Systematics of Protozoa

[Notice]
We thank following scientists and The Society of Protozoologists (The Journal of Protozoology) for quoting text descriptions from their papers.

1. The Subkingdom PROTOZOA

Systematic analysis; Mainly morphology.

2. The Kingdom PROTOZOA

Systematic analysis; Molecular phylogenetics.

3. Protist diversity

Systematic analysis; Ultrastructural identity.
David J. Patterson, 1999 (ref. ID; 5694)

4. ICZM

(The International Commission on Zoological Nomenclature) 1985: International Code of Zoological Nomenclature. Berkeley, Los Angeles

History of Classification

ref. ID; 4925, 4978, 5694, 5695

1. The Subkingdom Protozoa

[ref. ID; 923]

The Committee on Systematics and Evolution of The Society of Protozoologists
N.D. Levine (Chairman); J.O. Corliss; F.E.G. Cox; G. Deroux; J. Grain; B.M. Honigberg; G.F. Leedale; A.R. Loeblich, III; J. Lom; D. Lynn; E.G. Merinfeld; F.C. Page; G. Poljansky; V. Sprague; J. Vavra; and F.G. Wallace

The first Protozoa were seen by Antony van Leeuwenhoek in 1674. Linnaeus included 2 species of free-living Protozoa in the 1758 edition of his System Naturae, but he included no parasitic ones. At present, over 65,000 protozoan species (of which over half are fossil and ~10,000 are parasitic) have been named. Among living species, this includes ~250 parasitic and 11,300 free-living sarcodines (of which ~4,600 are Foraminiferida); ~1,800 parasitic and 5,100 free living flagellates; ~5,600 parasitic "Sporozoa" (including Apicomplexa, Microspora, Myxospora, and Ascetospora); and ~2,500 parasitic and 4,700 free-living ciliates. There are undoubtedly thousands more species still unnamed. The classical taxonomic scheme of the Protozoa was developed about the turn of the century. In it they were considered a phylum and were divided into 2 subphyla, Plasmodroma (containing the classes Mastigophora, Sarcodina, and Sporozoa) and Ciliophora. This scheme was based primarily on organelles of locomotion. In 1964 the Society of Protozoologists introduced a new but fairly similar classification. It is remarkable how many important and necessary changes have been made in the classification since 1964. Every major group has been affected. The 1964 scheme was a necessary step in the development of the present one, but it is now obsolete. One of the principal sources of many new data of taxonomic significance has been electron microscopy.

As in the Society's 1964 Classification, phyla, subphyla, and superclasses end in "-a"; classes in "-ea"; subclasses in "-ia"; orders in "-ida"; and suborders in "-ina"; superorders, not used in the previous scheme, end in "-idea." These uniform endings conform to those recommended by Pearse (1936) and employed by Hall (1953) and Jahn & Jahn (1949); they differ from the more precise but longer rending suggested by Levine (1959). In general, the nomenclatural policies of this Committee are also essentially the same as those adopted by the authors of the 1964 scheme. Thus, a worker who originally proposed a new name at any level lower than that of suborder is not credited with the name of the new higher taxon, even if essentially the same word is used for it or even if the new taxon (e.g. order or class) contains only a single family. The responsibility for the name of the high-level taxon (suborder or above) is that of the person who established its actual level and its concept. The same situation obtains when a given higher taxon, e.g. an order, has been elevated to another level, e.g. a class, with retention of the original taxon (order)- the name of the higher taxon (class) is credited to the worker who created it. On the other hand, if a group, originally established at the class or subclass level, is now considered to contain several more recently created orders, one of which bears a name similar to that of the class or subclass, the authority and date of the name of either of the latter taxa is automatically employed for this order, with different authorships and dates of the others; the same procedure applies to suborders with in an order. While this Classification is the product of a committee, it should not be assumed that its every member, although responsible for his own group, is in agreement with the entire scheme. Indeed, probably none of them agrees with it completely; however, unanimity can hardly be expected. What were have produced is something with which we can live and which we can modify as suggested by our differing needs and ideas.

The Society's 1980 Classification

Phylum I. SARCOMASTIGOPHORA Honigberg & Balamuth, 1963

Single type of nucleus, except in heterokaryotic FORAMINIFERIDA; sexuality, when present, essentially syngamy; flagella, pseudopodia or both types of locomotor organelles. (See: ref. ID; 1663)

Subphylum I. MASTIGOPHORA Diesing, 1866

One or more flagella typically present in trophozoites; asexual reproduction basically by intrakinetal (symmetrogenic) binary fission; sexual reproduction known in some groups. (See: ref. ID; 3731)

Class 1. PHYTOMASTIGOPHOREA Calkins, 1909

Typically with chloroplasts; if chloroplasts lacking, relationship to pigmented forms clearly evident; mostly free-living. (See: ref. ID; 7291)

Order 1. CRYPTOMONADIDA Senn, 1900

Two subequal flagella arising subapically in ventral groove; chloroplasts brown, red, olive-green, blue or yellow; storage products starch and fat; cells flattened, naked, without wall or pellicle; flagellates, coccoid unicells and palmellae; sexual reproduction unknown.
Genus: Cryptomonas

Order 2. DINOFLAGELLIDA Butschli, 1885

Two heterodynamic flagella, inserted apically or laterally, one ribbon-shaped with paraxial rod and single row of fine hairs, other smooth or with 2 rows of stiffer hairs; chloroplasts typically golden-brown or green; storage product starch and fat; cells flattened or of complex symmetry with transverse and ventral grooves and often armor of cellulosic plates; nucleus unique among eukaryotes in having chromosomes that consist primarily one of nonprotein-complexed DNA; mitosis intranuclear; flagellates, coccoid unicells, colonies, and simple filaments; sexual reproduction present.
Genus: Ceratium, Gymnodinium, Prorocentrum

Order 3. EUGLENIDA Butschli, 1884

Two (rarely more) flagella, one or both emerging from an anterior invagination of the cell; emergent flagella with single row of fine hairs; flagella with paraxial rods; chloroplasts grass-green, absent in many general storage products; paramylon, fat, and cyclic metaphosphates; cell with helical symmetry, naked but with complex pellicle of interlocking proteinaceous strips; nonspindle intranuclear mitosis; flagellates or colonies. (See: ref. ID; 4226)

Order 4. CHRYSOMONADIDA Engler, 1898

Two unequal flagella, one directed anteriorly and bearing 2 opposite rows of mastigonemes, other trailing and smooth; chloroplasts golden-brown or absent; storage products chrysolaminarin and fat; cells naked, with richly patterned silicified scales, or with lorica; sexual reproduction present.
Genus: Dinobryon, Ochromonas, Synura

Order 5. HETEROCHLORIDA Pascher, 1912

Two unequal flagella; chloroplasts yellow-green; storage products oil and possibly chrysolaminarin; supposedly related to xanthophycean algae.
Genus: Chloramoeba, Heterochloris

Order 6. CHLOROMONADIDA Klebs, 1892

Two heterokont flagella; chloroplasts green; storage product oil; characteristic ring of Golgi bodies at anterior end; sexual reproduction by fusion of 2 flagellates.
Genus: Chattonella, Vacuolaria

Order 7. PRYMNESIIDA Hibberd, 1976

Two equal or subequal, smooth flagella inserted laterally or anteriorly, with unique 3rd appendage, the haptonema, between them; chloroplasts golden-brown; storage products chrysolaminarin (?) and fat; cells covered with delicate organic scales of diagnostic pattern; scales calcified to form coccoliths in coccolithophorids; sexual reproduction present.
Genus: Chrysochromulina, Coccolithus, Prymnesium

Order 8. VOLVOCIDA France, 1894

Two or 4 equal, smooth, apical flagella; chloroplasts grass-green; storage products starch and fat; sexual reproduction present.
Genus: Chlamydomonas, Volvox

