Empire Biota Posted 2007; modified July, 2009; December, 2010; March, 2013 (for Farris system); April, 2013 (to add
synoptic key and additons to Discussion sections for prokaryotes and eukaryotes and the Tally Table
legend); May, 2013 (Bacteria changed to 1 kingdom, additions to Discussion section for prokaryotes, changes
to Tables 5 and addition of majority consensus tree (Table 4)) 71 pp.
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 and Gram-s are monophyletic and Mendosicutes (Metabacteria, Archeobacteria) evolved from G+s; as in Gupta's results G-s are advanced but only in the strict consensus where the groups are reversed. Also presented is a phylogeny for eukaryotes. Both are designed to more accurately reflect evolutionary kinship. Prokaryotes (=bacteria) are considered as a single kingdom and the major groups are: Thermosiphia, Fervidobacteria, Thermotogae, Firmicutes, Mendosicutes, and Gracilicutes. The major supergroup is Contobacteria comprising Fervidobacteria, Thermotogae, Monodermata, and Gracilicutes. 2 cladistic analyses were done for eukaryotes, based on 297 characters and 27 taxons in the 1st analysis, and 301 and 25 in the 2nd, both based on morphology, chemistry, and physiology. The final table for it, however, repositions some groups to eliminate homoplasy and contains 10 eukaryote kingdoms, so 11 in all, which are Cyanidioschyzophyca (Schizophyca), Cyanidiophyca, Galdieriaphyca, Glaucophyca, Rhodophyca, Plantae, Conosa (the classical amebas, cercomonads, and slime molds), Fungi, Animalia, and Ochrobiota (Ochrista (Chromista), and Dinista (Retaria (forams and actinopods) and Dinobiota (alveolates and excavates)). The supergroups are Metakaryota, Neokaryota, Cellulosa, Contophora, and Unikonta (Conosa and Opisthokonta), Bikonta (Glaucophyca, Plantae, and Ochrobiota), and Metakonta (Plantae and Ochrobiota). Rhodophyca+Plantae (Archeoplastida), with or without Glaucophyca, Cercozoa, and Rhizaria are polyphyletic groups. Archeoplastida is proven polyphyletic by both classical and molecular evidence. The eukaryote-first hypothesis, the infallibility or superior reliability of genotypic evidence, and gradism as evolutionary or phylogenetic are rejected and refuted and a fusion origin for eukaryotes is proposed. A Farris system is used for rank prefixes. Also included are a comprehensive historical overview, utilitarian taxonomies, a tally table, 4 standardized suffix systems, and a key to the kingdoms. New taxons are Metasoma, Thermoacidophila, Cenosoma, Cenobacteria, Eugracilicutes, Metakaryota, Neokaryota, Cellulosa, Metakonta, Ochrobiota, Dinobiota, Metachrista, Neochrista, Unicellulares, Pluricellulares, and Celestina. A convenience classification is also presented, containing 4 kingdoms: Bacteria, Phyta, Mycota, and Zoa. The new names are Proteinomura, Heterotropha, Autotropha, Chemoorganotropha, Chemolithotropha, Scotoautotropha, Rhodophyca, Euglenista, Mycozoa, Neophyta, Apicophyta, Axopoda, Dinociliata, and Chloroplasta.
Un système de classification phylogénétique des bactéries est présenté, basé sur une analyse cladistique de morphologie, chimie, physiologie, et biologie moléculaire pour 23 taxons et 263 caractères, est la première phylogénie de haut niveau des prokaryotes basée sur l’evidence classique (phénotypique). Les résultats sont largement en accord avec les phylogénies de protéines de Gupta qui démontrent la position primitive de G+, l'évolution de Mendosicutes (Metabacteria ou Archeobacteria) de ceux-ci. Une analyse cladistique pour les eukaryotes est aussi présentée. Les 2 analyses dessinée pour refléter avec plus de précision les relations évolutionnaires. Les prokaryotes (=bactéries) sont considérés comme un seul règne et les groupes principaux sont: Thermosiphia, Fervidobacteria, Thermotogae, Gracilicutes, Firmicutes, et Mendosicutes. Le supergroupe principal est Contophora. 2 analyses cladistiques pour les eukaryotes ont été faites, le 1er avec 297 caractères et 27 taxons et le 2me avec 301 caractères et 25 taxons. Mais le arbre final est hypothétisé de contenir 10 royaumes, donc 11 en tout, qui sont: Cyanidioschyza, Cyanidiophyca, Galdieriaphyca, Glaucophyca, Rhodophyca, Plantae, Conosa (les amibes classiques, cercomonades, et "myxomycètes"), Fungi, Animalia, Ochrobiota (Ochrista (Chromista), et Dinista (Retaria (forams et actinopods) et Dinobiota (les alvéolés et excavés)). Les super-groupes sont: Metakaryota, Neokaryota, Contophora, Unikonta, Opisthokonta, Bikonta, et Metakonta (Plantae et Ochrobiota). Le groupement rhodopycées-plantes, incluant ou non les glaucophycées, Cercozoa, et Rhizaria sont polyphylétiques. Archéoplastida est prouvé polyphylétique par les preuves classiques comme moléculaires. L'infallibilité ou la supériorité des phylogénies moléculaires, le gradisme comme évolutionnaire ou phylogénétique, et l'idée des eukaryotes comme primitifs sont rejetés et refutés et une origine par fusion des eukaryotes est proposée. Un système Farris est utilisé pour les préfixes de rang. Aussi inclus sont un historique compréhensif, 2 taxonomies utilitaires, une table de totales, un des systèmes de suffixes standardisés, et une clé des royaumes. Une classification utilitaire est aussi présentée qui contient 4 royaumes: Bacteria, Phyta, Mycota, et Zoa. Les nouveaux taxons sont: Metasoma, Thermoacidophila, Cenosoma, Cenobacteria, Eugracilicutes, Metakaryota, Neokaryota, Cellulosa, Ochrobiota, Dinobiota, Metachrista, Neochrista, Unicellulares, Pluricellulares, et Celestina. Les nouveaux noms sont Proteinomura, Heterotropha, Autotropha, Chemoorganotropha, Chemolithotropha, Scotoautotropha, Rhodophyca, Euglenista, Mycozoa, Neophyta, Apicophyta, Axopoda, Dinociliata, and Chloroplasta.
(Internal links were created but soon became disfunctional and had to be removed.)
Introduction and Historical Overview
Some Words on Nomenclature
Taxonomy-Meaning and Methods
Methods and Materials
Methods and Materials
A Convenience Classification
Taxonomies for Bacteria (Page 3)
Taxonomies for the Algae and Higher Plants (Page 3)
Taxonomies for Protozoans (Page 3
Taxonomies for Opisthokonts (Page 3)
Glossary of terms for the general reader:
apomorphy- derived state (mostly advanced but may include losses or reversals)
cladistics (parsimony analysis)- a phylogentic method that determines polarity (direction of evolution) of a characteristic (trait or feature), either primitive (ancestral) or advanced (derived) and counts only advanced as these define evolutionary groups (this is relative as the characteristic is advanced outside the group, in a more inclusive group, but ancestral in it, the more inclusive group; counts steps taken by a character (1 step corresponds to 1 higher order, more inclusive grouping of taxons, and
the tree with the fewest steps is the correct 1, but in the event of several most parsimonious trees a consensus method,
usually strict or majority, is calculated).
CI (consistency index)- a measure of homoplasy (convergent, i.e., coincidental, characteristics, which do not reflect kinship;
a CI of 1 indicates no homoplasy, one of .75 indicates 25% homoplasy; divergent characters diverge ffrom the same
ancestor so reflect kinship).
plesiomorphy- ancestral (primitive) state
RI (retention index)- a better measure of homoplasy (antonym: homology).
symplesiomorphy- shared ancestral state
synapomorphy- shared derived state
Introduction and Historical Overview
In the 1800s a re-evaluation 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.
There were previous 3rd kingdoms, however. German medic and mathematician Gottfried Reinhold Treviranus (1802-22), who coined the word “biology” in its current meaning and, like de Monet (Lamarck), 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. French naturalist, geographer, and explorer Jean-Baptiste Bory de Saint-Vincent (1824) established the Règne 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, Rotifères, 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 Règne des Némazoaires by Gaillon (1833).
Russian botanist 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, Alexandrian philosopher 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), and Neushul (1974) established subkingdoms Prokaryonta and Eukaryonta.
The 1st modern 4 kingdom system was by American biologist 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 ( 1928) had 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), both similar to Copeland's, Whittaker (1957, 1959), Takhtajan (1973), and Leedale's pteropod scheme (Leedale, 1974), all including a kingdom protista except the last 2. Bold et al (1987) also recognized 4 kingdoms (the 4th being Animalia was , however, not included but was inplicit), Monera with 2 phylums, Bacteria and Cyanophyta: Myceteae (Fungi), with 3 phylums, Gymnomycota, Mastigomycota, and Amastigomycota; and Phyta (Plantae), arranged in some 20 consecutive phylums comprising cormophytes and algae. Parker's (1982) 4 kingdoms were Virus and Monera in superkingdom Prokaryotae and Plantae and Animalia in Eukaryotae, the former with subkingdoms Thallobionta (ncluding funguses as well as algae) and Embryobionta, the latter with subkingdoms Protozoa, Placaozoa, Parazoa, and Eumetazoa.
American botanist Henry Conard (1939), Russian botanist Vada (1952), and American ecologist and botanist Robert 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 (blue algae were included in Plantae), and the last only informally suggested them. Dodson's 3 kingdoms (1971) were somewhat different: Mychota (blue algae, bacteria, and viruses), Plantae (including all eukaryotic algae plus all fungi), and Animaiia (including Protozoa).
American evolutionist 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 ( 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. Stewart and Mattox (1980) proposed 2 eukaryotic kingdoms Bodonobiota (with flat cristae) and Dinobiota (with tubular cristae).
Gordon Leedale (1974), as well as the pteropod scheme, 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).
Mohn's (1984) also had 19 kingdoms, which 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).
Jahn and Jahn (1949) presented 6 kingdoms: Archetista (viruses), Monera (bacteria), Protista, Metaphyta, Metazoa, and Fungi. Charles Jeffrey's 7 kingdoms (1971) were 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). 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.
Peter Edwards (1976) had 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. Starobogatoff (1986) also presented 9 kingdoms but 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). Kussakin and Starobogatov and Kussakin and Drozdoff (1994, 1998) also published kingdom level taxonomies and apparently included dominions and empires but the works are unavailable even in Russian.
Cavalier-Smith had several 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. In 1981 he proposed 9 eukaryotic kningdoms and a 2nd scheme that had 6 over-all (yet said there were 7) which were Bacteria (including Archeobacteria) in Prokaryota, and Protozoa, Animalia, Fungi, Plantae, and Chromista in Eukaryota, which he presented also in 1983, 1986, 1998, and 2004. He had 8 kingdoms in 1991, 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. Mayr's system (1990) also had 6, 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). John Corliss's 6 eukaryotic kingdoms (Corliss, 1994, 1995) were similar to Cavalier-Smith's and included Archeozoa, Protozoa, Chromista, Plantae, Fungi, and Animalia.
All these were decidedly artificial and Diana 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 James 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.
Simpson and Roger (2004) presented 6 so-called real kingdoms, Opisthokonta, Amebozoa (which should be Amebobiota), Plantae (which should be Plantaria or Archeoplastida), Chromalveolata, Rhizaria, and Excavata, but Archeoplastida and Rhizaria are far from real as they are obviously artificial groupings, and Amebobiota needs to include Cercomonada. 2 other strange claims they make in the same article are that the 5-kingdom system was eukaryote-centric, but most species are, indeed, eukaryotic so most kingdoms will be eukaryotic, and that, at the time, realistic alternatives would involve dozens of kingdoms but no such system was ever presented and there would be no basis or reason for such a system in any case.
