EMPIRE BIOTA
Posted 2007; last modified December, 2010. Prokaryotes Algae, kn Methods and Materials Results In the 2nd eukaryote analysis there were 451 steps, a CI of .59, and an RI of .47. Galdieria+Cyanidium, Glaucophyca, Rhodophyca formed a basal series in all 17 trees. 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) appeared in all 17 trees. 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. Rhodophyca Hennig86 Wagner parsimony analysis and branch swapping was used on 86 genera and 137 phenotypic features resulting in 7 optimal trees of 475 steps with a CI of .52; Nelson (strict) consensus was applied. Table 5. Synapomorphies for Eukaryote Clades. Metakaryota-larger genome, larger chloroplast DNA size, sporulation 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. Butcher RW (1967) An Introductory Account of the Smaller Algae of British Coastal Waters. Part IV: Cryptophyceae. Fishery Leedale, G. F. 1967. Euglenoid Flagellates. Prentice-Hall, Englewood Cliffs , New Jersey . sbph. Postciliodesmatophora Gerassimova and Seravin 1976 Retarians, s.l. Forams The classification for forams, traditionally an order in subclass Rhizopoda in class Sarcodina, was 1st done by Glaesssner ( 1947) in which there were 7 super-families and 50 families. Loeblich and Tappan (1984) recognized it as an order and divided it into 5 sub-orders, 17 super-families, and 96 families. J.J. Lee (1990) states there are 1200 genera in 12 orders and 120 families. Tappan and Loeblich (1988) give the following putative phylogeny: sbph. Allogromina (Allogromida) Actinopods Ernst Haeckel, who referred to radiolarians as nature's works of art, and was an artist himself authoring and illustrating the 1st major treatise, a comprehensive report, in 1887, on these organisms based on samples collected from the renowned Challenger Expedition of 1873-76. He treated them as a class and divided it into 4 legions or tribes: Spumellaria, Acantharia, Nassellaria, and Pheodaria, with the 1st 2 grouped as subclass Porulosa and the latter 2 as Osculosa, based on the size and distribution of the pores in the central capsular walls, split each legion into 2 sublegions, and recognized 20 orders, 85 families, and 4, 318 species in total. Although his system is not regarded as phylogenetic, and is not easily applied to species identification, it was one of the more thorough-going treatments of that century and has remained until recently the major source of information on actinopod diversity and taxonomy. Kunstformen der Natur (Art Forms of Nature) is a book of lithographic and autotype prints originally published in 10 sets of ten between 1899 and 1904 and as a complete volume in 1904, and consists of 100 prints of various organisms done by Haeckel. sbph. Radiolaria Muller 1858 sbph/cl. Desmothoracida 1 ord., 1 family (Clathrulina, Hedriocystis) Myxofilosa (Myxomycota, Mycetozoa) has 8 orders, 19 families, 74 genera, and some 630 species. Usually recognized are subphylums Dictyostela, including 1 class and order, 2 families, 3 genera, and about 50 species, and Eumyxafilosa, with classes Protostelea, which counts 1 order, 4 families, 14 genera, and 32 species, and Myxofilosea (Myxomycetes), which includes 2 or 3 subclasses, 6 orders, 13 families, some 60 genera, and about 550 species. Dictyostela comprises cellular slime molds which have 3 phases in their life cycle: ameboid, microscopic, bacteria-feeding; multicellular, sorocarp and spore-producing (visible to the unaided eye), and an intermediary aggregation phase (the pseudoplasmodium formed by aggregating myxamebas). It used to also include the Acrasians. Myxofilosea has 2 phases in its life cycle, a trophic, diploid, plasmodial, wall-less, ameboid generation, and a reproductive, haploid, sporophoric, plasmodial, walled generation. The plasmodium-sporophore complex sets it apart from other organisms. Rhizopods Protolobosa (syns. Archamebae, Pelobiota, Karyoblastea) includes 3 families: Pelomyxidae Schultze 1877 (Pelomyxa Greef 1874 and Mastigina) and Mastigamebidae (Mastigella and Mastigameba (syn. for the latter: Phreatameba and Dinameba)). Pelomyxa palustris is known only from mud at the bottom of freshwater ponds, and was usually placed in Entamebidae. The number of species is unknown. The traditional classification comprised of class Sporozoa, established by Leuckart in 1879, which contained sucbclasses Telosporidia (orders Gregarinida, Coccidia, and Hemosporidia), Acnidosporidia (orders Sarcosporidia and Haplosporidia), and Cnidosporidia (orders Myxosporidia, Actinomyxidia, Microsporidia, and Helicosporidia). Microsporidians and myxozoans (myxosporidians) were separated out, going to Fungi and Animalia, respectively. Paramyxea, which also contains 3 genera (Paramyxa, Marteilia, and Paramarteilia) has an organelle similar to haplosporosomes (considered homologous) in Marteilia and Paramarteilia, the 2 genera forming a family, which warrants the recognition of Ascetosporea, established by Desportes and Nashed (1983). However, Paramyxea has singlet microtubules, like Apicomplexa, but this might be a primitive feature. Haplosporidia, at least, should be placed in Fungi alongside Microsporidia. A phylogeny for the phylum is as follows: Colpodella is definitely an apicomplexan, as it has an apical complex and micropores, but is separated out for unknown reasons and I don't know where it goes exactly in the phylum's scheme of things. Vertebrata sbph Myxinoidia (hagfish)
Summary
A phylogenetic classification system of bacteria is presented, based on a cladistic analysis of morphology, chemistry, physiology, and molecular biology for 23 taxons and 263 characters, and is the first comprehensive high level phylogeny of prokaryotes based on classical evidence. The results are in basic agreement with Gupta's protein phylogenies, i.e., Gram+s are primitive, Gram-s are advanced, and Mendosicutes (Metabacteria, Archeobacteria) evolved from G+s. G+s, G-s, and Metabacteria show up as monophyletic. Also presented is a phylogeny for eukaryotes. Both are designed to more accurately reflect evolutionary kinship. There are 6 bacterial kingdoms: Thermosiphia, Fervidobacteria, Thermotogae, Firmicutes, Mendosicutes, and Gracilicutes. The major supergroup is Contobacteria comprising Fervidobacteria, Thermotogae, Monodermata, and Gracilicutes. 2 cladistic analyses were done for eukaryotes, based on 297 characters and 27 taxons in the 1st analysis, and 301 and 25 in the 2nd. The final tree, however, repositions some groups to eliminate homoplasy and contains 10 eukaryote kingdoms, so 16 in all, which are Cyanidioschyzophyca, Cyanidiophyca, Galdieriaphyca, Glaucophyca, Rhodophyca, Plantae, Conosa (the classical amebas, cercomonads, and slime molds), Fungi, Animalia, and Ochrobiota (Ochrista (Chromista), and Dinista (Retaria (forams and actinopods) and Dinobiota (alveolates and excavates)). The supergroups are Metakaryota, Neokaryota, Cellulosa, Contophora, and Unikonta (Conosa and Opisthokonta), Bikonta (Glaucophyca, Plantae, and Ochrobiota), and Metakonta (Plantae and Ochrobiota). Rhodophyca+Plantae, with or without Glaucophyca, Cercozoa, and Rhizaria are polyphyletic groups. 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, and 4 standardized suffix systems. 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 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 qui démontrent la position primitive de G+, l'évolution de Mendosicutes (Metabacteria ou Archeobacteria) de ceux-ci. Une analyse cladistique pour les eukaryotes est aussi présentée. Les 2 analyses dessinée pour refléter avec plus de précision les relations évolutionnaires. Les 7 regnes bactériens sont Thermosiphia, Fervidobacteria, Thermotogae, Gracilicutes, Firmicutes, et Mendosicutes. Le supergroupe principal est Contophora. 2 analyses cladistiques pour les eukaryotes ont été faites, le 1er avec 297 caractères et 27 taxons et le 2me avec 301 caractères et 25 taxons. Mais le arbre final est hypothétisé de contenir 10 royaumes, donc 16 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. L'infallibilité ou la supériorité des phylogénies moléculaires, le gradisme comme évolutionnaire ou phylogénétique, et l'idée des eukaryotes comme primitives sont rejetés et refutés et une origine par fusion des eukaryotes est proposée. Un système Farris est utilisé pour les préfixes de rang. Aussi inclus sont un historique compréhensif, 2 taxonomies utilitaires, une table de totales, et un des systèmes de suffixes standardisés. Une classification utilitaire est aussi présentée qui contien 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 Heterotropha, Autotropha, Chemoorganotropha, Chemolithotropha, Scotoautotropha, Rhodophyca, Euglenista, Mycozoa, Neophyta, Apicophyta, Axopoda, Dinociliata, and Chloroplasta.
Introduction and Historical Overview
Some Words on Nomenclature
Taxonomy-Meaning and Methods
Eukaryotes 2nd
Prokaryotes
Methods and Materials
Results
Discussion
Eukaryotes
Methods and Materials
Results
Discussion
Conclusions
Latin Diagnoses
Acknowledgements
Taxonomies for the Principal Algal Groups
Taxonomies for Dinoflagellates and Euglenoids
Taxonomies for Protozoans
Taxonomies for Opisthokonts
A Convenience Classification
References
Author Profile (see astro-taxonomy.info; can only be accessed at the present time through the address bar at the top of the search engine screen)
(Internal links were created but soon became disfunctional and had to be removed.)
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. 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. Bory de Saint-Vincent (1824) established the Regne Psychodiaire (2-souled) for zoophytes, vorticellids, and diatoms which contained 3 classes, Ichnozoaires, Phytozoaires, and Lithozoaires(corals). In his animal kingdom were included the Microscopiques comprising 4 orders: Gymnodes, Trichodes, Stomoblephardes, Rotiferes, Crustodes. It was the 1st order which contained bacteria, along with green algae, monads, amebas, ciliates, and cercaria. There was also a Regnum Neutrum (von Munchhausen, 1765-66) for polyps, corals, funguses, and lichens and a Regne des Némazoaires by Gaillon (1833).
Horaninoff (1834) proposed 2 kingdoms of nature, the inorganic and the organic, each with 4 unranked divisions, fire, water, air, and circulum corporum plus Vegetabilia (4 classes: Plantae sporophorae, Pseudospermae, Coccophorae, and Plantae spermophorae), Phytozoa (4 classes: Fungi, Algae, Polyparii(polyps), and Acelaphae(sponges and cnidarians)), Animalia (12 classes), and Homo sapiens. In 1843 he elevated his kingdoms to worlds or orbits (Orbis Anorganicum and Orbis Organicum), the 8 unranked groups becoming kingdoms (Ethereum, Aqueum, Aereum, and Minerale; Vegetabile, Amphorganicum, Animale, and Hominis). The various classes were arranged in concentric rings.
Even before this, Ammonius Hermiae, in the 400s AD, recognized animals, plants, and zoophytes and may have been the 1st to use the term "zoophytes"(if not, the honour would go to Sextus Empiricus or Iamblichus, both in the late 200s AD). The group was 1st formally established as part of Animalia by Edward Wotton in 1552.
In the 20th century, Haeckel's final version appeared in 1904, and included kingdom Histonia, but a major step occurred in 1925 (Chatton, 1925) with Chatton's recognition of the eukaryote prokaryote division classed as superkingdoms Akaryonta and Karyonta (viruses being named Aphanobionta) by Novak (1930) and named eucaryotique, procaryotique by Chatton himself (Chatton, 1937). it was Dougherty who formally named them (1957), and Neushul (1974) established subkingdoms Prokaryonta and Eukaryonta.
The 1st modern 4 kingdom system was by H.F Copeland with subsequent revisions (Copeland 1938, 1947, 1956) the final version being: Mychota (blue algae and bacteria), Protoctista (other eukarytic algae, fungi, slime molds, and protozoans), Plantae (including only embryophytes and green algae), and Animalia (including sponges). His father, E.B. Copeland ( 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.
Conard (1939), Vada (1952), and Whittaker (1957) proposed a 3- kingdom scheme, which were fungi-bacteria, plants (algae and cormophytes), and animals (protozoans and metazoans), corresponding to the 3 nutrional modes and the ecologist’s functional communities. The 1st author used the names Mycetalia, Phytalia, and Animalia, the 2nd did not use an explicit rank nor names (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).
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).
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; these were distributed into the usual 2 superkingdoms with 6 suprakingdoms being Archeobacteria comprising the single kingdom Archeobacteriobionta; Neobacteria comprising kingdoms Bacteriobionta and Cyanobionta, and Aconta (with Erythrobionta and Rhodecyanobionta); Contophora (containing 8 kingdoms: Chlorobionta, Flagelloopalinida, Euglenophytobionta, Eumycota, Dinophytobionta, Cryptophytobionta, Colponemata, and Chloromonadaphytobionta); Cormobionta (with a single kingdom bearing the same name); Animalia, containing middle-kingdoms Parazoa (with kingdoms Porifera, Archeata, and Placozoomorpha), and Eumetazoa (with kingdoms Bilateria and Radiata).
Jahn and Jahn (1949) presented 6 kingdoms: Archetista (viruses), Monera (bacteria), Protista, Metaphyta, Metazoa, and Fungi. 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.
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). Corliss's 6 eukaryotic kingdoms (Corliss, 1994, 1995) were similar to Cavalier-Smith's and included Archeozoa, Protozoa, Chromista, Plantae, Fungi, and Animalia.
All these were decidedly artificial and Diana Lipscomb's eukaryotic system (1985, 1989, 1991), was the 1st based on cladistic analysis of classical evidence and contained 9 major groups and is discussed later.
Molecular phylogenies were published by Woese, Kandler, and Wheelis (1990) which was a 3 primary kingdom set up (Archea, Bacteria, Eucarya) and by 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.
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, Excavata, and Archeoplastida+Chromalveolata-Rhizaria, making 9 kingdoms (not named as such). Glaucophyca was sister group to Plantae+Haptophyca-Rhodophyca. Excavata was directly related to Archeoplastida+Chromalveolata-Rhizaria.
Tekle et al (2008) also did maximum likelihood genotypic analysis yielding a series of sister groups related to remaining eukaryotes: Choanozoa, Metazoa, Fungi, Polymastigota, Amebobiota, Glaucophyca, Rhodophyca, Plantae, Cryptophyca-Haptophyca+Malawimonidae, Euglenista-Heterolobosa+Jakobida, and Alveolata+Cercomonada-Heterokonta, making 11 unnamed) kingdoms. It is similar to my results in that the Glaucophyca, Rhodophyca, and Plantae part of the series, and the last 3 groupings form none other than Ochrobiota, but with Cercomonada misplaced as it should be with Amebobiota, and without the misplaced Polymastigota.
In 2010, Parfrey et al came out with another genotypic ML analysis which comprised 15 (unranked) kingdoms: Animalia, Mesomycetozoa, Fungi, and Apusomonada in 1 large clade, Ancyromonas, Breviata, Amebobiota, and anothe large clade comprising Excavata, cryptomonads (including Katablepharids), red algae, Centroheliozoa, glaucophycans, Telonema, plants, haptophycans, and SAR.
The classification of bacteria has had a checkered and relatively short past. They were “invented” by Leewenhoek (1683) who considered them animalcules and in the Linnean system(1735) they were placed as specia dubia in Vermes and regarded as infusorians by Ehrenberg (1838) who first named them “Bakterien” (the English cognate was coined in 1847) but were switched to Plantae by Cohn (1872) who realized that blue algae were related to bacteria and set up the order Schizosporeae to accommodate both groups with the latter as family Bacteriaceae and later integrated as Schizophyta (1875) and were placed in Fungi in Eichler’s Thallophyta (1883) as Schizomycetes. In the first taxonomic tree (Haeckel, 1871) they were in Moneres, along with amebas, in Protista. They were first recognized as a kingdom by Enderlein in 1925.
Notable internal arrangements for prokaryotes have been done by Cohn (1872, 1875) (4 tribes, Spherobacteria, Microbacteria, Desmobacteria, and Spirobacteria); Migula (1897), which was the most widely accepted system of its time and included all then- known species but was based only on morphology; Orla-Jensen(1909); Bergey (1925, with many subsequent editions); Stanier and van Neil (1941), as Kingdom Monera with 2 phyla, Myxophyta and Schizomycetae, the latter comprising classes Eubacteriae (3 orders), Myxobacteriae (1 order), and Spirochetae (1 order); Bisset (1962), 1 class and 4 orders, Eubacteriales, Actinomycetales, Streptomycetales, and Flexibacteriales, but also a tree which comprises 6 clades Spirillum-Vibrio, Spirochetes, Trichobacteria, a pseudomonadoid group, a Cytophaga-Myxobacteria group, G+s; Gibbons & Murray (1978), with 4 phyla, Gracilicutes, Firmicutes, Tenericutes (Mollicutes), and Mendosicutes (Metabacteria); Woese and Fox (loc cit), and Mohn (loc. cit.) recognizing Gramabacteria (G+s) placing spirochetes with clostridians (because of the clastic system which is probably homoplasious) and chlamydians with mycoplasmas and Agramabacteria, coextensive with Thiobacteria (excluding blue bacteria).
Macroscopic funguses were also, of course, known in Antiquity and, along with microscopic ones, including pseudofungi and slime molds, were 1st given regnal status by Necker (1783) and Fries(1832)(The Father of Mycology), the former as Regnum Mesymale, the latter as Regnum Mycetoideum.
Protozoa was named by Goldfuss in 1817 as a class divided into 4 orders: Infusoria, Phytozoa, Lithozoa, and Medusinae. Infusoria had 4 families, Monades, Vorticellae, Brachioni, and Polypi. This was replaced by Butschli's familiar system (1880-82) containing classes Sarkodina, Mastigophora, Sporozoa, and Infusoria (ciliates and suctorians) which has survived well into the 1960s. There were then only 10 to 15 metazoan phylums. Previously, J-B de Monet (Lamarck), in Tableau du Regne Animal from 1806, distiguished between vertebrates and invertebrates recognizing 12 classes, adding Infusoires and separating out Cirripedes in 1807 and adding Tunicata in 1816. A year later Georges Cuvier established his 4 embranchements: Phytozoa, Articulata, Mollusca, Vertebrata, in Regne Animal. In ancient times, Aristotle, in his History of Animals, recognized Anaima (with white blood, invertebrates) and Enaima (with red blood, vertebrates). Greene, in 1859, recognized Protozoa as a subkingdom. Doflein, in 1901, combined the 1st 3 of Butschli's classes as Plasmodroma. Lankester, in 1878, recognized Gymnomyxa and Corticata.
Algae, known by Theophrastus, the Father of Botany, and the other ancients, the word was coined in 1551, but known only from seaweeds and red tides, were organized by Linneus into 4 genera, the filamentous Conferva, the membranous Ulva, the thalloid Fucus, and the gelatinous Tremella. The few unicelluar algae then known, such as Volvox, he placed in Vermes and then Chaoticum. Lamouroux distinguished Fucacées, Floridées, and Ulvacées; Agardh (1824) recognized 6 orders: Diatomeae, Nostichinae, Confervoidea, Ulvaceae, Florideae, Fucoideae. Harvey (1836) established 3 subclasses: Chlorospermae(including blue bacteria and xanthophycans which would both be separated out later in the century), Melanospermae (brown algae), and Rhodospermae. Haeckel classified them as Archephyta (blue algae and most green algae), Characeae (stoneworts), Florideae (red algae), and Fucoidae (brown algae) in Plantae while placing Diatomae, Myxocystoda (Noctilucae), and Flagellata (Peridium, Volvox, and Euglena) in Protista. And Eichler (1883) divided them into the familiar Cyanophyceae, Rhodophyceae, Chlorophyceae, and Pheophyceae in his Thallophyta, and, of course, included also funguses, but the phylum was 1st proposed by Endlicher (1836), with phytoflagellates claimed also by many protozoologists.
