EMPIRE BIOTA
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, addition
of majority consensus (Table 4) plus an analysis for bacteria only); June, 2013 (to add Additional
Analyses, MRTs (most representative trees), and combined results for the 2 eukaryotic analyses, and replace
extended majority (plurality) consensus by majority consensus in Table 14); July, 2013 (to expand Taxonomy- Meaning and Methods); Dec., 2013 (to change Bacteria to multiple kingdoms) 84 pp.
Summary
A phylogenetic classification system of bacteria is presented, based on a cladistic analysis of morphology, chemistry, physiology, and molecular biology for 23 taxons and 263 characters, and is the first comprehensive high level phylogeny of prokaryotes based on classical evidence. The results are in basic agreement with Gupta's protein phylogenies, i.e., Gram positives and Gram negatives are monophyletic, and Mendosicutes (Archeota) are directly related to Gram positives; 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) have 6 kingdoms and the major groups are: Thermosiphia, Fervidobacteria, Thermotogae, Posibacteria, Mendosicutes, and Gracilicutes (Diderma). The major supergroup is Contobacteria comprising Fervidobacteria, Thermotogae, Monodermata, and Gracilicutes. Another analysis was done but for bacteria only, which resulted in the same major monophyletic groups: Monoderma, Posibacteria, Mendosicutes, and Gracilicutes. There are 4 kingdoms (including Heliobacteria in Posibacteria). Also, there is evidence of a symbiotic origin for Gracilicutes. However, Monoderma and Diderma have weak confidence support, which would make 2 kingdoms (Eubacteria and Metabacteria (Archeota)). 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 14 (or 12) 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). Additional analyses were also done on phototrophic bacterial and eukaryotic groups. 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, a key to the kingdoms, and the MRT (most representative tree) (a solution to the problem of multiple MPTs (equally parsimonious trees)). 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 Proteinomuri, Heterotropha, Autotropha, Chemoorganotropha, Chemolithotropha, Scotoautotropha, Rhodophyca, Euglenista, Mycozoa, Neophyta, Apicophyta, Axopoda, Dinociliata, and Chloroplasta.
Resumé
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 c'est à dire, les G+ et G- sont monophylétique. Une analyse cladistique pour les eukaryotes est aussi présentée. Les analyses sont dessinées pour refléter avec plus de précision les relations évolutionnaires. Les prokaryotes (=bactéries) ont 6 règnes, et les groupes principaux sont: Thermosiphia, Fervidobacteria, Thermotogae, Gracilicutes (Diderma), Firmicutes, et Mendosicutes (Métabactéries). Le supergroupe principal est Contophora. Une autre analyse a été faite, mais sans les eukaryotes, qui a donnée les même taxons monophylétiques principaux: Monoderma, Posibacteria, Mendosicutes, et Gracilicutes. Il y a 4 règnes (incluant Héliobacteria dans Posibacteria). Aussi, il y a des preuves que Gracilicutes ont une origine symbiotique. Cependant, les Monodermes et les Didermes ont un faible appuie de confiance, ce qui ferait 2 règnes. 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 la table finale est hypothétisé de contenir 10 règnes, donc 14 (ou 12) 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, une table de totales, un des systèmes de suffixes standardisés, une clé des règnes, une solution au problème des arbres les plus parcimonieux multiples, et un index d'homologie. 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 Proteinomuri, 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
Prokaryotes
Methods and Materials
Results
Discussion
Eukaryotes
Methods and Materials
Results
Discussion
Additional Analyses
Conclusions
Latin Diagnoses
Acknowledgements
A Convenience Classification
References
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 (with the 1st 2 being combined classical-molecular) and contained 9 major groups and is discussed below.
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 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
Gaillon 3
Munchausen 3
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, and the Bacteriological Code and bacteriology include Mendosicutes, so it is far preferable to use the name Eubacteria. Especially egregious and unacceptable is using the name Firmictues only for low G-C Posibacteria (Mollicutes and Endospora) and Choanozoa for protopisthokonts, which are an artificial assemblage to boot. The suffix –zoa for protozoan groups is inappropriate and inaccurate in phylogenetic taxonomies 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 except when there would be an unnecessary increase in redundant or empty ranks. 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
-florae
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
sbtribe -inae
(-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.
tera- (tr)
giga- (gg)
mega- (mg)
grand- (grd
hyper- (hp)
super- (sp)
sub- (sb)
infra- (inf)
parv- (pv)
micro- (mc)
nano- (nn)
pico- (pc)
Taxonomy- Meaning and Methods
As defined in the Penguin Dictionary of Botany, taxonomy is the scientific study of the principles and practices of classification, the study and description of variation in the natural world and subsequent compilation of classifications, and includes systematics, which is the scientific study and description of organisms and the relationships between them, and adds that the 2 words are often used synonymously. Strickberger points out that some authors use the terms "taxonomy," "classification," and "systematics" interchangeably, and that some, like Simpson, consider systematics a much broader field--the study of the diversity of organisms and all their comparative and evolutionary relationships. Simpson defined classification as a subtopic of systematics, as the ordering of organisms into groups, and taxonomy as the study of the principles and practices of classification. The Simpson view, which is lamentably widespread, obviously makes artificial, arbitrary, and illogical distinctions (not surprisingly coming from a gradist) as classification necessarily includes comparative biology, the study of diversity, and both the principles and the practices. The 3 terms, are rightfully treated as synonymous by Webster's 9th New Collegiate Dictionary, which also specifies that "classification" was coined in 1790, "taxonomy" c. 1828, and "systematics" in 1888. Obviously, the 3 are essentially the same thing and the differences, if any, trivial. However, "systematics" might be better used as a synonym for "systems science" as it does not refer specifically to classification but to systems, although it is used specifically to mean systems of classification. Taxonomy, then, is the scientific principles and practices of biological classification (although the word it is sometimes used in some other sciences, e.g., "soil taxonomy") and therefore includes nomenclature, identification, comparative biology, and the study of biodiversity, and is not necessarily evolutionary but usually is in our time.
Phylogenetics, naturally a subset of taxonomy, 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 paraphyletic, which is a type of polyphyly, 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 taxons 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, and it is often not based on any system nor even analysis, yet is touted as “evolutionary”. 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 recognize monophyly, paraphyly (which is continuous or simple polyphyly), and polyphyly (which is discontinuous or complex 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.
Natural 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. McKenna, 1987; Raff et al, 1987; Wyss, Novacek, and McKenna, 1987; Meyer, Cusanovich, & Kamen, 1998; Philippe & Adoutte, 1998; Doolittle, 1999). The only advantage to molecular taxonomy is that the character states are always the same--A, C, G, U.
Gradism is a great example of sophistic argument so it is unscientific, and molecular mania is a great example of considering only part of the evidence (in evaluating the merits of taxonomic methods), so it is unscientific also; one unscientific attitude has been replaced by another.
Cladistics was the 1st phylogenetic method and was originated in 1901 by P. C. Mitchell (for birds)(Schuh, 2000, p.7, citing Nelson and Platnick, 1980; Folinsbee, 2007) and subsequently used by Tillyard (for insects) in 1921 (Tillyard, 1921), and W. Zimmermann (for plants) in 1943 (Schuh, 2000). The word "clade" was introduced by Lucien Cuénot in 1940 (Cladistics-Wikipedia), "cladogenesis" in 1958 (Webster's, loc. cit.), "cladistic" by Cain and Harrison in 1960 (Cladistics-Wikipedia), and "cladistics" in 1966 (Webster's, loc. cit.). The method was formalized by Willi Hennig in 1950 in the classic work Grundzuge einer Theorie der phylogenetischen Systematik, which was translated in '66 as Phylogenetic Systematics. The groundplan divergence method was apparently introduced by Mitchell but formalized by William Wagner in '52 (Folinsbee, 2007).
Cladistics has developed several innovations in 6 major areas (Forey, 1992; Kitching, 1998):
parsimony (optimization) criteria
Camin-Sokal, 1965
Wagner ( Kluge and Farris, 1969; Farris, 1970)
Fitsch, 1971
Dollo (LeQuesne, 1969; Farris, 1977)
generalized, Sankoff and Rousseau, 1975
search strategies
NNI (nearest-neighbour interchange), Robinson, 1971
branch and bound, Hendy and Penny, 1982
SPR (subtree pruning and regrafting), Swofford and Olsen, 1990
TBR (tree bisection and reconnection), Swofford and Olsen, 1990
consensus methods
Adams, 1972
Nelson, 1979
majority, Margush and McMorris, 1980
strict, Sokal and Rohlf, 1980
combinable components(=semi-strict=loose), Bremer, 1990
(Bryant (2003) identifies 4 classes:
based on clade intersection: Adams and Neumann, 1983(and the Neumann extensions: Durschnitt, cardinality, and s-
consensus)
based on splits and clades (strict; majority; median (a complex mathematical formulation of majority consensus), Barthélemy and McMorris, 1986; combinable components; majority extended (also called greedy (Degnan et al, 2009); Nelson-Page (combining Nelson and Page, 1990); and asymmetrical median: Phillips and Warnow, 1996
based on subtrees (local, Kannan, Warnow, and Yooseph, 1998; prune and regraft (same as GAS (greatest agreement subtree), Gordon, 1979; Q*; and R*)
based on recoding: Buneman, 1971; MRP (maximum representation with parsimony), Ragan, 1992; average, Lapointe and Cucumel, 1997)
(there is also reduced consensus, Wilkinson, 1994, 1995 (Wilkinson, 1994, 1995))
group support (confidence) measures
jackknife, Lanyon, 1985
bootstrap, Felsenstein, 1985
Bremer support, 1994
symmetrical resampling, Goloboff et al, 2007
homology measures
CI (consistency index), Kluge and Farris, 1969
RI (retention index), Farris, 1989
RC (rescaled consistency index), Farris, 1989
HER (homoplasy excess ratio), Archie, 1989
DDI (data decisiveness index), Goloboff, 1991
a posteriori character weighting
dynamic, Farris, 1969
successive, Farris, 1969
implied, Goloboff, 1993
algorithm, software packages
PHYLIP, Felsenstein, 1980
PHYSIS, Mikevich and Farris, 1982
PAUP, Swofford
Mesquite, Maddison and Maddison
Hennig86, Farris, 1988
MacClade, Maddison and Maddison, 1986
TNT, Goloboff, Farris, Nixon, 1998
Winclada, Nixon, 1999
The jackknife is a statistical, resampling method used for variance and bias estimation invented by Quenouille in 1949 and extended by Tukey in 1958, who proposed the name as, like a Boy Scout's jackknife, it is a rough and ready tool that can solve a variety of problems (Jackknife (statistics)-Wikipedia). Bootstrapping is another statistical, resampling method. It assigns measures of accuracy to sample estimates that allows estimation of the sampling distribution of almost any statistic using only very simple methods (Bootstrap (statistics)-Wikipedia). It was introduced in 1979 by Bradley Efron and was inspired by the jackknife. A Bayesian extension was developed in 1981, the ABC procedure in 1992, and the BCA procedure in 1996. It is so-called from the phrase "picking oneself up by the bootstraps," meaning it relies on internal data and operations.