Order 9. PRASINOMONADIDA Christensen, 1962

One, 2, 4, or 8 flagella, typically covered with rows of finely patterned scales; chloroplasts grass-green; storage product starch; cells typically covered with one or more layers of intricately patterned Golgi-derived scales; sexual reproduction present.
Genus: Mesostigma, Prasinomonas

Order 10. SILICOFLAGELLIDA Borgert, 1891

One flagellum; chloroplasts golden-brown or green-brown; storage product apparently chrysolaminarin; with star-shaped siliceous skeleton composed of tubular elements; sexual reproduction unknown.
Genus: Dictyocha

Class 2. ZOOMASTIGOPHOREA Calkins, 1909

Chloroplasts absent; one to many flagella; ameboid forms, with or without flagella, in some groups; sexuality known in few groups; a polyphyletic group. (See: ref. ID; 7291, 7293)

Order 1. CHOANOFLAGELLIDA Kent, 1880

One flagellum, inserted apically, with proximal part surrounded by ring of tentacles (collar); with membranous sheath or basket-like lorica composed of siliceous costae; stalked or free-swimming; free-living.
Genus: Monosiga

Order 2. KINETOPLASTIDA Honigberg, 1963 emend. Vickerman, 1976

One or 2 flagella arising from depression; flagella typically with paraxial rod in addition to axoneme; single mitochondrion (nonfunctional in some forms) extending length of body as single tube, hoop, or network of branching tubes, usually containing conspicuous Feulgen-positive (DNA-containing) kinetoplast (nucleoid) located near flagellar kinetosomes; Golgi apparatus typically in region of flagellar depression, not connected to kinetosomes and flagella; parasitic (majority of known species) and free-living.

Order 3. PROTEROMONADIDA Grasse, 1952 emend. Vickerman, 1976

One or 2 pairs of heterodynamic flagella without paraxial rods; single mitochondrion, distant from kinetosomes, curing around nucleus, not extending length of body, without Feulgen-positive kinetoplast; Golgi apparatus encircling band-shaped rhizoplast passing from kinetosomes near surface of nucleus to mitochondrion; cysts present; parasitic.
Genus: Karotomorpha, Proteromonas

Order 4. RETORTAMONADIDA Grasse, 1952

Two to 4 flagella, one turned posteriorly and associated with ventrally located cytostomal area bordered by fibril; mitochondria and Golgi apparatus absent; intranuclear division spindle; "semiopen'" mitosis reported from 1 genus; cysts present; parasitic.
Genus: Chilomastix, Retortamonas

Order 5. DIPLOMONADIDA Wenyon, 1926 emend. Brugerolle, 1975

One or 2 karyomastigonts; genera with 2 karyomastigonts with two-fold rotational symmetry or, in one genus, primarily mirror symmetry; individual mastigonts with 1 to 4 flagella, typically one of them recurrent and associated with cytostome, or, in more advanced genera, with organelles forming cell axis; mitochondria, and Golgi apparatus absent; intranuclear division spindle; "semiopen" mitosis reported in one genus; cysts present; free-living or parasitic.

Order 6. OXYMONADIDA Grasse, 1952

One or more karyomastigonts, each containing 4 flagella typically arranged in 2 pairs in motile stage; one or more flagella may be recurrent, adhering to body surface for greater or lesser distance; kinetosomes of flagellar pairs connected by paracrystalline structure ("preaxostyle") in which are embedded anterior ends of axostylar microtubules; one to many axostyles per organism, contractile in many genera; mitochondria and Golgi apparatus (including Janicki-type parabasal apparatus) absent; division spindle intranuclear; cysts in some species; sexuality in some species; parasitic.
Genus: Monocercomonoides, Oxymonas, Pyrsonympha

Superorder 1. PARABASALIDEA Honigberg, 1973

[Notice] This superorder was proposed by Honigberg to include TRICHOMONADIDA Kirby and HYPERMASTIGIDA Grassi & Foa, which share several important characters and which must have had common ancestry. Since, on the basis of the presently available information, no other zoomastigophorean orders can be considered as closely related as the trichomonads and hypermastigotes, there appears no justification for establishment of other superorders within this class. Although this procedure does not conform to the commonly accepted usage, I consider the inclusion of the single superorder in the present scheme consistent with our attempt to indicate degrees of interrelationships among the higher taxa wherever possible.

Typically at least some kinetosomes, bearing flagella or barren, arranged in pattern and associated with rootlet filaments characteristic of trichomonads; one or more argentophilic Janicki-type parabasal apparatuses (Golgi complexes applied to filaments with Type A periodicity) present; mitochondria absent; division spindle extranuclear.

Order 7. TRICHOMONADIDA Kirby, 1947 emend. Honigberg, in Camp, Mattern & Honigberg, 1974

Typically karyomastigonts with 4 to 6 flagella, but with only 1 flagellum in one genus and no flagella in another; karyomastigonts and akaryomastigonts in one family with permanent polymonad organization; in mastigont(s) of typical genera one flagellum recurrent, free or with proximal or entire length adherent to body surface; undulating membrane, if present, associated with adherent segment of recurrent flagellum; pelta and noncontractile axostyle in each mastigont, except for one genus; hydrogenosomes present; true cysts infrequent, known in very few species; all or nearly all parasitic.
Genus: Dientamoeba, Histomonas, Monocercomonas, Trichomonas

Order 8. HYPERMASTIGIDA Grassi & Foa, 1911

Mastigont system with numerous flagella and multiple Janicki-type parabasal apparatus; "privileged" barren kinetosomes, resembling in arrangement kinetosomes of trichomonads and associated with rootlet filaments characteristic of these flagellates, present in many genera; flagella-bearing kinetosomes distributed in complete or partial circle, in plate or plates, or in longitudinal or spiral rows meeting in a centralized structure; one nucleus per cell; cysts in some species; sexuality in some species; all parasitic.

Subphyllum II. OPALINATA Corliss & Balamuth, 1963

Numerous cilia in oblique rows over entire body surface; cytostome absent; nuclear division acentric; binary fission generally interkinetal (symmetrogenic); known life cycles involve syngamy with anisogamous flagellated gametes; all parasitic.

Class 1. OPALINATEA Wenyon, 1926

With characters of the subphylum.

Order 1. OPALINIDA Poche, 1913

With characters of the class.
Genus: Opalina

Subphyllum III. SARCODINA Schmarda, 1871

Pseudopodia, or locomotive protoplasmic flow without discrete pseudopodia; flagella, when present, usually restricted to developmental or other temporary stages; body naked or with external or internal test or skeleton; asexual reproduction by fission; sexuality, if present, associated with flagellate or, more rarely, ameboid gametes; most species free-living.

Superclass 1. RHIZOPODA von Siebold, 1845

Locomotion by lobopodia, filopodia, or reticulopodia, or by protoplasmic flow without production of discrete pseudopodia. (See: ref. ID; 4598, 5753)

Class 1. LOBOSEA Carpenter, 1861

Pseudopodia lobose or more or less filiform but produced from broader hyaline lobe; usually uninucleate; multinucleate forms not flattened or much-branched plasmodia; no sorocarps, sporangia, or similar fruiting bodies.