In 2005, Adl and 27 other authors presented a classification of 6 supergroups: Amebobiota, Opisthokonta, Rhizaria, Archeoplastida, Chromalveolata, and Excavata, making 9 kingdoms, Opisthokonta having Animalia and Fungi, and Archeoplastida having glaucophycans, red algae, and plants, but Chromalveolata might be considered as 2 kingdoms.
Rodriguez-Ezpeleta et al (2007) undertook a genotypic study resulting in 8 unranked kingdoms in 3 major groups, Holozoa (Animalia)+Fungi, Amebobiota, and Malawimonada+(Archeoplastida+((Alveolata-Heterokonta+Cercomonada)+Excavata).
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.
Burki et al (2007) and Burki et al (2008) came out with molecular phylogenies based on maximum likelihood both comprising 3 large groups: the 1st SAR (stramenopiles (heterokonts, alvveolates, and rhizarians)+Haptomonada-Cryptomonada, and Archeoplastida (Plantae-Rhodophyca+Glaucophyca), the 2nd Excavata, and the 3rd Unikonta, making 8 kingdoms.
Hackett et al (2007) published a phylogenomic analysis using maximum likelihood, which resulted also in 8 kingdoms (not named as such): Animalia, Fungi, Amebobiota, Excavata, Plantae, Rhodophyca, Glaucophyca, and Chromalveolata-Rhizaria. The usual Opisthokonta was recognized but also Archeoplastida and Archeoplastida+Chromalveolata-Rhizaria. Excavata was the sister group of this latter cluster.
Kim and Graham (2008) did a maximum likelihood genotypic analysis which yielded 3 large clusters, the 1st comprising Glaucophyca + (Excavata+Plastidophila) as sister group to the 2nd, a Rhizaria+Heterokonta-Alveolata clade, and the 3rd being Unikonta (Amebobiota+Opisthokonta), making 9 kingdoms (not named as such) if we consider the 2nd grouping as 1 kingdom. Plastidophila has Rhodophyca as sister group to a Plantae+Haptophyca-Cryptophyca lineage. In a 2nd analysis there was a Unikont-Bikont dichotomy but with Rhodophyca included in the latter and with no Archeoplastida clade.
Yoon et al (2008) did a molecular study which resulted in 16 kingdoms. Opisthokonta was not monophyletic, glaucopyhycans, cryptophycans, and plants grouped together, forams grouped with red algae, and there was a large crown clade which comprised Haptophyca+((Thaumatomonadida+Cercomonada)+(Heterokonta+Alveolata)), along with some other smaller groups.
Hampl et al (2009) came out with another maximum likelihood phylogenomic study that contained 3 major "mega-groupings": Unikonta, Bikonta, Excavata, and Archeoplastida+Chromalveolata-Rhizaria, making 9 kingdoms (not named as such). Glaucophyca was sister group to Plantae+Haptophyca-Rhodophyca. Excavata was directly related to Archeoplastida+Chromalveolata-Rhizaria.
Tekle et al (2008) also did maximum likelihood genotypic analysis yielding a series of sister groups related to remaining eukaryotes: Choanozoa, Metazoa, Fungi, Polymastigota, Amebobiota, Glaucophyca, Rhodophyca, Plantae, Cryptophyca-Haptophyca+Malawimonidae, Euglenista-Heterolobosa+Jakobida, and Alveolata+Cercomonada-Heterokonta, making 11 unnamed) kingdoms. It is similar to my results in that the Glaucophyca, Rhodophyca, and Plantae part of the series, and the last 3 groupings form none other than Ochrobiota, but with Cercomonada misplaced as it should be with Amebobiota, and without the misplaced Polymastigota.
In 2010, Parfrey et al came out with another genotypic ML analysis which comprised 15 (unranked) kingdoms: Animalia, Mesomycetozoa, Fungi, and Apusomonada in 1 large clade, Ancyromonas, Breviata, Amebobiota, and anothe large clade comprising Excavata, cryptomonads (including Katablepharids), red algae, Centroheliozoa, glaucophycans, Telonema, plants, haptophycans, and SAR.
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.
Macroscopic funguses were also, of course, known in Antiquity and, along with microscopic ones, including pseudofungi and slime molds, were 1st given regnal status by Necker (1783) and Fries(1832)(The Father of Mycology), the former as Regnum Mesymale, the latter as Regnum Mycetoideum.
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 Règne Animal. In ancient times, Aristotle, in his History of Animals, recognized Anaima (with white blood, invertebrates) and Enaima (with red blood, vertebrates). Greene, in 1859, recognized Protozoa as a subkingdom. Doflein, in 1901, combined the 1st 3 of Butschli's classes as Plasmodroma. Lankester, in 1878, recognized Gymnomyxa and Corticata.
Algae, known by Theophrastus, the Father of Botany, and the other ancients, the word was coined in 1551, but known only from seaweeds and red tides, were organized by Linneus into 4 genera, the filamentous Conferva, the membranous Ulva, the thalloid Fucus, and the gelatinous Tremella. The few unicelluar algae then known, such as Volvox, he placed in Vermes and then Chaoticum. Lamouroux (1813) distinguished Fucacées, Floridées, Dictyotacées, and Ulvacées; Agardh (1824) recognized 6 orders: Diatomeae, Nostichinae, Confervoidea, Ulvaceae, Florideae, Fucoideae. Harvey (1836) established 3 subclasses: Chlorospermae (including blue bacteria and xanthophycans which would both be separated out later in the century), Melanospermae (brown algae), and Rhodospermae. Haeckel classified them as Archephyta (blue algae and most green algae), Characeae (stoneworts), Florideae (red algae), and Fucoidae (brown algae) in Plantae while placing Diatomae, Myxocystoda (Noctilucae), and Flagellata (Peridium, Volvox, and Euglena) in Protista. And Eichler (1883) divided them into the familiar Cyanophyceae, Rhodophyceae, Chlorophyceae, and Pheophyceae in his Thallophyta, which, of course, included also funguses, but the phylum was 1st proposed by Endlicher (1836), with phytoflagellates claimed also by many protozoologists.
It was Eichler who divided plants into Cryptogamae and Phanerogamae, the latter being seed plants, which he in turn divided into gymnosperms and angiosperms, the latter, also for the 1st time, were formally recognized as containing monocots and dicots. But in the Middle Ages, Albertus Magnus had already recognized monocots and dicots, Theophrastus (200s BC) distinguished between, trees, shrubs, undershrubs, and herbs, between annual, biennial, and perenial, centripetal and centrifugal, polypetalous and gamopetalous, and superior and inferior ovaries, and Parasara in Ancient India knew of the cell (rasakosa) and chlorophyll (ranjakena pakyamanat) and recognized several plant families (ganas), including the mustard, bean, and squash families. The descriptions of plant morphology was quite detailed. Chlorophyll was rediscovered and named by Joseph Pelletier and Joseph Caventou in 1816.
Engler and Prantl (1897-1915) had published a system, appearing in a monumental 20-volume work, with later editions by Engler and Gilg (1924) and Engler and Diels (1936), that was based mostly on Eichler's and was widely adopted well into the late 20th century. Like Eichler it was supposed to be phylogenetic but was largely artificial but as a convenience system it is still very useful today. It was originally written by Engler as part of a guide to the Botanical gardens at Breslau U.
Tippo (1942) had recognized 2 plant subkingdoms, Thallophyta (10 phylums) and Embryophyta (2 phylums, Bryophyta and Tracheophyta (vasculars, aka, Stelophyta), the latter containing classes Psilopsida, Lycopsida, Sphenopsida, and Pteropsida) and Bold (1973) divided the plant kingdom into 3 subkingdoms, Prokaryonta, Chloronta, and Achloronta. But Tippo's arangement was more of a synthesis instead of original as his scheme for non-vasculars followed Smith (1938) and for vasculars that of Eames (1936).
A phylogenetic plant kingdom (green algae + embryophytes) was recognized as monophyletic by the following:
Chlorobiota Jeffrey 1971
Chlorophyta C-S 1978
Viridiplantae C-S 1981
Chlorobionta Mohn 1984
Plantae Lipscomb 1985, 89, 91
Plantae Starobogatoff 1986
Plantae Corliss 1994, 1995
Viridiplantae Holt and Uidica 2007
A chloroplast kingdom was recognized as monophyletic by the following:
Plantae Takhtajan 1973
Plantae Leedale 1974
Phyta (Plantae) Bold et al 1987
The following is a tally of the various kingdoms proposed throughout history.
Aristotle 2 300s BC
Ammonius Hermiae 3 400s AD
Linneus 2 1735
Linneus 3 1767
Treviranus 3 1802-22
Bory de St. Vincent 3 1824
Horaninoff 1 1834
Horaninoff 4 1843
Owen 3 1859, 1861
Hogg 3 1860
Wilson and Cassin 3 1861
Haeckel 3 1866, 1904
Walton 1 1930
Conard 3 1939
Copeland 4 1938, 47, 56
Barkley 4 1939, 49
Rothmaler 4 1948
Jahn and Jahn 6 1949
Vada 3 1952
Whittaker 4 1957
Whittaker 4 1959
Grant 5 1963
Dillon 1 1963
Whitttaker 5 1969
Jeffrey 7 1971
Dodson 3 1971
Margulis 5 1971
Leedale 4, 19 1974
Margulis, Schwartz 5 1974, 1988, 98
Edwards 9 1976
Margulis, Whittaker 5 1978
Cavalier-Smith 6 1981, 83, 86, 98, 2004
Cavalier-Smith 8 1993
Jeffrey 5 1982
Takhtajan 4 1983
Mohn 19 1984
Bold et al 4 1987
Holt, Iudica 22 2007
for eukaryotes only
Cavalier-Smith 7 1978
Stewart, Mattox 2 1980
Cavalier-Smith 9 1981
Lipscomb 7 1985
Lipscomb 7 1989, 91
Starobogatoff 9 1986
Corliss 6 1994, 95
Baldauf et al 7 2000
Simpson and Lee 6 2004
Adl et al 9 2005
Burki et al 8 2007, 2008
Hackett et al 8 2007
Rodriguez-Expelata et al 8 2007
Kim and Graham 9 2008
Tekle et al 11 2008
Yoon et al 16 2008
Hampl et al 9 2009
Parfrey et al 15 2010
Some Words on Nomenclature
My nomenclatural system is presented in Tables 1 and 2. There is some merit to using the name Bacteria for Eubacteria as Mendosicutes has fundamental differences in ribosomes, cell wall, and lipid type, however, this is impractical, unnecessary, and confusing, as Mendosicutes is a very small group, the term "bacteria" used broadly is too inveterate, generic names in Mendosicutes often include the –bacterium suffix, the Bacteriological Code and bacteriology include Mendosicutes, and the group is phylogenetically part of Prokaryota. In other words, it is distinct but not separate so it is far preferable to say Eubacteria. Especially egregious and unacceptable is using the name Firmictues only for low G-C Firmicutes. 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-. For the higher prefixes I have added grand- (probably introduced by McKenna in 1975) in the middle and tera- on top. For the lower prefixes I have added the oft used parv- in the middle, replaced pico- with nano, and placed pico- at the bottom. The 3 highest and 3 lowest prefixes are the same as in the SI system, and the 6 in the middle are the same in number as those of the SI system.