Phenetics (from "phenotype") is based on overall similarity, and characteristics are considered of equal value. The modern version is numerical and was introduced by Sokal and Michener in 1958 as a response to the subjective procedures of gradism and uses cluster analysis and the pairwise distance method and the generated tree is called a phenogram. It does not distinguish between ancestral and derived. Its Bible is Numerical Taxonomy by Sokal and Sneath from '63, with the 2nd edition by Sneath and Sokal from '73. The molecular version, although contrary to the defintion or at least the etymology, has the same principles and methodology. Cluster analysis was originated in anthropology by Driver and Kroeber in 1932 and introduced to psychology by Zubin in 1938 and Tryon in 1939 (Bailey, and famously used by Cattell and others for personality typology eventually culminating in the Big 4 (usually seen as the Big 5). Computational complexity made clustering difficult before the advent of computers. Numerical phenetics did, however, pave the way for numerical analysis in molecular taxonomy and cladistics.
Cladistics was once equivalent to phylogenetics, but in recent decades some new methods have rendered the latter as inclusive of, but not limited to, the former. These new methods, used exclusively or almost exclusively in molecular taxonomy, are a technique that uses mostly ME (minimum evolution), which uses a parsimony principle, and probabilism (ML (maximum likelihood) and BI (Bayesian inference). The former is derived from molecular phenetics and uses an optimality criterion and additive trees.
Maximum likelihood is a probability method that, instead of scoring trees with number of steps as is done in cladistics, scores them with probability values. Its equation, which is based on Bayes theorem, invented by the Rev. Thomas Bayes, English cleric and mathematician, in the 1760s (published 2 years after his decease), goes:
posterior odds ratio = likelihood ratio x prior odds ratio
The 1st attempt to use ML for taxonomy was by Edwards and Cavalli-Sforza in 1963. Farris and Felsenstein, both in '73, published ML algorithms for phylogeny but they had limited applications because of computational problems. The 1st successful application of ML to taxonomy (for nucleotide sequences) was by Neyman in 1974. The 1st computationally efficient ML algorithm for phylogeny was introduced by Felsenstein in '81. (Folinsbee, 2007).
Bayesian inference is a method that grew out of ML. It attempts to calculate a different portion--the posterior portion--and assigns a value to the prior odds ratio. A major problem for it was that the priors, probability of data, and probability of hypothesis have to be specified. This was solved by the Markov chain-Monte Carlo (MCMC) simulation, which scans the tree space (the set of all possible trees) and parameter space. The 1st working methods in BI were independently developed by Li, Mau, and Rannalla and Yang in '96, all using MCMC, so it is the new kid on the block. (Folinsbee, 2007).
An advantage of probabilism is that, given the accuracy of a particular tree, a variety of evolutionary models can be tested within a statistical framework. A disadvantage is that a particular evolutionary model has to be decided on prior to the analysis.
The 1st algorithmic, software application in cladistics was by Camin and Sokal in '65, but it was unwieldy for large data sets and never effectively programmed (Folinsbee, 2007).
The following summarizes the characteristics of the various methods.
pars. polarity mnphyly data set optimality stat. tree tree type
criterion score
cladistics + + + + + + + A
clique analysis - ? + + + + + A
probabilism - ? + + + + + A
ME + ? ? + + + + A
molecular phenetics - - - + - + - U
standard phenetics - - - + - + - U
traditional phenetics - - - - - - - -
synthetics - + - - - - - -
natural utilitarian - - - - - - - -
monothetic - - - - - - - -
special purpose - - - - - - - -
chrct.-based pairwise distance overall similarity chrcts. of equal value
cladistics + - - -
clique analysis + - - -
probabilism + - ? -
ME - + ? -
molecular phenetics - + + +
standard phenetics + + + +
traditional phenetics + - + +
synthetics + - + -
natural utilitarian + - - -
monothetic + - - -
special purpose - - - -
A=additive, U=ultrametric
The following is a classification of classification:
phylogenetics (based on evolution, numerical)
cladistics (starts in 1901)
probabilism
ML (starts in '63)
BI (starts in '96)
clique analysis (character compatability) (starts in '65)
ME (starts in 1971)
phenetics
numerical phenetics (based on overall similarity and equal-value traits
molecular phenetics (claims to be evolutionary)
standard phenetics (does not claim to be evolutionary)(begins in '57)
traditional phenetics (starts with Adanson in 1763)
gradism (recognizes polarity and evolution but accepts grades)(starts in 1800s, especially with Haeckel)
natural utilitarian (use of many traits)( in modern times starts with Cesalpino, Bauhin, and Ray in 1500s and 1600s)
monothetic utilitarian (single trait, e.g. habit (Theophrastus), sexuality (Linneus)
special purpose-utilitarian (for a specific purpose such as medicinal or culinary uses)
Prokaryotes
1st Analysis
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.
Results
The majority consensus tree with the synapomorphies is given in Table 3, 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, Posibacteria, Firmicutes, Neosoma, Metasoma, Cenosoma, Parkaryota, Gracilicutes, Protogracilicutes, Metagracilicutes, and Neogracilicutes appear in all 8 trees.
As a consensus may not be as parsimonious as the MPTs (or is always less parsimonious (Lipscomb, Basics of Cladistic Analysis-gwu.edu)) a representational method should be used, whereby the most representative MPT (MRT), that is, the one with the closest fit with the majority consensus, is selected. However, there may not always be a single MRT, in which case the majority consensus would have to be used. In this analysis there were 2 MRTs.
Discussion
The phylogeny basically is in accordance with that of McMaster's Radhey Gupta (1998a,b, 2000), who uses conserved signature sequences of proteins. It agrees on 4 fundamental points: the monophyly of Gram-s, Gram+s, and Monoderma, and the position of Metabacteria (however, both Monoderma and Diderma have weak resampling support; see 2nd analysis). 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. It disagrees principally in being branching instead of linear and in having Metabacteria as monophyletic (without Eukaryota). Gupta (1998a, pp. 16-17) points out that most eubacterial taxonomies based on rRNA do not give any confidence measures and the few that do have most of the critical nodes at values in the range of 25-50%, which means they are not reliable, and that Woese himself acknowledges the lack of resolution of branching order. It should be added that even in later molecular taxonomies for bacteria the CI and RI are rarely given. The Gupta result in which Metabacteria arose from various subgroups of G+s (some methanogens and some thermoacidophiles from Clostridia and halophiles from Actinobacteria) is not supported by the phenotypic evidence. Metabacteria as directly related to Posibacteria is supported also by Skophammer et al (2007) and Valas and Bourne (2011). Lorraine Olendzenski et al (2000) also say G+ genes transfered laterally to Metabacteria. Cheryl Andam, David Williams, and J. Peter Gogarten say the same thing and specifically, "Acetoclastic methanogens in Methanosarcina, which today generates about 60% of the biogenic methane, became possible when the genes that encode enzymes to convert acetate to acetyl-S coenzyme A were acquired through HGT from cellulolytic Clostridia (Fournier and Gogarten, 2008)." But they also state, "Horizontal gene acquistion is not a random process--more transfers occur between more closely related organisms than between divergent ones. This preference of exchange partners consequently reinforces the identity of higher taxonomic groups." (Andam et al, 2010, p. 590-91 and 596).
Gupta (2000) explains the double membrane of Gracilicutes as evolution by normal mechanisms in response to the strong selection pressure exerted by antibiotics produced by certain groups of Gram-positives. However, astounding new information suggests something very different. Analyzing the flows of protein families, the Lake Lab (2009) has obtained evidence that Gram-negatives were formed as the result of a symbiosis between an ancient actinobacterium and an ancient clostridium! As Lake points out, the resulting taxon has been extraordinarily successful and has profoundly altered the evolution of life by providing endosymbiotes necessary for the emergence of eukaryotes and generating Earth's oxygen atmosphere, that their double-membrane architecture and the observed genome flows into them suggest a common evolutionary mechanism for their origin. If this endosymbiosis is true we would have to classify Gracilicutes separately as we do with Eukaryota and there would be 3 subempires -- Monoderma, Diderma, and Eukaryota -- and analyses would have to be done separately for each. I have done just such an analysis (see Bacteria-Page 3). Monoderma would comprise 2-5 kingdoms depending on the monophyly or polyphyly of Togabacteria, which might comprise 2 or 3 independent lineages, and its position, as it might belong in Posibacteria as opposed to being its sister group, or Monoderma might even be only 1 kingdom if Gupta's interpretation is right. But Gupta (2011) states the Lake proposal is based on a number of false assumptions and the data presented in its support are also of questionable nature, so he claims there is no reliable evidence to back up the endosymbiotic origin of double-membrane bacteria.
In any case, LGT, also called HGT, is highly exaggereated as maintained by the Swedish team of Kurland, Canbeck, and Berg (2003) at the U. of Uppsala, who state that rampant global LGT was significant only in the progenote population, and that, although LGT is an important evolutionary force, in modern organisms both its range and frequencies are constrained most often by selective barriers, and as a consequence those LGT events that do occur most often have little influence on genome phylogeny, and classical Darwinian lineages are the dominant mode of evolution. They point out that an estimate of frequencies of events such as gene loss, gene duplication, novel sequence genesis, and LGT in the cohort of fully sequenced genomes done by Snel and colleagues found less than 15% of such phylogenetically troublesome events as ascribable to HGT in eubacterial and metabacterial genomes. An explicit estimate of the influences of biased and variable mutation rates was not presented in the study, so even this modest estimate is likely to be inflated. They also underline that anomalous phylogenetic reconstructions may be generated, as well , by improper clade selection, which often means examining too few clades or relying on inadequate phylogenetic methods. The contribution of LGT has been estimated to vary between 0% and 17% with a mean of 6% in eubacterial genomes.
Recently, the 1000s of coding sequences found in 5 taxons of photosynthetic bacteria were reduced to a set of 188 orthologous lineages by Raymond et al that could not be resolved into a single tree. Kurland et al point out that from this failure alone it was concluded that HGT was responsible for the phylogenetic ambiguity of the selected data set, yet there was a complete absence of any direct indication of HGT. No attempts were made to identify the impact of segregating paralogs, gene loss, extreme mutation rates, nor biased mutation rates on the reconstructions of this subset of orthologs.