Subclass 1. GYMNAMOEBIA Haeckel, 1862

Without test. (See: ref. ID; 6796)

Order 1. AMOEBIDA Ehrenberg, 1830

Typically uninucleate; mitochondria typically present; no flagellate stage. (See: ref. ID; 7594, 7615)

Order 2. SCHIZOPYRENIDA Singh, 1952

Body with shape of monopodial cylinder, usually moving with more or less eruptive, hyaline, hemispherical bulges; typically uninucleate, nuclear division promitotic; temporary flagellate stages in most species. (See: ref. ID; 7594, 7755)
Genus: Naegleria, Tetramitus, Vahlkampfia

Order 3. PELOBIONTIDA Page, 1976

Body with shape of thick cylinder; monopodial, with true bidirectional fountain flow of cytoplasm common; typically multinucleate; lacking mitochondria but with symbiotic bacteria; in microaerobic habitats; no flagellate stage known, but numerous nonmotile cils visible at fine-structural level, with variations of usual microtubular pattern.
Genus: Pelomyxa

Subclass 2. TESTACEALOBOSIA De Saedeleer, 1934

Body enclosed by test, tectum, or other complex membrane external to plasma membrane and glycocalyx.

Order 1. ARCELLINIDA Kent, 1880

Test, tectum, or other external membrane with single aperture and composed of either organic or inorganic material or both. (See: ref. ID; 6790, 7745)
Genus: Arcella, Cochliopodium, Difflugia

Order 2. TRICHOSIDA Mobius, 1889

Test composed of fibrous sheath and, in at least one extensive stage of life cycle, with calcareous spicules, and multiple apertures through which short, conical pseudopodia extend; locomotion by broad lobopodium; marine
Genus: Trichosphaerium

Class 2. ACARPOMYXEA Page, 1976

Small plasmodia or much-expanded similar uninucleate forms, usually branching, sometimes forming reticulum of coarse branches advancing tips lobose; no regular reversal of streaming; no test; no spores or fruiting bodies known.

Order 1. LEPTOMYXIDA Pussard, 1973

Typically thin sheets, often polyaxial; sometimes more cylindrical, limax-like forms; cysts produced by soil and freshwater species. Genus: Leptomyxa, Rhizamoeba

Order 2. STEREOMYXIDA Grell, 1966

Marine ameboid organism with more or less branched pseudopodia producing only very slow motion or serving as floating organelles.
Genus: Corallomyxa, Stereomyxa

Class 3. ACRASEA Schroter, 1886

Uninucleate amebae with eruptive, lobose pseudopodia; amebae aggregating to form pseudoplasmodium which gives rise to fruiting bodies without stalk tube; flagellate cells known in only one species; sexuality unknown.

Order 1. ACRASIDA Schroter, 1886

With characters of the class.
Genus: Acrasis

Class 4. EUMYCETOZOEA Zopf, 1884

Myxamebae with filiform subpseudopodia; flagella, when present nonmastigonemate, in unequal, less often equal, apical pair; producing aerial fruiting bodies; stalk tube typically present in fruiting bodies of first 2 subclasses and in some members of 3rd.

Subclass 1. PROTOSTELLIA Olive & Stoianovitch, 1966

Trophic stage varying from single amebae to plasmodia which lack shuttle streaming; flagellate cells present or absent; fruiting bodies consisting of one to several spores on narrow, hollow stalk; sexuality known in one species.

Order 1. PROTOSTELIIDA Olive & Stoianovitch, 1966

With characters of the subclass.
Genus: Ceratiomyxa, Protostelium

Subclass 2. DICTYOSTELIIA Lister, 1909

Amebae aggregate of form multicellular pseudoplasmodium that gives rise to multispored fruiting body stalk tube present no flagellate cells; sexuality indicated in some species.

Order 1. DICTYOSTELIIDA Lister, 1909

With characters of the subclass.
Genus: Dictyostelium

Subclass 3. MYXOGASTRIA Fries, 1829

Major trophic stage multinucleate plasmodium typically with shuttle streaming; fruiting bodies multispored; flagellate cells present; syngamy and meiosis in life cycle.

Order 1. ECHINOSTELIIDA Martin, 1961

Sporangia stalked, minute; plasmodium small, ameba-like, nonreticulate.
Genus: Echinostelium

Order 2. LICEIDA Lister, 1909

Spore mass usually light-colored; lime usually absent from sporocarps; true capillitium lacking; pseudo-capillitum often present.
Genus: Licea

Order 3. TRICHIIDA Masse, 1892

Spore mass usually light-colored; lime usually absent from sporocarps; true capillitium present.
Genus: Trichium

Order 4. STEMONITIDA Masse, 1892

Spore mass usually dark-colored; lime, when present, restricted to substrate, stipe, and columella.
Genus: Stemonitis

Order 5. PHYSARIDA Masse, 1892

Spore mass usually dark-colored; peridium and/or capillitium calcareous.
Genus: Physarum

Class 5. PLASMODIOPHOREA Cook, 1928

Obligate intracellular parasites with minute plasmodia; zoospores produced in zoosporangia and bearing anterior pair of unequal, nonmastigonemate flagella; resting spore formed in compact sori of loose clusters within host cells; sexuality reported in some species.

Order 1. PLASMODIOPHORIDA Cook, 1928

With characters of the class.
Genus: Plasmodiophora, Sorosphaera

Class 6. FILOSEA Leidy, 1879

Hyaline, filiform pseudopodia, often branching, sometimes anastomosing; no spores or flagellate stage known. (See: ref. ID; 4224)

Order 1. ACONCHULINIDA De Saedeleer, 1934

Without external skeletal material; filopodia produced from main mass of cell, not from hyaline lobe.
Genus: Nuclearia, Vampyrella

Order 2. GROMIIDA Claparede & Lachmann, 1859

Body enclosed by test or rigid external membrane with distinct aperture.
Genus: Euglypha, Gromia

Class 7. GRANULORETICULOSEA De Saedeleer, 1934

Delicate, finely granular or hyaline reticulopodia or, rarely, finely pointed, granular but nonanastomosing pseudopodia.

Order 1. ATHALAMIDA Haeckel, 1862

Naked.
Genus: Arachnula, Biomyxa

Order 2. MONOTHALANMIDA Haeckel, 1862

With single-chambered organic or calcareous test, sometimes including foreign matter; no alternation of generations.
Genus: Liberkuehnia

Order 3. FORAMINIFERIDA D'Orbigny, 1826

Test with one to many chambers; pseudopodia protruding from aperture, wall perforations or both; reproduction with alternation of sexual and asexual generations, of which one may be secondarily repressed; gametes usually flagellate, rarely ameboid; nuclear dimorphism in developmental stages of some species.

Class 8. XENOPHYOPHOREA Schulze, 1904

Multinucleate plasmodium enclosed in branched-tube system composed of transparent organic substance; numerous barite crystals in cytoplasm; fecal pellets retained outsides organic tube system as conspicuous dark masses; test of foreign matter surrounding tube system and fecal-pellet masses; marine.

Order 1. PSAMMINIDA Poche, 1913

Without linellae (threads forming part of test); body more or less rigid.
Genus: Psammetta, Psammina

Order 2. STANNOMIDA Tendal, 1972

With linellae (threads forming part of test); body flexible.
Genus: Stannophyllum

Superclass 2. ACTINOPODA Calkins, 1909

Often spherical, usually planktonic; axopodia with microtubular stereoplasm; skeleton, when present, composed of organic matter and/or silica, or else of strontium sulfate; reproduction asexual and/or sexual; trophic cells rarely flagellated; in many species small flagellated stages whose exact nature (gametes or spores) is still usually uncertain.

Class 1. ACANTHAREA Haeckel, 1881

Strontium surface skeleton, usually composed of 20 radial or 10 diametral spines oriented according to Muller's Law, rarely 16 diametrical or 32 radial spines oriented according to Haeckel's Law; sometimes many more spines randomly oriented; spines more or less joined in cell center extracellular outer (cortex) and inner envelops usually present; inner envelope (called "capsular membrane") often closely lining central cell mass; marine, usually planktonic.

