, along with amebas, in Protista. They were first recognized as a kingdom by Enderlein in 1925.
Notable internal arrangements for prokaryotes have been done by Cohn(1872, 1875) (4 tribes, Spherobacteria, Microbacteria, Desmobacteria, and Spirobacteria); Migula (1897), which was the most widely accepted system of its time and included all then- known species but was based only on morphology; Orla-Jensen(1909); Bergey(1925, with many subsequent editions); Kluyver and van Neil (1936); Stanier and van Neil (1941), as Kingdom Monera with 2 phyla, Myxophyta and Schizomycetae the latter comprising classes Eubacteriae (3 orders), Myxobacteriae(1 order), and Spirochetae(1 order); Bisset (1962), 1 class and 4 orders, Eubacteriales, Actinomycetales, Streptomycetales, and Flexibacteriales, but also a tree which comprises 6 clades Spirillum-Vibrio, Spirochetes, Trichobacteria, a pseudomonadoid group, a Cytophaga-Myxobacteria group, G+s; Gibbons & Murray (1978), with 4 phyla, Gracilicutes, Firmicutes, Tenericutes(Mollicutes), and Mendosicutes(Metabacteria); Woese and Fox (loc cit), and Mohn (loc. cit.) recognizing Gramabacteria (G+s) placing spirochetes with clostridians(because of the clastic system which is probably homoplasious) and chlamydians with mycoplasmas and Agramabacteria, coextensive with Thiobacteria (excluding blue bacteria).
Methods and Materials
The data set is divided into 4 sections and 242 characteristics: morphology(19), chemistry(83), physiology (43), and molecular biology (97) in 263 columns. All the characters are ordered and there are 9 complex (branching) ones (cell shape, protein types, peptide bridge for cross-linkage A(deactivated), amino acids at position 3(deactivated), cytochromes, carotenoids, quinone classes, bacteriochlorophylls, and chlorophylls). And 7 simple ones have been deactivated, as well, (23-27, 84-86, 139, 146, 170, 235, 250) as they were superfluous since the matrix was reformatted and simplified. The computer calculation phase was performed by James Carpenter. A TNT (Tree analysis using New Technology) program, Wagner parsimony, TBR branch swapping with c. 176 mln. rearrangements, and strict concensus were used. All 4 algorithms were used: ratchet, sectorial search, tree-drifting, and tree-fusing (Goloboff, 1999; Nixon, 1999). Random seed was set at 1, no constraints were used, and the search level was set at 100. Temporary collapsing was done for consensus calculation. There was no outgroup but all of the polarities were very to fairly easily determined.
Results
These are tabulated in Table 3 with the synapomorphies, the modified version (eliminating homoplasy, accounting for missing data, and being dichotomous (using semistrict consensus)) with the synapomorphies in Table 4 and Figure 2, with the taxon list in Table 5, data set in Table 6, the data matrix in Table 7, the probable taxonomy for Actinobacteria in Table 8, and the taxon tallies in Table 9. The synapomorphies serve as formal descriptions of the new names and groups. There were 8 equally most parsimonious trees, 315 steps, a CI of .67, and an RI of .76. The trees differ only in the positions of Fervidobacterium and Thermotoga; Halobacteria and Methanobacteria; and Rickettsiae, Cyanobacteria, and Cloroxybacteria. Aerobia, Monoderma, Firmicutes, Parkaryota, Gracilicutes, Protogracilicutes, Metagracilicutes, and Neogracilicutes appear in all 8 trees.
Discussion
The phylogeny basically is in accordance with Gupta (2000) so that molecular methods, although less reliable for, at least, prokaryotes, nonetheless, have considerable value and merit. It agrees on 3 fundamental points: the monophyly of G-s, the primitiveness of G+s and advanced nature of G-s, and the position of Metabacteria. It disagrees principally in being branching instead of linear and in having Metabacteria as monophyletic without Eukaryota. The claim that the former arose from various subgroups of G+s is not at all supported by the phenotypic evidence.
There are a few groups that might be misplaced due to missing data. These are Fervidobacterium and Thermotoga in 4 of the retained trees might belong in/with Actinobacteria but are for now retained as separate kingdoms. Molecular data indicates Thermotoga is part of Firmicutes (Kyrpides and Olsen, 1999) although this is based on maximum likelihood which isn't as reliable as parsimony. Archeoglobus should probably be with Methanobacteria and Thermoplasma with Sulfobacteria. 4 groupings (Chloroheliobacteria, Metagracilicutes, Neogracilicutes, and Rickettsiae + Cyano + Chloroxy) are represented by homoplasious traits. Heliobacteria with Clostridia is an artefact in molecular analyses and belongs with Oxyphotobacteria as bchl g is related to chlorophylls and the latter goes to Thiobacteria for reasons stated later. It is highly unlikely that photosynthesis would be acquired through LGT and that it would arise more than once. Thermus possibly belongs in Deinobacteria. The similarity in GC content between them was mistakenly omitted which might have grouped them together and are a clade in molecular phylogenies.
Thermosiphia (with the single genus Thermosipho) has the largest number of primitive traits which are: heterotrophy, hyperthermophilia, fermentation, anaerobiosis, nonmotility, with a single membrane, thin wall, unicellularity, small SRP, absence of LSP layer, outer membrane, spores, cytochromes, quinones, catalase, and carotenoids so is probably the ancestral group as indicated also by molecular evidence and was used as the root. The Pirellulae clade concurs with genotypic data, as well, but because of the adenylate system Rickettsiae probably goes with Chlamydiae. Chloroflexi is also in the same position in molecular taxonomies.
There were a few errors in the data set which are the following: the 1st character 200 was excluded as there were 2 character 200s and bchl g (128) was not placed with chlorophylls. In the matrix 133 was improperly coded and tends to place Chloroflexi with Thiobacteria, as was 188, so that it comes up as a synapomorphy for Monoderma when it is really for Neosoma, instead, and 112 and 190 are empty characters so should be excluded, too. These, however, have little or no effect on the outcome except for 128, which is mentioned earlier, and 133.