In their review of the HGT data, Gogarten and colleagues present a selected cohort of 30 instances of putative gene transfer. This list is used to support the notion that the genomes of bacteria that share a common environment may be mosaics created by the rampant exchange of sequence domains from both rRNA and proteins. Kurland and colleagues note that even if each of these had been rigorously identified as examples of HGT, the list is far too short to justify the conclusion that HGT is rampant and that these examples were culled from nearly as many genomes, which means that they represent a minute fraction of the many 1000s of proteins encoded by those genomes, so their impact on genome phylogeny would be correspondingly minute.
Four 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 4 molecular taxonomies (see Page 3), but usually Togabacteria 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 (signal recognition particle), and absence of LPS (lipopolysaccharide) 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 Proteinomuri (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, and 111, 188, and 191 are empty characters so should be excluded, too. These, however, have little or no effect on the outcome except perhaps for 127. Also, Heliobacteria was incorrectly coded as Gram- and probably 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 be due to reticulate evolution. But, if Eukaryota is factored in, as in my analysis, 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 (as in the 2nd analysis). Metabacteria or Crenarcheota are sister group to Eukaryota in the molecular taxonomies of Gogarten et al (1989) and Iwabe et al (1989), Brown et al (2001), Battistuzzi, Feijao, and Hedges (2004), Ciccarelli et al (2006), and Pisani et al (2007).
Whether eukaryotes evolved through a fusion event, that is, a fusion between an archeobacterium 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 fusion theory was first proposed by Wolfram Zillig and colleagues (1989) and is also proposed by Maria Rivera and James Lake (2004) as the ring of life model and a Crenarcheota-Alphaprotei symbiosis.
The endosymbiotic origin for eukaryotes is generally accepted, but there is no consensus on details, and over 20 such theories have been put forward, the most prominent ones, besides the fusion theory, being the serial endosymbiosis of Lynn Margulis (1996) in which there are the Thermoplasma-Spirochetes symbiosis providing flagella, the symbiosis with an alpha-proteobacterium providing mitochondria, and finally the symbiosis for chloroplasts, with sulfur metabolism being incorporated into the theory by Margulis et al (2000); the Thermoplasma-(S-dependent) Alphaprotei syntrophy by Searcy and Hixon (1991), going back to Searcy and colleagues in 1978; the Methanobacteria-(sulfur-reducing) Deltaprotei syntrophy by Lopez-Garcia and Moreira (2006); and the Methanobacteria-Alphaprotei hydrogen origin by Martin and Muller (1998). In Searcy and Hixon and Martin and Muller, the origin of eukaryotes concurrs with the origin of mitochondria. So there are 3 main types of theories: the SET, the syntrophic, and the hydrogen, although the later version of SET is also a syntrophy and perhaps also a fusion theory.
A major difference between the Lopez-Garcia and Moreira model and other chimeric models is that a selective force for the origin of the nucleus is advanced: metabolic compartmentalization. In this, the nucleus originated not to isolate the genetic material from the cytoplasm, as is generally believed, but to allow the coexistence of 2 interdependent metabolic pathways in the protoeukaryotic cell; the cytoskeleton and other eukaryotic properties are products of symbiotic innovation; and the primary symbiosis leading to eukaryotes took place in microbial communities thriving in the widespread anaerobic environments that characterized the Archeozoic.
However, Kurland and colleagues (loc. cit.) point out that another systematic source of inflated HGT estimates has come from the uncritical use of BLAST (Basic Local Alignment Search Tool) to identify the most similar homologs in pairwise comparisons of eubacterial, metabacterial, and eukaryotic sequences. The most closely related pairs in the different domains are identified then as members of orthologous lineages. For example, in this protocol a protein from the genome of a eukaryote found to be most similar to a protein from a eubacterium is identified as a eubacterial gene that has been transferred horizontally, so in this way eukaryotic proteins could be classified as more closely related to bacterial homologs. It was found that eukaryotic operational genes (those involved in intermediary metabolism) often were related more closely to eubacterial homologs, whereas those with informational functions (transcription, translation, and related processes) (which transfer much more often than the former; the complexity hypothesis (based on the fact that informational processes are more complex) has been put forward by Jain, Rivera, and Lake (1999) to explain this) were identified more closely with metabacterial sequences, which gave rise to the fusion theory. In contrast, phylogeny by more demanding methods casts doubt on such simplistic interpretations of the best-match searches for alien sequences. BLAST does not distinguish the different phylogenetic anomalies from genuine HGT events, so they maintain that there are no indications in global phylogenetic reconstructions of these intermediary metabolism enzymes suggesting that they were transfered from eubacteria to eukaryotes.
Jin and colleagues (Inferring Phylogenetic Networks by the Maximum Parsimony Criterion: a Case Study, on-line) make the same point--even advanced approaches, such as whole-genome sequencing, are sensitive to differential selection pressures, uneven evolutionary rates, and biased sampling, which can all give rise to false identification of HGT events.
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 endosymbiosis 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 eukaryotic ribosome could be primitive, 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.
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, Wallin proposing it for chloroplasts in 1926, 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 reasons (see for example Strickberger, 1996, and Lecture 21 in the Teaching Company's Origins of Life course).
Two 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. 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 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 Thaumarcheota, Crenarchaeota, and Korarcheota, as well as the recently proposed phylum Aigarcheota (Guy and Ettema, 2011).
2nd Analysis
Methods and Materials
14 new traits were added and 30 were deactivated because they were autopomorphies, repititions, null characters, or errors, making a total of 261. All the characters were ordered and the root was Togabacteria. The computer calculation phase was done by Dr. James Carpenter. A TNT (Tree analysis using New Technology) program, Wagner parsimony, and TBR (Tree Bisection and Reconsrtuction) branch swapping (a heurisric method and variant of SPR) with c. 15 mln. rearrangements were used. Random seed was set at 1 and no constraints were used. All 4 algorithms were used: ratchet, sectorial search, tree-drifting, and tree-fusing (Goloboff, 1999; Nixon, 1999).
Results
There were 347 steps, 64 MPTs, and the CI was .58 and the RI .67. The majority consensus is given in Table 4 as are the list of taxons, and the characters added and deactivated. There were 4 MRTs.
As with the 1st analysis, Monoderma, Posibacteria, Mendosicutes, and Gracilicutes are monophyletic, and Gracilicutes is advanced in the strict consensus and primitive in the majority consensus. Different are the position of Heliobacteria and the internal arrangment for Gracilicutes, Posibacteria, and Metabacteria. Heliobacteria was sister group to the rest of Deuterobacteria in half the MPTs and in the other half, sister group to Gracilicutes. In half the MPTs Mollicutes was the sister group to Endospora + Actinobacteria, as in the last analysis, but in the other half Actinobacteria was sister group to Mollicutes+Endospora. The Chromobacteria clade was in 60 (94%) of the MPTs, Proteinomura was in 52 (81%), With the majority consensus set at 51% there would be a Mureinomura (in 40 MPTs (63%))(as sister group to Proteinomura)(in 40 MPTs (63%) and a Eugracilicutes (in 33 MPTs (51%))(as sister group to Thermales). Archeoglobi was sister group to Methanobacteria + Crenobacteria in half the trees, while in the other half it was sister group to Methanobacteria. Metachromobacteria, Neochromobacteria, and Cenochromobacteria are defined by homoplasies.
Discussion
Contrary to the 1st analysis, I included a monophyletic Togabacteria as it has 10 or 12 genera which would be too cumbersome to include separately, it does have a synapomorphy or 2, and is monophyletic in molecular taxonomies. It might still be polyphyletic, however. Also, I separated Chlorobia and Saprospirae from what was otherwise (except for the exclusion of Rickettsiae) Proteobacteria. And, of course, I excluded Eukaryota. Korarcheota, Thaumarcheota, Nanarcheota, and Aigarcheota were again excluded due to lack of information.
The uncertain position of Heliobacteria is probably because it is photosynthetic yet is likely a Gram +, which might lend support to the probable symbiotic nature of Gracilicutes. Its position as ancestor to Gracilicutes or to Deuterobacteria indicates its primitive nature as in the results of Gupta's analysis of phototrophic bacteria (Gupta, 2003), and as it is possibly a Posibacteria group, a primitive nature for Posibacteria is also suggested as maintained by Gupta, a nature it would have if Gracilicutes arose from the symbiosis of 2 firmicutes. Also, the primitive nature of Chloroflexi among Gram negative phototrophic groups corroborates most molecular analyses. A surprise was the relatively low position of Acidobacteria, which shows up close to Proteobacteria in molecular analyses and has phenotypic similarities with it. There is no surprise in the low placement of Aquificae and Spirochetes. And as in the 1st analysis, Thermales and Deinobacteria do not form a clade and Rickettsiae does not turn up close to Proteobacteria.
Halobacteria has the most primitive ribosomal structure in Metabacteria (it has only the bill) and this shows up in this analysis, in which I coded Archeoglobi and Thermoplasmata as having the same ribosomal structure as Methanobacteria and Sulfobacteria, respectively, contrary to the previous analysis in which I coded them as unknown for this characteristic, as I was never able to find any data on ribosomal structure for Archeoglobi nor Thermoplasmata. Archeoglobi as sister group to Methanobacteria in half the MPTs agrees with molecular phylogenies, which place both in Euryarcheota.
For this analysis a resampling group support measure was done. Such group support is the result of interaction between characteristics that favour the group and those that contradict it. This particular method is symmetrical resampling, which is a combination of bootstrapping and jacknifing, devised by Pablo Goloboff et al (2003). When the characters have different prior weights or some different state transformation costs, the frequencies under either bootstrapping or jackknifing can be distorted, producing either under- or overestimations of the actual group support. The method avoids the problem as the probability p of increasing the weight of a character equals the probability of decreasing it. Stability, which can be considered as a measure of support, relies on certain factors such as the addition or recoding of characters and the addition of taxons--if a taxon maintains itself across these factors then it is stable. Out of 1000 replicates the following 5 had a support value of over 50.