Order 1. HOLACANTHIDA Schewiakoff, 1926

Usually 10, sometimes 16 diametral spines, crossing in center; inner envelope far outside central cell mass, or absent; encystment before sporogenesis, at least in several species.
Genus: Acanthochiasma, Acanthocolla, Acanthoplegma

Order 2. SYMPHYACANTHIDA Schewiakoff, 1926

Twenty radial spines totally fused in cell center or forming there small sphere by apposition of their basal pyramids; inner envelop far outside central cell mass; encystment before sporogenesis, at least in some species.
Genus: Acantholithium, Amphilithium, Pseudolithium

Order 3. CHAUNACANTHIDA Schewiakoff, 1926

Twenty radial spines with bases more or less loosely articulated; inner envelop at some distance outside central cell mass, or absent; encystment before sporogenesis in most or perhaps all species.
Genus: Conacon, Gigartacon, Stauracon

Order 4. ARTHRACANTHIDA Schewiakoff, 1926

Usually 20 radial spines joined at cell center by apposition of bases; inner envelope usually closely lining central cell mass; no cysts.

Order 5. ACTINELIIDA Haeckel, 1885

Variable number of radial spines, not disposed according to Muller's Law; mostly planktonic, one benthic genus.
Genus: Actinelius, Astrolophus, Podactinelius

Class 2. POLYCYSTINEA Ehrenberg, 1838

Siliceous skeleton present in most species; made up usually of solid elements, consisting of one or more latticed shell with or without radial spines, or of one or more isolated spicules; capsular membrane composed usually of grossly polygonal plates and containing many more than 3 pores; axonemes often originating from axoplast in endoplasm; marine, planktonic.

Order 1. SPUMELLARIDA Ehrenberg, 1875

Capsular membrane with uniformly distributed pores.

Order 2. NASSELLARIDA Ehrenberg, 1875

Capsular membrane with pores gathered at a single pole; skeleton of one piece, often basket-shaped.
Genus: Eucoronis, Plagiacantha, Plagonium

Class 3. PHAEODAREA Haeckel, 1879

Skeleton (sometimes absent) of mixed silica and organic matter, consisting of usually hollow spines and/or shells; very thick capsular membrane with astropyle (functioning as cytopharynx) at one pole; 2 smaller parapylae, penetrated by axopodia, usually at other pole; ectoplasm with phaeodium (group of dark corpuscles and debris); marine, planktonic.

Order 1. PHAEOCYSTIDA Haeckel, 1879

Skeleton absent, or consisting of spicules either free or radiating from common junction point.
Genus: Astracantha, Aulacantha, Phaeodina

Order 2. PHAEOSPHAERIDA Haeckel, 1879

Skeleton consisting mainly of very large latticed shell with wide polygonal meshes.
Genus: Aulosphaera, Cannosphaera, Sagosphaera

Order 3. PHAEOCALPIDA Haeckel, 1887

Skeleton consisting mainly of small shell, usually with numerous pores, often with one large opening; shell texture usually porcellanous, sometimes alveolar, never diatomaceous; radial spines often present.
Genus: Castanella, Circoporus, Tuscarora

Order 4. PHAEOGROMIDA Haeckel, 1879

Skeleton consisting mainly of small diatomaceous or alveolar shell with one large opening; shell, sometimes greatly reduced, may bear spines.
Genus: Atlanticella, Challengeron, Medusetta

Order 5. PHAEOCONCHIDA Haeckel, 1879

Skeleton consisting of 2 thick, usually hemispherical valves pressed against each other.
Genus: Concharium, Conchopsis, Neosphaeroconchidium

Order 6. PHAEODENDRIDA Haeckel, 1908

Skeleton consisting of 2 noncontiguous valves, from which originate long, branching spines with ramifications that may produce enormous external latticed spongious shells.
Genus: Coelodendrum, Coelographis, Coelothamnus

Class 4. HELIOZOEA Haeckel, 1866

Without central capsule; skeletal structures, if present, siliceous or organic; axopodia radiating on all sides; most species freshwater, some marine. (See: ref. ID; 3960, 7656, 7737)

Order 1. DESMOTHORACIDA Hertwig & Lesser, 1874

Cell enclosed in usually spherical, latticed organic capsule stalked in most species; no centroplast; microtubular stiffening elements, not discernible as axonemes, present in axopodia of some species; uni- or diflagellate zoospores.
Genus: Clathrulina

Order 2. ACTINOPHRYIDA Hartmann, 1913

No skeleton; no centroplast or axoplast; microtubular stiffening elements of axopodia usually discernible as axonemes by light microscopy; some with flagella or flagellated stage; sexuality known in some genera.
Genus: Actinophrys, Actinospharium, Ciliophrys

Order 3. TAXOPODIDA Fol, 1883

Bilaterally symmetrical, planktonic cells with siliceous spines; swimming by rowing action of axopodia arranged in parallel longitudinal rows; axopodia insert on complex, thick nucleotheca; small biflagellated species; marine.
Genus: Sticholonche

Order 4. CENTROHELIDA Kuhn, 1926

Frequently with a skeleton of siliceous plates and/or spines or of organic spicules; with centroplast or axoplast on which axonemes insert or, if centroplast absent, with large, eccentric nucleus; microtubular elements of axopodia frequently discernible by light microscopy as axonemes; some species with flagella or flagellated stages. (See: ref. ID; 4884)
Genus: Acanthocystis, Gymnosphaera, Raphidiophrys

Phylum II. LABYRINTHOMORPHA phyl. n.

[Notice] LABYRINTHOMORPHA phyl. n. was created by F.C. Page, with the diagnosis given in the body of this classification.

Trophic stage, ectoplasmic network with spindle-shaped or spherical, nonameboid cells; in some genera ameboid cells move within network by gliding; with sagenogenetosome, unique cell-surface organelle, associated with ectoplasmic network; heterokont zoospores produced by most species; saprobic and parasitic on algae, mostly in marine and estuarine waters.

Class 1. LABYRINTHULEA Levine & Corliss, 1963

With characters of the phylum.

Order 1. LABYRINTHULIDA Lankester, 1877

With characters of the class.
Genus: Labyrinthula, Thraustochytrium

Phylum III. APICOMPLEXA Levine, 1970

All species parasitic.

Phylum IV. MICROSPORA Sprague, 1977

Obligatory intracellular parasites in nearly all major animal groups.

Phylum V. ASCETOSPORA Sprague, 1978

All species parasitic.

Phylum VI. MYXOZOA Grasse, 1970 emend.

All species parasitic.

Phylum VII. CILIOPHORA Doflein, 1901

[Notice] The present classification of CILIOPHORA is a compromise between that of Corliss (1977) and that of de Puytorac et al. (1974). Publications, some 4 to 6 years ago suggested revolutionary changes in the concepts and bases for classification of the ciliates over the essentially Faurean scheme. Although, for the most part, the French and American proposals differed rather little, some additional refinements and/or criticisms have been made since the time of the original schemes, and still newer data have been accumulating. Thus, the Committee's ciliatologists have been faced with the formidable task of finding a single agreeable "compromise" classification for the present paper. To meet such a need and yet recognize the legitimacy of significant differences of opinion, footnotes have been used throughout this section-they generally contain comments of greatest value to specialists on the systematics of the groups concerned. In general, spellings of taxonomic names and data on authorships and dates conform to those used in Corliss (1977, 1979), except for the slight modification, here, of the suffixes on class and subclass names.