If ranks above tera- are needed they would start with supertera, etc., and if ranks below pico- are needed they would start with subpico-, etc. The abbreviations, which are my own, 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 would predominate. In cladistics ranks are designated according to branching order but at some point there is sometimes a ranking that is based on degree of difference and long-standing ranks for particular groups should be conserved for the most part. There should also be parsimony in the number of taxons of any particular rank so a lower rank is preferred.
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
order -oidia -ales alia ida
sbtord -oidina -ineae alina -ina
sprfam - ikea -areae -idiona oidea
fam. -ikae -aceae -ideae idae
sbtfam -ikinae -oideae idina -inae
tribe -ikineae -eae idini -ini
(-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.
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 taxons 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 monophyletic but in order to be monophyletic a taxon must have an immediate common ancestor unique to it. To aggravate matters most 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 21. 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 or superior and groups are regarded as necessarily and automatically phylogenetic based only on this type of evidence when it is not 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). Also, 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.
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 chloroplasts, given they evolved from bacteria, could have appeared before them, how a complex structure like the ribosome could have evolved de novo, and how the wholesale loss of a complex structure like the cytomembrane system could occur. The whole idea of eukaryotes coming before bacteria is, in fact, so bizarre that it can hardly be taken seriously and has gained very little acceptance.
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 in 2006. A TNT (Tree analysis using New Technology) program, Wagner parsimony, TBR branch swapping with c. 176 mln. rearrangements, a heuristic search, 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.
The strict consensus tree with the synapomorphies is given in Table 3, the majority consensus is given in Table 4 , the modified version (eliminating homoplasy and being dichotomous (using semistrict consensus)) with the synapomorphies is given in Table 5, with the taxon list in Table 6, data set in Table 7, the data matrix 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 Chloroxybacteria. Aerobia, Monoderma, Firmicutes, Neosoma, Metasoma, Cenosoma, Parkaryota, Gracilicutes, Protogracilicutes, Metagracilicutes, and Neogracilicutes appear in all
The phylogeny basically is in accordance with that of McMaster's Radhey Gupta (1998, 2000), who uses conserved signature sequences of proteins, so that molecular methods, although less reliable for, at least, prokaryotes, nonetheless, can have considerable value and merit. It agrees on 3 fundamental points: the monophyly of Gram-s, the monophyly Gram+s and the position of Metabacteria. It disagrees principally in being branching instead of linear and in having Metabacteria as monophyletic (without Eukaryota). The Gupta result in which Metabacteria arose from various subgroups of G+s is not at all supported by the phenotypic evidence. The primitiveness of G+s and advanced nature of G-s in Gupta's results agrees only with mine in the strict consensus which reverses the groups.
4 groupings (Chloroheliobacteria, Metagracilicutes, Neogracilicutes, and Rickettsiae + Cyano + Chloroxy) are represented by homoplasious traits. Thermus probably 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. Some molecular data indicate Thermotoga might be part of Firmicutes (Gupta, 1998b), but it is basal in at least 3 molecular taxonomies (see Page 3), but usually Togobacteria is monophyletic, including also Marinitoga, Geotoga, and Petrotoga. 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 LPS 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 Proteinomura (Pirellulae) clade concurs with genotypic data, as well, but because of the adenylate system Rickettsiae might go with Chlamydiae.
There were a few errors in the data set which are the following: the 1st character 199 was excluded as there were 2 character 199s and bchl g (127) was not placed with chlorophylls. In the matrix, 132 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 111, 188, and 191 are empty characters so should be excluded, too. These, however, have little or no effect on the outcome except for 127, which is mentioned earlier, and 132. Also, Heliobacteria was incorrectly coded as Gram- and belongs in Firmicutes as it is G+ and has endospores and shows up as G+ in molecular phylogenies.
The largest group is Thiobacteria, which is largely the Proteobacteria of molecular taxonomies but with Chlorobia (green sulfurs) and Cytophagales included and Rickettsiae excluded, See Bacteria in Page 3 for details.
Prochlorobacteria (Chloroxybacteria), which contains 3 genera (Prochloron, Prochlorothrix, and Prochlococcus) but may not be monophyletic, belong in, not just with, Cyano on account of both classical and molecular data. For example, Synechococcus in Chroococcales (which is a grade) has a cytology comparable to Prochlorococcus, the latter has phycobilins, which otherwise occur only in Cyano among bacteria, and Prochloron and Synechococcus are both symbiotes of ascidians.
Euryarcheota, combining Halobacteria with Methanobacteria, showed up in 4 of the 8 trees and is found in molecular analyses. The synapomorphies would be halophilia and AB'B" RNA polymerase.
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 (1998). 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). It is possible Metabacteria arose through LGT also and it usually shows up as separate from Eubacteria in molecular taxonomies.
The endosymbiosis hypothesis goes back some way, originating with German pathologist, histologist, and anatomy professor Richard Altmann in 1890, who discovered the mitochondrion (naming it "bioblast,"; he developed an histological staining method for this organelle, and coined the term "nucleic acid" as a synonym or replacement for Friedrich Miescher's "nuclein" when it was found to have acidic properties), with Russian botanist Konstantin Merezhkovsky doing important research in it and coining the term "symbiogenesis" in 1910 and perhaps 1st formulating the theory, French zoologist and marine biologist Paul Portier presenting the 1st detailed description in 1918, and Lynn Margulis popularizing, elaborating, and synthesizing it in the late '60s.
And a symbiotic origin to life has been proposed by British-American theoretical physicist Freeman Dyson (1985) (who united the various formulations of QED into a single, general theory) in which there are 2 origins: 1 based on proteins and 1 on some form of replicating RNA nucleotides, the latter "infecting" the cell and which later became incorporated as a more helpful symbiote that improved host-cell replication in a cooperative chemical coupling (this is a metabolism 1st theory as opposed to a genetics 1st, RNA World theory, the latter being mainstream but not very plausible for several resons (see for example Strickberger, 1996, and Lecture 21 in the Teaching Company's Origins of Life course).
2 new genera of metabacteria proposed as independent groups, Korarcheum, discovered in Yellowstone's Obsidian Pool (formerly called Jim Black's Pool) (Barns et al, 1995) and Nanoarcheum, discovered in a hydrothermal vent on the Icelandic coast (Huber et al, 2002), were not included in the analysis for lack of information at the time. Korarcheota is basal in Metabacteria in 16S analysis but the sister group of Euryarcheota+Nanarcheota in concatenated ribosomal protein analysis (Pester et al, 2011). Nanoarchaeum equitans (Huber et al, 2002; Das et al, 2006) was discovered in 2002 in a hydrothermal vent off the coast of Iceland on the Kolbeinsey Ridge by Karl Stetter. Strains of this microbe were also found on the Sub-polar Mid Oceanic Ridge and in the Obsidian Pool in Yellowstone. It is a very small (.4 microns, perhaps the smallest organism known), hyperthermophilic, obligate parasite of Ignicoccus in Sulfobacteria. In 16S analysis it branches with Crenarcheota and in concatenated ribosomal protein analysis it is instead the sister group of Euryarcheota (Pester et al, 2011). Korarcheota is basal in Metabacteria in 16S analysis but the sister group of Euryarcheota+Nanarcheota in concatenated ribosomal protein analysis (Pester et al, 2011). But both most probably belong to Sulfobacteria (Elkins et al, 2008; Brochier et al, 2005), with Korarcheota related specifically to Thermococcales (Brochier et al, 2005), which is placed with methanogens in genotypic phylogenies but is a sulfobacterial order according to its phenotype.
Thaumarchaeota (Thaumabacteria) (Muller et al, 2010; Schleper and Nicol, 2010; Pester et al, 2011), aerobic ammonia-oxidizers containing Nitrososphera, Nitrosopumilus, and Crenarcheum, is not new but has been completely overlooked and omitted from textbooks. Jed Fuhrman’s team and Ed DeLong reported its discovery in 1992 from ocean surface waters. Initially classified as a mesophilic sister group to hyperthermophilic Crenarchaeota, phylogenetic analyses based on more SSU and SLU rDNA sequences and comparative genomics (Brochier-Armanet et al, 2008; Pester et al, 2011; Gupta and Shami, 2011) have recently suggested they might form a separate and deep-branching taxon within Metabacteria. Information from the first available genomes of the group indicate that its metabolism is fundamentally different from that of their eubacterial counterparts, involving a highly copper-dependent system for ammonia oxidation and electron transport, as well as a novel carbon fixation pathway that has recently been discovered in hyperthermophilic metabacteria. So its phenotype indicates it belongs with Sulfobacteria. Extrapolating from the wide substrate of copper-containing membrane-bound monoxygenases, to which the taxon belongs, the use of substrates other than ammonia for generating energy by some members of Thaumarchaeota seems likely.
Ammonia oxidation, the first and rate-limiting step in nitrification, the 2nd step being the oxidation of the nitrites to nitrates, is the only biological process converting reduced to oxidized inorganic nitrogen. Nitrification, a chemolithautotrophic process, which was discovered by the renowned Ukrainian-Russian microbiologist, microbial ecologist, and soil scientist Sergei Winogradsky in the 1880s (for which he won the Leewenhoek Prize; he also invented the enrichment culture technique, also called Winogradsky's columns, still used today), plays a central role in the nitrogen cycle. For over 100 years, this process was thought to be mediated only by autotrophic beta-proteobacteria and gamma-proteobacteria (Thiobacteria) occasionally supported by heterotrophic nitrifiers in soil environments. The widespread distribution of putative metabacterial ammonia monoxygenase (amo) organisms and their numerical dominance over their eubacterial counterparts in most marine and terrestrial environments suggests that thaumabacteria play a major role in global nitrification, but our understanding of their evolution and metabolism is still in its infancy.
Also proposed has been the TACK superphylum that comprises the Thaumarchaeota, Crenarchaeota, and Korarchaeota, as well as the recently proposed phylum Aigarchaeota (Guy and Ettema, 2011).
Table 3. Empire Biota-Strict Consensus Tree.
Thermus Brock and Freeze 1969
Proteinomura new name (Pirellulae)(Chlamydiae+Planctobacteria)
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
Metasoma: potentially coaxial helices, core histones
Table 4. Majority Consensus for Bacteria (Eukaryota removed).
Proteinomura (Chlamydiae +Planctobacteria)
Table 5. Prokaryotes.
sbemp. Prokaryota (Chatton 1937) Dougherty 1957
kgdm. Bacteria Ehrenberg 1835
sbk. Thermosiphia stat. nov., nom. nov.
phyl./Thermosiphia stat. nov.
sbk. Contobacteria tax. nov.
grdph. Gracilicutes (Gibbons & Murray 1978, Cavalier-Smith 1987, Didermata Gupta 1998)
phyl. Deinothermi nom. nov. (Deinobacteria Cavalier-Smith 1986) stat. nov.
phyl. Spirochetes (Spirochetae Ehrenberg 1855)
phyl. Chloroflexi Garrity and Holt 2002, emend. Hugenholtz and Stackebrandt 2004
phyl. /cl. Proteinomura nom. nov.
ord. Chlamydirickettsiae nom. nov. stat. nov.
ord. Planctobacteria Cavalier-Smith 1998 stat. nov.
phyl. Chlorobia nom. nov.
phyl. Bacteroidetes Krieg et al 2012
phyl. Proteobacteria Stackebrandt et al 1988
grdph. Monodermata Gupta 1998 (Unibacteria Cavalier-Smith 1998) stat. nov.
hpph. Firmicutes Gibbons & Murray 1978 (Teichobacteria Cavalier-Smith 1998)
spph./phyl. Mollicutes Edward and Freundt 1967 (Tenericutes Gibbons & Murray 1978)
spph. Eufirmicutes nom. nov., stat. nov.
phyl. Clostridia Rainey 2010
phyl. Actinobacteria Margulis 1974
hpph. Mendosicutes Gibbons & Murray 1978 (Archeobacteria Woese and Fox 1977, Metabacteria Hori
& Osawa 1979 (including only Halobacteria), Hori, Itoh, and Osawa 1982 (including also
Sulfolobus, Thermoplasma, and the methanogens) stat. nov.
spph. Archeoglobi stat. nov.
spph. Metamendosicutes tax. nov.
phyl. Neobacteria (Cavalier-Smith 2002 (including only Methano- and Halobacteria
and Archeoglobi)) tax. nov.
spcl. Cenobacteria tax. nov.
cl. Sulfobacteria Cavalier-Smith 1986 ( Crenarcheota Woese, Kandler, and Wheelis 1990,
Caldaria Mohn 1984, Eocyta Lake 1984)
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.