Deuterobacteria 100
Metabacteria 100
Crenobacteria 72
Posibacteria 67
Anabacteria 52
So there is strong support for the 1st 2, moderate support for Crenobacteria and Posibacteria, and weak support for Anabacteria and the other 7, which were Cenochromobacteria (31), Firmicutes (19), Monodermata (18), Methanobacteria+Crenobacteria (13), Proteinomuri (7), Gracilicutes (5), and Proteobacteria+Saprospirae (2). However, other measures (which might be equally valid) must be considered: the number of MPTs the group appears in, the measure of homology, which can be calculated for nodes, and stability. Also, missing data can cause low estimates in resampling measures. Proteinomuri has a solid synapomorphy, is stable, as it appears in both analyses, and occurs in most molecular phylogenies. Gracilicutes, Monoderma, and Posibacteria have 7, a good dozen, and 5 synapomorphies, respectively, and have stability and are corroborated by Gupta's phylogenies as already mentioned, and Gracilicutes is corroborated by Lake. Deuterobacteria (equivalent to Metaerobia with Eukaryota removed) is recovered also in Woese, Battistuzzi and Hedges, and Yarza et al (see Page 3). It is true, though, that some molecular results do not recover Proteinomura and most do not recover Gracilicutes nor Monoderma and the values for Gracilicutes and Proteinomura are so low they may not be due to missing data.
The disagreement of these results especially for Gracilicutes with the previous analysis and with molecular taxonomies, and the discordance within the latter, highlight the lack of resolution in the internal taxonomy of Gram negatives.
Table 3. Empire Biota - Majority Consensus (set at 75%)
Thermosiphia
Aerobia
Thermotoga
Fervidobacteria
Metaerobia
Gracilicutes
Protogracilicutes
Thermus
Metagracilicutes
Spirochetes
Neogracilicutes
Proteinomuri (Chlamydiae +Planctobacteria)
Rickettsiae+Cyanobacteria+Chloroxybacteria
Cenogracilicutes
Chloroflexi+Heliobacteria
Thiobacteria+Deinobacteria
Monoderma
Posibacteria
Mollicutes
Firmicutes
Endospora
Actinobacteria
Neosoma
Archeoglobus
Metasoma
Thermoplasma
Cenosoma
Halobacteria
Methanobacteria
Parkaryota
Sulfobacteria
Eukaryota
Synapomorphies
Aerobia: large STK, loss of long chain diabolic acids, aerobism, loss of hyperthermophily, catalase
Monoderma: non-formylated methionine, glutaminyl synthase tRNA glutamine transamidation, tRNA mischarging, proteasoman alpha-amylase primary structure, proteasoman serine protease 3D structure, tyrosine kinases, serine/threonine kinases, type 1 fatty acid synthase, Ku with HEH domain, calmodulin homologs, chitin
Posibacteria: DOXY pathway; foliate derivative as RNA methionine methyl donour; actinomycin, novobiocin, and penicillin sensitivity, DNAP uracil, loss of DNAP exonuclease function
Firmicutes: 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. 2nd Analysis-Prokaryotes Only-Majority Consensus (set at 75%)(in parentheses are the number of trees the clade appeared in; kingdoms in bold).
infemp./kgdm. Togabacteria Cavalier-Smith 1992, orthog. emend. stat. nov.
infemp. Deuterobacteria tax nov. (64)
pvemp./kgdm. Heliobacteria stat. nov.
pvemp./kgdm. Gracilicutes Gibbons & Murray 1978 (Negibacteria Cavalier-Smith 1987, Didermata Gupta 1998) (64)
mcemp. Thermales stat. nov.
mcemp. Spirochetes (Spirochetae Ehrenberg 1855) stat. nov.
mcemp. Acidobacteria Cavalier-Smith 2002 stat. nov.
mcemp. Metagracilicutes tax. nov. (60)
mgph. Rickettsiae stat. nov.
mgph. Neogracilicutes tax. nov. (60)
grdph. Aquificae Reysenbach 2002 stat. nov.
grdph. Chromobacteria tax. nov. (60)
hpph. Chloroflexi stat. nov.
hpph. Metachromobacteria tax. nov. (60)
spph. Neochromobacteria tax. nov. (64)
Deinobacteria Cavalier-Smith 1986
Saprospirae (Bacteroidetes)
Proteobacteria Mohn 1984 emend.
spph. Cenochromobacteria tax. nov. (64)
Chlorobia
Cyanobacteria
mcemp. Proteinomuri stat. nov. (52)
Chlamydiae
Planctobacteria Cavalier-Smith 1998
pvemp. Monodermata Gupta 1998 (Unibacteria Cavalier-Smith 1998) stat. nov. (64)
kgdm. Posibacteria Cavalier-Smith 1987 (Teichobacteria 1992) (64)
Mollicutes (Tenericutes Gibbons & Murray 1978)
Actinobacteria Margulis 1974
Endospora Margulis and Schwartz 1988
kgdm. 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 methanogens) (64)
hpph. Halobacteria stat. nov.
hpph. Anabacteria tax. nov. (64)
spph. Archeoglobi
spph. Methanobacteria
spph. Crenobacteria Woese, Kandler, and Wheelis 1990 (Caldaria Mohn 1984, Eocyta
Lake 1984) (64)
Thermoplasmata
Sulfobacteria Cavalier-Smith 1986
Table 5.
Majority Consensus (set at 75%)(in parentheses are the number of trees the clade appeared in) Across the 2 Bacterial
Analyses (in parentheses are the percentages).
Deuterobacteria (100)
Heliobacteria
Gracilicutes (100)
Thermus/Thermales
Spirochetes
Rickettsiae
Proteinomuri (91)
Chloroflexi
Cyanobacteria
Deinobacteria
Monoderma (100)
Posibacteria (100)
Mollicutes
Endospora
Actinobacteria
Metabacteria (100)
Archeoglobus/Archeoglobi
Thermoplasma/Thermoplasmata
Halobacteria
Methanobacteria
Sulfobacteria
List of Taxons
0 Togabacteria, 1 Thermales, 2 Deinobacteria, 3 Rickettsiae, 4 Chlamydiae, 5 Planctobacteria, 6 Spirochetes, 7 Chloroflexi, 8 Aquificae, 9 Saprospirae, 10 Chlorobia, 11 Acidobacteria, 12 Proteobacteria, 13 Cyanobacteria, 14 Heliobacteria, 15 Mollicutes, 16 Endospora, 17 Actinobacteria, 18 Archeoglobus, 19 Thermoplasmata, 20 Halobacteria, 21 Methanobacteria, 22 Sulfobacteria
Added Characters
263. reaction center type 0 PS1 1 PS2
264. reaction center and antenna proteins 0 1 1 multiple
265. reaction center and antenna dimers 0 homodimer 1 heterodimer
266. carotenoids
267. chlorophylls 0 bchl a 0 bchl b 0 bchl g 0 chl a and b 1 c 1 d 1 e
268. 0 bchl a 0 bchl b 0 bchl g 0 chl a and b 0 c 1 d 1 e
269. 0 bchl a 0 bchl b 0 bchl g 0 chl a and b 0 c 0 d 1 e
270. 0 bchl a 0 bchl c 0 bchl d 0 e 1 bchl b 1 bchl g 1 chl a and b
271. 0 bchl a 0 bchl c 0 bchl d 0 e 0 bchl b 1 bchl g 1 chl a and b
272. 0 bchl a 0 bchl c 0 bchl d 0 e 0 bchl b 0 bchl g 1 chl a and b
273. oxidase
274. dissimilatory iron reduction
275. C DNA polymerases 0 Class I 1 Class II 2 Class III
276. H degradation
Deactivated Characters
5, 24-28, 40, 85-87, 111, 123-129, 140, 145, 154, 169, 191, 235, 249, 257
Synapomorphies
Deuterobacteria: large STK, aerobism, catalase, loss of long chain diabolic acids, loss of hyperthermophily
Firmicutes: DNAP uracil, DNAP exonuclease function, LL-DAP acid, teichoic acids, peptide bridge for A with dicarb
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, (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 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.
Gracilicutes: large citrate synthase, flagellar ring, outer membrane, LPS, invagination, large succinate thiokinase, NADH resistance
Eugracilicutes: thin cell wall, cell wall with DAP acid
Chromobacteria: photosynthesis, autotrophy, carotenoids, sporulation, hydrocarbon degradation, aa3 cytochrome
Anabacteria: ribosome with bill, gap, lobe, and platform split.
Table 6. - List of Taxons for Data Matrix-1st Analysis.
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 Endospora, 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+Eukaryota
all of the states are 0 absent and 1 present except where otherwise indicated; in TNT the taxons are numbered starting with 0
morphology
flagella
0. proterokonty
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
13. capsule
14. fimbrias
15. toga
16. prosthecas
17. sheathed filaments
18. carboxysomes
chemistry
cell wall
19. peptidoglycan 0 pep 1 psdpep 2 -
20. heteropolysaccharides
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
35. KDO (ketodeoxyoctanate)
36. LPS
37. cell wall with glycoprotein hexagonal array
storage products
38. type 0 PHB 1 a-1-4 amino acids
39. LSP 0 with DAP acid 1 with AAA acid
40. glutamine I type
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)
50. proteasomes
51. protein secretion mech. 0 post-translational 1 co-translational
52. protein secretion chaperone 0 SecA 1 SecB
enzymes
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 (succinate thiokinase) size 0 small 1 large
59. catalase
60. tyrosine kinases
61. oligosaccharyl transferases
62. split glutamate synthase
63. FDP (fructose diphosphate) 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 alpha-carotene 0 A 0 M 0 beta-gamma-car. 1 H
73. 0 A 0 M 0 beta-gamma-car. 0 H 1 a-car.
74. 0 a-car. 0 M 0 beta-gamma-car. 0 H 1 A
75. 0 a-car. 0 beta-gamma-car. 0 H 0 A 1 M
76. 0 a-car. 0 M 0 H 0 A 1 beta-gamma-car.
77. quinones
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
81. sphingolipids
82. sulfonolipids
83. archeol
84. caldarcheol
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
91. waxes
92. PI
93. PIM
94. lipid formation pathway 0 malonate 1 mevalonate
95. DOXY pathway
general
96. cellulose accumulation
97. chitin
98. glycosylation 0 O 1 N
99. S deposition 0 ext 1 int
100. DPA
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
111.
112. sulfur compound oxidation
113. sulfate reduction
114. iron oxidation
115. CO oxidation
116. hydrogen oxidation
117. nitrate reduction
118. methanogenesis
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
130. phycobilins
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 (aminolevulinate) 0 glycine succinyl Co A 1 L-glutamate
reproduction
137. cell division 0 with septum 1 without septum
138. sporulation
139. sporulation position 0 internal 1 external
140. myxospores
141. budding movement
142. motility
143. gliding
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
180. H
181. G
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
188.
189. 1-methylpseudouridine 0 + 1 -
190. N, N -dimethylguanosine
191.