Simple cilia or compound ciliary organelles typical in at least one stage of life cycle; with subpellicular infraciliature present even when cilia absent; 2 types of nuclei, with rare exception; binary fission transverse, basically homothetogenic and generally parakinetal, but budding and multiple fission also occur; sexuality involving conjugation, autogamy, and cytogamy, nutrition heterotrophic; contractile vacuole typically preset; most species free-living, but many commensal, some truly parasitic, and large number found as symphorionts on variety of "hosts". (See: ref. ID; 1663, 4132)

Class 1. KINETOFRAGMINOPHOREA de Puytorac, Batisse, Bohatier, Corliss, Deroux, Didier, Dragesco, Fryd-Versavel, Grain, Groliere, Hovasse, Iftode, Laval, Roque, Savoie & Tuffrau, 1974

[Notice] Because of the large number of authors responsible for the names of this and some of the other ciliophoran taxa included in the present classification, all the author's names are given only once, in connection with the first name of their authorship cited in this scheme. Subsequently, this "authority" is referred to as "de Puytorac et al., 1974".

Oral infraciliature only slightly distinct from somatic infraciliature and differentiated from anterior parts, or other segments, of all or some of somatic kineties; stomatogenesis generally telokinetal; cytostome often apical (or subapical) or mid-ventral, on surface of body or at bottom of atrium or vestibulum; cytopharyngeal apparatus commonly prominent; compound ciliature, oral or somatic, typically absent.

Subclass 1. GYMNOSTOMATIA Butschli, 1889

Cytostomal area superficial, apical or subapical; circumoral infraciliature without kinetosomal differentiation other than closer packing of kinetosomes, insertion of supplementary segments of kineties, or pairing (not as dyads) of kinetosomes; cytopharyngeal apparatus of rhabdos type toxicysts common; somatic ciliation usually uniform.

Order 1. PROSTOMATIDA Schewiakoff, 1896

Cytostome apical or subapical; circumoral infraciliature involving anterior parts of all somatic kineties; typical polyploid independent macronucleus; body often large; commonly carnivorous.

Order 2. PLEUROSTOMATIDA Schewiakoff, 1896

Cytostome slit-like, lateral; circumoral infraciliature including anterior parts of only few somatic kineties and showing differentiation into left and right components; body often large, laterally compressed; macronucleus possibly of low ploidy number; voracious carnivores. (See: ref. ID; 7355)
Genus: Amphileptus, Litonotus, Loxophyllum

Incertae sedis in subclass GYMNOSTOMATIA

[Notice] The Incertae sedis category is used here advisedly, although with some reluctance. The problem of a homokaryotic ciliate has been complicated by preliminary findings in an ultrastructural (as yet unpublished) study of Stephanopogon - a number of its characteristics appear to be significantly flagellate -like! In the case if the karyorelictids, which French workers generally place in the order PLEUROSTOMATIDA, the location of Geleia has become particularly controversial: Nouzarede (1977) has recently created a new order for it, the PROTOHETEROTRICHIDA (not included in the present scheme), in the class POLYHYMENOPHORA.

Order PRIMOCILIATIDA Corliss, 1974

Nuclei homokaryotic, with prominent RNA-rich nucleolus or endosome; cytostome apical, slit-like; somatic ciliature sparse, ventral; small, marine benthic forms, thigmotactic, often algivorous.
Genus: Stephanopogon

Order KARYORELICTIDA Corliss, 1974

Macronucleus diploid (with possible exceptions) and nondividing; fragile, highly thigmotactic; oral area apical or ventral slit; somatic toxicysts; postciliodesmata characteristically present; contractile vacuoles absent; mainly interstitial sand-dwelling forms, often carnivorous. (See: ref. ID; 4875)
Genus: Geleia, Kentrophoros, Loxodes, Trachelocerca

Subclass 2. VESTIBULIFERIA de Puytorac et al., 1974

Apical or near-apical (occasionally at posterior pole) vestibulum commonly present, equipped with cilia derived from anterior parts of somatic kineties (normal or reorganized) and leading to cytostome; stomatogenesis sometimes involving 2 anlagen; cytopharyngeal apparatus resembling rhabdos; free-living or parasitic, especially in digestive tract of vertebrates and invertebrates.

Order 1. TRICHOSTOMATIDA Butschli, 1889

No reorganization of somatic kineties at level of vestibulum other than more packed alignment of kinetosomes or addition of supernumerary segments of kineties; many species endocommensals in vertebrate hosts.

Order 2. ENTODINIOMORPHIDA Reichenow, in Doflein & Reichenow, 1929

Oral and somatic ciliature functioning as syncilia; somatic ciliature in form of unique ciliary tufts of bands, otherwise body naked; oral area sometimes retractable; pellicle generally firm, sometimes drawn out into processes; skeletal plates in many species; stomatogenesis apokinetal; commensals in mammalian herbivores, including anthropoid apes.
Genus: Cycloposthium, Entodinium, Ophryoscolex, Troglodytella

Order 3. COLPODIDA de Puytorac et al., 1974

Vestibular ciliature and infraciliature highly organized by reorganization of parts of somatic kineties in vestibulum, but stomatogenesis basically telokinetal (sometimes involving 2 anlagen); body often contorted, rendering morphogenetics of division complex; somatic kinetids typically with kinetosomes in pairs; cysts common; mostly free-living, often in edaphic habitats. (See: ref. ID; 4692, 7466 (Grossglockneriids), 7537, 7706)
Genus: Colpoda, Platyophrya, Tillina, Woodruffia

[Notice] Platyophrya: Grain (in Dragesco et al., 1977) has recently proposed a new order, PLATYOPHRYIDA (in a superorder PLATYOPHRYIDEA), for this problematic genus and several alleged relatives (e.g., Cyrtolophosis and Woodruffia), placing it as the most primitive group in the subclass HYPOSTOMATA. Such a taxonomic arrangement, although endorsed by McCoy (1978) and others, is not followed here, awaiting further data with regard to the ultrastructure of the cytopharyngeal apparatus, especially.

Subclass 3. HYPOSTOMATIA Schewiakoff, 1896

[Notice] French workers (de Puytorac & Grain 1976, de Puytorac et al. 1974) have insisted on insertion of superordinal taxa among the several orders comprising this large subclass of kinetofragminophorans; these are adapted here, except for PLATYOPHRYIDEA and SUCTORIDEA, although Corliss (1977, 1979) maintains that they are of limited taxonomic value at the present state of our knowledge. The most striking and most extensive changes in the present ciliate scheme over that of the Society's earlier classification are to be seen among the groups here assembled under the HYPOSTOMATIA-dozens of significant papers have been published on them within the past 10-20 years, one of the most heuristic being Faure-Fremiet's (1967) succinct but perceptive contribution.

Cytostome nonpolar, on ventral surface; body cylindrical or flattened dorsoventrally, often with reduction of somatic ciliature; cytopharyngeal apparatus typically of cyrtos type; oral area may be sunk into atrium, with atrial ciliature present; morphogenesis often complex, with stomatogenesis of advanced telokinetal type or even para- or buccokinetal-like; some species astomatous free-living or ecto- or endocommensals, principally of invertebrates.

Superorder 1. NASSULIDEA Jankowski, 1967

[Notice] Two suborders, the SYNHYMENIIA and the NASSULOPSINA, have been recognized by some workers as comprising this order, following the original proposal of de Puytorac et al. (1974); but Corliss (1979) and others believe that more data are needed firmly to establish such a suprafamilial separation.

Hypostomial frange of many pats, running obliquely across anterior end of ventral surface, or extremely reduced to few adoral "pseudomembranelles" (sometimes in oral atrium); body often cylindrical, with complete somatic ciliature; cyrtos of numerous nematodesmata; free-living, most often in freshwater habitats.

Order 1. SYNHYMENIIDA de Puytorac et al., 1974

Parts of generally extensive hypostomial frange more or less fused (= synhymenium); kineties bipolar; body often cylindrical, with complete ciliation; stomatogenesis parakinetal-like. (See: ref. ID; 7403)
Genus: Nassulopsis, Orthodonella, Scaphidiodon

Order 2. NASSULIDA Jankowski, 1967

Parts of hypostomial frange individualized, limited to left side of ventral surface, sometimes reduced to few "pseudomembranelles", distinct preoral suture; stomatogenesis para- or buccokinetal-like.