Metamendosicutes: 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
Photobacteria: photosynthesis, autotrophy, aa3 cytochrome
Table 6. - List of Taxons for Data Matrix
0 Thermosipho, 1 Rickettsiae, 2 Chlamydiae, 3 Planctobacteria, 4 Spirochetes, 5 Chloroflexi, 6 Thiobacteria,
7 Cyanobacteria, 8 Chloroxybacteria, 9 Thermus, 10 Deinobacteria, 11 Heliobacteria, 12 Clostridia, 13 Mollicutes,
14 Actinobacteria,15 Fervidibacteria, 16 Thermotoga, 17 Halobacteria, 18 Archeoglobus, 19 Methanobacteria,
20 Thermoplasma, 21 Sulfobacteria, 22 Eukaryota
Table 7. 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
1. (proterokontic ) position 0 polar 1 lateral 2 internal
2. no. of poles 0 monopolar 1 bipolar
3. no. of polar flagella 0 single 1 multiple
4. (proterokontic) BB 0 with inner rings 1 with outer rings
5. (protk.) pass through outer membrane 0 absent 1 present
6. (prtk.) (rotation) 0 with rt-handed helix 1 with left-handed helix general
7. cell shape 0 coccoid 0 bacillary 0 coryneform 0 vibrioid 0 spiral 1 oval 1 ell.
8. 0 coccoid 0 bacillary 0 coryneform 0 vibrioid 0 spiral 0 oval 1 ellip.
9. 0 coccoid 0 oval 0 ellip. 1 bacillary 1 coryneform 1 vibrioid 1 spiral
10. 0 coccoid 0 oval 0 ellip. 0 bacillary 0 coryneform 0 vibrioid 0 spiral 1 coryneform
11. 0 coccoid 0 oval 0 ellip. 0 bacillary 0 coryneform 1 vibrioid 1 spiral
12. 0 coccoid 0 oval 0 ellip. 0 bacillary 0 coryneform 0 vibrioid 1 spiral
17. sheathed filaments
19. peptidoglycan 0 pep 1 psdpep 2 -
21. protein 0 - 1 + 1 glycoprotein
22. 0 - 0 + 1 glycoprotein
23. murein 0 N-acetylated 1 N-glycolated
24. peptide cross linkage 0 A anchors at subunit position 3 and 4 1 B at pos. 2 and 4
25. peptide bridge for A 0 none 1 all
26. 0 1 monocarb 2 dicarb
27. 0 1 polymerized subunits
28. peptide bridge for B 0 L-amino acid 1 D-amino acid
29. amino acids at pos. 3 0 lysine 1 ornithine 1 DAP acid
30. 0 lysine 0 ornithine 1 DAP acid
31. peptidoglycan layer 0 thin 1 thick
32. teichoic acid
33. mycolic acid
34. cell wall outer membrane
37. cell wall with glycoprotein hexagonal array
38. type 0 PHB 1 a-1-4 amino acids
39. LSP 0 with DAP acid 1 with AAA acid
40. glutamine I type 0 ? ??? proteins general
41. cytochromes 0 c 0 a1 0 aa3 0 d 1 b 1 o
42. 0 c 0 a1 0 aa3 0 d 0 b 1 o
43. 0 c 0 b 0 o 0 d 1 a1 1 aa3
44. 0 c 0 b 0 o 0 d 0 a1 1 aa3
45. 0 c 0 b 0 o 0 a1 0 aa331 d
46. flagellar protein 0 flagellin 1 pilin-like
47. HSP 90
48. actin-tubulin folding chaperonins, no. of subunits 0 7(Group I) 1 8 (thermosome)(Group II) 2 9 (Group II)(TRIC(CCT))
49. actin-tubulin folding chaperones 0 GROES 1 GROEL/GIMC(2 subunits) 2 GROEL/GIMC (6 subunits)
51. protein secretion mech. 0 post-translational 1 co-translational
52. protein secretion chaperone 0 SecA 1 SecB
53. citrate synthase with N-terminal helix
54. citrate synthase sensitvity/inhibition to NADH
55. citrate synthase NADH inhibition AMP reactivation
56. citrate synthase inhibition by alpha-oxoglutarate
57. citrate synthase size 0 small 1 large
58. STK size 0 small 1 large
60. tyrosine kinases
61. oligosaccharyl transferases
62. split glutamate synthase
63. FDP aldolases
64. FDP-activated lactate dehydrogenase
65. serine proteases 3-D structure
66. superoxide dismutase (SOD) 0 FeMn 1 CuZn coenzymes
67. factor 420
68. methanopterin lipids
69. membrane lipids 0 straight chain fatty acids with ester bond 1 branched chain aliphatic acids with ether bond
70. diether/tetraether ratios 0 high/low 1 low/high
71. triterpenes 0 - 1 hopanoids 2 sterols
72. carotenoids 0 a-car. 0 A 0 M 0 gm-car. 1 H
73. 0 A 0 M 0 gm-car. 0 H 1 a-car.
74. 0 a-car. 0 M 0 gm-car. 0 H 1 A
75. 0 a-car. 0 gm-car. 0 H 0 A 1 M
76. 0 a-car. 0 M 0 H 0 A 1 gm-car.
78. quinone types 0 benzoquinones 0 anthraquinones 0 anthracyclinones 1 naphthaquinones
79. 0 benzoquinones 0 anthracyclinones 0 naphthaquinones 1 anthraquinones
80. 0 benzoquinones 0 anthraquinones 0 naphthaquinones 1 anthracyclinones
85. unsaturated fatty acids 0 monoenoic 0 polyenoic 1 cyclopropane 1 10-methyl
86. 0 monoenoic 0 polyenoic 0 cyclopropane 1 10-methyl
87. 0 monoenoic 0 cyclopropane 0 10-methyl 1 polyenoic
88. fatty acid pathway 0 anaerobic 1 Desaturase I 2 Desat. II
89. fatty acid synthase 0 type II 1 type I
90. long chain diabolic acids
94. lipid formation pathway 0 malonate 1 mevalonate
95. DOXY pathway
96. cellulose accumulation
98. glycosylation 0 O 1 N
99. S deposition 0 ext 1 int
101. EM pathway 0 without PFK 1 with PFK
102. EM pathway reversal general
103. metabolism 0 fermentation 1 respiration
104. type of respiration 0 anaerobic 1 aerobic
105. carbon sources 0 CH O (heterotrophic) 1 CO (autotrophic)
106. energy sources 0 chemical compounds(chemotrophic) 1 light(phototrophic)
107. electron or H donors 0 organic compounds(organotrophic) 1 inorganic compounds and C(lithotrophic)
108. hyperthermophily 0 + 1 -
109. TCA cycle 0 incomplete 1 complete
110. CO fixation(assimilation) pathway 0 hydroxyproprionate 1 reverse TCA 2 Calvin-Benson
112. sulfur compound oxidation
113. sulfate reduction
114. iron oxidation
115. CO oxidation
116. hydrogen oxidation
117. nitrate reduction
119. clastic system
120. adenylate ADP-ATP exchange system photosynthesis
121. chlorophyllian photosynthesis
122. reaction center pigments 0 bacteriochlorophylls 1 chlorophylls
123. bacteriochlorophylls 0 c 0 a 0 b 0 d 0 g 1 e
124. 0 c 0 e 1 d 1 a 1 b 1 g
125. 0 c 0 e 0 d 1 a 1b 1 g
126. 0 c 0 e 0 d 0 a 0 g 1 d
127. 0 c 0 e 0 d 0 a 0 d 1 g
128. chlorophylls 0 a 1 b 2 c
129. 0 a 0 b 1 c
131. carotenoid structure 0 aryl 1 aliphatic 2 alicyclic
132. antenna pigments 0 bchl a or b 1 bchl c, d, or e 2 phycobilins and chl a
133. photosynthetic system 0 chlorosomes 1 cytoplasmic membrane 2 phycobilisomes
134. metabolic type 0 anoxygenic 1 oxygenic
135. electron donours 0 H2 1 S or H2S 2 HO2
136. ALA 0 glycine succinyl Co A 1 L-glutamate
137. cell division 0 with septum 1 without septum
139. sporulation position 0 internal 1 external
141. budding movement
144. longitudinal gliding motility
145. magnetotaxis mol. biol. ribosomes
146. small subunit 0 without bill, lobe, gap, or platform split 1 with bill only 2 with bill + lobe, gap, and platform split
147. large subunit lobe
148. LSU filled gap
149. LSU bulge
150. 70S subunit association 0 tight 1 loose 5S secondary structure
151. no. of helices 0 4 1 5
152. helix IV base loop nucleotides 0 3 1 4
153. potentially coaxial helices 5S tertiary structure
154. helices 0 4 1 5
155. region E loop
156. G region 0 long 1 short
157. 5S rRNA 5’ termini with 0 monophosphate 1 triphosphate ribosomal A protein
158. C- terminal region
159. N-terminal region
160. valine content 0 high 1 low
161. size (no. of residues) 0 large 1 small r-proteins
162. no. 0 54-65 1 60- 65 2 70-80
163. acidity 0 low 1 high
164. r-subunit protein LX
165. IF hypusine
166. mol. mass of hypusine 0 low 1 high
167. EF-1 aminoacyl tRNA-to-ribosome catalysis 0 EF-Tu 1 EF-alpha
168. EF-1 G affinity
169. EF-1 inserts 0 4-amino acid 1 11-amino acid
170. EF-2 0 without diphthamide 1 with diphthamide
171. peptidyl tRNA translocation 0 EF-G 1 EF-2
172. EF-2 compatibility 0 + 1 -
173. subunit “ RNA
174. RNAP type 0 simple 1 multicomponent
175. no. of RNAP subunits 0 4 1 8 or more
176. RNAP A
177. RNAP A structure 0 split 1 integral
178. RNAP B
179. RNAP B structure 0 split 1 integral
182. protein encoded nuclear genes with 0 cis-splicing of miniexons 1 trans-splicing
183. SRP size 0 4.5S 1 7S
184. SRP helices 1-4
185. protein-RNA mass ratio 0 low 1 high
186. tRNA initiator methionine 0 formylated 1 nonformylated
187. G tetra- and pentaphosphates
189. 1-methylpseudouridine 0 + 1 -
190. N, N -dimethylguanosine
192. archeosine (in D loop)
193. queuine 0 + 1 -
194. RNA modification levels 0 low 1 high
195. tRNA anticodon loop 0 + 1 -
196. tRNA transamidation of asparagine 0 asparaginyl synthase 1 aspartyl synthase
197. tRNA transamidation of glutamine 0 glutamyl synthase 1 glutaminyl synthase
198. tRNA mischarging
199. tRNA spacers 0 + 1 -
200. tRNA 3’ terminal CCA added posttranscriptionally
201. mRNA ends 0 without cap or tail 1 with tail only 2 with cap and tail
202. RNA methionine methyl donor 0 S-adenosylmethionine 1 folate derivative DNA
204. topoisomerase II gyrase activity 0 + 1-
205. 2-stranded DNA repair Ku protein with C-terminal HEH domain
206. type II DNAP VI meiotic protein
207. B DNAPs, no. of subunits per ring 0 1 1 2 2 3 3 4
208. DNA helicase 0 DNAB 1 MCM
209. DNA binding protein 10b
210. G-C ratio 0 low 1 medium 2 high
211. sliding clamp
antibio sensitvity RNA polymerase
214. actinomycin D
216. DNA polymerase aphidicolin butylphenyl-dGTP protein synthesis ribosome-targeted
217. antibio group A 0 high 1 low
218. antibio group B 0 high 1 low
219. antibio group C 0 low 1 high
220. antibio overall 0 high 1 low
221. antibio very high
222. antibio high
223. antibio low
226. fusidic acid
227. penicillins 0 lo 1 hi
228. introns 0 - 1 self-splicing 2 protein splicing
229. promoter type 0 eubacterial 1 box A
230.box A in ICR
231 TATA-binding protein(TBP)
232. SECIS binding protein
233. genome size 0 small 1 large
234. silybin stimulation
235. flagella 0 external 1 internal
236. gas vacuoles
239. wall peptidoglycan with LL-DAP acid
240. wall peptidoglycan with L- and D-lysine
241. wall peptidoglycan with arabose-galactose
243. oligosaccaryl transferases