It was Eichler who divided plants into Cryptogamae and Phanerogamae, the latter being seed plants, which he in turn divided into gymnosperms and angiosperms, the latter, also for the 1st time, were formally recognized as containing monocots and dicots. But in the Middle Ages, Albertus Magnus had already recognized monocots and dicots, Theophrastus (200s BC) distinguished between, trees, shrubs, undershrubs, and herbs, between annual, biennial, and perenial, centripetal and centrifugal, polypetalous and gamopetalous, and superior and inferior ovaries, and Parasara in Ancient India knew of the cell (rasakosa) and chlorophyll (ranjakena pakyamanat) and recognized several plant families (ganas), including the mustard, bean, and squash families. The descriptions of plant morphology was quite detailed.
Engler and Prantl (1897-1915) had published a system, appearing in a monumental 20-volume work, with later editions by Engler and Gilg (1924) and Engler and Diels (1936), that was based mostly on Eichler's and was widely adopted well into the late 20th century. Like Eichler it was supposed to be phylogenetic but was largely artificial but as a convenience system it is still very useful today. It was originally written by Engler as part of a guide to the Botanical gardens at Breslau U.
Tippo (1942) had recognized 2 plant subkingdoms, Thallophyta (10 phylums) and Embryophyta (2 phylums, Bryophyta and Tracheophyta (vasculars, aka, Stelophyta), the latter containing classes Psilopsida, Lycopsida, Sphenopsida, and Pteropsida) and Bold (1973) divided the plant kingdom into 3 subkingdoms, Prokaryonta, Chloronta, and Achloronta. But Tippo's arangement was more of a synthesis instead of original as his scheme for non-vasculars followed Smith (1938) and for vasculars that of Eames (1936).
A phylogenetic plant kingdom (green algae + embryophytes) was recognized as and by the following:
Chlorobiota Jeffrey 1971
Chlorophyta C-S 1978
Viridiplantae C-S 1981
Chlorobionta Mohn 1984
Plantae Lipscomb 1985, 89, 91
Plantae Starobogatoff 1986
Plantae Corliss 1994, 1995
Viridiplantae Holt and Uidica 2007
A chloroplast kingdom was recognized as and by the following:
Plantae Takhtazhan 1973
Plantae Leedale 1974
Phyta (Plantae) Bold et al 1987
The following is a tally of the various kingdoms propsed 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
8 1993
Jeffrey 5 1982
Takhtazhan 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
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 is worthy of supraregnal status because of fundamental differences in ribosomes, cell wall, and lipid type, however, this is impractical as Mendosicutes is a very small group, the term used broadly is too inveterate, and generic names in Mendosicutes often include the –bacterium suffix, and the group is nested in Prokaryota. In other words, it is distinct but not separate so it is preferable to say Eubacteria. The suffix –zoa for protozoan groups is inappropriate and inaccurate and should be avoided in phylogenetic nomenclature and likewise for –phyta for non-plants. A prefix system for ranks is shown in Table 2. Based on the Farris system (1976) groups can be inserted without changing ranks of the taxons already included, for instance, between and hyper- and mega- one can add superhyper-. Ranks above giga- start with supergiga, ranks below nano- start with subnano-, etc. The abbreviations are given in parentheses. Rank names between basic units should be assigned as half and half, for example, if there are 6 levels the top 3 would be subtertaxic and the bottom 3 suprataxic and if there is an odd number the suprataxic would predominate. In cladistics ranks are designated according to branching order but at some point there is sometimes a ranking that is based on degree of difference and long-standing ranks for particular groups should be conserved for the most part. There should also be parsimony in the number of taxons of any particular rank so a lower rank is preferred.
Table 1. Suffix Systems
bacteria plants algae fungi animals
phyl. -bacteria -phyta -phycota -mycota
sbtph. -bacterina -phytina -phycotina -mycotina
sprcl. -arae -icae -mycetia
class -bacteriae, ariae -opsida -phyceae -mycetes -zoa, -acea
sbtcl. -arinae -idae -phycidae -mycetinae
sprord -oidiona -ionales, arae, -aliona
-florae
order -oidia -ales alia ida
sbtord -oidina -inales alina -ina
sprfam - ikea -areae -idiona oidea
fam. -ikae -aceae -ideae idae
sbtfam -ikinae -oideae idina -inae
tribe -ikineae -eae idini -ini
sbtribe -ineae
(-bacteria can, as well as a type plural, alternatively be used to designate any rank. spr-(supra) refers to any rank above and sbt-(subter) refers to any rank below the basic rank.)
Table 2. Rank Prefix System.
giga- (gg.)
mega- (meg)
hyper- (hpr)
super- (sp)
sub- (sb)
infra- (inf)
micro- (mc)
nano- (nn)
nano- replaces pico- and the abbreviations are mine.
Taxonomy- Meaning and Methods
Phylogenetics (=cladistics) is the only method that is truly and completely phylogenetic being based entirely on monophyly and phylogeny. Gradism(synthetic taxonomy), on the other hand, admits grades, which are polyphyletic, as well as paraphyletic, and considers factors external to phylogeny so it is arbitrary, contradictory, inconsistent, and subjective. The deliberate inclusion of known polyphyletic groups such as Protista, Protozoa, Pteridophyta, and Agnatha which are called "paraphyletic" and the deliberate exclusion of taxa from others to which they are known to belong thereby causing them to be trunchated, in other words splitting obviously monophyletic taxa and creating obviously polyphyletic ones is artificial and hardly a serious attempt at phylogeny. It is often not based on any system nor even analysis yet is touted as “evolutionary” or “evolutive”. Gradists do not believe evolution should be included in taxonomy or, at least, not in any serious or consistent manner, yet claim their method is phylogenetic and regard paraphyletic groups as necessarily monophyletic but in order to be monophyletic a taxon must have an immediate common ancestor unique to it. To aggravate matters many cladists acquiesce recognizing monophyly, paraphyly, and polyphyly as separate entities which makes paraphyly a completely ambiguous concept and use the especially Confusionese term and nonsense word “non-monophyletic” as distinct from polyphyletic when they are obviously synonymous. Utilitarian taxonomy is necessary and is stable and practical, but must be used in parallel with phylogenetics not in combination with it. I present just such a convenience classification in Table 18. The purposes of utility and phylogeny are irreconcilable within the same taxonomy but are complimentary as parallel systems.
Also, there is a disturbing overreliance on genotypic evidence which is considered foolproof and groups are regarded as necessarily and automatically phylogenetic based only on this type of evidence when it is no more reliable than the phenotypic sort, and might even be less so, as it is given to many pitfalls: random noise, long branch attraction, different evolutionary rates, mutational saturation, paralogous genes, the use of different methods, and insufficient sampling. Similar conclusions have been reached by others (cf. Felsenstein, 1978; McKenna, 1987; Raff et al, 1987; Wyss, Novacek, and McKenna, 1987; Meyer, Cusanovich, & Kamen, 1998; Philippe & Adoutte, 1998, Doolittle, 1999). It is widely believed that there is little classical evidence among bacteria of value, which is such a bizarre concept it is amazing it is almost universally held, but nothing could be further from the truth and my data set, matrix, and results prove it.
Eukaryotes 2nd
The notion that prokaryotes evolved from eukaryotes is completely contradicted by all kinds of evidence, morphological, physiological, chemical, molecular, and fossil as well as by the fusion hypothesis. Also, it is difficult to imagine how chloroplasts, given they evolved from bacteria, could have appeared before them, how a complex structure like the ribosome could have evolved de novo, and how the wholesale loss of a complex structure like the cytomembrane system could occur. The whole idea of eukaryotes coming before bacteria is, in fact, so bizarre that it can hardly be taken seriously.
The data set is divided into 4 sections and 242 characteristics: morphology(19), chemistry(83), physiology (43), and molecular biology (97) in 263 columns. All the characters are ordered and there are 9 complex (branching) ones (cell shape, protein types, peptide bridge for cross-linkage A(deactivated), amino acids at position 3(deactivated), cytochromes, carotenoids, quinone classes, bacteriochlorophylls, and chlorophylls). And 7 simple ones have been deactivated, as well, (23-27, 84-86, 139, 146, 170, 235, 250) as they were superfluous since the matrix was reformatted and simplified. The computer calculation phase was performed by James Carpenter. A TNT (Tree analysis using New Technology) program, Wagner parsimony, TBR branch swapping with c. 176 mln. rearrangements, and strict concensus were used. All 4 algorithms were used: ratchet, sectorial search, tree-drifting, and tree-fusing (Goloboff, 1999; Nixon, 1999). Random seed was set at 1, no constraints were used, and the search level was set at 100. Temporary collapsing was done for consensus calculation. There was no outgroup but all of the polarities were very to fairly easily determined.
Results
These are tabulated in Table 3 with the synapomorphies, the modified version (eliminating homoplasy and being dichotomous (using semistrict consensus)) with the synapomorphies in Table 4 and Figure 2, with the taxon list in Table 5, data set in Table 6, the data matrix in Table 7, the probable taxonomy for Actinobacteria in Table 8, and the taxon tallies in Table 9. The synapomorphies serve as formal descriptions of the new names and groups. There were 8 equally most parsimonious trees, 315 steps, a CI of .67, and an RI of .76. The trees differ only in the positions of Fervidobacterium and Thermotoga; Halobacteria and Methanobacteria; and Rickettsiae, Cyanobacteria, and Cloroxybacteria. Aerobia, Monoderma, Firmicutes, Neosoma, Metasoma, Cenosoma, Parkaryota, Gracilicutes, Protogracilicutes, Metagracilicutes, and Neogracilicutes appear in all 8 trees.
Discussion
The phylogeny basically is in accordance with Gupta (2000) so that molecular methods, although less reliable for, at least, prokaryotes, nonetheless, have considerable value and merit. It agrees on 3 fundamental points: the monophyly of G-s, the primitiveness of G+s and advanced nature of G-s, and the position of Metabacteria. It disagrees principally in being branching instead of linear and in having Metabacteria as monophyletic without Eukaryota. The claim that the former arose from various subgroups of G+s is not at all supported by the phenotypic evidence.
4 groupings (Chloroheliobacteria, Metagracilicutes, Neogracilicutes, and Rickettsiae + Cyano + Chloroxy) are represented by homoplasious traits. Heliobacteria with Clostridia is an artefact in molecular analyses and belongs with Oxyphotobacteria as bchl g is related to chlorophylls and the latter goes to Thiobacteria for reasons stated later. It is highly unlikely that photosynthesis would be acquired through LGT and that it would arise more than once. Thermus possibly belongs in Deinobacteria. The similarity in GC content between them was mistakenly omitted which might have grouped them together and are a clade in molecular phylogenies. Some molecular data indicate Thermotoga might be part of Firmicutes (Cavalier-Smith, 1992; Gupta, 1998b).
Thermosiphia (with the single genus Thermosipho) has the largest number of primitive traits which are: heterotrophy, hyperthermophilia, fermentation, anaerobiosis, nonmotility, with a single membrane, thin wall, unicellularity, small SRP, absence of LSP layer, outer membrane, spores, cytochromes, quinones, catalase, and carotenoids so is probably the ancestral group as indicated also by molecular evidence and was used as the root. The Pirellulae clade concurs with genotypic data, as well, but because of the adenylate system Rickettsiae probably goes with Chlamydiae. Chloroflexi is also in the same position in molecular taxonomies.
There were a few errors in the data set which are the following: the 1st character 200 was excluded as there were 2 character 200s and bchl g (128) was not placed with chlorophylls. In the matrix 133 was improperly coded and tends to place Chloroflexi with Thiobacteria, as was 188, so that it comes up as a synapomorphy for Monoderma when it is really for Neosoma, instead, and 112 and 190 are empty characters so should be excluded, too. These, however, have little or no effect on the outcome except for 128, which is mentioned earlier, and 133.
The largest group is Thiobacteria and contains most taxons of Proteobacteria. Myxobacteria and Bacteroidikae are related to Chlorobia because of sphingolipids and the third is akin to Beggiatoikae because of sulfur oxidation which relates to Cyanobacteria because of longitudinal gliding. Crenothrix goes to Cyano as these are colourless blue bacteria as they possess thylakoids. As well as most photosynthesizers autotrophism occurs in methylmonanads, nitromonads, the hydrogen oxidizers(included in Pseudomonada), and Thiobacillus and lithotrophy in sulfomonads, Beggiatoikae, desulfomonads, Siderobacteria, Magnetobacteria, Nitrobacteria, Hydrogenobacteria, Methylmonada, Hyphomicrobikae, Pseudomonada, green sulfurs , and purple sulfurs. Corkscrew motion relates Spirillikae to Beggiatoikae, magnetosomes Magnetobacteria to the former, carboxysomes unite Nitrobacterikae, Pseudomonadikae, and Cyanobacteria, sheathed flagella Caulobacteria, Enterobacteria, and Spirillikae, iron/manganese oxidation Sulfomonada (Thiobacilli), Chlamydobacteria, and Pseudomonada, sheathed filaments Beggiatoikae, Cytophagikae, Chlamydobacteria, and Cyanobacteria, flexing motion Beggiatoikae and Cytophagikae, hydrogen oxidation Hydrogenobacteria, Cytophaga (Flavobacterium), and Pseudomonada while slime capsules occur in Neisserikae, Cyclobacteria, Myxobacteria, Enterobacteria, Beggiatoikae, and Cytophagikae, methanol utilization in Methylomonada, Hyphomicrobium, and Acetobacterikae (Acidomonas), nitrogen compound oxidation in Pseudomonada, Nitrobacteria, Enterobacteria, Neisserikae, and Methylmonada(Methylococcus), iron inclusions in Caulobacteria and Chlamydobacteria, and acetate production by fermentation in Bacteroidikae, Acetobacteria, and Veillonellikae, and Cyclobacteria goes to Methylmonada as one genus (Ancylobacter) is (facultatively) methylotrophic. So there are many similarities that indicate interrelationship between all these groups. One will notice that Cyanobacteria is very close to Proteobacteria in Woese (1987).
The synapomorphy for Archeoactinobacteria is peptide cross-linkage B at position 2 and 4, Neoactinobacteria is united by mycelia and acid-fastness, and Sporactinobacteria by arthrospores and aerial mycelia; mycolic acids are lost in Propionibacteria and Madurobacteria, arabogalactans are lost in Propionibacteria and Actinobacteria, and acid-fastness and coryneform cells are wanting in Madurobacteria; proteasomes occur in Euactinobacteriae, waxes in Corynebacteriae and Mycobacteria, and phosphatidylinositol is present in all groups; Propionibacterikae is of uncertain position but would belong in Corynebacteriae if it has a 2-layered wall. Butyrivibrio, a genus with both G+ and G- traits, most likely belongs in Proprionibacteria as it produces propionic acid.
The many traits between Metabacteria and Eukaryota could well be due to reticulate evolution. But, if Eukaryota is factored in, the results show a polyphyletic Metabacteria. As there are many characteristics shared particularly by Sulfobacteria with eukaryotes its polyphyly is maintained especially by Lake (loc. cit.) as earlier mentioned but also Lake et al (1984) and Gupta (1998). However, an analysis excluding Eukaryota would result in a monophyletic Metabacteria. Whether eukaryotes evolved through a fusion event, that is, a fusion between a sulfobacterium and a eubacterium, is unclear at this point but there is much good evidence for this(e.g., Gupta and Singh, 1994, but it would be with an actinobacterium, instead of a G- as that is where most of the similarities lie) and the analysis tends to indicate this, as well, as eukaryotes probably diverge before G-s in it but really diverge later, and it would explain the nuclear double membrane and the discrepancy between molecular evidence categories but the nucleus is part of the cytomembrane system which evolved through infoldings of the plasma membrane. This is explained by Gupta (1998).
2 new genera of metabacteria, Korarcheum, discovered in Yellowstone's Obsidian Pool (formerly called Jim Black's Pool) (Barns et al, 1995) and Nanoarcheum, discovered in a hydrothermal vent on the Icelandic coast, (Huber et al, 2002), were not included in the analysis for lack of information at the time, but both most probably belong to Sulfobacteria based on both phenotypic and genotypic data (Elkins et al, 2008; Brochier et al, 2005).
Sulfobacteria contains 16 genera (including the above 2 genera) in 6 families and 3 orders (Sulfoloboidia, Thermoprotoidia, and Thermococcoidia) which inhabit Icelandic geothermal sources, Yellowstone geysers and hot springs, carbon mine refuse, and submarine volcanic eruption fluids. Sulfolobus and Thermoprotoidia have glycoprotetinaceous walls arranged in a hexagonal pattern.
Methanogens have walls of pseudopeptidoglycan, protein, glycoprotein, and heteropolysaccharides, and contain 18 genera 7 families and in 3 orders: Methanobacteroidia, Methanococcoidia, and Methanomicrobioidia, which inhabit sewage sediments, animal intestines, bogs, swamps, and estuaries. They are responsible for marsh gas which accounts for 90% of natural gas and produce over 2 bln. tons of methane per year.
Halobacteria contain only 1 order, Halobacteroidia, 2 families, and 6 genera, which dwell in hypersaline habitats such as salt lakes, salt ponds, soda lakes (2 genera), salt flats, brine, and salted fish and meats. Its salt concentrations are up to 5.5 M NaCl (32%), which is at the saturation limit. The walls contain glycoproteins and heteropolysaccharides.
The orders and families are based on descriptions in Holt et al (1994), but which does not use ranks for them.
Thermoplasmata has only 1 genus and branches deeply here and also in Woese (1997) and Barns et (1996), where it groups with methanogens. It has no walls but has derived features in common with Sulfobacteria, sulfur metabolism and hyperthermoacidophilia, and also with methanogens, histone-like proteins.
Archeoglobi, like Thermoplasmata, has also only 1 genus and branches deeply both here and in molecular phylogenies.
Table 3.