Superorder 2. PHYLLOPHARYNGIDEA de Puytorac et al., 1974

Cyrtos complex, embedded in foliated or laminated phagoplasm; commonly relatively few but distinctive nematodesmata, often partly recurved, with "teeth-like" capitula; circumoral ciliature restricted to 3 short rows of kinetosomes near oral opening; somatic ciliature only on ventral surface, in 2 dissymmetric fields; preoral suture skewed to left; macronucleus commonly heteromerous.

Order 1. CYRTOPHORIDA Faure-Fremiet, in Corliss, 1956

Three rows of oral ciliature arising from kineties of left field, composed of pairs of kinetosomes with inverted polarity; body dorsoventrally flattened or laterally compressed; ventral ciliature often thigmotactic; many species with "glandular" adhesive organelle near posterior end.

Order 2. CHONOTRICHIDA Wallengren, 1895

Variously vase-shaped, sessile and sedentary forms; naked, except for ciliature of ventral surface (displaced to apical end of body); cytopharynx without nematodesmata; adhesive organelle active in stalk production; macronucleus heteromerous; reproduction by budding; marine and freshwater species, ectocommensal principally on crustaceans.

Superorder 3. RHYNCHODEA Chatton & Lwoff, 1939

Aberrant, small rostrate forms, with sucking tube and toxicysts; body of mature stage often nearly naked or with somactic ciliature limited to thigmotactic field; buds or "larvae" typically ciliated (in 2 fields); commensal or pathogenic, most commonly on gills of marine bivalves.

Order 1. RHYNCHODIDA Chatton & Lwoff, 1939

With characters of the superorder.
Genus: Ancistrocoma, Gargarius, Sphenophrya

Superorder 4. APOSTOMATIDEA Chatton & Lwoff, 1928

Cytostome inconspicuous or, in certain stages of polymorphic life cycle, absent; glandular complex (rosette) typically near oral area; in mature forms somatic ciliature spiraled, often widely space; commonly anterior thigmotactic ciliary field; stomatogenesis specialized, derived from telokinetal type; life cycle complex, sometimes involving alternation of hosts (unique in phylum); palintomy and cysts common; most species associated with marine crustaceans.

Order 1. APOSTOMATIDA Chatton & Lwoff, 1939

With characters of the superorder.

Subclass 4. SUCTORIA Claparede & Lachmann, 1858

[Notice] The SUCTORIA present at least 2 problems: (a) whether or not they should be considered taxonomically closer to the hypostomes [by incorporation there as a separate superorder, as originally suggested by de Puytorac et al. (1974) and (b) whether or not the order SUCTORIDA should be composed of 2 [after Corliss 1977), 3 [after Corliss 1979], or 7[after Batisse 1975] distinct suborders. The generally more conservative positions have been taken here; i.e., the subclass has been considered deserving a separate status at the subclass level (many workers have made the separation at even higher ranks; see reviews in Corliss 1968, 1979) and the number of suborders has been placed at the intermediate figure of 3 (formerly, none has been recognized).

Suctorial tentacles, generally multiple (polystomy), containing haptocysts; adult body sessile and sedentary, seldom with cilia; reproduction by budding; stalk commonly present, noncontractile, produced by scopuloid; conjugation of the involving micro- and macroconjugants; migratory larva ciliated (with right field and possibly vestigial left field), without tentacles or stalk; widespread on marine and freshwater organisms, occasionally endocommensal.

Order 1. SUCTORIDA Claparede & Lachmann, 1858

With characters of the subclass.

Class 2. OLIGOHYMENOPHOREA de Puytorac et al., 1974

Oral apparatus, at least partially in buccal cavity, generally well defined, although absent in one group; oral ciliature, clearly distinct from somatic ciliature, consisting of paroral membrane (stichodyad) on right side and small number of compound organelles (membranelles, peniculi, or polykineties) on left side; stomatogenesis parakinetal or buccokinetal; cytostome usually ventral and/or near anterior end, present at bottom of buccal or influndibular cavity; cysts not uncommon; various species loricate; colony-formation common in some groups. (See: ref. ID; 3915, 4125)

Subclass 1. HYMENOSTOMATIA Delage & Herouard, 1896

[Notice] Some workers (e.g., see Lynn et al. 1978) would elevate the hymenostomatid suborder PENICULINA of ordinal status, very likely a good idea (but arriving too late for detailed consideration by the Committee). French specialist (e.g., see de Puytorac et al. 1974, 1976) suggest amalgamation of the 2nd and 3rd scuticociliated suborders, with others (see Corliss 1979) arguing for their separation; all 3 orders are tentatively retained here.

Body ciliation often uniform and heavy; buccal cavity, when present, ventral; kinetodesmata regularly present, usually conspicuous; sessile forms and stalk, colony, and cyst formation relatively rare; freshwater forms predominant.

Order 1. HYMENOSTOMATIDA Delage & Herouard, 1896

Buccal cavity well defined, containing membranelles or peniculi with infraciliary bases typically 3-4 rows of kinetosomes wide; oral area on ventral surface, usually in anterior half of body; no scutica appearing during stomatogenesis.

Order 2. SCUTICOCILIATIDA Small, 1967

Body uniformly to sparsely ciliated; thigmotactic area common in many species buccal ciliature often dominated by tripartite (anterior, middle, and posterior segments) paroral membrane on right side; mucocysts, director-meridian, and caudal cilia common; stomatogenesis buccokinetal, with appearance of prominent unique scutica during morphogenesis; mitochondria long, interkinetal, sometimes fused to form gigantic "chondriome"; no nematodesmata and probably no trichocysts; cysts common. (See: ref. ID; 7213)

Order 3. ASTOMATIDA Schewiakoff, 1896

Body usually large or long, uniformly ciliated; mouth absent; complex infraciliary endoskeleton and often elaborate holdfast organelles (hooks, spines, or sucker) may be present at anterior end; silverline system resembling that of hymenostomatids; fission may be by budding, with chain-formation; cytoproct absent; contractile vacuoles present; all endoparasitic, mostly in oligochaetes (soil, freshwater, marine); few species in other annelids, molluscus, and turberllarians; one major group in caudate amphibians.
Genus: Anoplophrya, Cepedietta, Intoshellina, Radiophrya

Subclass 2. PERITRICHIA Stein, 1859

Oral ciliary field prominent, covering apical end of body and dipping into infundibulum; paroral membrane, generally called "haplokinety", and adoral membranelles, "polykineties", becoming "peniculi" in infundibulum present; somatic ciliature reduced to temporary posterior circlet of locomotor cilia; stomatogenesis buccokinetal; widely distributed species, many stalked and sedentary, others mobile, all with aboral scopula; dispersal by migratory telotroch (larval form); mucocysts and pellicular pores universal; myonemes associated with strong contractility of stalk or parts of body; conjugation total, involving fusion of micro- and macroconjugants.

Order 1. PERITRICHIDA Stein, 1859

With characters of the subclass.