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
203. histones
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
212. rifampicin
213. streptolydigin
214. actinomycin D
215. novobiocin
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
EF-targeted antibios
224. kirromycin
225. pulvomycin
226. fusidic acid
227. penicillins 0 lo 1 hi
miscellaneous
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
addenda
235. flagella 0 external 1 internal
236. gas vacuoles
237. rosettes
238. mycelia
239. wall peptidoglycan with LL-DAP acid
240. wall peptidoglycan with L- and D-lysine
241. wall peptidoglycan with arabose-galactose
242. calmodulin
243. oligosaccaryl transferases
244. proton pumping H-ATPase catalytic subunit insertion 0 F 1 V
245. rhodopsin
246. C40-biphytanyl diol chains 0 acyclic 1 mono and bicyclic 2 tri and tetracyclic
247. S oxidation
248. hyperacidophily
249. corkscrew motion
250. EF-5A
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 -
256. plasmologens
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
0Thermosipho
0------00100000100000000????????000-00?00-----000000000?00000000000000-0-----0---000000000100000000-0000-00000--0000000000---------------00-0010-00000000000000000000000000000000-0-000000000000000000000000000000?00000000000000000000001000000100000-000000000 000-000
1Rickettsiae
???????001000010000000000000-110001010001[01][01][01][01][01]00000000??????0000000000-10000[01]1000[01]00010000000000000-0001100010?-0000000010---------------00-0010-00000000000000000000000000000000-0-000000000000000000000000000000?000000000000000000000010?0000000000-000000000010-010
2Chlamydiae
0------0010000000000010------------010?01-[01][01]0[01]00000000?????00000000000-0000000---000010000000001000-0001000010?-0000000010---------------00-0010-00000000000000000000000000000000-0-0000000000 000000000000000000000000000000000000000000000-000-000000-0000 00000010-010
3Planctobacteria
???????0010000000000010-------------10?01?0?0[01]00000000??????0000000000-0000000---000010000000001000-0001100010?-0000000000---------------00-011[01]-00000000000000000000000000000000-0-0000000000 00000000000000000000?00000000000000000000001000[01]0-000000-0 00000000010-010
4Spirochetes
1---100001011000000000000000-1[01]0001010?01?0[01]0[01]00000000?????00000000000-00000[01]0---000010000000000000-0001[01]000101-0000000100---------------00-0010-00000000000000000000000000000000-0-000000000000000000000000000000100000000000000000000001010000000000-000000000[01]10-010
5Chloroflexa
0----0 -?000 00000000000000000-100001000-01?????00000000?????000 00000000-000[01]0[01]1000000010000000001000-00010010[12]0?0000000000100[01][01]00--000000000-00[01]1000000000000000000000000000000000-0-00000000000000000000000000000010000000000000000000 00010-0000000000-000000000010-010
6Thiobacteria
[01][01]0[01]1[01]0[01][01][01]0[01][01][01][01]0[01][01]0000000000[01]100[01]1[01]10[01]0[01][01][01][01][01][01]00000000[01][01][01]11[01]0000000000-[01][01]0[01]0[01][01][01][01]0[01][01]00100000[01]000[01][01]001000 [01][01][01][01][01][12][01][01][12][01][01][01][01][01][01]000[01]0[01][01][01][01]0--0[01][01][01]0[01][01]0[01]1[01][01][01][01][01][01]0000000000000000000000000000000-0-00000000000000000[01]000000000000[012]0000000000000000000000[01]00[01][01]00000000-0000[01]0000[01]10-01 [01]
7Cyanobacteria
0------?????1000010000000000-111001010[01]01?000000000000????110000000000-[12]00[01][01][01]1[01]000[01]0010110000001000-0001111110[01]2000[01]0000011-----0012021210[01]100[01][01]100000000000000 000000000000000000-0-000000000000000000000000000000[02]000000000000000000000010-1000000000-000000000010-010
8Chloroxybacteria
0------?????0000000000000000-110001010?01????000000000?????00000000000-000[01]0[01]1000000010000000000000-0001100010?200000000011-----100?0212?00-00?0-00000000000000000000000000000000-0-0 00000000000000000000000000000?000000000000000000000010-0000 000000-000000000010-010
9Thermus
0------001000000000000000000-100001100?01??[01]0[01]000000000???100000000000-0000000---000010000000000000-00011000001-0000010000---------------00-0010-00000000000000000000000000000000-0-000000 000000000000000000000000?00000100000000000000001000000000000-000000000011-010
10Deinobacteria
0------00[01]000000000000000000-100001000?01?[01][01]0[01]00000000?????10000000000-0000000---000010000000001000-0001100011?-00000[01]0000--------------00-0010-00000000000000000000000000000000-0-00 000000000000 000[01]000000000000?0000000000000000000000100000 0000000-000000000010-000
11Heliobacteria
[01]1--1-0001000000000000000000-100001000?00?????00000000?????00000000000-0?????0---000010000000001000-1001001010??0000000001001101--0??10??00-001[01]-00000000000000000000000000000000-0-0 00000000000000000000000000000?0000000000000000000000100000 0000000-000000000010-000
12Clostridia
11--0 -000[01]0000000000000000[01]0-[01][01]1100--0?01[01][01][01]000 00000000-???[01]0000100000-0-----11000000100[01]0000001100-100[01][01]101[02]0020[01]0[01][01][01]0100---------------0100010-0000000000000 0000000000000000000-0-00000000000000000010001000000000001100 0000000001000001000001000000-0000[01][01]000[01]00-00[02]
13Mollicutes
0------ 00[01]0[01]0000000-----------------00?01-----000000000-???00000000 000-0-----0000000000000000001000-0001[01]000101-0000000000---------------00-0[01][01][01]000000000000000000000000000000000-0-0000000 10000000000100010000000000011000000000001000000-00000000000-00000[01]000000-000
14Actinobacteria
[01]1--0-0[01]0[01][01][01]00000000000[01][01][01][01]0[01][01][01]11[01]0-00101[01][01][01]0[01]0000[01][01]00[01]?001[01][01]000[01][01]0000-[02][01]100[01]11000000[01][01]0[01][01]0[01][01][01]010[01]0-[01]00[01] [01]000[12]01-00000[01]0000---------------0[01]100[01]0-00000000000000000000000000000000-0-00000001000000000010[01]0100[01]00002000 [01][01]0000000000010000010000[01][01]0[01][01]000-0000[01]0000[01]0 0-000
15Fervidobacterium
1???0-000100000000000000????????000-00?00-----000000000?00000000000000-0-----0---000000000100000000-0000-00000--000000 0000------- --------00-0010-00000000000000000000000000000000-0-0000000000000 00000000000000000?00000000000000000000001000000100000-000000 000001-000
16Thermotoga
1[01]?00-000100000100000000????????000-00?00-----000000000?0000 0000000000-0-----0---000000000100000000-0 000-0 0000--0000000000----- ----------00-0010-00000000000000000000000000000000-0-000000000000 000000000000000000?00000000000000000000001000000100000-00000 0000000-000
17Halobacteria
100?0-100[01]0000100002[01]11-----------0--1?00[01][01][01][01]0111111110???1?0111?0?001000000[01]1100000000000000010001-0101[01]01020?30000000000---------------00-0010-010000[01]101110111111110110111 1111110011100110111111110101100001111?111001110211011002100 1100000---0111-0001001110000002
18Archeoglobus
????0-?000000000000?0??-----------0--1?00?????111???????????0???? 0?111?0000000---001100000000010001-01110[01]0000?-0100001000----- ----------00-0010-02101???0???0????????01101111111110????????00? ??00?00?0110000????????00???0???????0?000??00000---0??0?000?0 00?00000000
19Methanobacteria
[01]0??0-000[01][01][01]00100001[01]11-----------0--1?00?????11111111??????0111?0?111[01]0000000---001100000000010001-0111010120?30000001000---------------00-0010-02[01]0[01]00[01]1???01111[01][01]110110 111111111011110011001111?110101102001111?1110011101001110021001[01]00000---01100000100011000010[01]
20Thermplasma
????0-?000000000000---0-----------0--1?00?????111???????????0????0100110000000---001100000000010001-0111[01]00010?-0000000000------ ---------00-0010-021010111???0????????01101111111111111101?100?? ?00100?0110200??????1100?010111111100?00?010000---0??0[01]110? 000?00001000
21Sulfobacteria
[01]0010-000[01]0000000012011-----------0--1?10?????11211111??????0111?0?00110000001100001100000000010001-0111[01]10000?-0000000000---------------10-0010-021011111???1????1?111111111111111111111 111101111111011110210111111110011102112111021111010000---0110 [12]1101000110002100
22Eukaryota
0------ [01][01][01]0[01]000000120[01][01]-----------0--011?[01][01][01][01]0-0111110?????-1110?12000-[12] 0[01]00[01][01][01][01]0001100[01][12]10 [01]0010[01][01]1-001[01][01]000[12]0[01]20000000000---------------1[01]10 [01][01][01] [01]02111111111111111200111111101111111000110111100 01100[01]011102111110[01] 111001001010011002111111000[01]---011 [01]-000100111[01]00210[01];
cc ] 24.28 85.87 140 145 169 235 249;
Table 9. Taxon Totals for the 14 Kingdoms.
phyla classes orders families genera species
eukaryotes
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
Gracilicutes 3 7 c 60 c. 160 c. 800 c. 5000
Posibacteria 3 7 20 c.100 c. 700 c. 4000
Metabacteria 4 5 9 17 42 c. 300
Togabacteria 1 1 1 1 11 c. 30
total 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.
Eukaryotes
1st Analysis
Materials and Methods
The data set (Table 10, Page 2) 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).
Results
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 4. Alveolates are probably a grade as the cortical alveoli occur also in Glaucophyca and forams and the micropores occur only in Apicomplexa, and these are the only "synapomorphies." 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).
Another type of implied weighting is successive weighting (or successive approximations weighting), although sometimes the 2 techniques are considered distinct, invented by James Farris (1969) and is based on the degree to which a character conforms to a heirarchy, which is related to homology, so that homoplasious characters are devalued. The CI is used as the weighting factor. The data matrix is reanalyzed for the MPT, and the new tree is compared to the previous one. The process ends when the form of the tree no longer differs between iterations, that is, until weights stabilize between searches. Farris suggested that each character could be considered independently with respect to a weight implied by frequency of change. However, the final tree depended strongly on the starting weights and the finishing criteria.
Goloboff's implied weighting is non-iterative, does not require independent estimations of weights, and is based on searching trees with maximum total fit, with character fits defined as a concave function of homoplasy. When comparing trees, differences in steps occurring in characters which show more homoplasy on the trees are less influential. The reliability of the characters is estimated during the reanalysis as a logical implication of the trees being compared. The fittest trees imply that the characters are maximally reliable and, given character conflict, have fewer steps for the characters which fit the tree better. If other trees save steps in some characters, it will be at the expense of gaining them in characters with less homoplasy. In other words, the trees which maximize the concave function of homoplasy resolve character conflict in favour of the characters that have more homology and imply that the average weight for the characters is as high as possible. The method was invented by Pablo Goloboff (1993).