Empire Biota
Thermosiphia
Aerobia
Fervidobacterium
Thermotoga
Metaerobia
Monoderma
Firmicutes
Mollicutes
Eufirmicutes
Clostridia
Actinobacteria
Neosoma
Archeoglobus
Metasoma
Thermoplasma
Cenosoma
Halobacteria
Methanobacteria
Parkaryota
Sulfobacteria
Eukaryota
Gracilicutes
Protogracilicutes
Chloroflexa+Heliobacteria
Thiobacteria+Deinobacteria
Metagracilicutes
Thermus
Neogracilicutes
Spirochetes
Pirellulae
Chlamydiae
Planctobacteria
Rickettsiae+Cyanobacteria+Chloroxybacteria
Synapomorphies
Aerobia: large STK, loss of long chain diabolic acids, aerobism, loss of hyperthermophily, catalase
Monoderma: non-formylated methionine, glutaminyl synthase tRNA glutamine transamidation, tRNA mischarging, proteasoman alpha-amylase primary structure, proteasoman serine protease 3D structure, tyrosine kinases, serine/threonine kinases, type 1 fatty acid synthase, Ku with HEH domain, calmodulin homologs, chitin
Firmicutes: DOXY pathway; foliate derivative as RNA methionine methyl donour; actinomycin, novobiocin, and penicillin sensitivity, DNAP uracil, loss of DNAP exonuclease function
Eufirmicutes: teichoic acid, naphthaquinones
Neosoma: wall with glycoprotein hexagonal array, loss of murein, pilin-like flagellar protein, HSP 90, thermosomes, ether lipids, archeol, mevalonate LFP, N-linked glycosylation, EM pathway with PFK, EM pathway reversal, ribosome SSU with bill, ribosome LSU with lobe, ribosome LSU with bulge, EF-1 aminocyl, tRNA-to-ribosome catalysis with EF-?, EF-2 with diphthamide, peptidyl tRNA translocation, with EF-2, EF-2 compatability, ribosome subunit, multiple RNAP enzymes, 8 or more RNAP subunits, RNAP subunit A, RNAP subunit B, mRNA with tail cap and tail
Metasoma: potentially coaxial helices, core histones
Euryarcheota: halophilia
Table 4.
sbemp. Bacteria (Ehrenberg 1835)
infemp. Thermosiphia stat. nov., nom. nov.
kgdm. Thermosiphia stat. nov.
infemp. Contobacteria tax. nov.
mgk./kgdm. Fervidobacteria
mgk. Metacontobacteria
hprk./kgdm. Thermotogae
hprk. Neocontobacteria
spk. Monodermata (Gupta 1998, Unibacteria Cavalier-Smith 1998)) stat. nov.
kgdm. Firmicutes (Gibbons & Murray 1978, Teichobacteria Cavalier-
Smith 1998)
spph./phyl. Mollicutes (Tenericutes Gibbons & Murray 1978)
spph. Eufirmicutes nom. nov., stat. nov.
phyl. Clostridia
phyl. Actinobacteria (Margulis 1974)
kgdm. Mendosicutes (Archeobacteria Woese and Fox 1977; Gibbons & Murray 1978; Metabacteria Hori
& Osawa 1992) stat. nov.
sbk./phyl./cl. Archeoglobi stat. nov.
sbk. Thermoacidophila tax. nov.
spph./phyl./cl. Thermoplasmata
spph. Cenobacteria tax. nov.
phyl. Euryarcheota (Woese, Kandler, and Wheelis 1990)
cl. Halobacteria
cl. Methanobacteria
phyl. Crenarcheota (Woese, Kandler, and Wheelis 1990) (Caldaria Mohn 1984, Eocyta
Lake 1984)
cl. Sulfobacteria (Cavalier-Smith 1986)
spk./kgdm. Gracilicutes (Gibbons & Murray 1978; Cavalier-Smith 1987, Didermata Gupta 1998)
sbk. Eugracilicutes tax. nov.
spph. Photobacteria (Gibbons & Murray 1978) tax. nov.
phyl. Chloroflexi stat. nov.
phyl. Thiobacteroidia
sbph. Thiobacteria stat. nov. (Mohn 1984 emend.)
sbph. Deinobacteria (Cavalier-Smith 1986) stat. nov.
spph. Spirochetes (Spirochetae Ehrenberg 1855)
sbk./phyl. Pirellulae stat. nov. emend.
cl. Rickettsiae
cl. Pirellulae
ord. Chlamydiae stat. nov.
ord. Planctobacteria Cavalier-Smith 1998 stat. nov.
Synapomorphies
Firmicutes: DNAP uracil, DNAP exonuclease function, LL-DAP acid, teichoic acids, peptide bridge for A with dicarb
Monoderma: (post-transcriptional) addition of tRNA(3’-terminal) CCA, proteasomes
Actinobacteria: coryneform cell, mycolic acids, peptide cross-linkage B at position 2 and 4
Mendosicutes: wall with glycoprotein hexagonal array, pilin-like flagellar protein, HSP 90, thermosomes, ether lipids, archeol, mevalonate LFP, N-linked glycosylation, EM pathway with PFK, EM pathway reversal, ribosome SSU with bill, ribosome LSU with lobe, ribosome LSU with bulge, EF-1 aminocyl, tRNA-to-ribosome catalysis with EF-a, EF-2 with diphthamide, peptidyl tRNA translocation, with EF-2, EF-2 compatability, ribosome subunit, 8 or more RNAP subunits, RNAP subunit A, RNAP subunit B, mRNA with tail cap and tail, nonformylated methionine, multicomponent RNAPs, introns, B DNAPs, PCNA sliding clamp, high no. of r-proteins, RNAP, DNAP, and protein synthesis antibio resistance, DNAP VI, DNA 10b MCM, N-linked glycosylation, neosoman 5S 3D structure, co- translational protein secretion, vacuolar proton-pumping ATPase, oligosaccharyl transferases, SECIS- binding protein, ubiquitin- directed proteolysis, fibrillarin, replication factor C, RNA-binding proteins, ribosomal subunit compatability, EF-2 with diphthamide, IF-2 and 5A, absence of EF compatability, loss of murein, HSP 10, and SEC A.
Euryarcheota: halophilia, AB'B" polymerase.
Thermoacidophilia: larger LSU lobe, LSU bulge, thermacidophilic 5S secondary structure, cyclopentanol C40- biphytanol chains, hyperacidity.
Gracilicutes: large citrate synthase, flagellar ring, outer membrane, LPS, invagination, large succinate thiokinase, NADH resistance
Eugracilicutes: spiral cell
Photobacteria: photosynthesis, autotrophy, aa3 cytochrome
Thiobacterina: sulfide respiration, rubisco, lithotrophy
Thiobacteria: tRNA transamidation of asparagine by aspartyl synthase
Table 5. - List of Taxons for Data Matrix
0. Thermosipho 1. Rickettsiae 2 Chlamydiae 3. Planctobacteria 4. Spirochetes 5. Chloroflexi 6. Thiobacteria 7. Cyanobacteria 8. Chloroxybacteria 9. Thermus lO.Deinobacteria 11. Mollicutes 12. Heliobacteria 13. Clostridia 14. Fervidibacteria 15. Thermotoga 16. Actinobacteria 17. Halobacteria 18. Archeoglobus 19. Methanobacteria 20. Thermoplasma 21. Sulfobacteria 22. Eukaryota
Table 6. Data Set - Bacteria
all of the states are 0 absent and 1 present except where otherwise indicated; in TNT the taxons are numbered starting with 0
morphology
flagella
1. proterokonty
2. (proterokontic ) position 0 polar 1 lateral 2 internal
3. no. of poles 0 monopolar 1 bipolar
4. no. of polar flagella 0 single 1 multiple
5. (proterokontic) BB 0 with inner rings 1 with outer rings
6. (prot.) pass through outer membrane 0 absent 1 present
7.(prt.) (rotation) 0 with rt-handed helix 1 with left-handed helix general
8. cell shape 0 coccoid 0 bacillary 0 coryneform 0 vibrioid 0 spiral 1 oval 1 ell.
9. 0 coccoid 0 bacillary 0 coryneform 0 vibrioid 0 spiral 0 oval 1 ellip.
10. 0 coccoid 0 oval 0 ellip. 1 bacillary 1 coryneform 1 vibrioid 1 spiral
11. 0 coccoid 0 oval 0 ellip. 0 bacillary 0 coryneform 0 vibrioid 0 spiral 1 coryneform
12. 0 coccoid 0 oval 0 ellip. 0 bacillary 0 coryneform 1 vibrioid 1 spiral
13. 0 coccoid 0 oval 0 ellip. 0 bacillary 0 coryneform 0 vibrioid 1 spiral
14. capsule
15. fimbrias
16. toga
17. prosthecas
18. sheathed filaments
19. carboxysomes
chemistry
cell wall
20. peptidoglycan 0 pep 1 psdpep 2 -
21. heteropolysaccharides
22. protein 0 - 1 + 1 glycoprotein
23. 0 - 0 + 1 glycoprotein
24. murein 0 N-acetylated 1 N-glycolated
25. peptide cross linkage 0 A anchors at subunit position 3 and 4 1 B at pos. 2 and 4
26. peptide bridge for A 0 none 1 all
27. 0 1 monocarb 2 dicarb
28. 0 1 polymerized subunits
29. peptide bridge for B 0 L-amino acid 1 D-amino acid
30. amino acids at pos. 3 0 lysine 1 ornithine 1 DAP acid
31. 0 lysine 0 ornithine 1 DAP acid
32. peptidoglycan layer 0 thin 1 thick
33. teichoic acid
34. mycolic acid
35. cell wall outer membrane
36. KDO
37. LPS
38. cell wall with glycoprotein hexagonal array
storage products
39. type 0 PHB 1 a-1-4 amino acids
40. LSP 0 with DAP acid 1 with AAA acid
41. glutamine I type 0 ? ??? proteins general
42. cytochromes 0 c 0 a1 0 aa3 0 d 1 b 1 o
43. 0 c 0 a1 0 aa3 0 d 0 b 1 o
44. 0 c 0 b 0 o 0 d 1 a1 1 aa3
45. 0 c 0 b 0 o 0 d 0 a1 1 aa3
46. 0 c 0 b 0 o 0 a1 0 aa331 d
47. flagellar protein 0 flagellin 1 pilin-like
48. HSP 90
49. actin-tubulin folding chaperonins, no. of subunits 0 7(Group I) 1 8 (thermosome)(Group II) 2 9 (Group II)(TRIC(CCT))
50. actin-tubulin folding chaperones 0 GROES 1 GROEL/GIMC(2 subunits) 2 GROEL/GIMC (6 subunits)
51. proteasomes
52. protein secretion mech. 0 post-translational 1 co-translational
53. protein secretion chaperone 0 SecA 1 SecB
enzymes
54. citrate synthase with N-terminal helix
55. citrate synthase sensitvity/inhibition to NADH
56. citrate synthase NADH inhibition AMP reactivation
57. citrate synthase inhibition by alpha-oxoglutarate
58. citrate synthase size 0 small 1 large
59. STK size 0 small 1 large
60. catalase
61. tyrosine kinases
62. oligosaccharyl transferases
63. split glutamate synthase
64. FDP aldolases
65. FDP-activated lactate dehydrogenase
66. serine proteases 3-D structure
67. superoxide dismutase (SOD) 0 FeMn 1 CuZn coenzymes
68. factor 420
69. methanopterin lipids
70. membrane lipids 0 straight chain fatty acids with ester bond 1 branched chain aliphatic acids with ether bond
71. diether/tetraether ratios 0 high/low 1 low/high
72. triterpenes 0 - 1 hopanoids 2 sterols
73. carotenoids 0 a-car. 0 A 0 M 0 gm-car. 1 H
74. 0 A 0 M 0 gm-car. 0 H 1 a-car.
75. 0 a-car. 0 M 0 gm-car. 0 H 1 A
76. 0 a-car. 0 gm-car. 0 H 0 A 1 M
77. 0 a-car. 0 M 0 H 0 A 1 gm-car.
78 quinones
79. quinone types 0 benzoquinones 0 anthraquinones 0 anthracyclinones 1 naphthaquinones
80. 0 benzoquinones 0 anthracyclinones 0 naphthaquinones 1 anthraquinones
81. 0 benzoquinones 0 anthraquinones 0 naphthaquinones 1 anthracyclinones
82. sphingolipids
83. sulfonolipids
84. archeol
85. caldarcheol
86. unsaturated fatty acids 0 monoenoic 0 polyenoic 1 cyclopropane 1 10-methyl
87. 0 monoenoic 0 polyenoic 0 cyclopropane 1 10-methyl
88. 0 monoenoic 0 cyclopropane 0 10-methyl 1 polyenoic
89. fatty acid pathway 0 anaerobic 1 Desaturase I 2 Desat. II
90. fatty acid synthase 0 type II 1 type I
91. long chain diabolic acids
92. waxes
93. PI
94. PIM
95. lipid formation pathway 0 malonate 1 mevalonate
96. DOXY pathway
general
97. cellulose accumulation
98. chitin
99. glycosylation 0 O 1 N
100. S deposition 0 ext 1 int
101. DPA
102. EM pathway 0 without PFK 1 with PFK
103. EM pathway reversal general
104. metabolism 0 fermentation 1 respiration
105. type of respiration 0 anaerobic 1 aerobic
106. carbon sources 0 CH O (heterotrophic) 1 CO (autotrophic)
107. energy sources 0 chemical compounds(chemotrophic) 1 light(phototrophic)
108. electron or H donors 0 organic compounds(organotrophic) 1 inorganic compounds and C(lithotrophic)
109 hyperthermophily 0 + 1 -
110 TCA cycle 0 incomplete 1 complete
111 CO fixation(assimilation) pathway 0 hydroxyproprionate 1 reverse TCA 2 Calvin-Benson
112.
113. sulfur compound oxidation
114. sulfate reduction
115. iron oxidation
116. CO oxidation
117. hydrogen oxidation
118. nitrate reduction
119. methanogenesis
120. clastic system
121. adenylate ADP-ATP exchange system photosynthesis
122. chlorophyllian photosynthesis
123. reaction center pigments 0 bacteriochlorophylls 1 chlorophylls
124. bacteriochlorophylls 0 c 0 a 0 b 0 d 0 g 1 e
125. 0 c 0 e 1 d 1 a 1 b 1 g
126. 0 c 0 e 0 d 1 a 1b 1 g
127. 0 c 0 e 0 d 0 a 0 g 1 d
128. 0 c 0 e 0 d 0 a 0 d 1 g
129. chlorophylls 0 a 1 b 2 c
130. 0 a 0 b 1 c 131. phycobilins
132. carotenoid structure 0 aryl 1 aliphatic 2 alicyclic
133. antenna pigments 0 bchl a or b 1 bchl c, d, or e 2 phycobilins and chl a
134. photosynthetic system 0 chlorosomes 1 cytoplasmic membrane 2 phycobilisomes
135. metabolic type 0 anoxygenic 1 oxygenic
136. electron donours 0 H2 1 S or H2S 2 HO2
137. ALA 0 glycine succinyl Co A 1 L-glutamate
reproduction
138. cell division 0 with septum 1 without septum
139. sporulation
140. sporulation position 0 internal 1 external
141. myxospores
142. budding movement
143. motility
144. gliding
145. longitudinal gliding motility
146. magnetotaxis mol. biol. ribosomes
147. small subunit 0 without bill, lobe, gap, or platform split 1 with bill only 2 with bill + lobe, gap, and platform split
148. large subunit lobe
149. LSU filled gap
150. LSU bulge
151. 70S subunit association 0 tight 1 loose 5S secondary structure
152. no. of helices 0 4 1 5
153. helix IV base loop nucleotides 0 3 1 4
154. potentially coaxial helices 5S tertiary structure
155. helices 0 4 1 5
156. region E loop
157. G region 0 long 1 short
158. 5S rRNA 5’ termini with 0 monophosphate 1 triphosphate ribosomal A protein
159. C- terminal region
160. N-terminal region
161. valine content 0 high 1 low
162. size(no. of residues) 0 large 1 small r-proteins
163. no. 0 54-65 1 60- 65 2 70-80
164. acidity 0 low 1 high
165. r-subunit protein LX
166. IF hypusine
167. mol. mass of hypusine 0 low 1 high
168. EF-1 aminoacyl tRNA-to-ribosome catalysis 0 EF-Tu 1 EF-alpha
169. EF-1 G affinity
170. EF-1 inserts 0 4-amino acid 1 11-amino acid
171. EF-2 0 without diphthamide 1 with diphthamide
172. peptidyl tRNA translocation 0 EF-G 1 EF-2
173. EF-2 compatibility 0 + 1 -
174. subunit “ RNA
175. RNAP type 0 simple 1 multicomponent
176. no. of RNAP subunits 0 4 1 8 or more
177. RNAP A
178. RNAP A structure 0 split 1 integral
179. RNAP B
180. RNAP B structure 0 split 1 integral
181. H
182. G
184. protein encoded nuclear genes with 0 cis-splicing of miniexons 1 trans-splicing
185. SRP size 0 4.5S 1 7S
186. SRP helices 1-4
187. protein-RNA mass ratio 0 low 1 high
188. tRNA initiator methionine 0 formylated 1 nonformylated
189. G tetra- and pentaphosphates
190.