244. proton pumping H-ATPase catalytic subunit insertion 0 F 1 V
246. C40-biphytanyl diol chains 0 acyclic 1 mono and bicyclic 2 tri and tetracyclic
247. S oxidation
249. corkscrew motion
251. DNAP uracil sensitivity
252. DNAP exonuclease function 0 + 1 -
253. tRNA 5’ terminal base, molecular stalk, paired
254. (complex) replication factor C
255. HSP 10 0 + 1 -
257. STK size 0 small 1 large
258. rotund bodies
259. LSU lobe size 0 small 1 intermediate 2 large
260. epsilon B DNAP
261. division by invagination
262. halophily 0 - 1 moderate 2 extreme
Table 8. Data Matrix
0------0010000000000010------------010?01-000000000?????00000000000-0000000---000010000000001000-0001000010?-0000000010---------------00-0010-00000000000000000000000000000000-0-0000000000 000000000000000000000000000000000000000000000-000-000000-0000 00000010-010
???????0010000000000010-------------10?01?0?000000000??????0000000000-0000000---000010000000001000-0001100010?-0000000000---------------00-011-00000000000000000000000000000000-0-0000000000 00000000000000000000?000000000000000000000010000-000000-0 00000000010-010
0----0 -?000 00000000000000000-100001000-01?????00000000?????000 00000000-00001000000010000000001000-000100100?000000000010000--000000000-001000000000000000000000000000000000-0-00000000000000000000000000000010000000000000000000 00010-0000000000-000000000010-010
010000000000000100110000000000110000000000-00000100000000001000 00000--00010000000000000000000000000000000-0-0000000000000000000000000000000000000000000000000000000000000-0000000010-01 
0------?????0000000000000000-110001010?01????000000000?????00000000000-00001000000010000000000000-0001100010?200000000011-----100?0212?00-00?0-00000000000000000000000000000000-0-0 00000000000000000000000000000?000000000000000000000010-0000 000000-000000000010-010
0------00000000000000000000-100001000?01?000000000?????10000000000-0000000---000010000000001000-0001100011?-000000000--------------00-0010-00000000000000000000000000000000-0-00 000000000000 000000000000000?0000000000000000000000100000 0000000-000000000010-000
1--1-0001000000000000000000-100001000?00?????00000000?????00000000000-0?????0---000010000000001000-1001001010??0000000001001101--0??10??00-001-00000000000000000000000000000000-0-0 00000000000000000000000000000?0000000000000000000000100000 0000000-000000000010-000
11--0 -00000000000000000000-1100--0?01000 00000000-???0000100000-0-----110000001000000001100-100101002000100---------------0100010-0000000000000 0000000000000000000-0-00000000000000000010001000000000001100 0000000001000001000001000000-000000000-00
0------ 0000000000-----------------00?01-----000000000-???00000000 000-0-----0000000000000000001000-0001000101-0000000000---------------00-0000000000000000000000000000000000-0-0000000 10000000000100010000000000011000000000001000000-00000000000-00000000000-000
1--0-00000000000000110-001010000000?0010000000-10011000000000100-00 00001-000000000---------------01000-00000000000000000000000000000000-0-00000001000000000010010000002000 00000000000100000100000000-000000000 0-000
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
1?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
100?0-100000010000211-----------0--1?000111111110???1?0111?0?0010000001100000000000000010001-010101020?30000000000---------------00-0010-010000101110111111110110111 1111110011100110111111110101100001111?111001110211011002100 1100000---0111-0001001110000002
????0-?000000000000?0??-----------0--1?00?????111???????????0???? 0?111?0000000---001100000000010001-011100000?-0100001000----- ----------00-0010-02101???0???0????????01101111111110????????00? ??00?00?0110000????????00???0???????0?000??00000---0??0?000?0 00?00000000
????0-?000000000000---0-----------0--1?00?????111???????????0????0100110000000---001100000000010001-011100010?-0000000000------ ---------00-0010-021010111???0????????01101111111111111101?100?? ?00100?0110200??????1100?010111111100?00?010000---0??0110? 000?00001000
0010-0000000000012011-----------0--1?10?????11211111??????0111?0?00110000001100001100000000010001-011110000?-0000000000---------------10-0010-021011111???1????1?111111111111111111111 111101111111011110210111111110011102112111021111010000---0110 1101000110002100
0------ 0000000120-----------0--011?0-0111110?????-1110?12000- 000000110010 00101-001000020000000000---------------110  02111111111111111200111111101111111000110111100 01100011102111110 111001001010011002111111000---011 -00010011100210;
cc ] 24.28 85.87 140 145 169 235 249;
Table 9. Taxon Totals for the 11 Kingdoms.
phyla classes orders families genera species
Animalia 25 84 c 360 c 3600 c100, 000 c 1.1 mln.
Plantae 15 23 c 130 c 700 c 16,000 c 300, 000
Fungi 7 17 c 80 c 250 c 5000 c 50, 000
Ochrobiota 10 33 c 220 c 800 c 3000 c 40, 000
Rhodophyca 1 2 17 67 c 600 c 4000
Conosa 1 3 17 36 163 c 1500
Glaucophyca 1 1 1 1 9 13
Galdieria 1 1 1 1 1 4
Cyanidiophyca 1 1 1 1 1 3
Schyzophyca 1 1 1 1 1 1
total 60 c160 c800 c5200 c 132,000 c 1.5 mln.
Bacteria 11 21 c50 c90 c.550 c. 5,000
From Parker (1982), Barnes (1984), and Lee at al (1985), Margulis et al (1990), and Holt et al (1994); all totals
are for known and extant groups. Estimates of the number of unknown species has ranged between 3 and 100 mln. (May, 2011), but is reasonably estimated at between c. 4-14 mln. (Stork, 1993; Odegaard, 2000) and Mora et al (2011) calculate about 10 mln.--some 3/4 are insects. And the number of extinct species is estimated at perhaps several 100s of mlns., but Discovery Channel (How many species have actually gone extinct?-dicovery.com) reports an estimate range of 1-4 bln., so the normal or background extinction rate might be about 1 species per year. The average species life span is 5-10 mln. years (Lawton and May, 1995). The total number of individual bacteria is estimated at 3 decillion (3x1033) (Whitman et al, 1998) and they are the majority so the total number might be c. 4 decillion.
Materials and Methods
The data set (Table 10, Page 2) for the 1st eukaryote analysis contained 27 taxons and 260 characters, 20 branched (complex), in 283 columns excluding 14 deactivated characters and was divided into 4 sections, chloroplasts (29), morphology (139), chemistry (34), and physiology (58), excluding the addenda section. The data matrix is presented in Table 11 (Page 2). The computer calculations were done by Dr. James Carpenter using the TNT (Tree analysis using New Technology) computer program (Goloboff, 1999; Nixon, 1999) in 2007. All 4 new technologies were used (ratchet, tree drifting, fusing, sectorial search) and TBR (tree bisection and reconnection) branch swapping was employed, random seed was set at 1, constraints were off, and there were 208 mln. rearrangements. Cyanidioschyzon was used as the root. (I am not able to insert an image so the cladogram is not included). For the 2nd eukaryote analysis, Plasmodiophorae and Spongomonada were excluded, the 14 deactivated characters were included, and 4 myosin characters were added. The computer calculatiions were done by Dr. Pablo Goloboff in 2009 also using TNT and a heuristic search.
In the 1st analysis for eukaryotes there were 448 steps and 13 most parsimonious trees (mpts) resulted. The CI was .58 and the RI .45. The following showed up as monophyletic in all 13 trees: Plantae + Opisthokonta (Megabiota), ((Plantae +Opisthokonta) + Ochrista), Opisthokonta, Cercomyxa (Cercomonada+Myxofilosa), Retaria, Protoamebae, Cyanidium-Galdieria, and Neoexcavata (Heterolobosa+ Polymastigota). Cyanidium+ Galdieria, Glaucophyca, Rhodophyca, Plasmodiophorae, and Spongomonada formed a basal series in all 13 trees. Dinociliata and Ochrista appeared as monophyletic in 12 trees, Excavata in 9, and Alveolata in 6. Apicomplexa grouped with Dinociliata 6 times, more than with any other group. Protoamebae was on top in all 13 trees. The strict consensus tree was not well resolved so implied weighting was used producing only 1 mpt (Table 13a). 7 groups are based on homoplasies, Cyanidium+ Galdieria, and Supergroups 5, 6, 7, 8, 9, and 10. The majority consensus tree (done by myself) is in Table 13b.
In the 2nd eukaryote analysis there were 17 MPTs, the CI was .59 and the RI was .47. As in the 1st analysis Galdieria+Cyanidium, Glaucophyca, Rhodophyca formed a basal series in all trees. Appearing in all 17 trees were Metakaryota, Galdieria-Cyanidium, Neokaryota, Cellulosa, Contophora, Anisokonta, Euchrista, Neolobosa+Protolobosa (Protoamebae), Opisthokonta, Actinopoda+Foraminifera (Retaria), Dinobiota (Dinociliata+ Excavata)(with or without Apicomplexa), Ciliata+Dinoflagellata (Dinociliata), Excavata, and Neoexcavata (Heterolobosa-Polymastigota). Ochrista showed up in 15, Protoexcavata (Euglenista+Jakobida) in 12, Myxofilosa+Opisthokonta in 10, Retaria+Dinobiota in 9, Megabiota (Plantae+Opisthokonta) in 6, and Megabiota + Ochrista in 6. Cercomonada grouped with Protoamebae in 6 and with Myxofilosa ("Myxomycetes")+Opisthokonta also in 6. Apicomplexa grouped with Retaria 4 times, with Dinociliata+Excavata 4 times also, twice with Dinoflagellata where it is usually placed in molecular phylogenies (forming Miomonada or Myzomonada) and twice with Dinociliata, so was in Dinista in 12 trees. Dinobiota was on top in 10, Ochrista in 6, and Opisthokonta in 1. The synapomorphies are in Table 15.