Seven 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. The putative synapomorphies for Megabiota are gibberelins, ergolines, and the MSD myosin subfamily. This group+Ochrista is also recovered in the molecular analyses of Sogin et al (1989) and Bhattacharya et al (1990). A plant-animal or plant-fungal grouping is recovered by Gouy and Li (1989), Wolf et al (2004), Gayle et al (2005), Yang et al (2005), and Philip et al (2005).
2nd 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. There were 17 MPTs and 451 steps, the CI was .59, and the RI was .47. As in the 1st analysis Galdieria+Cyanidium, Glaucophyca, and 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 (reduced consensus, which removes rogue (wandering) taxons) did not fair much better, but Euchrista and Dinobiota were recovered. A majority consensus was also done, set at 51%, which gave much better resolution (Table 14), but I also did one set at 75%, which includes only those clades that are strongly supported. In this case, the same results are obtained with a 2/3 consensus as all the clades there are 82% or over. Two groups are based on homoplasies, Galdieria-Cyanidium and Myxofilosa+Opisthokonta.
Of the 8 consensus methods -- majority, strict, combinable components (semistrict), Adams, Nelson, median, GAS (greatest agreement subtree)(probably same as MAST (maximum agreement subtree), and reduced -- the 1st 2 are the most popular, strict the more popular, devised by Sokal and Rohlf in '81, but it is majority consensus, devised by Margush and McMorris (1981), I favour as it usually produces better resolution and is simple, unlike the last 5. Strict consensus tends to yield polytomies and can exclude monophyletic groups. TNT does only strict consensus. The MRT is presented in Table 14 also. The consensus method was 1st devised for different data sets instead of for multiple MPTs by Adams in '72, and the consensus tree is always less resolved than the MPTs (Carpenter, 1988). The following 10 clades have 100% support across the 2 analyses: Metakaryota, Galdieria-Cyanidium, Neokaryota, Cellulosa, Contophora, Euchrista, Neochrista, Neolobosa+Protolobosa (Protamebae), Opisthokonta, and Actinopoda+Foraminifera (largely Retaria), with Dinobiota, Dinociliata, Excavata, and Neoexcavata also having strong support. The results for the combined analysis are given in Table 14 as well; the MRT is the same for it, too.
Some groups are misplaced because of homoplasy so I have repositioned them (Table 16) according to classical and molecular data. Ochrobiota (similar to Chromalveolata) is composed of Ochrista, Retaria, and Dinobiota (Apicomplexa, Dinociliata, and Excavata (Discicristata)), and is the supergroup with the most synapomorphies with 12. Dinaria might be on top in Bikonta instead of Ochraria. A key is also presented.
Table 12. Diana Lipscomb's Classification (1989 and 1991)-8 kingdoms.
Rhodophyca
Supergroup 1
Plantae
Supergroup 2
Cryptomonada
Supergroup 3
Amebae+Oomycota+Chromobiota+Heliozoa
Supergroup 4
Polymastigota
Animalia +(Choanozoa+Fungi)
Opalinida+Dinociliata+Euglenaria
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 consensus was applied.
Table 13. Eukaryota-1st Analysis.
a. Implied Weighting Tree
Cyanidioschyza
Metakaryota
Cyanidium+Galdieria
Glaucophyca
Cellulosa
Rhodophyca
Contophora
Plasmodiophorae
Supergroup 4
Pelomyxida+Neolobosa
Spongomonada
Supergroup 5
Dinista (Dinobiota+Retaria)
Dinobiota
Dinoflagellata+Ciliata
Excavata
Euglenaria
Apicomplexa
Jakobida+(Heterolobosa +Polymastigota)
Foraminifera+Axopoda
Supergroup 6
Cercomyxa (Cercomonada+Myxofilosa)
Supergroup 7
Megabiota
Plantae
Fungi+Animalia
Ochrista
Chlorarachnia
Euchrista
Haptomonada
Cryptomonada+Heterokonta
b. Majority Consensus Tree (set at 75%).
Cyanidioschyza
Metakaryota (13)
Cyanidium+Galdieria (13)
Glaucophyca
Cellulosa (13)
Rhodophyca
Contophora (13)
Plasmodiophorae
Supergroup 4 (13)
Spongomonada
Supergroup 5 (13)
I Supergroup 6 (13)
II Supergroup 7 (11)
III Supergroup 8 (13)
Megabiota (13)
Plantae
Fungi+Animalia (13)
Ochrista (12)
Chlorarachnia
Euchrista (13)
Haptomonada
Cryptomonada+Heterokonta (13)
III Cercomyxa (Cercomonada+Myxofilosa) (13)
III Foraminifera+Axopoda (13)
II Dinobiota (13)
Apicomplexa
Dinoflagellata+Ciliata (11)
Euglenaria
Jakobida
Heterolobosa +Polymastigota (13)
I Protolobosa+Neolobosa (13)
c. MRT for the 1st Eukaryotic Analysis
Cyanidioschyza
Metakaryota (13)
Cyanidium+Galdieria (13)
Glaucophyca
Cellulosa (13)
Rhodophyca
Contophora (13)
Plasmodiophorae
Supergroup 4 (13)
Spongomonada
Supergroup 5 (13)
I Supergroup 6 (13)
II Supergroup 7 (11)
III Supegroup 8
IV Supergroup 9 (13)
Megabiota (13)
Plantae
Fungi+Animalia (13)
Ochrista (12)
Chlorarachnia
Euchrista (13)
Haptomonada
Cryptomonada+Heterokonta (13)
IV Cercomyxa (Cercomonada+Myxofilosa) (13)
III Foraminifera+Axopoda (13)
II Dinobiota (13)
Supergroup 10 (6)
Apicomplexa
Excavata (8)
Euglenaria+Jakobida (8)
Heterolobosa +Polymastigota (13)
Dinoflagellata+Ciliata (11)
I Protolobosa+Neolobosa (13)
Table 14. Majority Consensus and MRT for Eukaryota- 2nd analysis, and Combined Results for the 2 Analyses,
najority consensus (51%) 13 Kingdoms (numbers in parentheses indicate the number
of trees the group appears in).
sbemp. Eukaryota (Chatton 1937) Dougherty 1959 stat. nov.
infemp. Cyanidiochyza stat. nov.
kgdm. Cyanidioschyza stat. nov.
infemp. Metakaryota Cavalier-Smith 1993 tax. nov. (17)
pvemp. Galdieria-Cyanidium stat. nov., nom. nov.
kgdm. Galdieria-Cyanidium stat. nov. (17)
pvemp. Cenokaryota tax. nov. (17)
mcemp. Glaucophyca stat. nov., nom. nov.
kgdm. Glaucophyca
mcemp. Cellulosa tax. nov. (17)
ggk. Rhodophyca stat. nov., nom. nov.
kgdm. Rhodophyca
ggk. Contophora Mohn 1984 emend., stat. nov. (17)
mgk. Plantae Haeckel 1856 (excluding green algae) stat. nov. (Isokonta Blackman and Tansley 1902 (as
Isokontae))
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)
mgk. Anisokonta nom. nov., stat. nov. (Tubulicristata Starobogatov emend.) (11)
grdk.//kgdm. Ochrista (Cavalier-Smith 1986, name only)(Chromista Cavalier-Smith 1981) stat. nov. (15)
sbk./phyl. Chlorarachnia stat.nov.
sbk. Euchrista tax. nov. (17)
spph./phyl. Haptophyca stat. nov., nom., nov.
spph. Neochrista tax. nov. (17)
phyl. Heterokonta Luther 1899 (as Heterokontae)
phyl. Cryptophyca nom. nov.
grdk. Metanisokonta tax. nov. (9)
hpk./kgdm. Eulobosa (Protamebae) nom. nov. (Rhizopoda von Siebold 1845) (17)
cl. Neolobosa nom. nov.
cl. Protolobosa nom. nov. ( Pelobiota Page 1976)
hpk./kgdm. Cercolobosa nom. nov.
cl. Cercomonada Poche 1913 (as order)
hpk. Myxokonta tax. nov. (11)
spk./kgdm./phyl. Myxofilosa nom. nov., stat. nov.
spk. Opisthokonta Cavalier-Smith 1987 (17)
kgdm. Animalia Linneus 1758 emend.
kgdm. Fungi Linneus 1753 emend.
hpk./kgdm. Foramaxia nom. nov. (Retaria Cavalier-Smith 1999, emend.) (17)
phyl. Actinopoda Calkins 1909
phyl. Foraminifera d’Orbigny 1826
hpk./kgdm. Dinobiota Stewart and Mattox 1980, tax. nov. (10)
sbk./phyl. Apicomplexa Levine 1970
sbk./phyl. Metadinobiota (11)
phyl. Dinociliata nom. nov. (17) /
spcl. Ciliata Perty 1852 (Ciliophora Doflein 1901, Heterokaryota Hickson 1903) stat. nov.
spcl. Dinoflagellata Butschli 1885 stat. nov.
phyl. Excavata Cavalier-Smith 2002 (16)
spcl. Protoexcavata nom. nov. (14)
cl. Euglenaria nom. nov.
cl. Jakobea Cavalier-Smith 1993 (as order) stat. nov.
spcl. Neoexcavata tax. nov. (14)
cl. Polymastigota Blochman 1895 (as order)
cl. Heterolobosa Page and Blanton 1985 (as Heterolobosea)
majority consensus (set at 75%)
Cyanidioschyza
Metakaryota (17)
Galdieria-Cyanidium (17)
Cenokaryota (17)
Glaucophyca
Cellulosa (17)
Rhodophyca
Contophora (17)
Plantae
Ochrista (15)
Chlorarachnia
Euchrista (17)
Haptophyca
Neochrista (17)
Heterokonta
Cryptophyca
Eulobosa (17)
Neolobosa
Protolobosa
Cercolobosa
Myxofilosa
Opisthokonta (17)
Animalia
Fungi
Foramaxia (17)
Actinopoda
Foraminifera
Apicomplexa
Dinociliata (17) /
Ciliata
Dinoflagellata
Excavata (16)
Protoexcavata (14)
Euglenaria
Jakobea
Neoexcavata (14)
Polymastigota
Heterolobosa
MRT for 2nd Analysis for Eukaryotes- 12 kingdoms.
sbemp. Eukaryota (Chatton 1937) Dougherty 1959 stat. nov.
infemp. Cyanidiochyza stat. nov., nom. nov.
kgdm. Cyanidioschyza stat. nov.
infemp. Metakaryota Cavalier-Smith 1993 (name only) tax. nov. (17)
pvemp. Galdieria-Cyanidium stat. nov., nom. nov.