191. 1-methylpseudouridine 0 + 1 -
192. N ,N -dimethylguanosine
193. X
194. archeosine(in D loop)
195. queuine 0 + 1 -
196. RNA modification levels 0 low 1 high
197. tRNA anticodon loop 0 + 1 -
198. tRNA transamidation of asparagine 0 asparaginyl synthase 1 aspartyl synthase
199. tRNA transamidation of glutamine 0 glutamyl synthase 1 glutaminyl synthase
(200. tRNA mischarging)
200. tRNA spacers 0 + 1 -
201. tRNA 3’ terminal CCA added posttranscriptionally
202. mRNA ends 0 without cap or tail 1 with tail only 2 with cap and tail
203. RNA methionine methyl donor 0 S-adenosylmethionine 1 folate derivative DNA
204. histones
205. topoisomerase II gyrase activity 0 + 1-
206. 2-stranded DNA repair Ku protein with C-terminal HEH domain
207. type II DNAP VI meiotic protein
208. B DNAPs, no. of subunits per ring 0 1 1 2 2 3 3 4
209. DNA helicase 0 DNAB 1 MCM
210. DNA binding protein 10b
211. G-C ratio 0 low 1 medium 2 high
212. sliding clamp
antibio sensitvity RNA polymerase
213. rifampicin
214. streptolydigin
215. actinomycin D
216. novobiocin
217. DNA polymerase aphidicolin butylphenyl-dGTP protein synthesis ribosome-targeted
218. antibio group A 0 high 1 low
219. antibio group B 0 high 1 low
220. antibio group C 0 low 1 high
221. antibio overall 0 high 1 low
222. antibio very high
223. antibio high
224. antibio low
EF-targeted antibios
225. kirromycin
226. pulvomycin
227. fusidic acid
228. penicillins 0 lo 1 hi
miscillaneous
229. introns 0 - 1 self-splicing 2 protein splicing
230. promoter type 0 eubacterial 1 box A
231.box A in ICR
232 TATA-binding protein(TBP)
233. SECIS binding protein
234. genome size 0 small 1 large
235. silybin stimulation
addenda
236. flagella 0 external 1 internal
237. gas vacuoles
238. rosettes
239. mycelia
240. wall peptidoglycan with LL-DAP acid
241. wall peptidoglycan with L- and D-lysine
242. wall peptidoglycan with arabose-galactose
243. calmodulin
244. oligosaccaryl transferases
245. proton pumping H-ATPase catalytic subunit insertion 0 F 1 V
246. rhodopsin
247. C40-biphytanyl diol chains 0 acyclic 1 mono and bicyclic 2 tri and tetracyclic
248. S oxidation
249. hyperacidophily
250. corkscrew motion
251. EF-5A
252. DNAP uracil sensitivity
253. DNAP exonuclease function 0 + 1 -
254. tRNA 5’ terminal base, molecular stalk, paired
255. (complex) replication factor C
256. HSP 10 0 + 1 -
257. plasmologens
258. STK size 0 small 1 large
259. rotund bodies
260. LSU lobe size 0 small 1 intermediate 2 large
261. epsilon B DNAP
262. division by invagination
263. halophily 0 - 1 moderate 2 extreme
Table 7. Data Matrix
0Thermosipho
0------00100000100000000????????000-00?00-----000000000?00000000000000-0-----0---000000000100000000-0000-00000--0000000000---------------00-0010-00000000000000000000000000000000-0-000000000000000000000000000000?00000000000000000000001000000100000-000000000 000-000
1Rickettsiae
???????001000010000000000000-110001010001[01][01][01][01][01]00000000??????0000000000-10000[01]1000[01]00010000000000000-0001100010?-0000000010---------------00-0010-00000000000000000000000000000000-0-000000000000000000000000000000?000000000000000000000010?0000000000-000000000010-010
2Chlamydiae
0------0010000000000010------------010?01-[01][01]0[01]00000000?????00000000000-0000000---000010000000001000-0001000010?-0000000010---------------00-0010-00000000000000000000000000000000-0-0000000000 000000000000000000000000000000000000000000000-000-000000-0000 00000010-010
3Planctobacteria
???????0010000000000010-------------10?01?0?0[01]00000000??????0000000000-0000000---000010000000001000-0001100010?-0000000000---------------00-011[01]-00000000000000000000000000000000-0-0000000000 00000000000000000000?00000000000000000000001000[01]0-000000-0 00000000010-010
4Spirochetes
1---100001011000000000000000-1[01]0001010?01?0[01]0[01]00000000?????00000000000-00000[01]0---000010000000000000-0001[01]000101-0000000100---------------00-0010-00000000000000000000000000000000-0-000000000000000000000000000000100000000000000000000001010000000000-000000000[01]10-010
5Chloroflexa
0----0 -?000 00000000000000000-100001000-01?????00000000?????000 00000000-000[01]0[01]1000000010000000001000-00010010[12]0?0000000000100[01][01]00--000000000-00[01]1000000000000000000000000000000000-0-00000000000000000000000000000010000000000000000000 00010-0000000000-000000000010-010
6Thiobacteria
[01][01]0[01]1[01]0[01][01][01]0[01][01][01][01]0[01][01]0000000000[01]100[01]1[01]10[01]0[01][01][01][01][01][01]00000000[01][01][01]11[01]0000000000-[01][01]0[01]0[01][01][01][01]0[01][01]00100000[01]000[01][01]001000 [01][01][01][01][01][12][01][01][12][01][01][01][01][01][01]000[01]0[01][01][01][01]0--0[01][01][01]0[01][01]0[01]1[01][01][01][01][01][01]0000000000000000000000000000000-0-00000000000000000[01]000000000000[012]0000000000000000000000[01]00[01][01]00000000-0000[01]0000[01]10-01 [01]
7Cyanobacteria
0------?????1000010000000000-111001010[01]01?000000000000????110000000000-[12]00[01][01][01]1[01]000[01]0010110000001000-0001111110[01]2000[01]0000011-----0012021210[01]100[01][01]100000000000000 000000000000000000-0-000000000000000000000000000000[02]000000000000000000000010-1000000000-000000000010-010
8Chloroxybacteria
0------?????0000000000000000-110001010?01????000000000?????00000000000-000[01]0[01]1000000010000000000000-0001100010?200000000011-----100?0212?00-00?0-00000000000000000000000000000000-0-0 00000000000000000000000000000?000000000000000000000010-0000 000000-000000000010-010
9Thermus
0------001000000000000000000-100001100?01??[01]0[01]000000000???100000000000-0000000---000010000000000000-00011000001-0000010000---------------00-0010-00000000000000000000000000000000-0-000000 000000000000000000000000?00000100000000000000001000000000000-000000000011-010
10Deinobacteria
0------00[01]000000000000000000-100001000?01?[01][01]0[01]00000000?????10000000000-0000000---000010000000001000-0001100011?-00000[01]0000--------------00-0010-00000000000000000000000000000000-0-00 000000000000 000[01]000000000000?0000000000000000000000100000 0000000-000000000010-000
11Heliobacteria
[01]1--1-0001000000000000000000-100001000?00?????00000000?????00000000000-0?????0---000010000000001000-1001001010??0000000001001101--0??10??00-001[01]-00000000000000000000000000000000-0-0 00000000000000000000000000000?0000000000000000000000100000 0000000-000000000010-000
12Clostridia
11--0 -000[01]0000000000000000[01]0-[01][01]1100--0?01[01][01][01]000 00000000-???[01]0000100000-0-----11000000100[01]0000001100-100[01][01]101[02]0020[01]0[01][01][01]0100---------------0100010-0000000000000 0000000000000000000-0-00000000000000000010001000000000001100 0000000001000001000001000000-0000[01][01]000[01]00-00[02]
13Mollicutes
0------ 00[01]0[01]0000000-----------------00?01-----000000000-???00000000 000-0-----0000000000000000001000-0001[01]000101-0000000000---------------00-0[01][01][01]000000000000000000000000000000000-0-0000000 10000000000100010000000000011000000000001000000-00000000000-00000[01]000000-000
14Actinobacteria
[01]1--0-0[01]0[01][01][01]00000000000[01][01][01][01]0[01][01][01]11[01]0-00101[01][01][01]0[01]0000[01][01]00[01]?001[01][01]000[01][01]0000-[02][01]100[01]11000000[01][01]0[01][01]0[01][01][01]010[01]0-[01]00[01] [01]000[12]01-00000[01]0000---------------0[01]100[01]0-00000000000000000000000000000000-0-00000001000000000010[01]0100[01]00002000 [01][01]0000000000010000010000[01][01]0[01][01]000-0000[01]0000[01]0 0-000
15Fervidobacterium
1???0-000100000000000000????????000-00?00-----000000000?00000000000000-0-----0---000000000100000000-0000-00000--000000 0000------- --------00-0010-00000000000000000000000000000000-0-0000000000000 00000000000000000?00000000000000000000001000000100000-000000 000001-000
16Thermotoga
1[01]?00-000100000100000000????????000-00?00-----000000000?0000 0000000000-0-----0---000000000100000000-0 000-0 0000--0000000000----- ----------00-0010-00000000000000000000000000000000-0-000000000000 000000000000000000?00000000000000000000001000000100000-00000 0000000-000
17Halobacteria
100?0-100[01]0000100002[01]11-----------0--1?00[01][01][01][01]0111111110???1?0111?0?001000000[01]1100000000000000010001-0101[01]01020?30000000000---------------00-0010-010000[01]101110111111110110111 1111110011100110111111110101100001111?111001110211011002100 1100000---0111-0001001110000002
18Archeoglobus
????0-?000000000000?0??-----------0--1?00?????111???????????0???? 0?111?0000000---001100000000010001-01110[01]0000?-0100001000----- ----------00-0010-02101???0???0????????01101111111110????????00? ??00?00?0110000????????00???0???????0?000??00000---0??0?000?0 00?00000000
19Methanobacteria
[01]0??0-000[01][01][01]00100001[01]11-----------0--1?00?????11111111??????0111?0?111[01]0000000---001100000000010001-0111010120?30000001000---------------00-0010-02[01]0[01]00[01]1???01111[01][01]110110 111111111011110011001111?110101102001111?1110011101001110021001[01]00000---01100000100011000010[01]
20Thermplasma
????0-?000000000000---0-----------0--1?00?????111???????????0????0100110000000---001100000000010001-0111[01]00010?-0000000000------ ---------00-0010-021010111???0????????01101111111111111101?100?? ?00100?0110200??????1100?010111111100?00?010000---0??0[01]110? 000?00001000
21Sulfobacteria
[01]0010-000[01]0000000012011-----------0--1?10?????11211111??????0111?0?00110000001100001100000000010001-0111[01]10000?-0000000000---------------10-0010-021011111???1????1?111111111111111111111 111101111111011110210111111110011102112111021111010000---0110 [12]1101000110002100
22Eukaryota
0------ [01][01][01]0[01]000000120[01][01]-----------0--011?[01][01][01][01]0-0111110?????-1110?12000-[12] 0[01]00[01][01][01][01]0001100[01][12]10 [01]0010[01][01]1-001[01][01]000[12]0[01]20000000000---------------1[01]10 [01][01][01] [01]02111111111111111200111111101111111000110111100 01100[01]011102111110[01] 111001001010011002111111000[01]---011 [01]-000100111[01]00210[01];
cc ] 24.28 85.87 140 145 169 235 249;
Table 8. Phylum Actinobacteria.
sbphyl. Archeoactinobacteria
cl. Corynebacteriae stat. nov.
cl. Actinobacteriae
sbphyl. Neoactinobacteria tax. nov.
cl. Euactinobacteriae stat. nov.
spord. Mycobacteria stat. nov.
spord. Sporactinobacteria stat. nov.
ord. Nocardiae
ord. Madurobacteria
Table 9. Taxon Totals for the 16 Kingdoms.
phyla classes orders families genera species
eukaryotes
Animalia 25 84 c 360 c 3600 c100, 000 c 1.1 mln.
Plantae 12 20 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 30 67 c. 330 c. 3000
Firmicutes 3 7 15 15 c. 200 c. 2000
Mendosicutes 4 5 9 17 42 ?
Thermotogae 1 1 1 1 1 ?
Fervidobacteria 1 1 1 1 1 ?
Thermosiphia 1 1 1 1 1 ?
total (bact) 13 22 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.
Eukaryotes
Materials and Methods
The data set ( Page 2) for the 1st eukaryote analysis contained 27 taxons and 260 characters, 20 branched (complex), in 283 colulmns 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 2 (Page 2). The computer calculations were done by James Carpenter using the TNT (Tree analysis using New Technology) computer program (Goloboff, 1999; Nixon, 1999). All 4 new technologies were used (ratchet, tree drifting, fusing, sectorial search) and TBR (tree bisection and reconnection) branch swapping was employed. Cyanidioschyzon was used as the root. (Cladograms can't be done properly with computer graphics so it would be a hand made cladogram but I am not able to insert an image ).
For the 2nd eukaryote analysis, Plasmodiophorae and Spongomonada were excluded, the 14 deactivated characters were included, and 4 myosin characters were added. The computer calculatiions were done by Dr. Pablo Goloboff.
A strict consensus with no groups excluded yielded low resolution and one with Apicomplexa and Myxofilosa excluded did not fair much better. A majority consensus, set at 50+%, was also done, which gave much better resolution (Table 3). 3 groups are based on homoplasies, Galdieria-Cyanidium, Protomebae+Cercomonada, and Myxofilosa+Opisthokonta.
Of the 6 consensus methods, majority, strict, semistrict, Adams, Nelson, and combinable components, the 1st 2 are the most popular and it is majority consensus, devised by Margush and McMorris (1981), I favour as it usually produces better resolution and is simple. TNT does only strict consensus. The synapomorphies are in Table 4.
The following 9 clades have 100% support across the 2 analyses: Metakaryota, Galdieria-Cyanidium, Neokaryota, Cellulosa, Contophora, Euchrista, Neolobosa+Protolobosa (Protamebae), Opisthokonta, Actinopoda+Foraminifera (Retaria).
Some groups are misplaced because of homoplasy so I have repositioned them according to both phenotypic and genotypic features (Table 10). Ochrobiota (similar to Chromalveolata and (mostly) recognized also by Lipscomb) is composed of Ochrista, Retaria, and Dinobiota (Alveolata and Excavata (Discicristata)), and is the most strongly supported supergroup with a dozen synapomorphies. Also, Plantae probably belongs above Unikonta as it has more derived traits than either Animalia or Fungi.
Table for Diana Lipscomb's Classification ( her results from 1989 and 1991)-7 kingdoms.
Contophora
Plantae
Supergroup 2
Cryptomonada
Supergroup 3
Amebae+Oomycota+Chromobiota+Heliozoa
Supergroup 4
Polymastigota
Animalia +(Choanozoa+Fungi)
Opalinida+Dinociliata+Euglenaria
Table 3. Implied Weighting Tree- 1st Analysis, 9 Kingdoms.
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
Table 4. Majority Consensus for Eukaryota- 2nd analysis, 9 Kingdoms.
sbemp. Eukaryota Dougherty 1959 stat. nov.
infemp. Cyanidiochyza stat. nov., nom. nov.
kgdm. Cyanidioschyza stat. nov.
infemp. Metakaryota Cavalier-Smith 1993 tax. nov.
mcemp. Galdieria-Cyanidium stat. nov., nom. nov.
kgdm. Galdieria-Cyanidium stat. nov.
mcemp. Cenokaryota tax. nov.
nnemp. Glaucophyca stat. nov., nom. nov.
kgdm. Glaucophyca
nnemp. Cellulosa tax. nov.
ggk. Rhodophyca stat. nov., nom. nov.
kgdm. Rhodophyca
ggk. Contophora Mohn 1984 stat. nov. emend.
mgk. Plantae Haeckel 1856 emend. (Isokonta nom. nov., Isokontae Blackman and Tansley 1902)
kgdm. Plantae
mgk. Anisokonta nom. nov., stat. nov.
hprk./kgdm. Ochrista Cavalier-Smith 1986 stat. nov., emend.
sbk./phyl. Chlorarachnia stat.nov.
sbk. Euchrista Cavalier-Smith 1993 stat. nov.
spph./phyl. Haptophyca stat. nov., nom., nov.
spph. Neochrista tax. nov.
phyl. Heterokonta Cavalier-Smith 1986 (Heterokontae Luther 1899)
phyl. Cryptophyca nom. nov.
hprk. Metanisokonta
spk./kgdm./phyl. Homolobosa (Protoamebae + Cercomonada)
cl. Eulobosa (Protamebae) nom. nov. (Rhizopoda)
sbcl. Neolobosa nom. nov.
sbcl. Protolobosa nom. nov. ( Pelobiota Page 1976, orthogr. emend.)
cl. Cercomonada Poche 1913 (as order) (Cercolobosa nom. nov.)
spk. Myxokonta+Neanisokonta
kgdm. Myxofilosa+Opisthokonta (Myxokonta)
sbk. Myxofilosa nom. nov., stat. nov.
sbk. Opisthokonta stat. nov.
infk. Animalia Linneus 1758 emend.
infk. Fungi Linneus 1753 emend.
kgdm. Neanisokonta
sbk. Foramaxia nom.nov. (Retaria Cavalier-Smith 1999, emend.)
phyl. Actinopoda Calkins 1909
phyl. Foraminifera d’Orbigny 1826
sbk./phyl. Apicomplexa Levine 1970
sbk. Dinobiota tax. nov. Stewart and Mattox 1980
spph. Dinociliata nom. nov./spcl. Ciliata Perty 1852 (Heterokaryota Hickson 1903) stat. nov.
Dinoflagellata Butschli 1885 stat. nov.
spph./phyl. Excavata Cavalier-Smith 2002
sbph. Protoexcavata
cl. Euglenaria nom. nov.
cl. Jakobea Cavalier-Smith 1993 (as order) stat. nov.
sbph. Neoexcavata tax. nov.
cl. Polymastigota Blochman 1895 (as order)
cl. Heterolobosa Page and Blanton 1985 orthog. emend.
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, tubular cristas
Anisokonta- tubular cristas, AAA LSP, MYTH4FERM myosins, and TH 1 myosins.
Metanisokonta-thecal and capsular plate position, tranisitional cytoplasmic organization
Ochrista- chloroplast in ER (endoplasmic reticulum), nucleomorphs
Euchrista (Metachrista)- PR (periplastidial reticulum), chloroplast in SER (smooth ER), silica in walls, transitional
helix (including helical band in haptophycans)
Neochrista- epsilon- carotene, maastigonemes formed in nucleaer envelope and ER, tripartite mastigonemes
Cercomyxa-ppks, striated fiber emanates from anteriorly directed flagellum extending as cone and terminating in MTOC,
cercomyxan semicircle complex
Retaria - pheodarian-type pseudopods
Dinobiota- articulins, mastigoneme rows 1 and 0, kinetochore location on nuclear envelope, permanently condensed
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 10. sbemp. Eukaryota (Dougherty 1957)-10 kingdoms
infemp./kgdm. Cyanidioschyza
infemp. Metakaryota
mcemp./kgdm. Cyanidiophyca
mcemp. Neokaryota
ggk./kgdm. Galdieria
ggk. Cellulosa
mgk./kgdm. Rhodophyca
mgk. Contophora
hprk. Unikonta
spk./kgdm. Conosa
spk. Opisthokonta
kgdm. Animalia
kgdm. Fungi
hprk. Bikonta
spk./kgdm. Glaucophyca
spk. Metakonta
kgdm. Plantae
kgdm. Ochrobiota
sbk. Dinista
sbk. Ochrista
Discussion
Cyanidioschyzon merolae is most definitely the ancestral eukaryote as it has the fewest advanced traits with 12 and the highest percentage of primitive traits with 90 % (excluding inapplicable and missing data), and is the root. It is supported as basal by Seckbach (1994) and Nagashima et al (1993), having the most primitive chloroplast, only 1 mitochondrion, no vacuoles, no trienoic acids, and the smallest eukaryotic genome at 8 Mbp. Prerhodophyca (after Seckbach (1987), including all 3 genera, which are eukaryotic blue algae), has no synapomorphies and is obviously an artifact in genotypic analyses. Cyanidium, is considered as a bridge alga between Cyanobacteria and Rhodophyca by Klein (1970), Frederick (1976), and Seckbach (loc. cit.). It also lacks vacuoles and trienoic acids, and has only 1 chloroplast and 1 mitochondrion. Galdieria has only 1 chloroplast but numerous mitochondria, a vacuole, and trienoic acids. For the root, Lipscomb (loc. cit.) used red algae but these have fewer primitive features than some other groups like Parabasalia, Pelomyxidae, and Glaucophyca, the 1st 2 sometimes considered as a sister group to all other eukaryotes. Lipscomb was on target but did not hit the bull's eye. Cyanidium+Galdieria form the sister group to red algae in Saunders and Hommersand (2004) based on the the GB (Golgi Body, aka dictyosome) association with the ER and presence of peripheral thylakoids, and a chloroplast dividing ring occurs in Cyanidioschyzon and Cyanidium, the 3 characters not included in my analyses, but they may be plesiomorphic.
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 and Archeoplastida as polyphyletic is supported by molecular evidence (Hori and Osawa, 1987; Hori et al, 1990; Luttke, 1991; Nozaki et al, 2007) 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, the others recognizing another group as such, usually green algae, or not doing any internal arrangements.
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), either phenotypic or genotypic, have found such a link, and the monophyly of Fungi is well established.
Archeoplastida has weak support from molecular evidence (Baldauf et al, 2000; Stiller et al, 2001; Parfrey et al, 2007), is strongly refuted by Kim and Graham (2008) and 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 characters, Archeoplastida is not supported. The group is recovered in several recent analyses but Parfrey et al (2010) point out that Archeoplastida support comes primarily from phylogenomic analyses and these may be picking up misleading EGT (endosymbiotic gene transfer) signal of genes independently transfered from the plastid to the host nucleus in the 3 archeoplastid clades. As well, they use maximum likelihood which is not as reliable as parsimony. And Stiller and Harrell (2005) emphasize that the "clade" can be explained by "short-branch exclusion" and "subtle and easily overlooked biases can dominate the overall results of molecular phylogenetic analyses of ancient eukaryoyic relationships. Sources of potential phylogenetic artifact should be investigated routinely, not just when obvious 'long-branch attraction' is encountered." Archeoplastidans are not supported in my analysis as expected as they have no synapomorphies and are weakly supported genotypically.
Rhizaria is also not recovered, not surprisingly, as it is ill-defined and weakly supported in molecular phylogenies. Rhizaria and Cercozoa are artifacts in molecular phylogenies, as well, as they are ill-defined and weakly supported (Palfrey et al, 2007). Statistical support for Rhizaria is inconsistent in multigene genealogies with larger taxon sampling (Yoon et al, 2008). 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), 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) 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). With the long branch taxons removed Hampl et al (2009) has 8 kingdoms: Amebazoa, Animalia, and Fungi in Unikonta, and Excavata, Plantae, Rhodophyca, Haptophyca, and Chromalveolata-Rhizaria. In it Bikonta includes 2 supergroups: Excavata (or Discoba) and Archeoplastida (plants + red algae + haptomonads) + most of chromalveolates and rhizarians.
Ochrobiota has a dozen classical synapomorphies, more than any other eukaryote supergroup and an exhaustive search would probably recover it, as well as Bikonta. The Burki et al (2009) investigation lends support to the proposed chromalveolate clade, similar to Ochrobiota, as the SAR (stramenopiles (heterokonts), alveolates, and rhizarians (which includes Retaria)) group and there is a Haptophyca-Cryptophyca grouping within it. Hackett et al (2007) and Hampl et al (2007) results also support a chromalveolate clade. The group is recognized in Adl et al (2005) and Holt and Iudica (2007). It shows up also in Tekle et al (2008) also based on maximum likelihood genotypic analysis as Cryptophyca-Haptophyca+Malawimonidae, Euglenista-Heterolobosa+Jakobida, and Alveolata+Cercomonada-Heterokonta, so Cercomonada is misplaced and belongs with Amebobiota, and Polymastigota is misplaced outside of it. The over-all arrangement is similar also to my results in that therer is a Glaucophyca, Rhodophyca, and Plantae part of the series. In Parfrey et al (2010), SAR is also supported but without Cryptomonada and Haptophyca. Kim and Graham (2008) maintain that their analysis strongly refutes it. In Baldauf et al (2000) and by others Chromalveolata is not considered as strongly supported only because it excludes Cryptophyca or both it and Haptophyca, so it is, in fact, well supported, and these 2 groups properly belong in Chromista (Ochrista).