Class 3. POLYHYMENOPHOREA Jankowski, 1967

[Notice] Several taxonomic problems remain unresolved at this time. Is Bursaria no longer to be recognized as a heterotrich [see the startling announcement by Fernandez-Galiano (1978)]? Should the order OLIGOTRICHIDA be raised to (a 2nd) subclass in the class? Is Strobilidium more properly assigned to the tintinnines than the oligotrichines? Should the hypotrichs be subdivided into more than 2 suborders? But some very important changes over earlier "spirotrich" classifications are agreed on: for example, (a) removal of the entodiniomorphids to the VESTIBULIFERIA, of class KINETOFRAGMINOPHOREA [following findings of Grain (1969), Noirot-Timothee (1969), and Wolska (1971)]; (b) recognizing 6 separate suborders of heterotrichs [based especially on works of Albaret (1974) and Jankowski (1964, 1967)]; (c) clarifying problems within the oligotrich and hypotrich taxa [see Borror (1972), Deroux (1974), Faure-Fremiet (1970), Faure-Fremiet & Ganier (1970), Grain (1972), Laval (1973), Radoicic (1969), Remane (1969), Tappan & Loeblich (1968) and Tuffrau (1972)].

Dominated by well-developed, conspicuous adoral zone (AZM) of numerous buccal or peristomial organelles (para- or heteromembranelles), often extending out onto body surface; on right side, one or several lines of "paroral" ciliature (mono- or diplo- or poly-stichomonads or pairs of kinetosomes); stomatogenesis parakinetal or apokinetal; somatic ciliature complete or reduced, or appearing as cirri; cytostome at bottom of buccal cavity or infundibulum; somatic infraciliature rarely including kinetodesmata; postciliodesmata common and prominent; cytoproct often absent; cyst, and especially loricae, very common in some groups; often large and commonly free-living, free-swimming forms in great variety of habitats.

Subclass 1. SPIROTRICHIA Butschli, 1889

With characters of the class. (See: ref. ID; 4111)

Order 1. HETEROTRICHIDA Stein, 1859

Generally large to very large forms, often highly contractile, sometimes pigmented; body dominated by AZM, but also commonly bearing heavy holotrichous ciliation; macronucleus oval or, often, beaded; parasitic and free-living species.

Order 2. ODONTOSTOMATIDA Sawaya, 1940

Laterally compressed, wedge-shaped, with armor-like cuirass and often posterior spines; somatic ciliature reduced; AZM with only 8 or 9 membranelles and no paroral membrane cytoproct absent; several small species, chiefly in putrefying organic matter in freshwater habitats, few marine.
Genus: Epalxella, Mylestoma, Saprodinium

Order 3. OLIGOTRICHIDA Butschli, 1887

Body ovoid to elongate, sometimes with tail; pellicle thickened, with perilemma external to cell membrane in many species; somatic ciliature reduced; AZM (of paramembranelles) extensive, often separable into one part inside buccal cavity and another on nearby body surface; paroral membrane and its infraciliary base single (monostichomonad); stomatogenesis apokinetal; macronuclear reorganization bands present; cytoproct absent; free-swimming, macrophagous, mainly pelagic. (See: ref. ID; 4356)

Order 4. HYPOTRICHIDA Stein, 1859

Dorsoventrally flattened, highly mobile (yet often thigmotactic), with unique cursorial type of locomotion body dominated by compound ciliary structures, consisting of prominent AZM (of numerous paramembranelles) near anterior end, multiple paroral lines (diplo- or polystichomonads) on right side of peristomial field, and cirri on ventral surface; rows of widely spaced "sensory-bristle" cilia common on dorsal surface; complex fibrillar system; some species loricate, few colony-forming; stomatogenesis typically apokinetal; macronuclear reorganization bands common; species numerous and very widespread. (See: ref. ID; 3630, 4386, 4889, 7307, 7354, 7590, 7679)

2. The Kingdom Protozoa

[ref. ID; 4887 (Thomas Cavalier-Smith: 1996/97 version)]

Subkingdom EOZOA Cavalier-Smith 1996

Flagellate, amoeboflagellate or rarely amoeboid protozoa having discoid, often rigid, mitochondrial cristae or hydrogenosomes bounded by two membranes; pseudopods usually (exception Dientamoeba) eruptive.

Constituent phyla: TRICHOZOA, PERCOLOZOA, EUGLENOZOA

Phylum TRICHOZOA Cavalier-Smith 1996

Flagellates or rarely amoebae with hydrogenosomes and prominent Golgi dictyosomes; closed mitosis with extranuclear mitotic spindle. Constituent subphyla: Anaeromonada, Parabasala. The name TRICHOZOA (Greek trichos = hair) is chosen because the phylum consists predominantly of trichomonads and hypermastigotes, the latter having a very hairy appearance because of their numerous long cilia.

Subkingdom NEOZOA Cavalier-Smith 1996

Diagnosis as for infrakingdom NEOZOA Cavalier-Smith 1993.

Infrakingdom SARCODINA Hertwig & Lesser 1874 stat. nov. Cavalier-Smith 1996

Amoeboid Protozoa with non-eruptive pseudopods; mitochondrial cristae usually tubular, rarely vesicular or non-rigidly discoid; axopodia absent; mitochondria and peroxisomes rarely absent, but if so without hydrogenosomes.

Constituent superphlya: EOSARCODINA, HAPLOSPORIDA, NEOSARCODINA

Superphylum EOSARCODINA Cavalier-Smith 1996

Sarcodines with granular reticulopodia or with filose pseudopods and stalked aerial fruiting bodies.

Constituent phyla: RETICULOSA, MYCETOZOA

Remarks

RETICULOSA were previously included in the NEOSARCODINA, but 28S ribosomal RNA trees suggest that they are not closely related to the testaceafilosian Gromia and branch well below the megakaryote radiation near to MYCETOZOA (Pawlowski et al. 1994). Pawlowski et al. (1996) give evidence from 18S rRNA for a similar or even lower position for foraminifera, and suggest that the sequence studied by Wray et al. (1995) that groups foraminiferans with Apicomplexa may actually be from a parasite, not the foram itself. I have therefore excluded RETICULOSA from the NEOSARCODINA, and group them instead with MYCETOZOA as the new superphylum EOSARCODINA, on the assumption that their common ancestor was a tubulicristate sarcodine with an anisokont flagellate stage. Although EOSARCODINA is a paraphyletic group it is possible that the ability of pseudopodia to fuse together as reticulopodia in RETICULOSA, and for separate amoebae to fuse together to make plasmodia in the Myxogastrea, has a common mechanistic basis; such capacity for pseudopodial fusion is relatively rare in NEOSARCODINA, being found only in some chlorarachnean and LOBORETICULATIDA.

Superphylum HAPLOSPORIDA Cavalier-Smith 1996

Diagnosis as for sole constituent phylum HAPLOSPORIDIA Caullery and Mesnil, 1899 (Cavalier-Smith 1993)

Superphylum NEOSARCODINA Cavalier-Smith 1993 emend. 1996

Sarcodines with filose or lobose pseudopods but no stalked fruiting bodies; unstalked fruiting bodies or non-granular reticulopodia very rarely present.

Phylum RHIZOPODA Dujardin 1835 stat. nov. Haeckel 1866 emend. Cavalier-Smith 1995

Emended diagnosis

Amoeboflagellates with variable pseudopods or non-ciliate amoebae usually with filose pseudopods or sarcodine phase an intracellular microplasmodium; mitochondria (usually with tubular cristae) and Golgi dictyosomes present. Extrusomes often present.

Phylum AMOEBOZOA Luhe 1913 stat. nov. Corliss 1984 emend. Cavalier-Smith 1995

Emended diagnosis

Non-ciliate amoebae with lobose pseudopodia, multiciliated amoebae, or uniciliate amoebae; mitochondrial cristae tubular or mitochondria and peroxisomes absent; extrusomes absent. (See: ref. ID; 4944, 6789)

Subphylum ARCHAMOEBAE Cavalier-Smith 1983 stat. nov.

Subphylum HOLOMASTIGA subphy. nov. Cavalier-Smith 1996

Class HOLOMASTIGA cl. nov. Cavalier-Smith 1996

Multiciliated amoebae; sole order HOLOMASTIGIDA Lauterborn 1895 (as suborder HOLOMASTIGINA) and family MULTICILIIDAE Poche (HOLOMASTIGIDAE Lemmermann 1914) and genus Multicilia Cienkowski 1881.