The largest group is Thiobacteria and contains most taxons of Proteobacteria. Myxobacteria and Bacteroidikae are related to Chlorobia because of sphingolipids and the third is akin to Beggiatoikae because of sulfur oxidation which relates to Cyanobacteria because of longitudinal gliding. Crenothrix goes to Cyano as these are colourless blue bacteria as they possess thylakoids. As well as most photosynthesizers autotrophism occurs in methylmonanads, nitromonads, the hydrogen oxidizers(included in Pseudomonada), and Thiobacillus and lithotrophy in sulfomonads, Beggiatoikae, desulfomonads, Siderobacteria, Magnetobacteria, Nitrobacteria, Hydrogenobacteria, Methylmonada, Hyphomicrobikae, Pseudomonada, green sulfurs , and purple sulfurs. Corkscrew motion relates Spirillikae to Beggiatoikae, magnetosomes Magnetobacteria to the former, carboxysomes unite Nitrobacterikae, Pseudomonadikae, and Cyanobacteria, sheathed flagella Caulobacteria, Enterobacteria, and Spirillikae, iron/manganese oxidation Sulfomonada (Thiobacilli), Chlamydobacteria, and Pseudomonada, sheathed filaments Beggiatoikae, Cytophagikae, Chlamydobacteria, and Cyanobacteria, flexing motion Beggiatoikae and Cytophagikae, hydrogen oxidation Hydrogenobacteria, Cytophaga (Flavobacterium), and Pseudomonada while slime capsules occur in Neisserikae, Cyclobacteria, Myxobacteria, Enterobacteria, Beggiatoikae, and Cytophagikae, methanol utilization in Methylomonada, Hyphomicrobium, and Acetobacterikae (Acidomonas), nitrogen compound oxidation in Pseudomonada, Nitrobacteria, Enterobacteria, Neisserikae, and Methylmonada(Methylococcus), iron inclusions in Caulobacteria and Chlamydobacteria, and acetate production by fermentation in Bacteroidikae, Acetobacteria, and Veillonellikae, and Cyclobacteria goes to Methylmonada as one genus (Ancylobacter) is (facultatively) methylotrophic. So there are many similarities that indicate interrelationship between all these groups. One will notice that Cyanobacteria is very close to Proteobacteria in Woese (1987).
The synapomorphy for Archeoactinobacteria is peptide cross-linkage B at position 2 and 4, Neoactinobacteria is united by mycelia and acid-fastness, and Sporactinobacteria by arthrospores and aerial mycelia; mycolic acids are lost in Propionibacteria and Madurobacteria, arabogalactans are lost in Propionibacteria and Actinobacteria, and acid-fastness and coryneform cells are wanting in Madurobacteria; proteasomes occur in Euactinobacteriae, waxes in Corynebacteriae and Mycobacteria, and phosphatidylinositol is present in all groups; Propionibacterikae is of uncertain position but would belong in Corynebacteriae if it has a 2-layered wall. Butyrivibrio , a genus with both G+ and G- traits, most likely belongs in Proprionibacteria as it produces propionic acid.
The many traits between Metabacteria and Eukaryota could well be due to reticulate evolution. But, if Eukaryota is factored in, the results show a polyphyletic Metabacteria. As there are many characteristics shared particularly by Sulfobacteria with eukaryotes its polyphyly is maintained especially by Lake (loc. cit.) as earlier mentioned but also Lake et al (1984) and Gupta (loc. cit.). However, an analysis excluding Eukaryota would result in a monophyletic Metabacteria. Whether eukaryotes evolved through a fusion event, that is, a fusion between a sulfobacterium and a eubacterium, is unclear at this point but there is much good evidence for this(e.g., Gupta and Singh, 1994, but it would be with an actinobacterium, instead of a G- as that is where most of the similarities lie) and the analysis tends to indicate this, as well, as eukaryotes probably diverge before G-s in it but really diverge later, and it would explain the nuclear double membrane and the discrepancy between molecular evidence categories but the nucleus is part of the cytomembrane system which evolved through infoldings of the plasma membrane. This is explained by Gupta (1998).
Some Words on Nomenclature
My nomenclatural system is presented in Tables 1 and 2. There is considerable merit to using the name Bacteria for Eubacteria as Mendosicutes is worthy of supraregnal status because of fundamental differences in ribosomes, cell wall, and lipid type, however, this is impractical as Mendosicutes is a very small group, the term used broadly is too inveterate and generic names in Mendosicutes often include the –bacterium suffix, and the group is nested in Prokaryota. In other words, it is distinct but not separate so it is preferable to say Eubacteria. The suffix –zoa for protozoan groups is inappropriate and inaccurate and should be avoided in phylogenetic nomenclature and likewise for –phyta for non-plants. A prefix system for ranks is shown in Table 2. Based on the Farris system (1976) groups can be inserted without changing ranks of the taxons already included, for instance, between and hyper- and mega- one can add superhyper-. Ranks above giga- start with supergiga-, ranks below nano- start with subnano, etc. The abbreviations are given in parentheses. Rank names between basic units should be assigned as half and half, for example, if there are 6 levels the top 3 would be subtertaxic and the bottom 3 suprataxic and if there is an odd number the suprataxic predominates.
Table 1. Suffix Systems
bacteria plants algae fungi animals
phyl. -bacteria -phyta -phycota -mycota
sbtph. -bacterina -phytina -phycotina -mycotina
sprcl. -arae -icae -mycetia
class -bacteriae, ariae -opsida -phyceae -mycetes -zoa, -acea
sbtcl. -arinae -idae -phycidae -mycetinae
sprord -oidiona -ionales, arae, -aliona
-florae
order -oidia -ales -alia -ida
sbtord -oidina -inales -alina -ina
sprfam - ikea -areae -idiona -oidea
fam. -ikae -aceae -ideae -idae
sbtfam -ikinae -oidea -idina -inae
tribe -ikineae -eae -idini -ini
sbtribe -ineae
(-bacteria can, as well as a type plural, alternatively be used to designate any rank. spr-(supra) refers to any rank above and sbt-(subter) refers to any rank below the basic rank.)
Table 2. Rank Prefix System.
giga- (gg.)
mega- (meg)
hyper- (hpr)
super- (sp)
sub- (sb)
infra- (inf)
micro- (mc)
nano- (nn)
nano- replaces pico- and the abbreviations are mine.
Table 3.
Empire Biota
Thermosiphia
Aerobia
Fervidobacterium
Thermotoga
Metaerobia
Monoderma
Firmicutes
Mollicutes
Eufirmicutes
Clostridia
Actinobacteria
Neosoma
Archeoglobus
Metaneosoma
Thermoplasma
Cenoneosoma
Halobacteria
Methanobacteria
Parkaryota
Eukaryota
Gracilicutes
Protogracilicutes
Chloroflexa+Heliobacteria
Thiobacteria+Deinobacteria
Metagracilicutes
Thermus
Neogracilicutes
Spirochetes
Pirellulae
Chlamydiae
Planctobacteria
Rickettsiae+Cyanobacteria+Chloroxybacteria
Synapomorphies
Aerobia: large STK, loss of long chain diabolic acids, aerobism, loss of hyperthermophily, catalase
Monoderma: non-formylated methionine, glutaminyl synthase tRNA glutamine transamidation, tRNA mischarging, proteasoman alpha-amylase primary structure, proteasoman serine protease 3D structure, tyrosine kinases, serine/threonine kinases, type 1 fatty acid synthase, Ku with HEH domain, calmodulin homologs, chitin
Firmicutes: DOXY pathway; foliate derivative as RNA methionine methyl donour; actinomycin, novobiocin, and penicillin sensitivity, DNAP uracil, loss of DNAP exonuclease function
Eufirmicutes: teichoic acid, naphthaquinones
Neosoma: wall with glycoprotein hexagonal array, loss of murein, pilin-like flagellar protein, HSP 90, thermosomes, ether lipids, archeol, mevalonate LFP, N-linked glycosylation, EM pathway with PFK, EM pathway reversal, ribosome SSU with bill, ribosome LSU with lobe, ribosome LSU with bulge, EF-1 aminocyl, tRNA-to-ribosome catalysis with EF-?, EF-2 with diphthamide, peptidyl tRNA translocation, with EF-2, EF-2 compatability, ribosome subunit, multiple RNAP enzymes, 8 or more RNAP subunits, RNAP subunit A, RNAP subunit B, mRNA with tail cap and tail Metaneosoma: potentially coaxial helices, core histones
Table 4.