Both Haptophyca and Cryptophyca are nested within Heterokonta in Williams (1991) and Haptophyca, also, in Saunders, Potter, and Andersen (1997), the former based on phenotypic data and the latter on phenotypic, molecular, and combined data, but excluding Cryptophyca. However, in the latter the combined data show Haptophyca as sister group to Heterokonta, with the strict consensus for the phenotypic results not well resolved and the molecular results grouping Haptophyca with Alveolata+Heterokonta. Chlorarachnia was excluded from both studies.
Retaria appears not to have been widely tested but is corroborated in Moreira et al (2006), along with Excavata and Conosa, but where, notably, Cercomonas, Plantae, red algae, a truncated Conosa, and Nuclearia are misplaced. It is also supported in Parfrey et al (2010). Contrary to the title the Parfrey et al 2010 results are not well resolved as there is a polytomy of 7 taxons (Haptophyca, Plantae, Telonema, glaucophycans, Centroheliozoa, Rhodophyca, and Cryptomonada) and another of 3 (minor groups). The 7 plus SAR and Excavata form a clade. The remaining group is Opisthokonta.
Like other unikonts, cercomonads have posterior to anterior flagellar transformation and share a derived feature with chytrids, the PNB (paranuclear body), and like other conosans an mt cone, and share at least 3 kinetid features with Myxofilosa as listed in the Synapomorphy Table (Table 5).
Groups included in some terminals should be specified and are as follows:
Pelobiota contains Pelomyxidae (Pelomyxa, Mastigina), Mastigamebae (Mastigameba, Mastigella), Phalansterium,
and Entamebidae (Entameba, Endolimax).
Neolobosa contains Gymnolobosa and Testalobosa.
Spongomonada comprises Spongomonadidae (Spongomonas, Rhipidiodendron)
Cercomonada comprises Cercomonas and Heteromita.
Heterolobosa comprises Acrasidae (Acrasis, Fonticula, Guttulina, Guttulinopsis) and Schizopyrenida (Vahlkampfidae,
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.
Conclusions
Open and shut cases are the high value and merit of classical evidence including among bacteria, the phylogenetic quality and nature of cladistics and the lack of same for gradism, the primitiveness of prokaryotes, the derived status of Metabacteria, the advanced condition of Methanobacteria and Sulfobacteria, the polyphyly of Protista and Protozoa, the position of Choanozoa and Myxozoa in Animalia, Microsporodia in Fungi, green algae in Plantae, chytrids in Fungi, an bicocesids, opalinates, and proteromonads in Heterokonta, and the unity of Heterokonta and Eukaryota. Very high probabilities exist for the monophyly of Monoderma, Firmicutes, Actinobacteria, Gracilicutes, Photobacteria, and Thiobacteria.
The most important points can be summed up as follows:
1. red algae are ancestral, a position supported by both genotypic and phenotypic evidence.
2. archeoplastidans are a polyphyletic group with no support from classical evidence, only weak
support from molecular data, and much robust support for their polyphyly.
3. Rhizaria is a heterogenous assemblage with no support from classical data and therefore should be considered polyphyletic and the genotypic taxonomies that do support it are artifactual; the same goes for Cerozoa, included in it.
4. Protozoa and Protista are polyphyletic assemblages with no support from classical nor molecular evidence.
5. Metakaryota, Neokaryota, Cellulosa, Contophora, Alveolata, Excavata, Dinobiota, Ochrista, Opisthokonta, Protoamebae, and Retaria, are monophyletic groups, and Ochrobiota, Conosa, Ochraria, Unikonta, and Bikonta probably are also.
6. molecular methods are highly overrated and not superior to classical evidence and LGT is highly exaggerated.
7. the obvious existence of important phenotypic data in bacteria.
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 and now administrative editor, and Dr. Pablo Goloboff, of CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), past president of the Willi Hennig Society, for their invaluable assistance.
Taxonomies for the Largest Algal Groups
Red Algae
The internal phylogenetic classification for red algae, based on Saunders and Hommersand (2004), is presented in Table 11. In this, the Golgi Body association with the ER and peripheral thylakoids include also Cyanidium+Galdieria which form a sister group to red algae. They recognize 25 orders but I recognize 17 (Dixon (1982) recognized 10), and 84 families, Dixon (loc. cit.) recognized 67. Chadefaud (1960) had recognized 11 orders in subphyla Proto-Floridées and Floridées, the usual subgroups (called also Bangiophycidae (or -phyceae) and Florideophycidae (or -phyceae), respectively, the former being polyphyletic and paraphyletic, and containing Bangiales (Porphyridiaceae and Bangiaceae) with Compsogonales (1 genus) (Porphyridiales (3 families) and Rhodochetales (1 family) being added later by others), with the latter subphylum, containing 99% of red algal genera, divided into Eo-floridées (Acrocetales and Eu-Nemaliales), Meso-floridées (the remaining Nemaliales, plus Chetangiales, Gelidiales, Gigartinales, Cryptonemiales, and Rhodymeniales) and Meta-floridées (Bonnemaisoniales and Ceramiales). Magne (1989) established Archeorhodophycidae, Metarhodophycidae, and Eurhodophycidae. "Florideae" is properly a synonym for angiosperms and is a gross misnomer for red algae. Compsogonales is the most primitive order and Ceramiales is the most advanced. The largest family is Rhodomelaceae, in Ceramiales, with 100 genera and 500 species.
The kingdom is predominantly marine and benthic. In it we find Irish moss or carragheen (Chondrus), dulse (Palmaria), purple laver (Porphyra), coral weed (Corallina), threadweed (Nemalion), and pitcherweed (Ceramium), among other large and attractive forms.
Green Algae
Green algae are freshwater, marine (benthic or planktonic), or terrestrial. The 600 genera and 8000 species are cladistically divided into 6-8 phyla as shown in Table 12 (Page 3). The arrangment is based on classical evidence (largely Mishler and Churchill, 1985) but agrees with the molecular evidence (Lewis and McCourt, 2004). Here there are 6 phylums of green algae, although Klebsormidiales (3 gen., 40 sp.) might be a 7th (here it is placed with Zygnematales in Gamophyta), and Chetospheridium might be an 8th (here it is placed with Coleochete). Volvocophyta contains most prasinophycans, which are polyphyletic and apparently subsumed in Volvocopsida, volvocophycans (chlamydophycans) (misnamed as “chlorophytes”or "chlorophyceans" as the former name refers to all plants and the latter to all green algae), and most ulvophycans, thus the bulk of green algae, 14 orders. 22 orders are usually recognized with the most primitive being Volvocales and the most advanced Charales. The largest family is Desmidaceae in Gamophyta (order Zygnematales, class Conjugatophyceae ) with 30 genera and some 4000 species.
Volvocophyta has cruciate rootlets, Volvocopsida is distinguished by a collapsing interzonal telophase spindle in a phycoplast, and a theca, Volvocidae by a 1-7 o'clock cruciate arrangement and centripetal cleavage, Chlorellidae by a 12-6 arrangement and centrifugal cleavage, Oedogonidae by stephanokonty (a crown of flagella), Ulvopsida by proximal sheaths, terminal cap, and an 11-5 cruciate configuration, Ulvidae has well developed proximal sheaths, precocious cleavage, and unicellular sporophytes, and Siphonidae is totally siphonous, and possesses mannan, siphonein, and winged mt rootlets.
For convenience, 4 classes are recognized, based mostly on levels of organization: Prasinophyceae (Pedinomonadales, Monomastigales, Pyramimonadales, Chlorodendrales (Tetraselmidales)), Volvocophyceae (Volvocales, Tetrasporales, Chlorococcales, Chlorosarcinales, Spheropleales, Schizogoniales, Chetophorales, and Oedogoniales), Ulvophyceae (Ulotrichales, Ulvales, Cladophorales, Dasycladales, Caulerpales, Siphonocladales), and Charophyceae (Klebsormidiales, Zygnematales, Coleochetales, Charales). Another arrangement has 4 different classes in 3 subphylums: Zygophytina, Euchlorophytina, and Charophytina, the middle 1 having 2 classes: Prasinophyceae and Euchlorophyceae, the latter class containing 4 subclasses: Monadophycidae (Volvocales and Tetrasporales), Coccophycidae (Chlorococcales), Septophycidae (2 subgroups: isokontic and stephanokontic (Oedogoniales), the former also containing 2 subgroups: those with an axial chloroplast (Prasiolales) and those with a parietal 1, having 3 subgroups: 1 with a pyrenoid surrounded by starch (Ulotrichales, Chetophorales, Ulvales), 1 with pyrenoids not surrounded by starch ( Spheropleales, Acrosiphonales), and the 3rd having no pyrenoids and no starch ( Trentepohliales) ), and Siphonophycidae (Siphonocladales, Dasycladales, and Siphonales).
A simpler arrangement would be to recognize 3 classes: Unicellulares, with subclasses Monadophycidae and Coccophycidae; Cenocyta, the siphonous (tubular) forms, which are cenocytic (=syncytial) (multinucleate cytoplasm without cross-walls, i.e., a nonseptate condition); and Pluricellulares, containing subclasses Semi-Siphonidae, which is semi-siphonous (siphonocladous, i.e., filamentous-siphonous) (Cladophorales=Siphonocladales), Septophycidae, and Charophycidae, which are filamentous or foliose (thallose). Some orders have both unicellular and multicellular, and sometimes also siphonous or semi-siphonous forms; these are Chlorococcales (coccoid, filamentous, and siphonous), Ulotrichales (coccoid, filamentous, filamentous-siphonous, and foliose), and Zygonematales (coccoid and filamentous). Ulotrichales would go to Pluricellulares and Zygonematales to Unicellulares. Cenobial (a gelatinous colonial condition found in some Volvocales and Chlorococcales), palmelloid (a tetrasporal colonial condition), sarcinoid (a cubical packet of cells) levels of organization, and the ameboid (in Zygonematales) also occur. Most of these 9 levels of organization occur in most algal groups. The ameboid level occurs also in Chrysophyca, Xanthophyca, Haptophyca, and Dinophyca, and the siphonous level is present only in yellow, brown, and green algae.
Notable macroscopic forms are the green laver or sea lettuce (Ulva) and maiden's hair or sea grass (Enteromorpha) in Ulvales; Neptune's shaving brush (Penicillus) and the sea staghorn (Codium) in Caulerpales (aka Bryopsidales, Codiales, and Siphonales); mermaid's wineglass (Acetabularia) in Dasycladales; the stonewort and muskgrass (Chara) and nitella (Nitella) in Charales; and the water net (Hydrodictyon) in Chlorococcales.
A cladistic classification for seed plants, including only living groups is also presented in Table 12 (Page 3) as well as one for angiosperms.
Ochristan Algae
Table 13 contains my tentative taxonomy for a group corrresponding to Ochrobiota prior to the analyses.
The phylogeny for Ochrista, probably the crown group, being the most advanced, is given in Table 14 based on data by Williams (1991), Cavalier-Smith and Chao (1996), Saunders et al (1997). There are some 80 orders.
Cryptophycans, specifically Cryptomonas and Chilomonas, were 1st described by Ehrenberg in 1832, and 6 years later established for it the family Cryptomonadina. In 1841, Dujardin placed them in his Infusoires, dubbed Flagellaten by Cohn in 1853. Klebs, in 1892 placed them as 1 of 2 families in Chromomonadina, the other being Chrysomonadina. Pascher placed Cryptophyceae with chrysomonads in Pheochrysidales in 1911 and 3 years later in Pyrrhophyta and recognized only 2 orders: Cryptomonadales and Cryptococcales, for motile and nonmotile forms, respectively. Families recognized in the 1930s and 1940s (as arranged by Pascher, Pringsheim, and Skuja) were: Cryptochysidaceae, Cryptomonadaceae, Cyathomonadaceae, Kathablepharidaceae, and Senniaceae.
The group is now divided into 3-5 orders: Cryptomonadales, Thecomonadales, Cyathomonadales, Katablepharidales, and Goniomonadales. Butcher (1967) recognized 3 families, 13 gen,. and 60 sp.; Bourelly (1970) listed 8 families and 23 gen.; Van Den Hoek (1995) reports 12 gen. and 200 sp., 100 freshwater (mostly lakes) and 100 marine (nanoplankton (2-20 microns) in mostly tidal pools); 15 gen. are covered in Lee et al ( 1997) but are not classified.
Chlorarachnians, found in cultures of tropical or subtropical siphonous green algae, have an ameboid-plasmodial stage with reticulopds (forming a web, hence the name), a walled coccoid stage, and a uniflagelllate stage, and can form zoospores. They have a 4-membrane chloroplast envelope, a chloroplast in the RER (rough ER), a nucleomorph, chlorophyll a and b, paramylon as the storage product, and tubular cristas. There are 5 genera and 6 species (Chlorarachnion, Gymnochlora, Lotharella, Cryptochlora, and Bigelowiella); 4 genera are monotypic, Lotharella has 2 species.
Investigations, Series IV. Ministry of Agriculture, Fisheries & Food, Her Majesty's Stationary Office, London.
Bourelly, P. (1970). Les algues d'eau douce. III: Les algues bleues et rouges. Les Eugleniens, Peridiniens, et Cryptomonadines,
pp. 1-512. Paris.
The most familiar examples of haptophycans, the coccolith-bearing species, were discovered by Ehrenberg in 1835, the coccoliths (name coined by Huxley in 1858) being calcified plates or scales, often invested with elaborate ornamentation. The distinctive organelle, the haptonema, was described as a "3rd flagellum" by Scherffel in 1900 but in the 1950s, in a series of articles, Parke et al demonstrated that the organelle was really a thin filamentous appendage, differently structured from a flagellum, which they named a haptonema, hence the descriptive name for the group.
The great majority of haptophycans are unicellular and flagellate (monadoid) but some species also have ameboid, coccoid, palmelloid, or filamentous stages. The great majority, also, are marine and planktonic (nanoplanktonic (2-20 microns or picoplanktonic ( .2-2 microns)). Some also have an alternation of generations.
Some 50-75 genera and about 500 species are usually recognized. The traditonal convenience classification has 4 orders: Pavlovales, Prymnesiales, Isochrysidales, containing those species with isokontic flagella, and Coccolithophorales, containing those species with coccoliths. A more phylogenetic arrangement, recognized by some (e.g., Christensen, 1980; Green and Jordan, 1994; Jordan and Green, 1994), has only 2 orders, subsuming the other 2, Pavlovales, without plate-scales and with anisokontic flagella, and Prymnesiales, with plate-scales, and with isokontic flagella.
Pheophyceae (brown algae ) is traditionally divided into subclasses Pheosporeae, where the zooids are either unilocular, unicellular, and forming several reproductive elements, or pluirlocular, multicellualr, and forming only 1 reproductive element, where there are both spores and gametes (alternation of generations), and where is isogamy, anisogamy, or oogamy, variously occur, and Cyclosporeae, which has only gametes and oogamy, and is usually interpreted as having no alternation of generations, only a diploid, sporophyte generation, but some believe the gametophyte is reduced and included in the sporophyte (a case comparable to/analogous with the female prothallus gametophyte (embryo sac) of angiosperms). Cyclosporae contains only 1 order, Fucales, but often Acroseirales and Durvillaeales are separated out, while Pheosporae is divided into the following:
Isogeneratae (sporophyte and gametophyte generations are morphologically identical (isomorphic))
haplostichous
Ectocarpales
polystichous
Sphacelariales
Dictyotales
Cutleriales (both iso- and heteromorphic)
Heterogeneratae (generations dissimilar, the gametophyte being a microscopic, more or less branching prothallus)
haplostichous
Chordariales
Sporochnales
Desmarestiales
polystichous
Dictyosiphonales
Scytosiphonales
Laminariales
A phylogenetic arrangement is presented by Van Den Hoek (1995) where Ectocarpales forms 1 clade, Sphacelariales, and Dictyotales form a 2nd, Scytosiphonales and Cutleriales form a 3rd, and Heterogeneratae+Cyclosporeae forms a 4th. Heterogeneratae has 2 groups: Dictyosiphonales+Chordariales and Sporochnales+(Desmarestiales+ Laminariales) but the latter is grouped with Cyclosporeae. An evolutuinary link by others also is postulated between Chordaria, Dictyosiphonales, and Cyclosporeae as they share cryptostomas, conceptacles, and apical growth, and there is a striking similarity between the mastigotes of the unilocular structure in the conceptacles. Sporochnales, Desmarestiales, and Laminariales share a heteromorphic life history, anisogamy, female pheromones eliciting 2 responses, reduction of the male plurilocular gametangia, and filamentous gametophytes. The 3rd clade should be united with the 4th on the basis of heteromorphic generations and trichothallic meristems. The recently disovered (in 1999) genus (with 2 species) Bolidomonas, probably goes to brown algae because of pigmentation and laterally inserted flagella, instead of with diatoms based only on genotypic data, and comprises a family and order included in the Pheophyca totals.
The most primitive order is Ectocarpales and the most advanced is Fucales. The largest families are Ectocarpaceae and Chordariaceae, both with about 30 genera. The largest families in Ochrista are probably Fragillariaceae and Bacillariaceae ( in Diatomae).
Brown algae are almost entirely marine and benthic and inhabit the intratidal and subtidal zones, especially rocky shores. In these algae we find the kelps (Laminaria and Macrocystis) (the blade and giant or great kelp can grow to 50 yards long!), which make enchanting underwater kelp forests, a productive and dynamic ecosystem, sea lace, bootlace weed, or mermaid's tresses (Chorda), winged kelp (Alaria), and sea colander (Agarum) in Laminariales; rockweed or wrack (Fucus), knotted wrack, yellow tang, or sea whistle (Ascophyllum), and sargassum weed (Sargassum) in Fucales; and mermaid's hair and landlady's wig (Desmarestia) in Desmarestiales, among other large algae (Lee, 1977, 1986; Lamoureux, 1985).
(Sources: Parker (1982), Margulis et al (1990), Encyclopedie Universalis (1995), Van Den Hoek (1995)).
Internal Taxonomies for Dinoflagellata and Euglenophyca
Dinoflagellates
A phylogeny for dinoflagellates, after Van Den Hoek et al (1995) is presented in Table 15. Ebrids and ellobiophycans are not mentioned, but ebrids have a dinokaryon and share an internal siliceous skeleton with some genera and an inverted Y-shape in 1 (Dicroerisma), and ellobiophycans are 1 of 4 subclasses recognized by Loeblich (1982), the others being Dinophycidae, Ebriophycidae, and Syndiniophycidae (1 order, no dinokaryon). There is the plate increase model (where thecal plate increase is considered apomrphic (advanced)) and plate decrease model (where the opposite is considered apomorphic), the latter being adopted by Van Den Hoek et al (loc. cit.) as comparative morphology and the fossil record support it. Thoracospherales and Pyrocystales are sometimes recognized also, separated from Peridiniales and Gonyaulacales, respectively, solely on differences in life cycle. Groups are distinguished by their thecal organization and the thecal patterns (tabulations) are numbered and noted according to the Kofoid System.
There are about 50 families, 130 genera, and 2000 living species (2000 are fossils). Much like euglenoids, some 50% are colourless. Most are microscopic, but some are larger, the largest is Noctiluca at 2 mm. so is visible to the naked eye and was the 1st discovered; this was in 1753 by Henry Baker. Stein, in 1883, regarded them as animalcules and placed them as a suborder. arthrodele Flagellaten, in his order Flagellaten, arranging them into 5 families: Prorocentrinen, Noctilucide, Peridiniden, Dinophysiden, and Cladopyxiden. Pascher, staring in the 1920s, partitioned them into 3 groups, Desmokontae, Cryptophyceae, and Dinophyceae. Fritsch and Graham separated out Cryptophyceae and the former regarded the 2 remaining groups ( renaming Dinophyceae as Dinokontae) as forming class Dinphyceae.