kgdm. Galdieria-Cyanidium stat. nov.
pvemp. Cenokaryota tax. nov. (17)
mcemp. Glaucophyca stat. nov., nom. nov.
kgdm. Glaucophyca
mcemp. Cellulosa tax. nov. (17)
nnk. Rhodophyca stat. nov., nom. nov.
kgdm. Rhodophyca
nnk. Contophora Mohn 1984 emend., stat. nov. (17)
ggk. Plantae stat. nov.
kgdm. Plantae Haeckel 1866 (excluding green algae) (Isokonta Blackman and Tansley 1902 (as Isokontae),
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 1981)
ggk. Anisokonta nom. nov., stat. nov. (11)
mgk.//kgdm. Ochrista (Cavalier-Smith 1986, name only)(Chromista Cavalier-Smith 1981) stat. nov. (15)
sbk./phyl. Chlorarachnia stat.nov.
sbk. Euchrista tax. nov. (17)
spph./phyl. Haptophyca stat. nov., nom., nov.
spph. Neochrista tax. nov. (17)
phyl. Heterokonta Luther 1899 (as Heterokontae)
phyl. Cryptophyca nom. nov.
mgk. Metanisokonta (9)
grdk./kgdm. Eulobosa (Protamebae) nom. nov. (Rhizopoda) (17)
cl. Neolobosa nom. nov.
cl. Protolobosa nom. nov. (Pelobiota Page 1976)
grdk. Neanisokonta (5)
hpk. Myxokonta tax. nov. (11)
spk./kgdm./phyl. Myxofilosa nom. nov., stat. nov.
spk. Opisthokonta Cavalier-Smith 1987 (17)
kgdm. Animalia Linneus 1758 emend.
kgdm. Fungi Linneus 1753 emend.
hpk. Cenanisokonta tax. nov. (6)
spk./kgdm. Cercolobosa
spk./kgdm. Ananisokonta tax. nov. (8)
sbk. Foramaxia nom. nov. (Retaria Cavalier-Smith 1999, emend.)(17)
phyl. Actinopoda Calkins 1909
phyl. Foraminifera d’Orbigny 1826
sbk. Dinobiota (Stewart and Mattox 1980) tax. nov. (10)
infk./ phyl. Apicomplexa Levine 1970
infk. Neodinobiota (11)
/ spph./phyl. Dinociliata nom. nov. (17) /
spcl. Ciliata Perty 1852 (Ciliophora Doflein 1901, Heterokaryota Hickson 1903) stat. nov.
spcl. Dinoflagellata Butschli 1885 stat. nov.
spph. Excavata Cavalier-Smith 1998 (Discicristata Cavalier-Smith 2002) (16)
spcl. Protoexcavata nom. nov. (14)
cl. Euglenaria nom. nov.
cl. Jakobea Cavalier-Smith 1993 (as order) stat. nov.
spcl. Neoexcavata tax. nov. (14)
cl. Polymastigota Blochman 1895 (as order)
cl. Heterolobosa Page and Blanton 1985 (as Heterolobosea)
Majority Consensus (set at 75%) for Combined Results-Eukaryotic Analysis 1 and 2 (in parentheses are the percentages of
the combined frequencies (number of trees group appears in))(MRT is same as above).
Cyanidioschyza
Metakaryota (100)
Galdieria-Cyanidium (100)
Cenokaryota (100)
Glaucophyca
Cellulosa (100)
Rhodophyca
Contophora (100)
Plantae
Ochrista (90)
Chlorarachnia
Euchrista (100)
Haptophyca
Neochrista (100)
Heterokonta
Cryptophyca
Eulobosa (100)
Neolobosa
Protolobosa
Cercolobosa
Myxofilosa
Opisthokonta (100)
Animalia
Fungi
Foramaxia (100)
Actinopoda
Foraminifera
Dinobiota (93)
Apicomplexa
Dinociliata (92)
Ciliata
Dinoflagellata
Excavata (77)
Euglenaria
Jakobea
Neoexcavata (91)
Polymastigota
Heterolobosa
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
chloroplasts
Contophora- gametic meiosis, stigmas, open mitosis
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
Foramaxia - pheodarian-type pseudopods
Dinobiota- articulins, mastigoneme rows 1 and 0, kinetochore location on nuclear envelope, permanently condensed
chromosomes
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
infemp./kgdm. Cyanidioschyza
infemp. Metakaryota
pvemp./kgdm. Cyanidiophyca
pvemp. Neokaryota
mgk./kgdm. Galdieriae
mgk. Cellulosa
grdk./kgdm. Rhodophyca
grdk. Contophora
hpk. Bikonta (Cavalier-Smith 1993) tax. nov.
spk./kgdm. Glaucophyca
spk. Metakonta tax. nov.
kgdm. Plantae (Chlorophyta)
kgdm. Ochrobiota tax. nov.
sbk. Dinaria nom. nov.
infk. Alveolata
infk. Excavata
sbk. Ochraria nom. nov.
infk. Retaria
infk. Ochrista
hpk. Unikonta Cavalier-Smith 1987 stat. nov.
spk./kgdm. Conosa Cavalier-Smith 1998, stat. nov.
spph. Euobosa
spph. Cercomyxa
spk. Opisthokonta
kgdm. Fungi
kgdm. Animalia
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
posterior. Opisthokonta
13 Nutrition osmotrophic; wall mostly chitinous; mostly sessile; mycelia present; diploid; meiosis
gametic; reproduction sporogenic;mitosis mostly closed; no true tissue; without embryonic
development. Fungi
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 flagella usually 2; MLS in many; autotrphy in many. Bikonta
14 DHFR-TS gene fusion absent; cyanelles present; sexuality
absent. Glaucophyca 14 DHFR-TS gene fusion present; cyanelles absent; sexuality
present. Metakonta
15 Chloroplasts, when present, with 2 membranesd and chlorophyll b. cristas lamellar; storage
product
alpha 4. Plantae
15 Chloroplasts, when present, with 3 or 4 membranes and chlorophyll c; cristas usually tubular;
storage product beta 1-3 or alpha- 4. Ochrobiota
Discussion
Cyanidioschyzon merolae has the fewest advanced traits with 12 and the highest percentage of primitive traits with 90 % (excluding inapplicable and missing data). 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), includes all 3 genera. 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.
Cyanidium+Galdieria form the sister group to red algae in Saunders and Hommersand (2004) based on 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 1st and 3rd characters not included in my analyses, peripheral thylakoids occur also in Glaucosphera and are probably apomorphic as they occur in higher algae, and Cyanidium, Galdieria, and Rhodophyca have endospores, which might be apomorphic as well, but the monophyly of Prerhodophyca and Rhodophyca sensu lato is further contradicted by my other analyses (see below).
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. 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 analysis and combined 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 or branch-and-bound 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 (together as Cercomyxa): ppks, striated fiber emanating from anteriorly-directed flagellum extending as cone and terminating in MTOC, cercomyxan semicircle complex.
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, Guttulina, Guttulinopsis ) and Schizopyrenida (Vahlkampfidae,
Percolomonadidae).
Glaucophyca contains Glaucocystis, Cyanophora, Gleochete, and Glaucosphera (this last maybe goes to red algae (ss) as
earlier mentioned).
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.
Additional Analyses
4 analyses were done with the computer calculations being done by me. Phylip (Phylogeny Inference Package), designed by Joseph Felsenstein in 1980, which is the most widely used phylogeny software with some 20, 000 users, was used, specifically the Pars, Dolpenny, and Penny programs. Pars uses the 3 major heuristic search strategies (NNI (Nearest Neighbour Interchange), SPR, and TBR). The latter 2 programs use exact search (branch and bound, not exhaustive). Penny uses Wagner parsimony, as does Pars, and Dolpenny uses Dollo parsimony. Phylip does not do CI, RI, nor synapomorphy plots, and the resampling meaure program didn't work. But the CI can be calculated by dividing the minimum numerber of steps possible by the actual number of steps in the MPT (s).
In the 1st analysis, for phototrophic bacteria, all 7 photosynthetic bacterial groups were included, Togabacteria, was the outgroup, and 31 characters were used. Only 1 MPT was generated, it had 39 steps, and the CI was .79, and is as follows:
Togabacteria
Heliobacteria
Photobacteria (Supergroup 1)
Supergroup 2
Chlorobacteria
Chloroflexi
Chlorobia
Supergroup 3
Porphyrobacteria
Chromatia
Rhodobacteria
Cyanobacteria
Chloracidobacteria
Again this shows the primitiveness of Heliobacteria and Chloroflexi and the unity of Gracilicutes. The data set and matrix are shown in Page 3.
In the 2nd version only photosynthetic features were included, so there were 18, the results had only 1 tree and 22 steps, and the CI was .82.
Togabacteria
SG 1
SG 2
Chloroflexi+Heliobacteria
Chloracidobacteria+Chlorobia
Cyanobacteria
Chromatia
Rhodobacteria
The 2nd analysis was for phototrophic eukaryotes and was done to test the polyphyly of Prerhodophyca and Rhodophyca s.l. by using an outgroup and including a couple of characteristics which might indicate monophyly and which were excluded in the previous analyses. All 12 photosynthetic groups were included and Sulfobacteria was the outgroup. In the 1st stage only photosynthetic features were included (along with storage glycan to complete the storage characteristics). Carotenoid synthesis pathways, carotenes, and xanthophyll cycle were excluded as they would not be informative concerning these groups. On the 1st run 97 MPTs were generated and there were 83 steps. The CI was .52. The majority consensus (in parentheses are the number of MPTs the group appeared in), set at 51%, is as follows:
Sulfobacteria
Rhodophyca s. l. (61)
Prerhodophyca s. l. (70)(((Cyanidioschizon+Glaucophyca)+Galdieria)+Cyanidium)
Rhodophyca s. s.
Plantae
Euglenoida
Chlorarachnia
Dinobiota (60)
Dinoflagellata
Ochrista (64)
Cryptophyca
Haptophyca-Heterokonta
On the 2nd run there were 29 MPTs and 82 steps, and the majority consensus was different only in the position of Chlorarachnia, which was sister group to Dinobiota and on top. Prerhodophyca was in 20 trees, Prerhodophyca + Rhodophyca was in 17, and Dinobiota + Chlorarachnia was in 19.
But when 17 other characteristics were added, only 8 MPTs were found, in 119 steps, with both Rhodophyca s.l. and Prerhodophyca turning up as polyphyletic. The CI was .50. The only difference in the 8 trees was the position of Rhodophyca, which was sister group to Bikonta in half the MPTs and sister group to Cenokaryota in the other half, and the position of Euglenoida, which was sister group to Plantae + (Dino+Ochrista) (and on top) in half the trees and to Metakonta (under it) in the other half. As expected, in both versions, there is no Archeoplastida.