sbemp. Bacteria (Ehrenberg 1835)
infemp. Thermosiphia stat. nov., nom. nov.
kgdm. Thermosiphia stat. nov.
infemp. Contobacteria tax. nov.
spk. Monoderma Gupta 1998) stat. nov.
kgdm. Firmicutes (Gibbons & Murray 1978)
spph. Mollicutes
spph. Metafirmicutes
phyl. Clostridia
phyl. Actinobacteria (Margulis 1974)
kgdm. Mendosicutes (Gibbons & Murray 1978; Metabacteria Hori & Osawa 1992) stat. nov.
spph. Euryarcheota stat. nov.
phyl. Halobacteria stat. nov.
phyl. Methanobacteria
spph. Thermacidophilia tax nov. nov.
phyl. Thermoplasmata stat. nov.
phyl. Sulfobacteria(Cavalier-Smith1986)
spk. Gracilicutes (Gibbons & Murray 1978; Diderma Gupta 1998)
kgdm. Eugracilicutes tax. nov.
sbk. Photobacteria (Gibbons & Murray 1978) tax. nov.
srph. Chloroflexi stat. nov.
srph. Thiobacteroidia
spph. Thiobacteria stat. nov. (Mohn 1984 emend.)
spph. Deinobacteria (Cavalier-Smith 1986) stat. nov.
sbk. Spirochetes
kgdm. Pirellulae stat. nov. emend.
spph. Rickettsiae
spph. Pirellulae
phyl. Chlamydiae sta. nov.
phyl. Planctobacteria stat. nov.
Synapomorphies
Firmicutes: DNAP uracil, DNAP exonuclease function, LL-DAP acid, teichoic acids, peptide bridge for A with dicarb
Monoderma: (post-transcriptional) addition of tRNA(3’-terminal) CCA, proteasomes
Actinobacteria: coryneform cell, mycolic acids, peptide cross-linkage B at position 2 and 4
Mendosicutes: wall with glycoprotein hexagonal array, pilin-like flagellar protein, HSP 90, thermosomes, ether lipids, archeol, mevalonate LFP, N-linked glycosylation, EM pathway with PFK, EM pathway reversal, ribosome SSU with bill, ribosome LSU with lobe, ribosome LSU with bulge, EF-1 aminocyl, tRNA-to-ribosome catalysis with EF-a, EF-2 with diphthamide, peptidyl tRNA translocation, with EF-2, EF-2 compatability, ribosome subunit, 8 or more RNAP subunits, RNAP subunit A, RNAP subunit B, mRNA with tail cap and tail, nonformylated methionine, multicomponent RNAPs, introns, B DNAPs, PCNA sliding clamp, high no. of r-proteins, RNAP, DNAP, and protein synthesis antibio resistance, DNAP VI, DNA 10b MCM, N-linked glycosylation, neosoman 5S 3D structure, co- translational protein secretion, vacuolar proton-pumping ATPase, oligosaccharyl transferases, SECIS- binding protein, ubiquitin- directed proteolysis, fibrillarin, replication factor C, RNA-binding proteins, ribosomal subunit compatability, EF-2 with diphthamide, IF-2 and 5A, absence of EF compatability, loss of murein, HSP 10, and SEC A.
Euryarcheota: halophilia.
Thermoacidophilia: larger LSU lobe, LSU bulge, thermacidophilic 5S secondary structure, cyclopentanol C40- biphytanol chains, hyperacidity.
Gracilicutes: large citrate synthase, flagellar ring, outer membrane, LPS, invagination, large succinate thiokinase, NADH resistance Eugracilicutes: spiral cell Photobacteria: photosynthesis, autotrophy, aa3 Thiobacterina: sulfide respiration, rubisco, lithotrophy Thiobacteria: tRNA transamidation of asparagine by aspartyl synthase
Table 5. - List of Taxons for Data Matrix
0. Thermosipho 1. Rickettsiae 2 Chlamydiae 3. Planctobacteria 4. Spirochetes 5. Chloroflexi 6. Thiobacterria 7. Cyanobacteria 8. Chloroxybacteria 9. Thermus lO.Deinobacteria 11. Mollicutes 12. Heliobacteria 13. Clostridia 14. Fervidibacteria 15. Thermotoga 16. Actinobacteria 17. Halobacteria 18. Archeoglobus 19. Methanobacteria 20. Thermoplasma 21. Sulfobacteria 22. Eukaryota
Table 6. Data Set Bacteria
all of the states are 0 absent and 1 present except where otherwise indicated; in TNT the taxons are numbered starting with 0
morphology
flagella
1. proterokonty
2. (proterokontic ) position 0 polar 1 lateral 2 internal
3. no. of poles 0 monopolar 1 bipolar
4. no. of polar flagella 0 single 1 multiple
5. (proterokontic) BB 0 with inner rings 1 with outer rings
6. (prot.) pass through outer membrane 0 absent 1 present
7.(prt.) (rotation) 0 with rt-handed helix 1 with left-handed helix general
8. cell shape 0 coccoid 0 bacillary 0 coryneform 0 vibrioid 0 spiral 1 oval 1 ell.
9. 0 coccoid 0 bacillary 0 coryneform 0 vibrioid 0 spiral 0 oval 1 ellip.