Tending to predominate in warm water communities they are particularly abundant in the Indian Ocean and Red Sea. Links to marine luminescence were demonstrated by Michaelis in 1830. At least 30 species in 5 autotrophic (Gonyaulax, Protogonyaulax, Pyrodinium, Pyrocystis, Ceratium) in the Peridiniarae complex, and 2 heterotrophic genera (Noctiluca, Protoperidinium) in the Gymnodiniarae complex, contain scintillons, particles/organelles that cause luminescence, a blue flash of 1 tenth of a second duration, hence the name fire algae and Pyrrhophyceae for the entire class. Its purpose is unknown but it may be to ward off predators. The ocellus, which is present in all 7 genera of Warnowiaceae (Gymnodiniales) has a remarkable resemblance to the animal eye at the subcellular level. "Blooms", especially of Gonyaulax, cause red tides in which dangerous toxins are secreted by several genera including Protogonyaulax. 90% of dinophycans are marine, the other 10 % being fresh or brackish water, terrestrial ( as snow algae), or intrazoic. Zooxanthellas, symbiotic in colonial radiolarians, were described and named by Karl Brandt in the 1880s.
Euglenoids
The earliest classification of euglenoids was in Infusoria, as they were named by Ledermuller in 1763. Although described by O. F. Muller in 1786 in his Animalcula Infusoria, the 1st comprehensive treatment on infusorians, Ehrenberg's Die Infusoriensthier of 1836 was more influential. Flagellata was then established and was divided into 5 subgroups: Protomastigina, Polymastigina, Euglenoidina, Chloromonadina, and Chromomonadina. In 1892 Klebs configured the euglenoids into 3 families named by Senn 8 years later according to botanical nomomenclature as Euglenaceae, Astasiaceae, and Peranemaceae. In 1898, Engler established the euglenoids as the order Euglenales. In 1900 Senn divided Flagellata into 7 subgroups: Protomastigineae, Pantostomatineae, Distomatineae, Chrysomonadineae, Cryptomonadineae, Chloromonadineae, and Euglenineae, and in 1903, treated Flagellata as a phylum and the 7 groups as orders. Pascher, in 1931 elevated the euglenoids to phylum status as Euglenophyta. The 3 families grouped together the chlorophyllian, saprophytic, and holozoic genera and species, respectively, and the families were recognized as artificial. In 1933, G. M. Smith established the family Colaciaceae for the single genus Colacium, a chlorophyllian, nonmotile group forming into dendroid colonies in a gelantinous sheath and having a stalk system, and in 1938 created an order for it. In 1948, Skuja added 2 more families: Rhynchopodaceae and Rhizaspidaceae.
Leedale presented a scheme including 6 orders: Eutreptiales, Euglenales, and Euglenomorphales, Rhabdomonadales (Menoldidae) (osmotrophic), Sphenomonadales (osmotrophic or phagotrophic), Heteronematales (phagotrophic), the 1st 3 being green or colourless, the 1st 2 being mostly with a stigma and flagellar swelling, and the last 3 being heterotrophic and without a stigma or flagellar swelling. It is now most commonly used but is basically unclassified and no families are recognized. Much better arrangements were done by Mignot (1966) and Johnson (1968). The former had suborders Euglenina ( families Euglenidae (including Menoldidae), Distigmidae, Eutreptidae, and Euglenomorphidae) and Poranomina ( families Poranomidae, Petalomonadidae, and Scytomonadidae), and the latter had 3 suborders, the 1st having 2 families, Euglenidae and Menoldidae, the 1st of these being divided into 3 subfamilies (Eutreptinae, Euglenomorphinae, and Eugleninae). Leedale (1978) did, however, present a putative phylogeny in which Distigma was the root and lead to 2 lines, Sphenomonadales+(Eutreptales-Euglenomorphales+Euglenales) and Rhabdomonadales+Heteronematales.
Later, Kinetoplastida, Diplonemida (Diplonema (Isonema)), Pseudociliata (Stephanopogon), and Hemimasigota were rightly added, because of fine structural affinities (confirmed by molecular methods, except possibly Hemimastigota) forming an extended/expaned Euglenoida/Euglenophyca or Euglenista/Euglenaria. The 1st order, the (blood parasitic) hemoflagellates, is the largest, with 2 families, 16 genera, and 600 species, created by Honigberg in 1963. The others all have only 1 genus, except for Hemimastigota, which has 4.
Euglenoids range in size frrom 15 microns to .5 mm. and are world-wide and found in mostly freshwater habitats, such as lakes, rivers, streams, ponds, and ditches. Marine forms, which are less common, occur in the open sea, tidal zones among seaweeds, and sandy beaches. Blooms occur in farmyard ponds, greenhouse tanks, agricultural drainage channels, dew ponds, and estuarine mudflats. Some forms favour very acidic environments such as peaty pools, sphagnum bogs, and sulfur lakes at pH 3-4. Terrestrial forms, which are rare, include those in snowfields, on trees, and in insectivorous plants.
Leedale, G. F. 1978. Phylogenetic criteria in euglenoid flagellates. Biosystems 10, 183–187
Mignot, J. P. 1966. Structure et ultrastructure de quelques euglénomonadines. Protistologica 2:51–140.
Table 11. Rhodophyca.
sbph. Rhodellophytina (1 order) (GB association is with both the ER and the nucleus)
sbph. Archeorhodophytina Magne 1989 emended (Metarhodophycidae Magne 1989; Metarhodophytina Saunders and
Hommersand 2004) (1 order; families Compsogonaceae, Erythropeltidaceae, Rhodochetaceae)
sbph. Eurhodophytina Saunders and Hommersand 2004 (Eurhodophycidae Magne 1989) (GB association with both ER
and mitochondrion)
cl. Porphyridiophyceae (1 order) (without peripheral thylakoids)
cl. Bangiopsidiophyceae (1 order)
cl. Bangiophyceae Wettstein 1901 (1 order) (no peripheral thylakoids in gametophyte)
cl. Neorhodophyceae nov. nom. (peripheral thylakoids and GB association with ER)
sbcl. Hildenbrandiophycidae Saunders and Hommersand 2004 (1 order)
sbcl. Cenorhodophycidae
infcl. Nemaliophycidae Christensen 1978 (5 orders)
infcl. Ahnfeltiophycidae Saunders and Hommersand 2004
hprord. Ahnfeltarae stat. nov. (1 order)
hprord. Rhodymeniarae stat. nov. (6 orders)
Table 13. Tubulicristata
sbk. Foraminifera ( [d’Orbigny1826] Eichwald 1830, stat. nov. Margulis 1974) stat. nov.
sbk. Metatubulicristata tax. nov.
infk. Axopoda stat. nov., nom. nov.
infk. Chromobiota (Jeffrey 1971) stat. nov., emend.
mck. Alveolata stat. nov., nom. nov.
mck. Chromaria stat. nov., nom. nov.
mgph. Euglenista tax. nov.
phyl. Euglenaria nom. nov. (replacing Euglenozoa)
phyl. Excavata (Cavalier-Smith 2004)
mgph. Chromista (Cavalier-Smith 1983) stat. nov.
hpph. Chlorarachnia (Cavalier-Smith 1993) stat. nov.
hpph. Euchromista (Cavalier-Smith 1993)stat. nov.
spph. Cryptomonada (Ehrenberg 1838)
spph. Ochrista (Cavalier-Smith 1993, emend.) stat. nov.
phyl. Haptomonada (Cavalier-Smith 1989)
phyl. Heterokonta (Luther 1866)
Table 14. Heterokonta.
sbph./cl. Hydromyxia (Labyrhinthulata)(slime nets)(1 order, 4 families, 8 genera, 40 species)
sbph. Neoheterokonta nom. nov.
infph./cl. Bicosecida (1 order, 4 families, 8 genera, 16 species)
infph. Gyrista
spcl. Bigyrista
cl. Opalinata Wenyon 1926 (aka paraflagellates, protociliates)(1 order, 2 families, 15 genera, 400 species)
cl. Pseudomycota nom. nov. (water molds)(7 orders, 14 families, 70 genera, 800 species)
spcl. Pheophyceae De Bary 1881 (Pheophyta Wettstein 1901)
cl. Diatomeae Dumortier 1821 (40 orders, 81 families, 200 genera, 10,000 species extant, 100, 000 extinct)
cl. Pheophycidae
sbcl. Hypogyra (Pelagococcales (1 genus), Pedinellales (10 genera), (Silicoflagellata or Dictyochae)
(1 genus), Sarcinochrysidales (1 genus), Rhizochromulinales (1gen.)
sbcl. Pheista
mgord. Phearia nom. nov. (Pheophyca (12 orders, 41 families, 260 genera, 2000 species),
Xanthophyca (6 orders, 20 families, 100 genera, 600 species), Chrysomeridales ( 1 genus))
mgord. Chrysaria nom. nov. (Chrysophyca (7 orders, 23 families, 120 genera, 1000 species),
Eustigmata (1 order, 1 family, 6 genera, 12 species), Raphidomonada (Chloromonada) (1 order,
2 families, 12 genera, 27 species), Oikomonadales (1 genus))
All are stat. nov.; the totals are from the same souces as for the Tally Table and the ones for genera and species are approximations.
Table 15. Dinoflagellata.
sbph./cl. Protodinophycidae (Oxyrhinnales)
sbph. Metadinophycidae
cl. Gymnodiniophycidae (11 orders) (gymnodinioid thecal organization)
cl. Syndinophycidae (fusion of thecal plates)
spord. Peridiniarae (Gonyaulacales, Peridiniales) (gonyaulacoid-peridinioid thecal type)
spord. Desmokonta (Desmocapsales, Desmomonadales, Prorocentrales) (prorocentroid thecal type and
desmokonty)
Internal Taxonomies for Protozoans
Ciliata
Traditionally called Infusoria and later subphylum Ciliophora and divided into classes Ciliata and Suctoria. Ciliata was split into subclasses Protociliata and Euciliata by Metcalf in 1918, the former containing the orders Holotricha, Spirotricha, Chonotricha, and Peritricha. Some 50 orders, 215 families, 1100 genera, and 7500 species are now usually recognized. Lynn recognizes 11 classes, 19 subclasses, and 52 orders. De Puytorac et al recognize 11 classes, 25 subclasses, and 70 orders. Corliss (1994) recognizes 8 classes.
The following classification combines the proposals for ciliate phylogeny by Small and Lynn (1992), de Puytorac (1994), and Baroin-Tourancheau et al (1992).
Ciliata Perty 1852 (Ciliophora Doflein 1901)
cl. Karyorelictea Corliss 1974
cl. Heterotrichea Stein 1859
sbph. Intramacronucleata Lynn 1996
spcl. Spirotricha Butschli 1889, as class
cl. Hypotrichea Stein 1859, as suborder
cl. Oligotrichea Butschli 1887, as suborder
spcl. Transversala de Puytorac et al 1993
cl. Colpodea Small and Lynn 1981
cl. Plagiopylea
spcl. Filicorticata de Puytorac et al 1993
cl. Litostomatea Small and Lynn 1981
cl. Vestibulifera
spcl. Epiplasmata de Puytorac et al 1993
cl. Ciliostomatophorea de Puytorac et al, 1993, as superclass (Phyllopharyngea de Puytorac et al 1974)
cl. Membranellophorea Jankowski 1975
sbcl. Nassophoria Small and Lynn 1981, as class
sbcl. Oligohymenophoria de Puytorac et al 1974, as class
The molecular analysis by Baroin-Tourancheau et al (1992) agrees very well with morphology at lower levels, with the grouping of Karyorelictea+Heterotrichea, and with the Ciliodesmatophora- Intramacronucleata split. The results for Intramacronucleata are as follows: ((Hypotricha+Oligotricha)+Colpodea))+(Nassophora ((Oligohymnophora+Protostoma)+(Litostoma))).
sbph. Protopolythalamia nom. nov.
cl. Fusulinea (extinct) (Fusulinida)
cl. Miliodea
spord. Miliodina+Silicoluculinida
spord. Lagenida
spord. Involutinida+Spirillinida
sbph. MetaPolythalmia nom. nov.
cl. Textularina (Textularida)
cl. Rotulina
sbcl. Carterinia (Carterinida)
sbcl. Rotulinia
spord. Robertina (Robertinida)
spord. Bilamella nom. nov. (Rotalida+Globigerinida)
Petrushevskaya (1977) proposed the following scheme for Actinopoda: superclasses Heliozoa and Radiolaria, the latter divided into classes Acantharia and Euradiolaria, the latter in turn divided into subclasses Pheodaria and Polycystina, with Polycystina split into the superorders Nassellaria, Spherellaria, Collodaria, and Albaillellaria.
Contrary to what is often stated, actinopods appeaer to be monophyletic. The MTOC is entirely surrounded by the nucleus in Dimorpha (in Heliozoa) as well as some other actinopods like the polycystines; the kinetocyst in Arthracantharia and Centrohelea has a spherical inner core and a sharp conical rodlet; the central capsule occurs in Polycystina, Pheodaria, and Acantharia; there are intracellular celestine crystals in each flagellum in Polycystina and Acantharia; a dodecagonal mt pattern is present in Holacanthida and the polycystine Periaxoplatidiata; a hexagonal mt pattern is present in Chauncantharia, Arthrancantharia, Taxopoda (1 genus: Stilolonche), and Axoplastohelida. In fact, most of Heliozoa may be subsumed by Euacantharia, with Holacantharia going to Polycystina, leaving only Desmothoracida and Exonucleoplastohelida (1 genus: Tetradimorpha), with the latter possibly going to Pedinellales, because of the shared triangular mt pattern with Ciliophrys.
Actinophrys, Actinospherium, Echinospherium (might be same as Actinospherium) in Actinophryida, and Ciliophrys in Ciliophryida, primtive heliozoans, have been transfered to Pedinellales, which prior to this had only Pedinella, Apedinella, and Pseudopedinella. Plegmacantharia contains a single genus separated from the heterogenous family Plegmacantharidae of Holoacantharia.
The following is the traditional, utilitarian taxonomy followed by my proposed phylogeny.
Convenience classification:
cl. Pheodaria Haeckel 1879 (7 orders; 6 named by Haeckel in 1887, 1 named by Cachon and Cachon in 1985)
cl. Polycystina Ehrenberg 1838 ( Spumellarida, Nassellarida)
cl. Acantharia Haeckel 1881
sbcl. Holacantharia Schewiakoff 1926 (Holacanthida)
sbcl. Euacantharia Cavalier-Smith 1987 (Chauncanthida, Symphiacanthida, Arthracanthida)
sbph. Heliozoa Haeckel 1866
cl. Cryptoaxohelea ( Desmothoracida and Taxopodida)
cl. Phaneraxohelea (Centrohelea Kuhn 1926) ( Axoplastohelida, Centroplastohelida
Endonucleoaxoplastohelida, Exonucleoaxoplastohelida)
Phylogenetic proposal:
sbph. Euactinopoda
spcl. Endoaxoplastohela 1 ord., 1 family (Dimorpha)
spcl. Radiolaria Muller 1858
cl. Pheodaria Haeckel 1879 (7 orders) 6 named by Haeckel in 1887, 1 named by Cachon and Cachon in 1985
cl. Celestina tax. nov. 6 orders
sbcl. Polycystina Ehrenberg 1838 (Spumellarida, Nassellarida)
sbcl. Acantharia Haeckel 1881
infcl. Plegmacantharia Reshniak 1981
infcl. Euacantharia Cavallier-Smith 1987
spord. Chauncantharia
spord. Symphiacantharia+Arthracantharia (periplasmic cortex in 2 sheets)
Heterolobosea, Polymastigota, and Jakobea
Class Heterolobosea contains the orders Acrasia (Guttulinida)(cellular slime molds), with 4 families, and Schizopyrenida (ameboflagellates), with 2 families. Polymastigota contains 42 genera and some 600-800 species in subclasses Metamonada (orders Diplomonada (2 families), Retortomonada (1 family), and Oxymonada (5 families)) and Parabasalia (orders Trichomonada (4 families) and Hypermastigota (15 families in suborders Lophomonada, Trichonympha, and Spirotrichonympha). Often the polymastigote subclasses are treated as classes and the suborders as orders. Jakobea has perhaps only 1 genus. Acrasians, as cellular slime molds, were once assigned to Dictyostela.
Myxofilosa
The convenience group Gymnolobosa is arranged as an order with 5 suborders and 9 families. Testalobosa has 2 orders (Arcellinida and Trichosida), 20 families, and 20-40 genera. Testafilosa comprises Euglyphida, with 4 families and about 20 genera, and 3 families (with 22 genera) left unclassified (but not designated as incertae sedis) in Lee at al (2000), and traditionally included also Gromida, which is now regarded as related to the forams. Gymnofilosa (Aconchulinida) had 2 families: Nuclearidae and Vampyrellidae. The former has discoid cristas so should be placed in Excavata and the latter was separated out based on fine structure ( vesicular cristas, osmiophilic granules, and ribosome arrays) and is considered incertae sedis. A Gymnamebae group is now recognized and configured as 3 orders, Euamebida, Centramebida, and Leptomyxida, with 14 families (including 3 of uncertain affinities), 58 genera, and c. 200 species.
Apicomplexans
2 taxons, parasites of marine invertebrates, Haplosporidia and Paramyxea, have also been separated out because they have no structures as in Apicomplexa, so do not warrant placement there, and are considered of contentious position. Haplosporidia, established by Caullery and Mesnil (1899), contains 3 genera (Haplosporidium, Minchinia, and Urosporidium) and about 30 species, and possesses haplosporosomes. It is regarded as closely related to Microsporidia (now known to be a fungus, based on both phenotypic and genotypic data), by Desportes and Nashed (1983) because of telling similarities: diplokaryosis, as in higher funguses, proliferation with vegetative stages alternating with sporulating ones where sporulation is initiated by the differentiatioon of sporonts which divide into sporoblasts producing spores, similar spindle pole bodies involved in nuclear division, presumably synaptonemal complexes in the sporont nuclei.
sbph. Perkinsia (1 genus)
sbph. Gamontomorpha (orthog. emend. from Gamontozoa Cavalier-Smith )
spcl. Gregarinia Dufour 1828 (4 orders)
spcl. Coccidiomorpha Doflein 1901
cl. Coccidia Leuckart 1879 (4 orders)
cl. Hematomorpha (orthog. emend. from Hematozoa Vivier 1982)
ord. Hemosporidia Danilewsky 1886
ord. Piroplasmida Wenyon 1926
Apicomplexans are parasitic and include 14 orders, 120 families, about 300 genera, and some 5000 species.
Baroin-Tourancheau, A., Delgado, P., Perasso, R., and Adoutte, A. 1992. A broad molecular phylogeny of ciliates:
identification of major evolutionary trends and radiations within the phylum. Proc. Natl. Acad. Sci. U S A 89: 9764–9768.
Caullery, M., and Mesnil, F. 1899. Sur le genre Aplosporidium (nov) et l'ordre nouveau des Aplosporidies. Comptes rendus
des séances de la Société de biologie et de ses filiales. Série 1, 51: 789-91.
Corliss. J.O. 1994. An Interim Utilitarian ("Usre-friendly") Heirarchical Classification and Characterization of the Protistans.
Acta Protozoologica 33: 1-51.
Desportes, I., and Nashed, N.N. 1983. Ultrastructure of sporulation in Minchinia dentali (Arvy), a haplposporean parsite of
Dentalium entale (Scaphopoda, Mollusca); taxonomic implications. Protistologica 19: 435-60.