Sulfobacteria
Cyanodioschizon
Metakaryota
Cyanidium
Neokaryota
Galdieria
Rhodophyca
Cenokaryota
Glaucophyca
Bikonta
Plantae
Ochrobiota
Dinochlorarachnia
Dinobiota
Dinoflagellata
Haptomonada+Heterokonta
Chlorarachnia
Euglenoida
Cryptophyca
The matrix for Penny and Dolpenny had to be modified as these 2 programs do not take multiple state characters. Here are the results:
3rd Analysis a (Penny, only photosynthetic features (20), 77 MPTs, 22 steps, CI .91)
majority consensus (set at 50%)
Supergroup
Chloroflexi
Chlorobia
Porphyrobacteria
Cyanobacteria
Chloracidobacteria
Heliobacteria
Togabacteria
3rd Analysis b (Penny, 33 characters, 1 MPT, 39 steps, .85, 85% searched)
SG 1
SG 2
SG 3
Chlorobacteria
Porphyrobacteria+ Cyanobacteria
Chloracidobacteria
Heliobacteria
Togabacteria
4th Analysis a (Dolpenny, 33 characters, 8 trees, 18 steps, 77 % searched)
majority consensus (set at 50%)
Monoderma (5) (Togabacteria+Heliobacteria)
Photobacteria (4)
SG 3 (4) Porphyrobacteria (8)+Cyanobacteria
SG 4 (5) Chloracidobacteria+Chlorobacteria (7)
(the synapomorphy for Chlorobacteria is bacteriochlorophyll c and for SG 4 is bacteriochlorophyll d).
4th Analysis b (Dolpenny, only photosynthetic features (20), 9 steps, 52 trees, 86% searched)
majority consensus (at 50%)
Togabacteria
Heliobacteria+Cyanobacteria (32)
Porphyrobacteria (49)
Chlorobacteria (39)
Chloracidobacteria
5th Analysis (Penny, eukaryotes, photosynthetic characters only, 47 characters, unrooted, search self-terminated at 80 steps, 16 trees, CI .59, 1 mln. trees looked at, and 2 % searched, majority consensus (at 51%))
Eukaryota
Cyanidium
Neokaryota
Galdieria
Cellulosa
Rhodophyca
Bikonta
Plantae
Ochrobiota
Euglenoida
Dinobiota
Dinoflagellata
Euchrista
Cryptophyca
Neochrista
Heterokonta
Haptomonada
Chlorarachnia
Glaucophyca+Cyanidioschizon
Sulfobacteria
6th Analysis (Dolpenny, eukaryotes, photosynthetic characters only, 47 characters, search self-terminated at 42 steps, 9 MPTs, 1 mln. trees looked at, and 30 % searched, majority consensus (at 51%))
Sulfobacteria+Cyanidioschizon
SG 1
Cyanidium
Neokaryota
Glaucophyca
Cenokaryota
Galdieria
Cellulosa
Rhodophyca
Bikonta
Plantae
Ochrobiota
Dinobiota
Ochrista
Heterokonta
Haptophyca
Cryptophyca+Chlorarachnia
Dinophyca
Euglenoida
In the 6th analysis, Sulfobacteria+Cyanidioschizon, and in the 5th analysis, Sulfobacteria on top, are obviously artefacts, It is the larger data matrix that is more accurate, so the analyses with only photosynthetic traits included are less meaningful, but the 2 B n B searches for photosynthetic eukaryotes provide still more support for the polyphyly of Prerhodophyca and Rhodophyca s.l. And the most accurate results came with the Dolpenny analysis for 33 characteristics for bacteria as it was the larger matrix, used an exact search, had a small number of MPTs, and was more parsimonious than Penny, as well as the 6th analysis, again with Dolpenny, for the same reasons. Of course, a matrix with more taxons would be more accurate still, but this would require modifications (in symbols) that would be too complex for a large matrix with the sequential format that Phylip and most phylogeny packages unfortunately use, instead of the tabular format, which is far easier to do and read.
I also did 2 analyses using Dolmove which combines parsimony with character compatibility but does not do clique analysis and allows the user to rearrange trees himself/herself. In the 1st of these, for phototrophic eukaryotes, the 7th additional analysis, which had 47 characters, the MPT was found at 44 steps with 37 characters compatible. The initial tree was 73 steps with 22 characters compatible.
Sulfobacteria
Eukaryota
Cyanidioschizon
Metakaryota
Cyanidium
Neokaryota
Galdieria+Glaucophyca
Cellulosa
Rhodophyca
Contaphora
Plantae
Ochrobiota
Euglenoida
Dinobiota
Dinophyca
Ochrista
Chlorarachnia+Cryptophyca
Haptophyca+Heterokonta
In the 2nd Dolmove analysis, for phototrophic bacteria, the 8th additional analysis, which had 33 characters, the MPT was found at 18 steps with 27 characters compatible. The initial tree was 34 steps with 15 characters compatible.
Monoderma
Togabacteria
Heliobacteria
Gracilicutes/Photobacteria
Chlorobacteria+Chloracidobacteria
Porphyrobacteria+Cyanobacteria
I did a 10th analysis (the 9th being for funguses and is in Page 3), this one including Cristidiscoida to test its monophyly and position with Fungi in molecular taxonomies. Pars was used and there were 16 taxons, 78 characters, 4 MPTs, and the CI was .50 rounded off. Cristidiscoida was monophyletic but nowhere near Fungi even with coding discoid cristas as present in Fungi, which is doubtful and would be rare, and with aggregation as present in animals and funguses even though this is rare in them, but occurs in Acrasia and Fonticula. The majority consensus is as follows (the numbers in parentheses are the number of trees the group appears in):
Cyanidioschizon
Cyanidium
Neokaryota (4)
Galdieria
Cenokaryota (4)
Cellulosa (3)
Rhodophyca
Contophora (4)
Megabiota (3)
Plantae
Opisthokonta (4)
Fungi
Animalia
Ochrobiota (3)
Discicristata
Dinobiota (4)
Dinophyca
Ochrista (4)
Euchrista (4)
Cryptophyca+Haptophyca (4)
Heterokonta
Chlorarachnia
Glaucophyca
Cristidiscoidia (4)
Nuclearia Cienkowsky 1865
Fonticula Worley, Raper, and Hohl 1979
There was only 1 MRT, it is the 1st tree, and is the same as the majority consensus. The strict consensus is as follows:
Cyanidioschizon
Cyanidium
Neokaryota
Galdieria
Cenokaryota
Rhodophyca
Contophora
Plantae
Opisthokonta
Fungi
Animalia
Discicristata
Dinobiota
Dinophyca
Ochrista
Euchrista
Cryptophyca+Haptophyca
Heterokonta
Chlorarachnia
Glaucophyca
Cristidiscoidea
Nuclearia
Fonticula
In Lipscomb's analyses, Fonticula is not included and Nuclearia groups with Polymastigota but based on homoplasies. The position of Cristidiscoidea is uncertain.
Conclusions
Open and shut cases are the high value and merit of classical evidence including among bacteria, the phylogenetic quality and nature of cladistics and the lack of same for gradism, the primitiveness of prokaryotes, the derived status of Metabacteria, the advanced condition of Sulfobacteria, the polyphyly of Protista and Protozoa, the position of Choanozoa and Myxozoa in Animalia, Microsporodia in Fungi, green algae in Plantae, chytrids in Fungi, and bicocesids, opalinates, and proteromonads in Heterokonta, and the unity of Heterokonta and Eukaryota.
The most important points can be summed up as follows:
1. red algae are ancestral, a position supported by both phenotypic and genotypic 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. Posibacteria, Metabacteria, 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.
8. Eukaryota is probably a chimera but may not have originated in a fusion event.
Latin Diagnoses
Euchrista-algae cum chloroplasta in reticulum endoplasmicum sine ribosomae et reticulum periplasmicum.
Neochrista- algae cum epsilon-carotena et mastigonemata tripartitae et tubulari.
Acknowledgements
I am extremely grateful to Dr. James Carpenter, of the Am. Mus. Nat. Hist., former editor-in-chief of Cladistics, former administrative editor, and administrator with the Willi Hennig Society, 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 23) 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.
In Bacteria Heterotropha, Anaerobia are parasitic (except for Desulfobacteria) and unpigmented (except for Enterobacteria), while Aerobia are free-living (except for a few in Pseudomonada and Flavobacteria) and pigmented (except for Planctobacteria and Caulobacteria). In Autotropha, the exceptions are Chloroflexi and Rhodobacteria, which are heterotrophic.
Table 23. Convenience Classification for Empire Biota.
spk. Prokaryota
kgdm. Bacteria
sbk. Eubacteria
spph. Gracilicutes
phyl. Heterotropha tax. nov.
cl. Anaerobia tax. nov.
cl. Aerobia tax. nov.
phyl. Autotropha tax. nov.
cl. Clatobacteria tax. nov.
cl. Photobacteria
spph. Mollicutes
spph. Firmicutes
cl. Togabacteria
cl. Endospora
cl. Actinobacteria
sbk. Metabacteria (Mendosicutes)
spk. Eukaryota stat. nov.
kgdm. Phyta (Chloroplasta nom. nov. )
sbk. Protophyta (Algae)
phyl. Ochrophyca
phyl. Rhodophyca
phyl. Chlorophyca
sbk. Metaphyta (Embryophyta, Cormophyta)
kgdm. Mycota stat. nov.
sbk. Protomycota (Mastigomycota)
sbk. Metamycota
phyl. Zygomycota (classes Tricho- and Zygomycetes)
phyl. Ascomycota (classes Disco-, Pyreno-, Plecto-, and Hemiascomycetes)
phyl. Basidiomycota (classes Archeo- and Neobasidiomycetes)
kgdm. Zoa
sbk. Protozoa
phyl. Zooflagellata
phyl. Sarcodina
phyl. Sporozoa
phyl. Ciliata
sbk. Metazoa
grdph. Diploblastica
grdph. Triploblastica
hpph. Protostomia
hpph. Deuterostomia
simplified
spk. Prokaryota
kgdm. Bacteria
sbk. Protobacteria (Eubacteria)
sbk. Metabacteria (Mendosicutes)
spk. Eukaryota
kgdm. Phyta (Chloroplasta)
sbk. Protophyta (Algae)
sbk. Metaphyta (Embryophyta)
kgdm. Mycota
sbk. Protomycota (Mastigomycota)
sbk. Metamycota
kgdm. Zoa
sbk. Protozoa
sbk. Metazoa
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