10. 0 coccoid 0 oval 0 ellip. 1 bacillary 1 coryneform 1 vibrioid 1 spiral
11. 0 coccoid 0 oval 0 ellip. 0 bacillary 0 coryneform 0 vibrioid 0 spiral 1 coryneform
12. 0 coccoid 0 oval 0 ellip. 0 bacillary 0 coryneform 1 vibrioid 1 spiral
13. 0 coccoid 0 oval 0 ellip. 0 bacillary 0 coryneform 0 vibrioid 1 spiral
14. capsule
15. fimbrias
16. toga
17. prosthecas
18. sheathed filaments
19. carboxysomes
chemistry
cell wall
20. peptidoglycan 0 pep 1 psdpep 2 -
21. heteropolysaccharides
22. protein 0 - 1 + 1 glycoprotein
23. 0 - 0 + 1 glycoprotein
24. murein 0 N-acetylated 1 N-glycolated
25. peptide cross linkage 0 A anchors at subunit position 3 and 4 1 B at pos. 2 and 4
26. peptide bridge for A 0 none 1 all
27. 0 1 monocarb 2 dicarb
28. 0 1 polymerized subunits
29. peptide bridge for B 0 L-amino acid 1 D-amino acid
30. amino acids at pos. 3 0 lysine 1 ornithine 1 DAP acid
31. 0 lysine 0 ornithine 1 DAP acid
32. peptidoglycan layer 0 thin 1 thick
33. teichoic acid
34. mycolic acid
35. cell wall outer membrane
36. KDO
37. LPS
38. cell wall with glycoprotein hexagonal array
storage products
39. type 0 PHB 1 a-1-4 amino acids
40. LSP 0 with DAP acid 1 with AAA acid
41. glutamine I type 0 ? ??? proteins general
42. cytochromes 0 c 0 a1 0 aa3 0 d 1 b 1 o
43. 0 c 0 a1 0 aa3 0 d 0 b 1 o
44. 0 c 0 b 0 o 0 d 1 a1 1 aa3
45. 0 c 0 b 0 o 0 d 0 a1 1 aa3
46. 0 c 0 b 0 o 0 a1 0 aa331 d
47. flagellar protein 0 flagellin 1 pilin-like
48. HSP 90
49. actin-tubulin folding chaperonins, no. of subunits 0 7(Group I) 1 8 (thermosome)(Group II) 2 9 (Group II)(TRIC(CCT))
50. actin-tubulin folding chaperones 0 GROES 1 GROEL/GIMC(2 subunits) 2 GROEL/GIMC (6 subunits)
51. proteasomes
52. protein secretion mech. 0 post-translational 1 co-translational
53. protein secretion chaperone 0 SecA 1 SecB
enzymes
54. citrate synthase with N-terminal helix
55. citrate synthase sensitvity/inhibition to NADH
56. citrate synthase NADH inhibition AMP reactivation
57. citrate synthase inhibition by alpha-oxoglutarate
58. citrate synthase size 0 small 1 large
59. STK size 0 small 1 large
60. catalase
61. tyrosine kinases
62. oligosaccharyl transferases
63. split glutamate synthase
64. FDP aldolases
65. FDP-activated lactate dehydrogenase
66. serine proteases 3-D structure
67. superoxide dismutase (SOD) 0 FeMn 1 CuZn coenzymes
68. factor 420
69. methanopterin lipids
70. membrane lipids 0 straight chain fatty acids with ester bond 1 branched chain aliphatic acids with ether bond
71. diether/tetraether ratios 0 high/low 1 low/high
72. triterpenes 0 - 1 hopanoids 2 sterols
73. carotenoids 0 a-car. 0 A 0 M 0 gm-car. 1 H
74. 0 A 0 M 0 gm-car. 0 H 1 a-car.
75. 0 a-car. 0 M 0 gm-car. 0 H 1 A
76. 0 a-car. 0 gm-car. 0 H 0 A 1 M
77. 0 a-car. 0 M 0 H 0 A 1 gm-car.
78 quinones
79. quinone types 0 benzoquinones 0 anthraquinones 0 anthracyclinones 1 naphthaquinones
80. 0 benzoquinones 0 anthracyclinones 0 naphthaquinones 1 anthraquinones
81. 0 benzoquinones 0 anthraquinones 0 naphthaquinones 1 anthracyclinones
82. sphingolipids
83. sulfonolipids
84. archeol
85. caldarcheol
86. unsaturated fatty acids 0 monoenoic 0 polyenoic 1 cyclopropane 1 10-methyl
87. 0 monoenoic 0 polyenoic 0 cyclopropane 1 10-methyl
88. 0 monoenoic 0 cyclopropane 0 10-methyl 1 polyenoic
89. fatty acid pathway 0 anaerobic 1 Desaturase I 2 Desat. II
90. fatty acid synthase 0 type II 1 type I
91. long chain diabolic acids
92. waxes
93. PI
94. PIM
95. lipid formation pathway 0 malonate 1 mevalonate
96. DOXY pathway
general
97. cellulose accumulation
98. chitin
99. glycosylation 0 O 1 N
100. S deposition 0 ext 1 int
101. DPA
102. EM pathway 0 without PFK 1 with PFK
103. EM pathway reversal general
104. metabolism 0 fermentation 1 respiration
105. type of respiration 0 anaerobic 1 aerobic
106. carbon sources 0 CH O (heterotrophic) 1 CO (autotrophic)
107. energy sources 0 chemical compounds(chemotrophic) 1 light(phototrophic)
108. electron or H donors 0 organic compounds(organotrophic) 1 inorganic compounds and C(lithotrophic)
109 hyperthermophily 0 + 1 -
110 TCA cycle 0 incomplete 1 complete
111 CO fixation(assimilation) pathway 0 hydroxyproprionate 1 reverse TCA 2 Calvin-Benson
112
113. sulfur compound oxidation
114. sulfate reduction
115. iron oxidation
116. CO oxidation
117. hydrogen oxidation
118. nitrate reduction
119. methanogenesis
120. clastic system
121. adenylate ADP-ATP exchange system photosynthesis
122. chlorophyllian photosynthesis
123. reaction center pigments 0 bacteriochlorophylls 1 chlorophylls
124. bacteriochlorophylls 0 c 0 a 0 b 0 d 0 g 1 e
125. 0 c 0 e 1 d 1 a 1 b 1 g
126. 0 c 0 e 0 d 1 a 1b 1 g
127. 0 c 0 e 0 d 0 a 0 g 1 d
128. 0 c 0 e 0 d 0 a 0 d 1 g
129. chlorophylls 0 a 1 b 2 c
130. 0 a 0 b 1 c 131. phycobilins
132. carotenoid structure 0 aryl 1 aliphatic 2 alicyclic
133. antenna pigments 0 bchl a or b 1 bchl c, d, or e 2 phycobilins and chl a
134. photosynthetic system 0 chlorosomes 1 cytoplasmic membrane 2 phycobilisomes
135. metabolic type 0 anoxygenic 1 oxygenic
136. electron donours 0 H2 1 S or H2S 2 HO2
137. ALA 0 glycine succinyl Co A 1 L-glutamate
reproduction
138. cell division 0 with septum 1 without septum
139. sporulation
140. sporulation position 0 internal 1 external
141. myxospores
142. budding movement
143. motility
144. gliding
145. longitudinal gliding motility
146. magnetotaxis mol. biol. ribosomes
147. small subunit 0 without bill, lobe, gap, or platform split 1 with bill only 2 with bill + lobe, gap, and platform split
148. large subunit lobe
149. LSU filled gap
150. LSU bulge
151. 70S subunit association 0 tight 1 loose 5S secondary structure
152. no. of helices 0 4 1 5
153. helix IV base loop nucleotides 0 3 1 4
154. potentially coaxial helices 5S tertiary structure
155. helices 0 4 1 5
156. region E loop
157. G region 0 long 1 short
158. 5S rRNA 5’ termini with 0 monophosphate 1 triphosphate ribosomal A protein
159. C- terminal region
160. N-terminal region
161. valine content 0 high 1 low
162. size(no. of residues) 0 large 1 small r-proteins
163. no. 0 54-65 1 60- 65 2 70-80
164. acidity 0 low 1 high
165. r-subunit protein LX
166. IF hypusine
167. mol. mass of hypusine 0 low 1 high
168. EF-1 aminoacyl tRNA-to-ribosome catalysis 0 EF-Tu 1 EF-alpha
169. EF-1 G affinity
170. EF-1 inserts 0 4-amino acid 1 11-amino acid
171. EF-2 0 without diphthamide 1 with diphthamide
172. peptidyl tRNA translocation 0 EF-G 1 EF-2
173. EF-2 compatibility 0 + 1 -
174. subunit “ RNA
175. RNAP type 0 simple 1 multicomponent
176. no. of RNAP subunits 0 4 1 8 or more
177. RNAP A
178. RNAP A structure 0 split 1 integral
179. RNAP B
180. RNAP B structure 0 split 1 integral
181. H
182. G
184. protein encoded nuclear genes with 0 cis-splicing of miniexons 1 trans-splicing
185. SRP size 0 4.5S 1 7S
186. SRP helices 1-4
187. protein-RNA mass ratio 0 low 1 high
188. tRNA initiator methionine 0 formylated 1 nonformylated
189. G tetra- and pentaphosphates
190.