Glaessner, M.F. 1947. Principles of Micropaleontology. Hafner.
Haeckel, E. 1887. Report on Radiolaria collected by H.M.S. Challenger during the years 1873-1876. In The Voyage of H.M.S.
Challenger, Vol. 18 (Thompson, C.W., Murray, J., eds.), Her Majesty's Stationary Office, London.
Lee, J.J. 1990. Granuloreticulosa. In Handbook of Protoctista (Margulis, L., Melkonian, M., Corliss, J.O., Chapman,
D.J., eds.). Jones and Bartlett, Boston.
Loeblich, A.R., Tappan, H. 1984. Suprageneric classification of the foraminifera (Protozoa). Micropaleontology 30: 1-70.
Lynn, D.H. and Small, E.B. 1997. A Revised Classification of the Phylum Ciliophora Doflein, 1901. Rev. Soc. Mex. Hist.
Nat. 47: 65-78
Petrushevskaya, M. G. 1977. On the origin of Radiolaria. – Zoologicheskii Zhurnal 56, 10.
Petrushevskaya MG. 1977. Radiolaria. In: Zuse AP, editor. Atlas of the Microorganisms in the Bottom Sediments of the
Oceans. Moscow: Nauka.
Puytorac, P de (1994): Phylum Ciliophora Doflein, 1901. In: P de Puytorac, ed., Traité de Zoologie, Tome II, Infusoires Ciliés,
Fasc. 2, Systématique. Masson, Paris. p. 1-15.
Reshetnjak, V.V. 1981. Akantarii. Fauna SSSR, 123, Akad. Nauk SSSR, Zool. Inst., Nauka, Leningrad, pp. 1-210.
Schewiakoff, W. 1926. Die Acantharia des Golfes von Neapel. Fauna Flora Golfo Napoli, Monogr. 37:1-755.
Tappan, H., Loeblich, A.R. 1988. Foraminiferal evolution, diversification, and extinction. Journal of Paleontology 62: 695- 714.
Taxonomies for the Opisthokonts
Contrary to Tehler’s (1988) phylogenetic analysis, which is, however, basically accurate, Chytridiomycotes might be monophyletic as he did not include rumposomes (occuring only in 2 orders, however), MLBs, nor flagellar architecture (but it shows up as polyphyletic in molecular analyses); and naked gametes, one of 3 characters denoting a Chytridiales + Metamycota clade, is a primitive feature. Also, oomycetes and hyphochytriomycetes belong in Heterokonta, but he included the former as part of Fungi (he used hyphochytriomyctes as the outgroup). With the exclusion of 3 or 4 small groups, which are probably phylums of their own, from Ascomycota, there still remains a core monophyletic Neascomycota. Basidiomycota and Dikaryomycota (with the inclusion of Zygomycota (Kickxellales is related to Trichomycetes because of septal structure, spore ontogeny, and serology, and has a dikaryon therefore belongs with Dikaryomycota) as well as Microsporidia) are confirmed as monophyletic making 8 phylums. A phyogeny, based on Tehler, is presented in Table 16.
Notable microscopic forms include angel wings, death trumpets, puffballs, earthstars, earthballs, truffles, agarics, amanitas, boletes, chantarelles, morels, cup mushrooms, fiber heads, jelly cones, and among lichens, reindeer moss, Iceland moss, British soldiers, and orchella.
The general animal phylogeny is presented in Table 17 (Page 3), based mostly on Zrzavy et al (1998), Nielsen (1995), Neilsen et al (1996), Eernisse et al (1992), Halanych (2004), and Giribet et al (2007) as well as phylogenies for holometabolous insects, mollusks, and extant mammals, vertebrates, and primates.
Eernisse, D.J., Albert, J.S., Anderson, F. E. 1992. Annelida and Arthropdoa are not sister taxa: a phylogenetic analysis of
spiralian metazoan morphology. Syst. Biol. 41: 305-30.
Giribet, G., Dunn, C.M., Edgecombe, CG.D., Rouse, G.W. 2007. A modern look at the Animal Tree of Life. Zootaxa 1668:
61-79.
Halanych, K.M. 2004. The New View of Animal Phylogeny. Annu. Rev. Ecol. evol. Syst. 35: 229-56.
Nielsen, C. Animal Evolution: Interrelationships of the Living Phyla. U. of Copenhagen Press/Oxford U. Press.
Nielsen, C., Scharff, N., Eibye-Jacobsen, D. 1996. Cladistic analyses in the animal kingdom. Biol. J. Linn. Soc. 57: 385-410.
Tehler, A. 1988. A cladistic outline of Eumycota. Cladistics 4: 227-277.
Zrzavy, J., Mihulka, S., Kepka, P., Bezdek, A., Tietz, D. 1998. Phylogeny of Metazoa Based on Morphological and 18S
Ribosomal DNA Evidence. Cladistics 14: 249-85.
Table 16. Fungi
sbk. Chytridiomycota (maybe polyphyletic)
sbk. Metamycota
infk. Dipodascomycota
infk. Argamycota nom. nov.
mck. Endomycota
mck. Neargamycota
mgph. Metadipodomycota
mgph. Cenargamycota
hpph. Eremascomycota
hpph. Dikaryomycota
spph. Microsporidiomycota
spph. Zygomycota (maybe polyphyletic)
spph. Neodikaryomycota
phyl. Ascomycota (Neascomycota)
phyl. Basidiomycota
Mollusca (Malacozoa)
sbph Aplacophora
cl Aplacophora
sbph Testaria
hpcl Polyplacophora
cl Polyplacophora
hpcl Conchifera
spcl Galeroconcha
cl Galeroconcha (Monoplacophora)
spcl Rhacopoda
cl Gastropda
cl Cephalopoda (Siphonopoda)
spcl Ancyropoda (Loboconcha)
cl Bivalvia (Acephela)
cl Scaphopoda
sbph Neovertebrata
infph Petromyzontia (lampreys)
infph Gnathostomata
mcph Chondrichthyes (cartilaginous fish)
mcph Osteognatha
nnph Actinoidia (ray-finned fish)
nnph Choanata
ggcl Dipnoi (lungfish)
ggcl Kinocrania
mgcl Actinistia (celacanths=tassel-finned fish)
mgcl Tetrapoda
hprcl Neoamphibia (modern amphibians)
hprcl Amniota
spcl Sauropsida
cl Diapsida
sbcl Archosauriomorpha
sbcl Lepidosauriomorpha
cl Anapsida
sbcl Testidunes (turtles)
sbcl Synapsida
leg Mammalia
leg Mammalia
ggcoh Multituberculata
ggcoh Metamammalia
mgcoh Monotremata
mgcoh Theria
hprcoh Metatheria (Marsupalia)
hprcoh Eutheria (Placentalia)
spcoh Edentomorpha (edentates, phliodonts, paleonodonts)
spcoh Epitheria
coh Ernotheria
spord Lipotyphla (shrews, moles, tenrecs)
spord Menotyphla (jumping shrews)
spord Glires (lagomorphs and rodents)
coh Neotheria
ggord Ungulata
mgord Protungulata
hprord Ferungulata
spord Ferae (creodonts, carnivores)
spord Perissodactyla
hprord Paraxonia
spord ordArtiodactyla
spord Ceti
mgord Penungulata
Tethytheria (elephants, manatees, desmostylians)
Hyracoida (hyrax or coney)
ggord Archonta
spord Volitantia
ord flying lemurs
ord Chiroptera (bats)
spord Primatomorpha
ord tree shrews
ord primates
Primates
subord Strepsirhini (lemurs and lorises )
subord Haplorhini
inford Tarsiformes (mostly extinct, only living genus Tarsius (tarsiers))
inford Simiformes
hypfam Platyrhini (New World monkeys)
hypfam Catarhini
spfam Cercopithicoidea (Old World monkeys)
spfam Hominoidea (Anthropoidea)
fam Hylobatidae gibbons
fam Hominidae (great apes)
sbfam Ponginae
sbfam Homininae
tribe Gorillini
gen Gorilla 2 sp (W and E)
tribe Hominini
gen Pan 2 sp (common or field and bonobo or pygmy chimps)
gen Homo 12 sp ( only 1 extant, which has 2 sbsp, only 1 extant)
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 an 4-kingdom arrangement (Table 18) without a protistan kingdom but with a protistan level is more useful and informative, unlike most modern alternative systems, which had a protistan kingdom of some sort.
The protistan subkingdoms are Protobacteria (Eubacteria) and Metabacteria (Archeota) and the 3 lower eukaryote subkingdoms, Algae or Protophyta, Mastigomycota or Protomycota, and Protozoa. The histonian subkingdoms are Metaphyta (Embryophyta or Cormophyta), Metamycota, and Metazoa. The 4 kingdoms are Bacteria (prokaryotic, mostly osmotrophic, and with typically a murein wall), Phyta (usualy autotrophic and with a typically cellulose wall), Mycota (osmotrophic, mostly with a chitinous wall), and Zoa (phagotrophic, with no wall). And the 2 superkingdoms are Prokaryota and Eukaryota.
The bases are, then, trophic mode/functional community, wall composition, and nuclear type. Lines can be drawn to indicate histonian and protistan levels and trophic mode sections and walled and unwalled sections. Similar taxonomies were Takhtajan’s, but ochrophycans were lumped with green algae, and blue bacteria were separated from eubacteria, and Leedale’s pteropod scheme, but there was no formal internal arrangement for the component kingdoms.
Table 18. Convenience Classification for Empire Biota.
spk. Prokaryota
kgdm. Bacteria
sbk. Eubacteria
spph. Gracilicutes
phyl. Heterotropha tax. nov.
cl. Chemorganotropha tax. nov.
cl. Chemolithobacteria tax. nov.
phyl. Autotropha tax. nov.
cl. Scotoautotropha tax. nov.
cl. Photobacteria
spph. Mollicutes
spph. Firmicutes
cl. Micrococci
cl. Clostridia
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
infk. Choanozoa
phyl. Choanozoa
infk. Metazoa
mgnph. Diploblastica
mgnph. Triploblastica
grdph. Protostomia
phyl. Helminthes
cl. Helminthes-Acelomata
cl. Helminthes-Pseudocelomata
cl. Helminthes-Celomata
phyl. Arthropoda
phyl. Mollusca
grdph. Deuterostomia
spph. Lophophorata
phyl. Lophophorata
spph. Epithelioneuria
phyl. Echinodermata
phyl. Chordata
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
References
Adl, S.M. et al. 2005. The new higher level classification of eukaryotes with emphasis on the taxonomy of protistans. J. Euk.
Microbiol. 52: 399-451.
Agardh, C.A. 1824. Systema Algarum. Berlingianis, Lund.
Ammonius Hermiae. 400s AD. Porphyri Isagogen.
Aristotle. 300s BC. History of Animals.
Atkinson, G.F. 1915. Phylogeny and Relationships in Ascomycetes. Ann.Miss. Bot. Gard. 2: 315-76.
Baldauf, S.L., Roger, A.J., Wenk-Siefert, I., & Doolittle, W.F. (2000). A kingdom-level phylogeny of eukaryotes based on
combined protein data. Science 290: 972-977.
Bapteste E., Brinkman H., Lee J.A., Moore D.V., Sensen C.W., Gordon P., Durufl L., Gaasterland T., Lopez P., Muller M.,
Philippe H. 2002. The analysis of 100 genes supports the grouping of 3 highly divergent amebas: Dictyostelium, Entameba,
and Mastigameba. Proc. NAS 99, 1414-1419.
Barkley, F.A. 1939. Keys to the Phyla of Organisms. U. of Montana Press, Massoula, Mon.
Barkley, F.A. 1949. Un esbozo de clasificcion de los organismos. Rev. Fac. Nac. Agron. 10, 83-103.
Barnes, R.S.K., ed. 1984. Synopsis and Classification of Living Organisms. Blackwell, London.
Barns, S.M., Fundyga, R.E., Jeffries, M.W., Pace, N.R. 1995. Remarkable archaeal diversity detected in a Yellowstone
National Park hot spring environment. Proc. Natl. Acad. Sci. USA 91: 1609–1613.
Barns, S.M., Delwiche, C.F., Palmer, J.D., Pace, N.R. 1996. Perspectives on archaeal diversity, thermophily, and monophyly
from environmental rRNA sequences. Proc. Natl. Acad. Sci. USA 93: 9188–9193.
Bisset, K.A. (1952). Bacteria, 1st ed. Livingston, London; 2nd ed. 1962.
de Bary, A. 1881. Untersuchengen uber die Peronosporeen und Saprolgnien und die Grundlagen ienes naturalischen der Pilze.
In Beitr. Morphol. Physiol. Pilze, A. de Bary and M. Woronin, 4: 1-145, Winter, Frankfurt.
Bold, H.C. 1973. Morphology of Plants. 3rd ed. harper and Row, NY.
Bold, H.C., Alexopoulos, C.J., Delevoryas, T. 1987. Morphology of Plants and Fungi. Harper and Row, New York.
Bory de Saint-Vincent, J-B. 1824. Psychodiaire (Regne). In Encyclopedie Methodique (J-V Lamouroux, J-B Bory de Saint-
Vincent, E. Deslongchamps, eds.), Vol. 138, pp. 657-63. Paris.
Bory de Saint-Vincent, J-B. 1824. Microscopiques. In Encyclopedie Methodique (J-V Lamouroux, J-B Bory de Saint-
Vincent, E. Deslongchamps, eds.), Vol. 138, pp. 515-43. Paris.
Brochier, C., Gribaldo, S., Zivanovic, Y., Confalonieri, F., Forterre, P. (2005). Nanoarchaea: representatives of a novel
archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? Genome Biol. 2005; 6(5): R42.
Burki, F., Shalchian-Tabrizi, K., Minge, M., Skjaeveland, A., Nikolaev, S.I., Jacobsen, K.S., Pawlovsky, J. 2007.
Phylogenomics reshuffles the eukaryotic super-groups. PLoS ONE 2e:790.
Burki, F., Shalchian-Tabrizi, K., Pawlovsky, J. 2007. Phylogenomics reveals a new 'megagroup' including most photosynthetic
eukaryotes. Biol. Letters 4: 366-69.
Burki F , Inagaki Y, Bråte J, Archibald J M, . Keeling PJ, Cavalier-Smith T, Sakaguchi M, Hashimoto T , Horak A,
Kumar S, Klaveness D, . Jakobsen KS, Pawlowski J, and Shalchian-Tabrizi, K. 2009. Large-Scale Phylogenomic
Analyses Reveal that 2 Enigmatic Protistan Lineages, Telonemia and Centroheliozoa, are Related to Photosynthetic
Chromalveolates. Genome Biology and Evolution 2009:231; doi:10.1093/gbe/evp022.
Bütschli, O. 1880-2. Protozoa. In: Bronn, H. G. (Ed.), Klassen und Ordnung des Their- Reichs in Wort und Bild, vol. 1.
Winter’sche, Leipzig and Heidelberg.
Cain, R.F. 1972. Evolution of the fungi. Mycologia 64: 1-14.
Cavalier-Smith, T. 1978. The evolutionary origin and phylogeny of microtubules, mitotic spindles, and eukaryote flagella.
BioSystems 10, 93-114.
Cavalier-Smith, T. 1981. Eukaryote kingdoms: 7 or 9? BioSystems 14 , 461-481.
Cavalier-Smith, T. 1983. A 6-kingdom Classification and a Unified Phylogeny. In Schwemmler, W., Schenk, H. E. A. (Eds.),
Endocytobiology II, deGruyter, Berlin, pp. 1027-1034.
Cavalier-Smith, T. 1986. The kingdoms of organisms. Nature 324, 416-417.
Cavalier-Smith, T. 1992. Bacteria and eukaryotes. Nature 356: 570.
Cavalier-Smith, T. 1993. Kingdom Protozoa and its 18 phyla. Microbiol. Revs. 57, 953-954.
Cavalier-Smith, T. 1998. A revised 6-kingdom system of life. Biol. Rev. 73, 203-266.
Cavalier-Smith, T. 2004. Only 6 kingdoms of life. Proc. Roy. Soc. Lond. B 271: 1251-62.
Cavalier-Smith, T, Chao, E. 1996. 18S RNA sequence of Heterosigma carterae (Raphidophyceae) and the phylogeny of
heterokont algae (Ochrophyta). Phycologia 35: 500-10.
Chadefaud, M. 1957. Les Champignons et les Algues. Ann. Univ. Paris 27: 5-22.
Chadefaud, M. 1960. Traité de botanique, tome 1. Masson.
Chadefaud, M., Emberger, L. 1960. Traite de Botanique Systématique, Vol. 1 (Les Végétaux Vasculaires). Masson.
Chatton, E. (1925). Pansporella perplexa: reflexions sur la biologie et la pliylogenie des protozoaires. In
Annales des Sciences Naturelles, Zoologie: l’anatomie, la physio1ogie, classification, et 1'histoire naturelle des
animaux. I0me series, volume 8. edited by Bouvier, M.E. L. Masson, Paris.
Chatton, E. (1937). Titres et travaux scientifique E. Chatton, Sete, France.
Conard, H. S. 1939. Plants of Iowa (Grinnell Flora 5th ed.). Iowa Acad Sci., Biol. Surv. Publ. 2, 1-92.
Copeland, E B. 1927. What is a plant? Science 65, 388-390.
Copeland, HF. 1938. The kingdoms of organisms. Quart. Rev. Biol. 13, 383-420.
Copeland, HF. 1947. Progress report on basic classification. Am. Nat. 8, 340-61.
Copeland, HF.(1956) The Classification of Lower Organisms. Pacific Books, Palo Alto, Cal.
Cohn, F. (1875). Untersuchungen uber Bakterien, II. Beitrage zur Biologie der Pfanzen 1: 141-207.
Cuvier, G. Regne Animal. 1817.
De Luca, P., Taddei, R., Varano, L. 1978. "Cyanidoschyzon merolae": a new alga of thermal acidic environments. Webbia 33:
37-44.
Demoulin, V. 1974. The Origin of Ascomycetes and Basidiomycetes-the case for a red algal ancestry. Bot. Rev. 40: 315-45.
Dillon, L. 1963. A reevaluation of the major groups of organisms based on comparative cytology. Syst. Zool. 12, 71-82.
Dixon, P.S. 1982. Rhodophycota. In Cybil Parker (ed.), Synopsis and Classification of Living Organisms, McGraw-Hill, New
York.
Dodson, G.O. (1971). The kingdoms of organisms. Syst. Zool. 20: 265-281.
Doolittle, W. F. (1999). Phylogenetic classification and the universal tree. Science 284: 2124-2128.
Dougherty, E. Neoligism needed for structures of primitive organisms 1- Types of nuclei. J. Protozool. 4,14.
Doflein, F. 1901. Die Protozoen als Parasiten und Krankheitserreger. Gustav Fischer, Jena.
Eames, A. J. 1936. Morphology of Vascular Plants-Lower Groups.
Edwards, P. (1976). A classification of plants into higher taxa based on cytological and biochemical criteria. Taxon 25: 529-
542.
Eichler, A.W. (1886). Syllabus der Vorlesungen uber specielle und Medicinisch-pharmaceutische Botanik, 4th ed. Borntraeger,
Berlin.
Elkins, J.G. 2008. A korarchaeal genome reveals insights into the evolution of the Archaea. Proc. Natl. Acad. Sci. USA 105:
8102–8107.
Enderlein, G. 1925. Bakterien-Cyclogenie. de Gruyter, Berlin.
Endlicher, S.L. 1836. Genera Plantarum.Vienna.Fries, E. 1821. Systema Mycologicum, vol 1. Berlinger, Lund.Necker, N. J.,
de. 1783. Traité sur la Mycitologie. Matthias Fontaine, Mannheim
Engler, A. 1886. Fuhrer durch den koniglichen Garten. Breslau.