A strict consensus with no groups excluded yielded low resolution and one with Apicomplexa and Myxofilosa excluded did not fair much better. A majority consensus, set at 50+%, was also done (by myself), which gave much better resolution (Table 15). 3 groups are based on homoplasies, Galdieria-Cyanidium, Protomebae+Cercomonada, and Myxofilosa+Opisthokonta.
Of the 6 consensus methods-- majority, strict, semistrict, Adams, Nelson, and combinable components-- the 1st 2 are the most popular and it is majority consensus, devised by Margush and McMorris (1981), I favour as it usually produces better resolution and is simple. TNT does only strict consensus. The following 9 clades have 100% support across the 2 analyses: Metakaryota, Galdieria-Cyanidium, Neokaryota, Cellulosa, Contophora, Euchrista, Neolobosa+Protolobosa (Protamebae), Opisthokonta, Actinopoda+Foraminifera (Retaria).
Some groups are misplaced because of homoplasy so I have repositioned them (Table 16) according to classical and molecular data. Ochrobiota (similar to Chromalveolata and (mostly) recognized also by Lipscomb) is composed of Ochrista, Retaria, and Dinobiota (Alveolata and Excavata (Discicristata)), and is the supergroup with the most synapomorphies with 12. Also, Plantae probably belongs above Unikonta as it has more derived traits than either Animalia or Fungi, although it might still be better placed below it, and Dinaria might be on top in Bikonta instead of Ochraria. A key is also presented.
Table 12. Diana Lipscomb's Classification ( her results from 1989 and 1991)-7 kingdoms.
Hennig86 Wagner parsimony analysis and branch swapping was used on 86 genera and 137 phenotypic features resulting in 7 optimal trees of 475 steps with a CI of .52; Nelson (strict) consensus was applied.
Table 13. Eukaryota-1st Analysis.
a. Implied Weighting Tree
b. Majority Consensus Tree.
I Supergroup 6
II Supergroup 7
III Supergroup 8
IV Supergroup 9
IV Cercomyxa (Cercomonada+Myxofilosa)
Table 14. Majority Consensus for Eukaryota- 2nd analysis, 11 Kingdoms.
sbemp. Eukaryota (Chatton 1937) Dougherty 1959 stat. nov.
infemp. Cyanidiochyza stat. nov., nom. nov.
kgdm. Cyanidioschyza stat. nov.
infemp. Metakaryota Cavalier-Smith 1993 tax. nov.
pvemp. Galdieria-Cyanidium stat. nov., nom. nov.
kgdm. Galdieria-Cyanidium stat. nov.
pvemp. Cenokaryota tax. nov.
mcemp. Glaucophyca stat. nov., nom. nov.
mcemp. Cellulosa tax. nov.
nnk. Rhodophyca stat. nov., nom. nov.
nnk. Contophora Mohn 1984 emend., stat. nov.
ggk. Plantae Haeckel 1856 (excluding green algae) stat. nov. (Isokonta Blackman and Tansley 1902 (as
kgdm. Plantae (Chlorophyta Pascher 1914 (including only green algae), Vegetabilia Linneus 1753
(excluding green algae), Chlorobiota Jeffrey 1971 (including also euglenoids), Chlorobionta Edwards 1976
(including also euglenoids), Viridiplantae Cavalier-Smith)
ggk. Anisokonta nom. nov., stat. nov.
mgk.//kgdm. Ochrista (Cavalier-Smith 1986, name only)(Chromista Cavalier-Smith 1981) stat. nov.
sbk./phyl. Chlorarachnia stat.nov.
sbk. Euchrista tax. nov.
spph./phyl. Haptophyca stat. nov., nom., nov.
spph. Neochrista tax. nov.
phyl. Heterokonta Luther 1899 (as Heterokontae)
phyl. Cryptophyca nom. nov.
grdk./kgdm. Lobosa stat. nov.
phyl. Eulobosa (Protamebae) nom. nov. (Rhizopoda)
cl. Neolobosa nom. nov.
cl. Protolobosa nom. nov. ( Pelobiota Page 1976)
phyl. Cercomonada Poche 1913 (as order) (Cercolobosa nom. nov.)
hpk. Myxokonta tax. nov.
spk./kgdm./phyl. Myxofilosa nom. nov., stat. nov.
spk. Opisthokonta Cavalier-Smith 1987
kgdm. Animalia Linneus 1758 emend.
kgdm. Fungi Linneus 1753 emend.
hpk./kgdm. Cenanisokonta tax. nov.
sbk. Foramaxia nom. nov. (Retaria Cavalier-Smith 1999, emend.)
phyl. Actinopoda Calkins 1909
phyl. Foraminifera d’Orbigny 1826
sbk. Dinobiota (Stewart and Mattox 1980) tax. nov.
spph. Alveolata Cavalier-Smith 1991
phyl. Apicomplexa Levine 1970
phyl. /phyl. Dinociliata nom. nov. /
spcl. Ciliata Perty 1852 (Ciliophora Doflein 1901, Heterokaryota Hickson 1903) stat. nov.
spcl. Dinoflagellata Butschli 1885 stat. nov.
spph. Excavata Cavalier-Smith 2002
cl. Euglenaria nom. nov.
cl. Jakobea Cavalier-Smith 1993 (as order) stat. nov.
phyl. Neoexcavata tax. nov.
cl. Polymastigota Blochman 1895 (as order)
cl. Heterolobosa Page and Blanton 1985 (as Heterolobosea)
Table 15. Synapomorphies for Eukaryote Clades.
Metakaryota-intermediate genome, intermediate chloroplast DNA size, sporulation
Neokaryota- lobate chloroplasts, large genome, large chloroplast DNA size, multiple mitochondria
Cenokaryota-flagella, cellulose, MLS
Cellulosa- pyrenoids, chloroplast DNA arrangement as scattered nodules, semi-open mitosis, multiple
Contophora- gametic meiosis, stigmas, open mitosis, tubular cristas
Anisokonta- tubular cristas, AAA LSP, MYTH4FERM myosins, and TH 1 myosins.
Metanisokonta-thecal and capsular plate position, tranisitional cytoplasmic organization
Ochrista- chloroplast in ER (endoplasmic reticulum), nucleomorphs
Euchrista (Metachrista)- PR (periplastidial reticulum), chloroplast in SER (smooth ER), silica in walls, transitional
helix (including helical band in haptophycans)
Neochrista- epsilon- carotene, maastigonemes formed in nucleaer envelope and ER, tripartite mastigonemes
Cercomyxa-ppks, striated fiber emanates from anteriorly directed flagellum extending as cone and terminating in MTOC,
cercomyxan semicircle complex
Retaria - pheodarian-type pseudopods
Dinobiota- articulins, mastigoneme rows 1 and 0, kinetochore location on nuclear envelope, permanently condensed
Excavata- discoid cristas, linked mts underlie entire cell membrane, feeding groove (ventral groove used for suspension
feeding), composite fiber, I fiber, B fiber, C fiber
Neoexcavata-polymastigote rootlets, singlet rootlet between right rootlet and BB runs along floor of groove
Dinociliata- dinociliate thecal vesicles
Protoamebae- transverse bipartite mts associated with centriole, conical pseudopods.
Opisthokonta- TZ constriction and striation, opisthokontic histones, ophiobolins, tryptophan pathway with nicotinic acid
Table 16. sbemp. Eukaryota (Chatton 1937) Dougherty 1957-10 kingdoms
hpk. Unikonta Cavalier-Smith 1987 stat. nov.
spk./kgdm. Conosa Cavalier-Smith 1998, stat. nov.
hpk. Bikonta (Cavalier-Smith 1993) tax. nov.
spk. Metakonta tax. nov.
kgdm. Plantae (Chlorophyta)
kgdm. Ochrobiota tax. nov.
sbk. Dinaria nom. nov.
sbk. Ochraria nom. nov.
Key to the Kingdoms.
1 Ribosomes 70S, RNA 16S; nucleus without membrane; cell wall generally with peptidoglycan; no meiosis, mitosis, nor
mitochondria; did not originate through endosymbiosis; tissue absent. Prokaryota
2 Flagella absent. Thermosipho
2 Flagella present. Kontobacteria
3 Lysine absent; without rotund bodies. Fervidobacterium
3 Lysine present in some; rotund bodies rare. Cenobacteria
4 Toga present; no aerobiosis; with hyperthermophily. Thermotoga
4 Toga absent; aerobiosis usually present; hyperthermophily usually absent. Aerobacteria
5 Wall with LPS; Gram negative (staining red); phtosynthesis in large group and based on
chlorophyll. Gracilicutes 5 Wall without LPS; Gram positive (staining purple) in some; phtosynthesis only in 1 small group and not
based on chlorophyll. Monoderma
6 Ribosome primitive; lipids ester-linked; Gram positive. Firmicures
6 Ribosome advanced; lipids ether-linked; Gram varies or inapplicable. Mendosicutes
1 Ribosomes 80S, RNA mostly 18S; nucleus with membrane; cell wall generally without peptidoglycan; meiosis, mitosis, and mitochondria usually present; originated through endosymbiosis; tissue often present. Eukaryota
7 Genome supersmall; no sporulation. Schizophyca
7 Genome small or larger; usually with sporulation. Metakaryota
8 Mitochondrion single. Cyanidophyca
8 Mitochondria 1 or many. Neokaryota
9 Meiosis absent; wall proteinaceous; unicellular. Galdieria
9 Meiosis present in most; wall typically celulosic or chitinous; unicellular or multicellular.
10 Kinetids absent; meiosis zygotic; mitosis closed or semiopen; with pit connections. Rhodophyca
10 Kinetids usually present; meiosis generally gametic; mitosis usually open; no
pit connections. Contophora
11 DHFS-R gene fusion absent; flagella usually 1; no MLS; autotrophy absent. Unikonta
12 Microtubules with conical array; ameboid form; flagella anterior. Conosa
12 Microtubules without conical array; ameboid form absent or rare; flagella typically
13 Nutrition osmotrophic; wall mostly chitinous; mostly sessile; mycelia present; diploid; meiosis
gametic; reproduction sporogenic;mitosis mostly closed; no true tissue; without embryonic
13 Nutrition phagotrophic; wall absent; mostly mobile; no mycelia; haploid; meiosis varies;
reproduction typically anisogamous; mitosis mostly open; true tissue in most; embryonic
development normally present. Animalia
11 DHFS-R present; flagella usually 2; MLS in many; autotrphy in many. Bikonta
14 Cyanelles present; sexuality absent. Glaucophyca 14 Cyanelles absent; sexuality
15 Chloroplasts, when present, with 2 membranesd and chlorophyll b. cristas lamellar; storage
product alpha 1-
15 Chloroplasts, when present, with 3 or 4 membranes and chlorophyll c; cristas usually tubular;
storage product beta 1-3 or alpha- 4. Ochrobiota
Cyanidioschyzon merolae is most definitely the ancestral eukaryote as it has the fewest advanced traits with 12 and the highest percentage of primitive traits with 90 % (excluding inapplicable and missing data), and is the root. It is supported as basal by Seckbach (1994) and Nagashima et al (1993), having the most primitive chloroplast, only 1 mitochondrion, no vacuoles, no trienoic acids, and the smallest eukaryotic genome at 8 Mbp. Prerhodophyca (after Seckbach (1987), including all 3 genera, which are eukaryotic blue algae), has no synapomorphies and is obviously an artifact in genotypic analyses. Cyanidium, is considered as a bridge alga between Cyanobacteria and Rhodophyca by Klein (1970), Frederick (1976), and Seckbach (loc. cit.). It also lacks vacuoles and trienoic acids, and has only 1 chloroplast and 1 mitochondrion. Galdieria has only 1 chloroplast but numerous mitochondria, a vacuole, and trienoic acids. 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 sometimes considered as a sister group to all other eukaryotes. Lipscomb was on target but did not hit the bull's eye. Cyanidium+Galdieria form the sister group to red algae in Saunders and Hommersand (2004) based on the the GB (Golgi Body, aka dictyosome) association with the ER and presence of peripheral thylakoids, and a chloroplast dividing ring occurs in Cyanidioschyzon and Cyanidium, the 3 characters not included in my analyses, but the 1st is common (but rare in red algae) and is plesiomorphic, peripheral thylakoids occur also in Glaucosphera and are probably symplesiomorphic, and the 3rd is probably also plesiomorphic, but would probably not affect the final classification, in any case, as there are more synapomorphies for Metakaryota and Neokaryota than for a Cyanidium+Galdieria or Prerhodophyca clade.