191. 1-methylpseudouridine 0 + 1 -
192. N ,N -dimethylguanosine
193. X
194. archeosine(in D loop)
195. queuine 0 + 1 -
196. RNA modification levels 0 low 1 high
197. tRNA anticodon loop 0 + 1 -
198. tRNA transamidation of asparagine 0 asparaginyl synthase 1 aspartyl synthase
199. tRNA transamidation of glutamine 0 glutamyl synthase 1 glutaminyl synthase
(200. tRNA mischarging)
200. tRNA spacers 0 + 1 -
201. tRNA 3’ terminal CCA added posttranscriptionally
202. mRNA ends 0 without cap or tail 1 with tail only 2 with cap and tail
203. RNA methionine methyl donor 0 S-adenosylmethionine 1 folate derivative DNA
204. histones
205. topoisomerase II gyrase activity 0 + 1-
206. 2-stranded DNA repair Ku protein with C-terminal HEH domain
207. type II DNAP VI meiotic protein
208. B DNAPs, no. of subunits per ring 0 1 1 2 2 3 3 4
209. DNA helicase 0 DNAB 1 MCM
210. DNA binding protein 10b
211. G-C ratio 0 low 1 medium 2 high
212. sliding clamp
antibio sensitvity RNA polymerase
213. rifampicin
214. streptolydigin
215. actinomycin D
216. novobiocin
217. DNA polymerase aphidicolin butylphenyl-dGTP protein synthesis ribosome-targeted
218. antibio group A 0 high 1 low
219. antibio group B 0 high 1 low
220. antibio group C 0 low 1 high
221. antibio overall 0 high 1 low
222. antibio very high
223. antibio high
224. antibio low
EF-targeted antibios
225. kirromycin
226. pulvomycin
227. fusidic acid
228. penicillins 0 lo 1 hi
miscillaneous
229. introns 0 - 1 self-splicing 2 protein splicing
230. promoter type 0 eubacterial 1 box A
231.box A in ICR
232 TATA-binding protein(TBP)
233. SECIS binding protein
234. genome size 0 small 1 large
235. silybin stimulation
addenda
236. flagella 0 external 1 internal
237. gas vacuoles
238. rosettes
239. mycelia
240. wall peptidoglycan with LL-DAP acid
241. wall peptidoglycan with L- and D-lysine
242. wall peptidoglycan with arabose-galactose
243. calmodulin
244. oligosaccaryl transferases
245. proton pumping H-ATPase catalytic subunit insertion 0 F 1 V
246. rhodopsin
247. C40-biphytanyl diol chains 0 acyclic 1 mono and bicyclic 2 tri and tetracyclic
248. S oxidation
249. hyperacidophily
250. corkscrew motion
251. EF-5A
252. DNAP uracil sensitivity
253. DNAP exonuclease function 0 + 1 -
254. tRNA 5’ terminal base, molecular stalk, paired
255. (complex) replication factor C
256. HSP 10 0 + 1 -
257. plasmologens
258. STK size 0 small 1 large
259. rotund bodies
260. LSU lobe size 0 small 1 intermediate 2 large
261. epsilon B DNAP
262. division by invagination
263. halophily 0 - 1 moderate 2 extreme
Table 7. Data Matrix
0Thermosipho
0------00100000100000000????????000-00?00-----000000000?00000000000000-0-----0---000000000100000000-0000-00000--0000000000---------------00-0010-00000000000000000000000000000000-0-000000000000000000000000000000?00000000000000000000001000000100000-000000000 000-000
1Rickettsiae
???????001000010000000000000-110001010001[01][01][01][01][01]00000000??????0000000000-10000[01]1000[01]00010000000000000-0001100010?-0000000010---------------00-0010-00000000000000000000000000000000-0-000000000000000000000000000000?000000000000000000000010?0000000000-000000000010-010
2Chlamydiae
0------0010000000000010------------010?01-[01][01]0[01]00000000?????00000000000-0000000---000010000000001000-0001000010?-0000000010---------------00-0010-00000000000000000000000000000000-0-0000000000 000000000000000000000000000000000000000000000-000-000000-0000 00000010-010
3Planctobacteria
???????0010000000000010-------------10?01?0?0[01]00000000??????0000000000-0000000---000010000000001000-0001100010?-0000000000---------------00-011[01]-00000000000000000000000000000000-0-0000000000 00000000000000000000?00000000000000000000001000[01]0-000000-0 00000000010-010
4Spirochetes
1---100001011000000000000000-1[01]0001010?01?0[01]0[01]00000000?????00000000000-00000[01]0---000010000000000000-0001[01]000101-0000000100---------------00-0010-00000000000000000000000000000000-0-000000000000000000000000000000100000000000000000000001010000000000-000000000[01]10-010
5Chloroflexa
0----0 -?000 00000000000000000-100001000-01?????00000000?????000 00000000-000[01]0[01]1000000010000000001000-00010010[12]0?0000000000100[01][01]00--000000000-00[01]1000000000000000000000000000000000-0-00000000000000000000000000000010000000000000000000 00010-0000000000-000000000010-010
6Thiobacteria
[01][01]0[01]1[01]0[01][01][01]0[01][01][01][01]0[01][01]0000000000[01]100[01]1[01]10[01]0[01][01][01][01][01][01]00000000[01][01][01]11[01]0000000000-[01][01]0[01]0[01][01][01][01]0[01][01]00100000[01]000[01][01]001000 [01][01][01][01][01][12][01][01][12][01][01][01][01][01][01]000[01]0[01][01][01][01]0--0[01][01][01]0[01][01]0[01]1[01][01][01][01][01][01]0000000000000000000000000000000-0-00000000000000000[01]000000000000[012]0000000000000000000000[01]00[01][01]00000000-0000[01]0000[01]10-01 [01]
7Cyanobacteria
0------?????1000010000000000-111001010[01]01?000000000000????110000000000-[12]00[01][01][01]1[01]000[01]0010110000001000-0001111110[01]2000[01]0000011-----0012021210[01]100[01][01]100000000000000 000000000000000000-0-000000000000000000000000000000[02]000000000000000000000010-1000000000-000000000010-010
8Chloroxybacteria
0------?????0000000000000000-110001010?01????000000000?????00000000000-000[01]0[01]1000000010000000000000-0001100010?200000000011-----100?0212?00-00?0-00000000000000000000000000000000-0-0 00000000000000000000000000000?000000000000000000000010-0000 000000-000000000010-010