Engler, A., Prantl, H. 1897-1915. Die naturalischen Pflanzenfamilien, 20 vols. Leipzig.
Engler, A., Diels, L. 1936. Syllabus der Pflanzenfamilien. Berlin.
Engler, A. Gilg, E. 1924. Syllabus der Pflanzenfamilien. Berlin.
Felsenstein, J. (1978). Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27: 401-
410.
Farris, J.S. (1976). Phylogenetic classification of fossils with recent species. Syst. Zool. 25: 271-282.
Frederick, J.F. 1976. Cyanidium caldarium as a bridge alga between between Cyanophyceae and Rhodophyceae: evidence
from immunodiffusion studies. Plant Cell Physiol. 17: 317-22.
Fries, E. 1821. Systema Mycologicum, vol 1. Berlinger, Lund.
Gaillon, B. 1833. Apercu d’histoire naturelle. In: Mémoires et Notices, Soc. Agric. Com. Arts, Boulogne-sur-mer, pp. 95-114.
Galdieri, A. 1899. Su di un'alga che cresce intorno alle fumarole della solfatura. Rend. R. Accad. Sci. Fis. Mat. Napoli 6: 160- 64.
Geitler, L., Ruttner, F. 1935. Die Cyanophyceen der deutschen limnologischen Sunda Expedition. Arch. Hydrobiol., suppl. 14:
371-481.
Gibbons, N.E. & Murray, R.E. (editors)(1978). Bergey’s Manual of Determinative Bacteriology, 9th ed. Williams & Wilkins,
Baltimore.
Goloboff, P. A. (1999). Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15: 415-428.
Goloboff, P.A., S.A. Catalano, J.M. Mirande, C.A. Szumik, J.S. Arias, M. Kallersjo, J.S. Farris. 2009. Phylogenetic analysis
of 73, 060 taxa corroborates major eukaryotic groups. Cladistics 25: 211-30.
Greene, R.R. 1859. Manual of the Subkingdom Protozoa, with a general introduction on the principles of zoology. Longman,
Green, and Roberts, London.
Griffin J.L. 1988. Fine structure and taxonomic positionof the giant ameboid flagellate Pelomyxa palustris. J. Protozool. 35,
300-315.
Gupta, R.S. (1998). Protein phylogenies and signature sequences: a reappraisal of
evolutionary relationships archeobacteria, eubacteria,and eukaryotes. Microbiol. Mol. Biol. Rev. 62: 1435-1491.
Gupta, R.S. 1998b. Life's 3rd domain: an established fact or an endangered paardigm. Theor. Popul. Biol.54: 91-104.
Gupta, R.S. (2000). The natural evolutionary relationships among prokaryotes. Crit. Rev. Microbiol. 26: 111-131.
Gupta, R.S. & Singh, B. (1994). Phylogenetic analysis of 70 kD HSP sequences suggests a chimeric origin for the eukaryotic
cell nucleus. Current Biol. 4: 1104-1114.
Hackett, J.D., Yoon, H.S., Li, S., Reyes-Prieto, A., Rummele, S.E., Bhattacharya, D. 2007. Phylogenomic analysis supports
the monophyly of crytophytes and haptophytes and the association of 'Rhizaria' with chromalveolates. Mol. Biol. Evol. 8:
1702-13.
Hampl, V., Hug, L., Leigh, J.W., Dacks, J.B., Lang, B.F., Simpson, A.G.B., Roger, A.L. 2009. Phylogenomic analyses
support the monophyly of Excavata and resovle relationships among eukaryote super-groups. Proc. NAS USA 106: 3859- 64.
Haeckel. E.H. (1866). Generelle Morphologie der Organismen. Reimer, Berlin.
Haeckel, E. 1878. Das Protistenreich. Gunther, Leipzig.
Haeckel, E. 1994. Systematische Phylogenie, Vol. 1. Reimer, Berlin.
Haeckel, E. 1904. The Wonders of Life. Harper, New York and London.
Harvey, W.H. 1836. Algae. In: J.T. Mackay(Ed.), Flora Hibenica., vol 2,.Curray, Dublin., pp. 157-256.
Holt, J.G., Krieg, N.R., Sneath, P.H.A., Staley, J.T., Williams, S.T. (editors)(1994). Bergey’s Manual of Determinative
Bacteriology, 9th edn. Williams & Wilkins, Baltimore.
Honogberg, B.M. et al. 1964. A revised classification of the phylum Protozoa. J. Protozool. 11: 7-20
Horaninow, P. 1834. Primae Lineae Systematis Naturae. St. Petersburg.
Horaninoff, P. 1843. Tetractys Naturae. Weinhoberianis, St. Petersburg.
Hori, H, Osawa, S. 1987. Origin and evolution of organismsas deduced from 5S rRNA sequences. Mol. Biol. Evol. 4, 445-
472.
Hori, H. Stow, Y, Inoue, I, and Chihara M. 1990. Origins of organelles and algae evolution deduced from 5S rRNA
sequences. In: Dardon, P., Gianinazzi- Pearson, V., Grenier, A.M., Margulis, L., Smith, D.C. (Eds. ), Endocytology IV,
INSA, Paris, pp. 557-559.
Huber, H. et al. (2002). A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:
63–67.
Jeffrey, C. (1971). Thallophytes and kingdoms: a critique. Kew Bull. 25: 291-299.
Jeffrey, C. (1982). Kingdoms, codes, and classification. Kew Bull. 37: 403-416.
Karpov S. 1999. Flagellate phylogeny. In: The Flagellates (Eds. Leadbeater, B.S.C., Green, J.C. Systematics Association
Special Volume 59, Taylor and Francis, London and New York, pp. 336-360.
Kim, E. Graham, L.E. 2008. EEF2 analysis challenges the monophyly of Archeoplastida and Chromalveolata. PLoS ONE 3:
e2621.
Klein, R.M. 1970. Relationships between blue-green and red algae. Ann. NY Acad. Sci. 175: 623-33.
Kussakin, O. G., Starobogatoff, Y.I.. 1973. On the very highest categories of the organic world. Problemy
Évolyutsii (Problems of Evolution), Nauka, Sibirskoe Otdelenie, Novosibirsk. 3 , 95-103; Pp. 215–226 (In Russian).
Kussakin, O.G., Drozdoff, A.L. 1994 (vol.1), 1998 (vol. 2), Phylums of the Living World (in Russian).
Lake, J.A. (1983). An alternative to archeobacterial dogma. Nature 319: 626.
Lake, J.A., Henderson, E., Oakes, M., Clark, M.W. (1984). Eocytes: a new ribosome structure indicates a new kingdom
with a close relationship to eukaryotes. Proc. NAS USA 81: 3786-3790.
Lake, J.A.(1986). Mapping evolution with 3-D ribosome structure. Syst. Appl. Microbiol. 7: 131-136.
Lake, J.A. (1988). Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences. Nature
331: 184-186.
Lamoureux, Gisèle (ed.). 1985. Plantes sauvages du bord de la mer. Fleurbec, Portneuf, Québec.
Lamouroux, J-V, Bory de St. Vincent, J-B, Deslongchamps, E. (Eds.). Agasse, Paris, pp. 657-63.
Lee, J.J., Hunter, S.H., Bovee, E.C. 1997. Illustrated Guide to Protozoa. Allen Press, Lawrence, Kansas.
Lee, T. F. 1986. The Seaweed Handbook. Dover (republication; originally published in 1977 by Mariner's Press).
Leewenhoek, A. van. (1683). Phil. Trans. Roy. Soc. London.
Lewis, L. A. & McCourt, R.M. (2004). Green algae and the origin of land plants. Am. J. Bot. 91: 1535- 1556.
Linder, D.H. 1940. Evolution of Basidiomycetes and its relation to the terminology of the basidium. Mycologia 32: 419-37.
Linneus (von Linne, C. (1735). Systema Naturae. 1st ed. Lugduni Batavorum, Stockholm.
Linneus, C. 1767. Mundus Invisibilis. In Amenitatis Academicae, vol. 7, pp. 385-408. Erlangen.
Lipscomb, D. (1989). Relationships among the eukaryotes. In The Hiearchy of Life , edited by B. Fernholm, K. Bremer, & H.
Jornvall, Elsevier, New York. pp. 161-178.
Lipscomb, D. (1991). Broad classification: the kingdoms and the protozoa. In Parasitic Protozoa,Vol. 1, 2nd eds. edited by
J.P. Kreier & J.R. Baker. Academic Press, San Diego. pp. 81-136.
Luttke, A. 1991. On the origin of chloroplasts and rhodoplasts: protein sequence composition. Endocyobiosis Cell Res. 8, 75-
82.
Magne, F. 1989. Classification et phylogénie des Rhodophycées. Cryptogamie Algologie 10: 111-13.
Margulis, L. Five-Kingdom classification. In Evolutionary Biology, Vol. 7, pp. 45-78, ed. T. Dobzhansky, M.K. Hecht, and
W.C. Steere, Plenum, NY.
Margulis, L, Schwartz, K. 1998. Five Kingdoms, 3rd ed. W.H. Freeman. NY.
Margulis, L., Melkonian, M., Corliss, J.O., Chapman, D.J. (eds.). 1990. Handbook of Protoctista. Jones and Bartlett, Boston.
Margush T, McMorris FR. 1981. Consensus n-trees. Bull. Math .Biol. 43, 239–244.
McKenna, M.C. (1987). Molecular and morphological analysis of higher level mammalian relationships. In Molecules and
Morphology, edited by C. Patterson,.Cambridge University Press, Cambridge. pp. 55-93.
Meneghini, G. 1839. Nuova specie di alga. Nuova Giornale de' Litterati 39: 67-68.
Meneghini, G. 1841. Monographia Nostichinearum italicarum. Accad. Sci., Torino; Mat. Fis., ser. 2, 5: 1-143.
Merola, A., Castaldo, R., De Luca, P., Gambardella, R., Musacchio, A., Taddei, R. 1981. Revision of Cyanidium caldarium: 3
species of acidophilic algae. Giorn. Bot. Ital. 115: 189-95.
Meyer, T.E., Cusanovich, M.A., & Kamen, MD. ( 1986). Evidence against use of bacterial amino acid sequence data for
construction of all-inclusive phylogenetic trees. Proc. NSA USA 83: 217-20.
Migula, W. (1897). System der Bakterien. Gustav Fischer, Jena.
Mishler, B.D., Churchill, S.P. (1985). Transition to a land flora: phylogenetic relationships of green algae and bryophytes.
Cladistics 1:305-328.
Mohn, E. (1984). System und Phylogenie der Lebewese. 2 vols. E. Schweizerbart’sche.
de Monet (Lamarck), J.B.J. 1806. Tableau du Regne Animal.
Moreira D., Heyden S, von der Bass, D., Lopez-Garcia P., Chao E., and Cavalier-Smith T. 2006. Globoal eukaryote
phylogeny: Combined S and LSU rDNA trees support monophyly of Rhizaria, Retaria, and Excavata. Mol. Phyl. Evol.
sciencedirect.com.
von Munchhausen, O.. 1765-76. Bibliotheca Botanico-Physico-Economica. Forsters, Hanover.
Nagashima, H. et al. 1993. Several new strains of thermal alga Cyanidioschyzon as the most primitive eukaryotes. In: Sato,
V, S., Ishida, M., Ishakawa, H.(Eds.), Endocytobiology, Tübingen U. Press,. pp. 279-285.
Nees Esenbeck, von . 1770. In : C. d’Orbigny( Ed.), Dictionnaire Universelle d’Histoire Naturelle.
Neushul, M. 1974. Botany. Hamilton; Santa Barbara.
Nixon, K.C. (1999). The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15: 407-414.
Novak, F.A. (1930). Systematika Botanika. J.R. Vilimek, Praha.
Nozaki H., Iseki M., Hasegawa M., Misawa K., Nakada T., Sasaki N., Watanabe M. 2007. Phylogeny of primary
photosynthetic eukaryotes as deduced from slowly evolving nuclear genes. Mol. Biol. Evol. 24, 1592-1595.
Nozaki, H. et al. 2007. Phylogeny of primary photosynthetic eukaryotes as deduced from slowly evolving nuclear genes. Mol.
Biol. Evol.
Orla-Jensen, W. (1909). Die Hauptlinien des naturalischen Bakteriensystems nebst einer Ubersicht der
Garungsphenomene. Zentr. Bakt. Parasitenk., II, 22: 305-346.
Parasara. 1st millenium BC. Vrikshayurveda (Botany).
Parfrey L., Barber E., Lasser E., Dunthorn M., Bhattacharya D., Patterson D.J., and Katz L. 2006. Evaluating support for the
current classification of eukaryotic diversity. PSOL Genetics 2, 220-38.
Parfrey, L., Grant, J., Tekle, Y.I., Lasek-Nesselquist, E., Morrison, H.G., Sogin, M.L., Patterson, D.J., Katz, L.A.
2010. Broadly Sampled Muligene Analyses Yield Well-Resolved Eukaryotic tree of Life. Syst. Biol. 59: 518-533.
Parker, C.(ed.). (1982). Synopsis and Classification of Living Organisms. McGraw-Hill, New York.
Pascher, A. 1931. Systematische Ubersicht uber die Flagellaten. Bot. Zentrlb. Beih, Abt. 2. 48: 317-32.
Philippe, H. & Adoutte, A. (1998). The molecular phylogeny of Eukaryota: solid facts and uncertainties. In Evolutionary
Relationships Among Protozoa edited by G.H. Coombs, K. Vickerman, M.A. Sleigh, and A. Warren, Systcs. Assc. Spl.
Vol. Srs. 56, KluwerAcademic, Dordrecht, The Netherlands, pp. 25-56.
Prévot, A.R. (1963). Manuel de Classification et Determination des Bacteries Anaerobies. 4th ed. Masson, Paris.
Raff, E.C., Diaz, H.B., Hoyle, H.D., Hutchens, J.A., Kimble, M., Raff, R.A., Rudolph, J.E., & Subler, M.A.
(1987). Origin of multiple gene families- are there both functional and regulatory constraints? In Development as an
Evolutionary Process, edited by R.A. RAFF & E.C. RAFF) Alan Liss, New York. pp. 203-238.
Ragan, M.A. 1997. A 3rd Kingdom of life: the history of an idea. Arch. Protistenkd. 148: 225-43.
Richards T. and Cavalier-Smith T. 2005. Myosin evolution and the primary divergence of eukaryotes. Nature 436, 1113-1118.
Rodriguez-Ezpeleta, N, et al. 2007. Towards resolving the eukaryotic tree: the phylogenetic positons of jakobids and
cercomonads. Curr. Biol. 17: 1420-25.
Sachs, J. 1874. Lehrbuch der Botanik, 4te umgearb. Engelmann, Leipzig.
Saunders G.W, Potter D., and Andersen R.A. 1997. Phylogenetic affinities of Sarcinochrysidales and Chrysomeridales
(Heterokonta) based on analyses of molecular and combined data. J. Phycol. 33, 310-318.
Saunders, G.W. and Hommersand, M.H. 2004. Assessing Supraordinal Red Algal Diversity and Taxonomy in the Context of
Contemporary Systematic Data. Am. J. Bot. 91: 1494-1507.
Savile, D.B.O. 1968. possible Interelationships between Fungal Groups. In Fungi, vol. 3, G.C. Ainsworth and A.S. Sussman
(eds.), pp. 649-75, Academic Press, NY and London.
Seckbach, J. 1987. Evolution of eukaryotic cells via bridge algae, the cyanidia connection. Ann. NY Acad. Sci. 503: 424-37.
Seckbach, J. 1994. The 1st eukaryotic cells-acid hot-spring algae. J. Biol. Physics 20, 335-345.
Smith, G.M. 1938. Cryptogamic Botany,Vol. 1 ( Algae and Fungi ). McGraw-Hill, NY.
Stanier, R.Y. & van Neil, C.B. (1941). The main outlines of bacterial classification. J Bacteriol 42: 437- 466.
Starobogatoff, Y.I. 1986. On the number of kingdoms of eukaryotic organisms. Trudy Zool. Inst. 144: 4-25 (in Russian).
Stiller J.W., Riley J., and Hall, BD. 2001. Are red algae plants? a critical evaluation of 3 key molecular data sets. J. Mol. Evol.
52, 527-539.
Tekle YI, Grant J, Cole JC, Nerad TA, Patterson DJ, Anderson OR, Katz LA. 2008. Phylogenetic placement of diverse
amoebae inferred from multigene analysis and assessment of the stability of clades within ‘Amoebozoa’upon removal of
varying fast rate classes of SSU-rDNA. Molecular Phylogenetics and Evolution 47: 339–352.
Theophrastus. 200s BC. Enquiry into Plants, 10 vols.(9 extant) (transl. A. Hort, 1916).
Tilden, J. 1898. Observations on some west American thermal algae. Bot. Gaz. 26: 89-105.
Tilden, J. 1910. Minnesota Algae, Vol. 1 (the Myxophyceae). U. Minn. Press, Minneapolis.
Tippo, O. 1942. A modern classification of the plant kngdom. Chron. Bot. 7; 203-6.
Treviranus, G. 1802-1822. Biologie. Gottingen.
van Neil, C.B. (1946). The classification and natural relationships of bacteria. Cold Spring Harb Symp. Quant . Biol 11:
285-301.
Walker G., Simpson A.G.B., Edgcomb. V., Sogin M.L., and Patterson D.J. 2001. Ultrastructural studies of Mastigameba
punctophora and simplex and Mastigella commutans and assesssment of hypotheses of relatedness of pelobiotes (Protista).
Eur. J. Protistol. 37, 25-49.
Walton, L. B. 1930. Studies concerning organisms occurring in water supplies with particular reference to those found in Ohio.
Bull. Ohio Biol. Surv. 24, 1-86.
Whittaker, R.H. 1957. The kingdoms of the living world. Ecology 38, 536-538.
Whittaker, R.H. 1959. On the broad classification of organisms. Quart. Rev. Biol. 34, 210-226.
Whittaker, R.H.(1969). New concepts of kingdoms. Science 163: 150-160.
Whittaker, R. Margulis, L. 1978. Protistan classification and the kingdoms of organisms. BioSystems 10: 3-18.
Williams D. 1991. Phylogenetic relationships among Chromista: a review and preliminary analysis. Cladistics 7, 141-156.
Woese, C.R. & Fox, G. E. (1977). The concept of cellular evolution. J Mol Evol 10: 1-6.
Woese, C.R.., Debrunner-Vossbrinck, B.A., Oyaizu, A., Stackebrandt, S., Ludwig, W. ( 1985). Gram-positive bacteria:
possible photosynthetic ancestry. Science 229: 762-765.
Woese, C.R.., Olsen, G.V. (1 986). Archaebacterial phytogeny: perspectives on the urkingdoms. Syst. Appl.
Microbiol. 7: 161-177.
Woese, C.R., (1987). Bacterial evolution. Microbiol. Rev. 51: 221-271.
Woese, C.R., Kandler, O, & Wheelis, M.L. (1 990). Towards a natural system of organisms: proposal for the
domains Archea, Bacteria, and Eucarya. Proc. NAS USA 87: 4576-4579.
Wheelis, M.L., Kandler, O, & Woese, C.R., ( 1992). On the nature of global classification. Proc. NAS USA 89:
2930- 2934. Wyss, Novacek, & McKenna(1987). Amino acid sequence versus morphological data and the
interordinal relationships of mammals. Mol. Biol. Evol. 4: 9-116.
Yoon HS, Grant J, Tekle YI, Wu M, Chaon BC, Cole JC, Logsdon JM, Patterson DJ, Bhattacharya D, Katz LA. 2008.
Broadly sampled multigene trees of eukaryotes. BMC Evolutionary Biology 8: 14.
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