The earliest descriptions of these thermoacidophilic organisms were by Meneghini (1839; 1841 (in Coccochloris (=Anaphorathece, Cyanobacteria)) and Tilden (1898 (in Protococcus, a green alga); 1910 (in Pleurocapsa, a cyanobacterium)), but these descriptions were invalid as they referred to mixed populations. The 1st valid description was by Galdieri in 1899 as Pleurococcus sulphurarius, and set up by Merola et al (1981) as a new genus Galdieria sulphuraria and referred to red algae and the other prerhodophycans. They established the new class Cyanidiophyceae and the families Cyanidiaceae, for Cyanidium and Cyanidioschyzon, and Galdieriaceae for Galdieria. The 2nd valid description was of Cyanidium caldarium by Geitler and Ruttner (1935) (Geitler is known for his influential classification of Cyanobacteria) but seen as a synonym with Pleurocapsa caldaria. Cyanidioschyzon merolae was discovered as part of Cyanidium caldarium by Tilden (1898) but recognized and named as such (because of its longitudinal fission) only in 1978 by De Luca et al, the 2 being previously designated as Cyanidium caldarium forma A and B, respectively.
The other groups that would be possible candidates for the root are Parabasalia or Polymastigota and Pelomyxa, Pelomyxidae or Pelomyxida but their seemingly primitive traits are reductions or losses due to their parasitic or otherwise symbiotic lifestyle and have affinities to other taxons. There are 4 apomorphies linking Pelomyxa to Mastigina, Mastigella, or Mastigameba: nuclei surrounded by apposed bacteria within vacuolar membranes linked to the nuclear membrane by vesicular membranes, densly vesiculated cytoplasm, bacteria apposed to the plasmalemma (Griffin, 1988), and fountain flow (Walker et al, 2001). If Pelomyxidae was separated as a terminal taxon, as it would need to be since Mastigamebidae has open mitosis, or if these traits were included as autopomorphies, then there would be 5 extra apomorphies making a total of 33. Even if we were to consider some chracteristics as plesiomorphic instead of apomorphic, and there would be 6 of these (single basal body, mt cone, radiating mts, intranuclear spindle, lobose pseudopods, and eruptive motion), then it would still have 23 derived traits, almost double Cyanidioschyzon, making 88 % primitive traits, lower than Cyanidioschyzon. As well, most molecular phylogenies support Protolobosa as derived rather than basal as does some of the morphology (pseudoflagella suggesting reduction, ED (electron dense) material or cryptons suggesting mitochondrial derivatives). And Mastigameba and Entameba uniquely share neo-inositol polyphosphates, the 2 together also well supported by molecular evidence (Bapteste et al, 2002). Dinoflagellates, often touted as the basal eukaryotes, have a lack of histones or of typical histones but this is a reversal and are now recognized as part of Alveolata, in any case. Their advanced position, along with that of Polymastigota and Euglenaria also occurs in Lipscomb’s arrangement.
The taxons with the fewest derived traits (20 or under) are Cynidioschyzon with 12, Galdieria with 16, and Cyanidium with 20. Spongomonada is the next highest with 28, Pelomyxida (Protolobosa) and Cercomonada have 30 each. Polymastigota has 50, Rhodophyca 68, Glaucophyca 34, Fungi 71, and Animalia 51. The ones with the most (over 90) are Heterokonta (151), Plantae (135), Euglenaria (99), and Dinoflagellata (94). The ones with the highest number of primitive traits are Glaucophyca with 190, at 84.8 %, Polymastigota with 167, and Pelomyxida with 153.
By way of comparison the bacterial taxons with the lowest number of derived traits (under 10) are Thermosipho, Fervidobacterium, and Thermotoga with 6, 7, and 8 respectively. The ones with the highest number are Thiobacteria (93), Methanobacteria (103), Halobacteria (106), and Sulfobacteria (117).
Glaucophyca is positioned in Heterokonta in Lipsomb (including only Cyanophora)(1991) and with Cryptophyca in Battacharya et al (1995) but with Glaucosphera with red algae. However, the phenotypic evidence is comprised of negative traits for this latter position-- no flagella nor basal bodies, with R-phycocyanin instead of C-phycocyanin, the latter occuring in other glaucophycans, and lack of peptidoglycan in its cyanelles; and lobate chloroplasts occur elsewhere. If Glaucosphera has open mitosis, which apparently it does, then it possibly belongs in Contophora (and, in fact, in Bikonta). It is a separate kingdom in Hackett et al (2007), Burki et al (2008), Tekle et al (2008), Kim and Graham (2008), Hampl et al (2009), Parfrey et al (2010).
Red algae as basal is supported by molecular evidence (Hori and Osawa, 1987; Hori et al, 1990; Luttke, 1991; Nozaki et al, 2007) and Archeoplastida as polyphyletic is also supported by molecular evidence (Hori and Osawa, 1987; Hori et al, 1990; Luttke, 1991; Olsen, 1994; Bhattacharya, 1995; Nozaki et al, 2007; Yoon et al, 2008; Kim and Graham, 2008; Tekle et al, 2008; Parfrey et al, 2010) as well as previous classical evidence (Lipscomb, 1985, 1989, 1991). Red algae as the most primitive eukaryotes is agreed to also by Starobogatov (who, as well, separated Cyanidium as phylum Cyanidiophyta, and placed Glaucophyca close to Cryptophyca and Centrohelida, a radiolarian group), Vada, Taylor, Cavalier-Smith in his '78 taxonomy, Edwards, Leedale, Jeffrey, Pascher (1931), Chadefaud (1960), Honigberg et al (1964), Copeland, Whittaker, Margulis (1974), and Mohn (1984), the others recognizing another group as such, usually green algae, or not doing any internal arrangements.
Archeoplastida has weak support from molecular evidence (Baldauf et al, 2000; Stiller et al, 2001; Parfrey et al, 2007), is strongly refuted by Stiller and Harrell (2005), and has no support from classical evidence as it has no synapomorphies so it is no surprise it shows up as polyphyletic in my analysis, also. Furthermore, Parfrey et al ( 2007) excluded Hori and Osawa (1987), Hori et al (1990) and Luttke (1991) which makes Archeoplastida even more weakly supported. In the genotypic phylogeny of Parfrey et al (2010) and the combined phenotypic-genotypic phylogeny of Goloboff et al (2009), the latter using over 73,000 taxons and over 600 characteristics, Archeoplastida is not supported. The group is recovered in several recent analyses but Parfrey et al (2010) point out that its support comes primarily from phylogenomic analyses and these may be picking up misleading EGT (endosymbiotic gene transfer) signal of genes independently transfered from the plastid to the host nucleus in the 3 archeoplastid clades. As well, they use maximum likelihood which is not as reliable as parsimony. And Stiller and Harrell (2005) emphasize that the "clade" can be explained by "short-branch exclusion" and "subtle and easily overlooked biases can dominate the overall results of molecular phylogenetic analyses of ancient eukaryoyic relationships. Sources of potential phylogenetic artifact should be investigated routinely, not just when obvious 'long-branch attraction' is encountered." Archeoplastida is not supported in my analysis as expected as it has no synapomorphies, is weakly supported genotypically, and is contradicted by Lipscomb's classical analyses, by 10 molecular analyses, and by Goloboff et al's combined analysis .
Red algae most likely evolved their plastids from Cyanobacteria which has chlorophyll a only and phycobilins, while plant plastids probably evolved from Chloroxybacteria which has chlorophyll a and b and no phycobilins. There probably were 5 secondary plastid symbiogeneses: chlorophyll c, chlorophyll b in chlorarachnians (from a green alga), chlorophyll b in euglenoids (also from a green alga), cryptomonad (from a red alga), and dinoflagellate (from a heterokont), hence the 4 fucoxanthins found also in dinoflagellates, and the symbiote is still recognizable.
Taylor (1978) and Mattox and Stewart (1980) emphasized the phylogentic importance of cristal structure, both recognizing a flat-tubular split, and the latter proposed a link between this split and plastid symbiogenesis--flat corresponding to chlorophyll b and tubular to chlorophyll c. This is generally the case, as plants and euglemoids have flat cristas and chlorophyll b, and the ochrobiotes have chlorophyll c and tubular cristas, however, chlorarachnians have chlorophyll b, and cryptomonads have flattened (albeit tubular) cristas.
An evolutionary link between red algae and funguses had been proposed by Sachs (1874), Chadefaud (e.g., 1957), Cain (1972), and Demoulin (1974), among others, who pointed out similarities between the 2 groups: trichogynes, spermatia, perforated septa, and trehalose storage, and favoured fungal polyphyly. This has been contradicted by deBary (1881), Atkinson (1915), Linder (1940), and Savile (1968), among others, who favoured fungal monophyly, as they are cases of convergence rather than actual kinship, and no phylogenetic analyses (including mine, which includes the 4 traits), either phenotypic or genotypic, have found such a link, and the monophyly of Fungi is well established.
Rhizaria is also not recovered, not surprisingly, as it is ill-defined and weakly supported in molecular phylogenies (Palfrey et al, 2007), statistical support for it is inconsistent in multigene genealogies with larger taxon sampling (Yoon et al, 2008), and it is ambiguously supported in Goloboff et al (2009). Cercozoa is, as well, an artifact in molecular phylogenies, as it is also ill-defined and weakly supported (Palfrey et al, 2007). And Amebobiota is simply Conosa without Cercomonada.
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.
Spongomonada probably belongs in Euglenista where it is placed in Lipscomb (1991) or in Heterokonta (Karpov, 1999). Plasmodiophorae is of uncertain position but could be akin to heterokonts.
In Baldauf et al (2000), a synthesis of molecular evidence, of the 15 groups surveyed, all were fairly to very well supported in molecular studies, except for Ochrobiota (largely Chromalveolata), Archeoplastida, and Excavata. Conosa was not included, however, “Amebozoa” (Neolobosa-Myxofilosa), which is more or less the same, was well supported. Strongly supported also are 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).
In Parfrey et al (2006), of the 6 groups surveyed, only Opisthkonta was strongly supported by molecular studies. Of the others, Archeoplastida, Rhizaria, and “Amebozoa” (Myxofilosa-Protoamebae) were weakly supported and Excavata and Ochrobiota were poorly supported. In the molecular phylogeny of Parfrey et al (2010), Rhizaria, "Amebozoa," and Excavata are supported, and Archeoplastida is not. In the molecular phylogeny of Hampl et al (2009), Rhizaria, "Amebozoa," and Excavata are supported, but also Archeoplastida. Excavata is recovered also in Hackett et al (2007). Amebobiota is recovered also by Hackett et al (2007) and Kim and Graham (2008).