9Thermus
0------001000000000000000000-100001100?01??[01]0[01]000000000???100000000000-0000000---000010000000000000-00011000001-0000010000---------------00-0010-00000000000000000000000000000000-0-000000 000000000000000000000000?00000100000000000000001000000000000-000000000011-010
10Deinobacteria
0------00[01]000000000000000000-100001000?01?[01][01]0[01]00000000?????10000000000-0000000---000010000000001000-0001100011?-00000[01]0000--------------00-0010-00000000000000000000000000000000-0-00 000000000000 000[01]000000000000?0000000000000000000000100000 0000000-000000000010-000
11Heliobacteria
[01]1--1-0001000000000000000000-100001000?00?????00000000?????00000000000-0?????0---000010000000001000-1001001010??0000000001001101--0??10??00-001[01]-00000000000000000000000000000000-0-0 00000000000000000000000000000?0000000000000000000000100000 0000000-000000000010-000
12Clostridia
11--0 -000[01]0000000000000000[01]0-[01][01]1100--0?01[01][01][01]000 00000000-???[01]0000100000-0-----11000000100[01]0000001100-100[01][01]101[02]0020[01]0[01][01][01]0100---------------0100010-0000000000000 0000000000000000000-0-00000000000000000010001000000000001100 0000000001000001000001000000-0000[01][01]000[01]00-00[02]
13Mollicutes
0------ 00[01]0[01]0000000-----------------00?01-----000000000-???00000000 000-0-----0000000000000000001000-0001[01]000101-0000000000---------------00-0[01][01][01]000000000000000000000000000000000-0-0000000 10000000000100010000000000011000000000001000000-00000000000-00000[01]000000-000
14Actinobacteria
[01]1--0-0[01]0[01][01][01]00000000000[01][01][01][01]0[01][01][01]11[01]0-00101[01][01][01]0[01]0000[01][01]00[01]?001[01][01]000[01][01]0000-[02][01]100[01]11000000[01][01]0[01][01]0[01][01][01]010[01]0-[01]00[01] [01]000[12]01-00000[01]0000---------------0[01]100[01]0-00000000000000000000000000000000-0-00000001000000000010[01]0100[01]00002000 [01][01]0000000000010000010000[01][01]0[01][01]000-0000[01]0000[01]0 0-000
15Fervidobacterium
1???0-000100000000000000????????000-00?00-----000000000?00000000000000-0-----0---000000000100000000-0000-00000--000000 0000------- --------00-0010-00000000000000000000000000000000-0-0000000000000 00000000000000000?00000000000000000000001000000100000-000000 000001-000
16Thermotoga
1[01]?00-000100000100000000????????000-00?00-----000000000?0000 0000000000-0-----0---000000000100000000-0 000-0 0000--0000000000----- ----------00-0010-00000000000000000000000000000000-0-000000000000 000000000000000000?00000000000000000000001000000100000-00000 0000000-000
17Halobacteria
100?0-100[01]0000100002[01]11-----------0--1?00[01][01][01][01]0111111110???1?0111?0?001000000[01]1100000000000000010001-0101[01]01020?30000000000---------------00-0010-010000[01]101110111111110110111 1111110011100110111111110101100001111?111001110211011002100 1100000---0111-0001001110000002
18Archeoglobus
????0-?000000000000?0??-----------0--1?00?????111???????????0???? 0?111?0000000---001100000000010001-01110[01]0000?-0100001000----- ----------00-0010-02101???0???0????????01101111111110????????00? ??00?00?0110000????????00???0???????0?000??00000---0??0?000?0 00?00000000
19Methanobacteria
[01]0??0-000[01][01][01]00100001[01]11-----------0--1?00?????11111111??????0111?0?111[01]0000000---001100000000010001-0111010120?30000001000---------------00-0010-02[01]0[01]00[01]1???01111[01][01]110110 111111111011110011001111?110101102001111?1110011101001110021001[01]00000---01100000100011000010[01] 20Thermplasma
????0-?000000000000---0-----------0--1?00?????111???????????0????0100110000000---001100000000010001-0111[01]00010?-0000000000------ ---------00-0010-021010111???0????????01101111111111111101?100?? ?00100?0110200??????1100?010111111100?00?010000---0??0[01]110? 000?00001000
21Sulfobacteria
[01]0010-000[01]0000000012011-----------0--1?10?????11211111??????0111?0?00110000001100001100000000010001-0111[01]10000?-0000000000---------------10-0010-021011111???1????1?111111111111111111111 111101111111011110210111111110011102112111021111010000---0110 [12]1101000110002100
22Eukaryota
0------ [01][01][01]0[01]000000120[01][01]-----------0--011?[01][01][01][01]0-0111110?????-1110?12000-[12] 0[01]00[01][01][01][01]0001100[01][12]10 [01]0010[01][01]1-001[01][01]000[12]0[01]20000000000---------------1[01]10 [01][01][01] [01]02111111111111111200111111101111111000110111100 01100[01]011102111110[01] 111001001010011002111111000[01]---011 [01]-000100111[01]00210[01];
cc ] 24.28 85.87 140 145 169 235 249;
Table 8. Phylum Actinobacteria.
sbphyl. Archeoactinobacteria
cl. Corynebacteriae stat. nov.
cl. Actinobacteriae
sbphyl. Neoactinobacteria tax. nov.
cl. Euactinobacteriae stat. nov.
spord. Mycobacteria stat. nov.
spord. Sporactinobacteria stat. nov.
ord. Nocardiae
ord. Madurobacteria
Table 9. Taxon totals for the 13 kingdoms.
phyla classes orders families genera species
Animalia 23 84 c 360 c 3600 c100, 000 c 1.1 mln.
Plantae 20 20 c 130 c 700 c 16,000 c 300, 000
Fungi 7 17 c 80 c 250 c 5000 c 50, 000
Ochrobiota 20 60 c 220 c 820 c 5000 c 55, 000
Rhodophyca 1 2 13 67 c 600 c 4000
Conosa 2 6 17 36 163 c 1500
Galdieria 1 1 1 1 1 4
Cyanidiophyca 1 1 1 1 1 3
Schyzophyca 1 1 1 1 1 1
Gracilicutes 6 ? c 30 67 c 330 c. 3000
Firmicutes 5 7 12 20 c 180 c. 2000
Thermosiphia 1 1 1 1 1 ?
Mendosicutes 5 5 12 12 41 ?
Total (bact) 19 ? c50 c90 c.550 c. 5,000
Total (eukts) 71 183 c800 c5200 c 132,000 1.5 mln.
from Holt et al (1994), Parker (1982)
Taxonomy- Meaning and Methods
Phylogenetics (=cladistics) is the only method that is truly and completely phylogenetic being based entirely on monophyly and phylogeny. Gradism(synthetic taxonomy), on the other hand, admits grades, which are polyphyletic, as well as paraphyletic, and considers factors external to phylogeny so it is arbitrary, contradictory, inconsistent, and subjective. The deliberate inclusion of known polyphyletic groups such as Protista, Protozoa, Pteridophyta, and Agnatha which are called "paraphyletic" and the deliberate exclusion of taxa from others to which they are known to belong thereby causing them to be trunchated, in other words splitting obviously monophyletic taxa and creating obviously polyphyletic ones is artificial and hardly a serious attempt at phylogeny. It is often not based on any system nor even analysis yet is touted as “evolutionary” or “evolutive”. Gradists do not believe evolution should be included in taxonomy or, at least, not in any serious or consistent manner, yet claim their method is phylogenetic and regard paraphyletic groups as necessarily monophyletic but in order to be monophyletic a taxon must have an immediate common ancestor unique to it. To aggravate matters many cladists acquiesce recognizing monophyly, paraphyly, and polyphyly as separate entities which makes paraphyly a completely ambiguous concept and use the especially Confusionese term and nonsense word “non-monophyletic” as distinct from polyphyletic when they are obviously synonymous. Utilitarian taxonomy is necessary and is stable and practical, but must be used in parallel with phylogenetics not in combination with it. I present just such a convenience classification in Table 16. The purposes of utility and phylogeny are irreconcilable within the same taxonomy but are complimentary as parallel systems.
Also, there is a disturbing overreliance on genotypic evidence which is considered foolproof and groups are regarded as necessarily and automatically phylogenetic based only on this type of evidence when it is no more reliable than the phenotypic sort, and might even be less so, as it is given to many pitfalls: random noise, long branch attraction, different evolutionary rates, mutational saturation, paralogous genes, the use of different methods, and insufficient sampling. Similar conclusions have been reached by others (cf. Felsenstein, 1978; McKenna, 1987; Raff et al, 1987; Wyss, Novacek, and McKenna, 1987; Meyer, Cusanovich, & Kamen, 1998; Philippe & Adoutte, 1998, Doolittle, 1999). It is widely believed that there is little classical evidence among bacteria of value, which is such a bizarre concept it is amazing it is almost universally held, but nothing could be further from the truth and my data set, matrix, and results prove it .
Phylogeny of Eukaryotes
The notion that prokaryotes evolved from eukaryotes is completely contradicted by all kinds of evidence, morphological, physiological, chemical, molecular, and fossil as well as by the fusion hypothesis. Also, it is difficult to imagine how a complex structure like the ribosome could have evolved de novo and the wholesale loss of a complex structure like the cytomembrane system. The whole idea of eukaryotes coming before bacteria is, in fact, so bizarre that it can hardly be taken seriously.
A cladistic classification of eukaryotes is presented in Table 11. For the root Lipscomb(loc cit) used red algae but these have fewer primitive features than some other groups like Parabasalia, Pelomyxidae, and Glaucophyca, the 1st 2 often considered as a sister group to all other eukaryotes. However, the 1st is suspect because of its parasitic life style indicating that its primitive features might well be reversals. Moreover, the pseudoflagellum of Pelomyxidae indicates reduction, and the group is related to one which is parasitic, Entamebidae, because of neo-inositol. Lipscomb was on target but did not hit the bull's eye. Cyanidioschyzon has the fewest derived traits and the highest % of primitive traits (excluding inapplicable and missing data) with 90 and is the root. Plantarians (red algae, glaucophycans, plants) are not supported as expected as they have no synapomorphies and are weakly supported genotypically. Rhizaria and "Cercozoa" are also not recovered, not surprisingly, as they are ill-defined and weakly supported in molecular phylogenies. Ochrista ("chromista"), Retaria (forams and actinopods), Discicristata, Excavata, Alveolata, Pelaria (pelobiotes and eulobosans), Cercobiota (cercomonads and myxofilosans (plasmodial slime molds)), and Opisthokonta (Mycozoa) are confirmed. There are several groups misplaced so I have repositioned some taxons according to both phenotypic and genotypic features. Ochrobiota is composed of Ochraria (Ochrista and Retaria) and Dinobiota (Alveolata and Discicristata). Ochrobiota is the most strongly supported supergroup with a dozen synapomorphies. In a synthesis of molecular evidence (Baldauf et al, 2000) strongly supported are "Amebozoa" + myxomonads, green algae in Plantae (9-1), heterokonts (6-0), Ciliata + Apicomplexa (8-2), euglenoids + kinetoplastids (7-2), weakly supported are: red algae + plants(5-7), glaucophyceans + plants(3-3), and moderately supported are microsporidians in fungi (5-4).
Chytriomycota and Microsporidia are included in Fungi, Myxozoa in Animalia, specifically Hydrozoa, and proteromonads in opalinates in Heterokonta.
Green algae are divided into 7 phyla as shown in Table 12. The arrangment is based on classical evidence(largely Mishler and Churchill, 1985) but agrees with the molecular evidence( Lewis and McCourt , 2004). There are 6 phylums of green algae, although Mesostigmataceae might be a 7th ( here it is placed in Charophyta) and Klebsormidiales might be an 8th (here it is placed with Zygnematales in Gamophyta); Volvocophyta contains prasinophycans, volvocophycans (chlamydophycans) (misnamed as “chlorophytes”as this name refers to all plants), and ulvophycans, thus the bulk of green algae.
Table 13 contains my tentative arrangement for a group I considered as probably natural previous to the analysis and which is probably so. Axopoda contains the bulk of actinopods with a few of them going to Heterokonta. Eulobosa contains the bulk of "amebozoans" equally misnamed as "rhizopods" as they are not mostly rhizopodian. Metamonada has a feeding groove as in euglenoids and jakobids(excavates) but also a honeycomb lattice as in Ameba and rootlet patterns similar to heterolobosans suggesting a probable kinship to Eulobosa and discoid cristas occur not only in Euglenoida but in Heterolobosa as well.
Contrary to Tehler’s phylogenetic analysis, which is, however, basically accurate, Chytridiomycotes might be monophyletic as he did not include rumposomes, MLCs, nor flagellar architecture, and naked gametes, one of 3 characters denoting a Chytridiales + Metamycota clade, is primitive. Also, oomycetes and hyphochytriomycetes belong in Heterokonta. With the exclusion of 3 or 4 small groups, which are probably phylums of their own, from Ascomycota there still remains a core monophyletic Neascomycota. Basidiomycota and Dikaryomycota (with the inclusion of Zygomycota (Kickxellales is related to Trichomycetes because of septal structure, spore ontogeny, and serology, and has a dikaryon therefore belongs with Dikaryomycota) as well as Microsporidia) are confirmed as monophyletic making 8 phylums. The phyogeny is presented in Table 14.
The animal phylogeny is presented in Table 15.