The monophyly of Cellulosa, Contophora, Ochrista, Dinobiota, Excavata, Protoamebae, and Opisthokonta is very solid. Alveolata also, even though it is not strongly supported in the analyses here it has strong support in molecular phylogenies and there are synapomorphies for it in classical data. Opisthokonta has the strongest support from genotypic characteristics of any eukaryotic supergroup and is well supported by phenotypic characteristics.
There are 5 groups that are probably clades: Bikonta (Glaucophyca+ (Plantae (this excludes, of course, red algae) +Ochrobiota)), Unikonta (Conosa+Opisthokonta), Ochrobiota (Ochrista, Retaria, and Dinobiota), Ochraria (Ochrista+Retaria), and Conosa (Protamebae+Cercomyxa or Lobosa+Myxofilosa), as these have several putative synapomorphies. Bikonta has DHFR-TS gene fusion, green-yellow photoaction spectrum, pyrenoid type D, stacked thylakoids, vesicular vacuoles, MLS (multi-layered structure), pantonematic flagella, and cortical (pellicular) alveoli (this last feature occurs in Glaucophyca, and Actinopoda as well as Alveolata); Unikonta, unikonty, radiating perpendicular mts, posterior-anterior flagellar transformation, cartwheel in BB (basal body), PNB (paranuclear body), CSP (carotenoid synthesis pathway) L, 3 myosin features (myosin TH2, class II myosins, SH3 domain tails); Ochrobiota has chlorophyll c, beta-1-3 storage, xanthophyll type C and D, B – D type stigma structure, cytoplasmic stigma, flagellar photoreceptor, flagellar swelling, paraxial rod, protein import mechanism by GB (Golgi Body) vesicles, CSP T, cytostome; Ochraria possesses axopods; 2 mastigoneme rows on 1 flagellum, none on the other; 2 mastigoneme rows on 1 flagellum and the other reduced; ED (electron dense) plaque in the TZ (transition zone); ED bodies with rectangular arrays; Conosa, with conical array of microtubules subtending the nucleus.
Bikonta is corroborated as well as the others by molecular evidence (Baldauf et al, 2000; Nozaki et al, 2003; Kim and Graham, 2008; Hampl et al, 2009) but, in spite of the name, cannot be defined by dikontic flagella as this is a primitive trait and occurs also in Unikonta, which is also well supported especially by myosin features (Richards and Cavalier-Smith, 2005) and in part by 2 Lipscomb phylogenies. And Metakonta, uniting Plantae with Ochrobiota, would have, for instance, the synapomorphy of stellate flagellar transition zone. Both Unikonta and Bikonta (but including also red algae) are supported in the molecular phylogeny of Hampl et al (2009) as well as Kim and Graham (2008). With the long branch taxons removed Hampl et al (2009) has 8 kingdoms: Amebazoa, Animalia, and Fungi in Unikonta, and Excavata, Plantae, Rhodophyca, Haptophyca, and Chromalveolata-Rhizaria. In it Bikonta includes 2 supergroups: Excavata (or Discoba) and Archeoplastida (plants + red algae + haptomonads) + most of chromalveolates and rhizarians.
Ochrobiota has a dozen classical synapomorphies, more than any other eukaryote supergroup and an exhaustive search would probably recover it, as well as Bikonta. The Burki et al (2009) investigation lends support to the proposed chromalveolate clade, similar to Ochrobiota, as the SAR (stramenopiles (heterokonts), alveolates, and rhizarians (which includes Retaria)) group and there is a Haptophyca-Cryptophyca grouping within it. Hackett et al (2007) and Hampl et al (2007) results also support a chromalveolate clade. The group is recognized in Adl et al (2005) and Holt and Iudica (2007). It shows up also in Tekle et al (2008) also based on maximum likelihood genotypic analysis as Cryptophyca-Haptophyca+Malawimonidae, Euglenista-Heterolobosa+Jakobida, and Alveolata+Cercomonada-Heterokonta, so Cercomonada is misplaced and belongs with Amebobiota, and Polymastigota is misplaced outside of it. The over-all arrangement is similar also to my results in that therer is a Glaucophyca, Rhodophyca, and Plantae part of the series. In Parfrey et al (2010), SAR is also supported but without Cryptomonada and Haptophyca. Kim and Graham (2008) maintain that their analysis strongly refutes it. In Baldauf et al (2000) and by others Chromalveolata is not considered as strongly supported only because it excludes Cryptophyca or both it and Haptophyca, so it is, in fact, well supported, and these 2 groups properly belong in Chromista (Ochrista).
Both Haptophyca and Cryptophyca are nested within Heterokonta in Williams (1991) and Haptophyca, also, in Saunders, Potter, and Andersen (1997), the former based on phenotypic data and the latter on phenotypic, molecular, and combined data, but excluding Cryptophyca. However, in the latter the combined data show Haptophyca as sister group to Heterokonta, with the strict consensus for the phenotypic results not well resolved and the molecular results grouping Haptophyca with Alveolata+Heterokonta. Chlorarachnia was excluded from both studies.
Retaria appears not to have been widely tested but is corroborated in Moreira et al (2006), along with Excavata and Conosa, but where, notably, Cercomonas, Plantae, red algae, a truncated Conosa, and Nuclearia are misplaced. It is also supported in Parfrey et al (2010). Contrary to the title the Parfrey et al 2010 results are not well resolved as there is a polytomy of 7 taxons (Haptophyca, Plantae, Telonema, glaucophycans, Centroheliozoa, Rhodophyca, and Cryptomonada) and another of 3 (minor groups). The 7 plus SAR and Excavata form a clade. The remaining group is Opisthokonta.
Like other unikonts, cercomonads have posterior to anterior flagellar transformation and share a derived feature with chytrids, the PNB (paranuclear body), and like other conosans an mt cone, and share at least 3 kinetid features with Myxofilosa as listed in the Synapomorphy Table (Table 15).
Groups included in some terminals should be specified and are as follows:
Pelobiota contains Pelomyxidae (Pelomyxa, Mastigina), Mastigamebae (Mastigameba, Mastigella), Phalansterium,
and Entamebidae (Entameba, Endolimax).
Neolobosa contains Gymnolobosa and Testalobosa.
Spongomonada comprises Spongomonadidae (Spongomonas, Rhipidiodendron)
Cercomonada comprises Cercomonas and Heteromita.
Heterolobosa comprises Acrasidae (Acrasis, Fonticula, Guttulina, Guttulinopsis) and Schizopyrenida (Vahlkampfidae,
Glaucophyca contains Glaucocystis, Cyanophora, Gleochete, and Glaucosphera (this last maybe goes to red algae(ss) as
Euglenaria contains Euglenoidia, Diplonema, Kinetoplastida, Pseudociliata, and Hemimastigota.
Malawimonas is included in Excavata.
Heterokonta necessarily includes opalinates, proteromonads, mycelial algae(pseudofungi), and bicoesids.
Cryptophyca includes katablepharids.
Plantae necessarily includes green algae.
Animalia necessarily includes Choanozoa, sponges, Myxozoa, and Mesozoa.
Fungi necessarily includes chytrids and microsporidians and probably includes also haplosporidians.
Groups excluded were Gymnofilosa, Gromida, and Euglyphida, these for lack of information, although the 1st and 3rd probably go to Neolobosa, and the 2nd one is often considered to be a member of the forams.
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, an bicocesids, opalinates, and proteromonads in Heterokonta, and the unity of Heterokonta and Eukaryota. Very high probabilities exist for the monophyly of Monoderma, Firmicutes, Actinobacteria, Gracilicutes, Photobacteria, and Thiobacteria.
The most important points can be summed up as follows:
1. red algae are ancestral, a position supported by both genotypic and phenotypic evidence.
2. archeoplastidans are a polyphyletic group with no support from classical evidence, only weak
support from molecular data, and much robust support for their polyphyly.
3. Rhizaria is a heterogenous assemblage with no support from classical data and therefore should be considered polyphyletic and the genotypic taxonomies that do support it are artifactual; the same goes for Cerozoa, included in it.
4. Protozoa and Protista are polyphyletic assemblages with no support from classical nor molecular evidence.
5. Metakaryota, Neokaryota, Cellulosa, Contophora, Alveolata, Excavata, Dinobiota, Ochrista, Opisthokonta, Protoamebae, and Retaria, are monophyletic groups, and Ochrobiota, Conosa, Ochraria, Unikonta, and Bikonta probably are also.
6. molecular methods are highly overrated and not superior to classical evidence and LGT is highly exaggerated.
7. the obvious existence of important phenotypic data in bacteria.
Euchrista-algae cum chloroplasta in reticulum endoplasmicum sine ribosomae et reticulum periplasmicum.
Neochrista- algae cum epsilon-carotena et mastigonemata tripartitae et tubulari.
I am extremely grateful to Dr. James Carpenter, of the Am. Mus. Nat. Hist., former editor-in-chief of Cladistics and now administrative editor, and Dr. Pablo Goloboff, of CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), past president of the Willi Hennig Society, for their invaluable assistance.
A Convenience Classification
If we are to design a convenience classification as was the convention prior to recently, but touted as “evolutionary”, and which we should, but separate and distinct, as it is as important and valid as a cladistic system, then a 4-kingdom arrangement (Table 21) without a protistan kingdom but with a protistan level is more useful and informative, unlike most modern alternative systems, which had a protistan kingdom of some sort.
The protistan subkingdoms are Protobacteria (Eubacteria) and Metabacteria (Archeota) and the 3 lower eukaryote subkingdoms, Algae or Protophyta, Mastigomycota or Protomycota, and Protozoa. The histonian subkingdoms are Metaphyta (Embryophyta or Cormophyta), Metamycota, and Metazoa. The 4 kingdoms are Bacteria (prokaryotic, mostly osmotrophic, and with typically a murein wall), Phyta (usualy autotrophic and with a typically cellulose wall), Mycota (osmotrophic, mostly with a chitinous wall), and Zoa (phagotrophic, with no wall). And the 2 superkingdoms are Prokaryota and Eukaryota.
The bases are, then, trophic mode/functional community, wall composition, and nuclear type. Lines can be drawn to indicate histonian and protistan levels and trophic mode sections and walled and unwalled sections. Similar taxonomies were Takhtajan’s, but ochrophycans were lumped with green algae, and blue bacteria were separated from eubacteria, and Leedale’s pteropod scheme, but there was no formal internal arrangement for the component kingdoms.
Table 23. Convenience Classification for Empire Biota.
phyl. Heterotropha tax. nov.
cl. Chemorganotropha tax. nov.
cl. Chemolithobacteria tax. nov.
phyl. Autotropha tax. nov.
cl. Scotoautotropha tax. nov.
spk. Eukaryota stat. nov.
kgdm. Phyta (Chloroplasta nom. nov. )
sbk. Protophyta (Algae)
sbk. Metaphyta (Embryophyta, Cormophyta)
kgdm. Mycota stat. nov.
sbk. Protomycota (Mastigomycota)
phyl. Zygomycota (classes Tricho- and Zygomycetes)
phyl. Ascomycota (classes Disco-, Pyreno-, Plecto-, and Hemiascomycetes)
phyl. Basidiomycota (classes Archeo- and Neobasidiomycetes)
sbk. Protobacteria (Eubacteria)
sbk. Metabacteria (Mendosicutes)
kgdm. Phyta (Chloroplasta)
sbk. Protophyta (Algae)
sbk. Metaphyta (Embryophyta)
sbk. Protomycota (Mastigomycota)
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