Table 11. sbemp. Eukaryota (Dougherty 1957)-9 Kingdoms.
infemp. Schyzophyca
infemp. Metakaryota
mcemp. Cyanidiophyca
mcemp. Neokaryota
ggk. Galdieria
ggk. Cellulosa
mgk. Rhodophyca
mgk. Contophora
hpk. Bikonta
kgdm. Plantae
kgdm. Ochrobiota
hpk. Unikonta
spk. Conosa
spk. Mycozoa
kgdm. Fungi
kgdm. Animalia
Table 12. Plantae
sbk. Volvocophyta (Oltsmann 1904, as order) stat. nov.
sbk. Metaphyta stat. nov.
infk. Chlorokybophyta stat. nov.
infk. Neophyta stat. nov., nom. nov.
bsk. Gamophyta stat. nov.
bsk. Streptophyta (Jeffrey 1967) stat. nov. (Phragmaphyta nom. nov.)
hpok. Coleochetophyta stat. nov.
hpok. Apicophyta stat. nov., nom. nov.
btk. Charophyta (Rabenhorst 1863) stat. nov.
btk. Embryophyta (Endlicher 1836) stat. nov. (Cormophyta Endlicher 1836)
ctk. Hepaticophyta
phyl. Hepaticophyta
ctk. Stomophyta
megph. Cerotophyta
megph. Coscinophyta nom. nov., stat. nov.
anph. Muscophyta
phyl. Muscophyta
anph. Polysporangiophyta
epph. Aglaophyta*
phyl. Aglaophyta
epph. Stelophyta
hprph. Horneophyta*
phyl Horneophyta
hprph. Eustelophyta
altph. Rhyniophyta*
phyl. Rhyniophyta
altph. Neostelophyta
srph. Lycophyta
phyl. Lycophyta
srph. Telomophyta
spph. Trimerophyta*
phyl. Trimerophyta
spph. Megaphylla
phyl. Calomophyta
phyl. Lignophyta
sbph. Aneurophytina*
sbph. Metalignophytina
infph. Archeophytina*
infph. Spermatophytina
*indicates extinct groups
Table 13. Tubulicristata
sbk. Foraminifera( [d’Orbigny1826] Eichwald 1830, stat. nov. Margulis 1974) stat. nov.
sbk. Metatubulicristata tax. nov.
infk. Axopoda stat. nov., nom. nov.
infk. Chromobiota (Jeffrey 1971) stat. nov., emend.
bsk. Ciliodinista stat. nov., nom. nov.(replacing Alveolata)
bsk. Chromaria stat. nov., nom. nov.
epph. Euglenista tax. nov.
phyl. Euglenaria nom. nov.(replacing Euglenozoa)
phyl. Excavata (Cavalier-Smith 2004)
epph. Chromista (Cavalier-Smith 1983) stat. nov.
altph. Chlorarachnia (Cavalier-Smith 1993)stat. nov.
altph. Euchromista (Cavalier-Smith 1993)stat. nov.
srph. Cryptomonada (Ehrenberg 1838)
srph. Ochrista (Cavalier-Smith 1993, emend.) stat. nov.
phyl. Haptomonada (Cavalier-Smith 1989)
phyl. Heterokonta (Luther 1866)
Table 14. Fungi
sbk. Chytridiomycota
sbk. Metamycota
infk. Dipodascomycota
infk. Argamycota
bsk. Endomycota
bsk. Neargamycota
altiph. Metadipodomycota
altiph. Cenargamycota
srph. Eremascomycota
srph. Dikaryomycota
spph. Microsporidiomycota
spph. Zygomycota
spph. Neodikaryomycota
phyl. Ascomycota (Neascomycota)
phyl. Basidiomycota
Table 15. Animalia
Choanozoa
Metazoa
Archeocyatha*
Neozoa
Demospongiae
Epitheliozoa
Placozoa
Euzoa (Enterozoa, Eumetazoa)
Cnidaria
Argazoa
Ctenophora
Artiozoa (Triploblastica)
Ecdysyzoa
Cephalorhyncha
Sensillozoa
Nematohelminthes
Panarthropoda
Onychophora
Arthropoda
Neartiozoa
Trochata
Tetrazoa
Platymorpha
Trochozoa
Kamptozoa
Eutrochozoa
Chetifera
Conchozoa
Molluscoidia
Nemertina
Molluscomorpha
Sipuncula
Mollusca(Malacozoa)
Deuterostomia
Chetognatha
Enterocela(Trimera)
Lophophorata
Bryozoa(Ectoprocta)
Phoronozoa
Brachiopoda
Phoronida
Epithelioneuria
Echinodermata
Stomochordata
Pterobranchia
Cyrtotreta
Enteropneusta
Chordata
Urochordata
Notochordata
Cephalochordata
Vertebrata
Table 16. Convenience Classification for Empire Biota
hprk. Prokaryota
kgdm. Eubacteria
sbk. Gracilicutes
infk. Heterotropha tax. nov.
mgnph..Chemorganotropha tax. nov.
mgnph.Chemolithobacteria tax. nov.
infk. Autotropha tax. nov.
phyl. Scotoautotropha tax. nov.
phyl. Photobacteria
sbk. Mollicutes
sbk. Firmicutes
cl. Micrococci
cl. Clostridia
cl. Actinobacteria
kgdm. Metabacteria(Mendosicutes)
hprk. Eukaryota stat. nov.
spk. Chloroplasta stat. nov., nom. nov.
kgdm. Ochrophyta
kgdm. Rhodophyta
kgdm. Chlorophyta
spk. Mycota stat. nov.
kgdm. Fungi
spk. Zoaria stat. nov., nom. nov.
kgdm. Protozoa
phyl. Sarcodina
phyl. Sporozoa
phyl. Ciliata
kgdm. Zoa
sbk. Choanozoa
phyl. Choanozoa
sbk. Metazoa
infrk. Diploblastica
infrk. Triploblastica
grdph. Protostomia
phyl. Helminthes
cl. Helminthes-Acelomata
cl. Helminthes-Pseudocelomata
cl. Helminthes-Celomata
phyl. Arthropoda
phyl. Mollusca
grdph. Deuterostomia
spph. Lophophorata
phyl. Lophophorata
spph. Epithelioneuria
phyl. Echinodermata
phyl. Chordata
Conclusions
Open and shut cases are the high value and merit of classical evidence including among bacteria, the phylogenetic quality and nature of cladistics and the lack of same for gradism, the primitiveness of prokaryotes, the derived status of Metabacteria, the advanced condition of Methanobacteria and Sulfobacteria, the polyphyly of Protista and Protozoa, the position of Choanozoa and Myxozoa in Animalia, Microsporodia in Fungi, green algae in Plantae, chytrids in Fungi, and bicoesids, opalinates, and proteromonads in Heterokonta, and amebas in Tubulicritata, and the unity of Heterokonta and Eukaryota. Very high probabilities exist for the monophyly of Monoderma, Firmicutes, Actinobacteria, Gracilicutes, Photobacteria, Thiobacteria, and the primitiveness of Firmicutes.
Hopefully, this article will generate interest in phenotypic evidence for bacteria.
Acknowledgements
I thank Dr. James Carpenter of the Am. Mus. Nat. Hist. in New York for his invaluable assistance.
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