Subphylum LOBOSA Carpenter 1861 stat. nov. Cavalier-Smith 1996

Diagnosis as for class LOBOSEA (Cavalier-Smith 1993) (See: ref. ID; 7079). Constituent classes AMOEBAEA and TESTACEALOBOSEA.

Infrakingdom ALVEOLATA Cavalier-Smith 1991

Superphylum MIOZOA Cavalier-Smith 1987

Superphylum HETEROKARYOTA Hickson 1903 stat. nov. Cavalier-Smith 1993

Infrakingdom ACTINOPODA Calkins 1902 stat. nov. Cavalier-Smith 1996

Infrakingdom and phylum NEOMONADA Cavalier-Smith 1996

Non-amoeboid aerobic flagellates with peroxisomes, mitochondria and Golgi dictyosomes; cristae tubular or flat, never discoid; cortical alveoli, rigid tubular ciliary hairs, axopodia and locomotory pseudopodia all absent; cilia 1, 2 or many, rarely (Corallochytrea) absent.

Remarks

MYCETOZOA were earlier grouped with OPALOZOA (See: ref. ID; 7292) as a superphylum OPALOMYXA and this taxon was grouped with CHOANOZOA as the parvkingdom CILIOMYXA (Cavalier-Smith 1993). However these two taxa now appear to be polyphyletic according to the recent molecular trees (Cavalier-Smith & Chao 1995, 1996) and are best abandoned. However, these trees also suggest that CHOANOZOA and APUSOZOA are more closely related to each other than to any other protozoan phyla (Cavalier-Smith & Chao 1995), so I have created the phylum and infrakingdom NEOMONADA for them. Both NEOMONADA and CHOANOZOA are monophyletic taxa, but are paraphyletic because of the derivation of both the kingdoms ANIMALIA and FUNGI from choanoflagellate ancestors (Cavalier-Smith 1987). NEOMONADA are all non-amoeboid zooflagellates and, as discussed below, probably arose from a neosarcodine amoeboflagellate by the loss of the amoeboid phase. Rather than retaining phylum rank for CHOANOZOA and creating a separate phylum for the other three neomonad subphyla, I have reduced CHOANOZOA in rank to subphylum in order to include all the non-alveolate and non-amoeboid neozoan zooflagellates in a single phylum, which will be more practically useful.

Infraphylum EXTRUMONADA Cavalier-Smith 1996

Apusozoans with extrusomes.

Infraphylum EURYMONADA Cavalier-Smith 1996

Apusozoans without extrusomes.
Classes ANISOMONADEA, EBRIDEA

[ref. ID; 4924 (Thomas Cavalier-Smith: 2003 version)]

These new insights have come not just from molecular sequence studies but by integrating them with numerous other lines of evidence, genetic, structural and biochemical. The classical view developed over two centuries that reliance on a single line of evidence or character is often very misleading for phylogeny and systematics is at last penetrating the previously over-dogmatic and over-self-confident field of molecular systematics.

Kingdom: PROTOZOA

Subkingdom: SARCOMASTIGOTA Cavalier-Smith 1993 emend.

Phylum 1: AMOEBOZOA Luhe 1913 stat. nov. Corliss 1984 emend. Cavalier-Smith 1998

(See: ref. ID; 4944)

Subphylum 1: PROTAMOEBAE+ Cavalier-Smith 2004

Subphylum 2: CONOSA Cavalier-Smith 1998

Infraphylum 1: ARCHAMOEBAE Cavalier-Smith 1983 stat. nov. 1998

Infraphylum 2: MYCETOZOA De Bary stat. nov.

Phylum 2: CHOANOZOA Cavalier-Smith 1981 emend. 1998

Subkingdom BICILIATA subkingd. nov.

Ancestrally biciliate unicellular eukaryotes in which dihydrofolate reductase and thymidylate synthase genes, if present, are fused into a single unit of translation; lacking plastids in the cytoplasm with double envelopes and lacking plastids within the rough endoplasmic reticulum or tubular ciliary hairs; mitochondrial cristae usually tubular or discoid (i.e. all bikonts excluding Plantae and Chromista).

Infrakingdom 1: RHIZARIA Cavalier-Smith 2002 emend.

(See: ref. ID; 6795)

Phylum 1: CERCOZOA Cavalier-Smith 1998 emend. 2002

(See: ref. ID; 7130)

Subphylum 1: FILOSA Cavalier-Smith 2003

Subphylum 2: ENDOMYXA Cavalier-Smith 2002 emend.

Phylum: RETARIA Cavalier-Smith 1999

Subphylum 1: RADIOZOA Cavalier-Smith 1987 emend.

(Ancestrally with axopodia having an open dodecagonal meshwork of microtubules and also to sequester strontium sulphate intracellularly)

Subphylum 2: FORAMINIFERA (D'Orbigny 1826) Eichwald 1830 stat. nov. Mikhalevich 1980

RHIZARIA incertae sedis

Class PHAEODAREA Haeckel 1879 (e.g. Aulacantha, Castanella)

Infrakingdom EXCAVATA Cavalier-Smith 2002

(See: ref. ID; 4980)

Phylum 1: LOUKOZOA Cavalier-Smith 1999 emend. 2003

Phylum 2: METAMONADA Grasse 1952 stat. nov. emend. Cavalier-Smith

Subphylum 1: ANAEROMONADA Cavalier-Smith 1996/7

Subphylum 2: TRICHOZOA Cavalier-Smith 1996/7 stat. nov. emend. 2003

Superphylum 1: DISCICRISTATA Cavalier-Smith 1993

Phylum 1: PERCOLOZOA Cavalier-Smith 1991 stat. nov.

Phylum 2: EUGLENOZOA Cavalier-Smith 1981

(See: ref. ID; 4898)

Subphylum 1: PLICOSTOMA Cavalier-Smith 1998

Subphylum 2: SACCOSTOMA Cavalier-Smith 1998

Infrakingdom ALVEOLATA Cavalier-Smith 1991

Phylum 1: MIOZOA Cavalier-Smith 1987 stat. nov. 1999

Subphylum 1: PROTALVELATA Cavalier-Smith 1991 em.

Subphylum 2: DINOZOA Cavalier-Smith 1981 em.

Infraphylum 1: ELLOBIOPSA infraph. nov.

Diagnosis as the for class ELLOBIOPSEA

Infraphylum 2: DINOFLAGELLATA Butschli 1885 stat. nov. Cavalier-Smith 1999

Subphylum 3: APICOMPLEXA Levine 1970 emend. stat. nov.

Infraphylum 1: APICOMONADA Cavalier-Smith 1993 stat. nov.

Infraphylum 2: SPOROZOA Leuckart 1879 stat. nov. Cavalier-Smith 1999

Phylum 2: CILIOPHORA Doflein 1901 (ciliates and suctorians)

(See: ref. ID; 4926)

Subphylum 1: POSTCILIODESMATOPHORA Gerassimova and Seravin 1976

Subphylum 2: INTRAMACORNUCLEATA Lynn, 1996

BICILIATA incertae sedes

1. Phylum APUSOZOA Cavalier-Smith 1996/7 stat. nov. 2003 emend. 2. Class TELONEMEA Cavalier-Smith 1993 (Telonema, Nephromyces)

PROTISTA incertae sedes (Protozoa or chromists)

Class HOLOSEA Cavalier-Smith 1993 (Luffisphaera); Order COMMATIIDA Cavalier-Smith 1996/7 (Commation); Order DISCOCELIDA Cavalier-Smith 1997 (Discocelis)

[ref. ID; 4979 (Thomas Cavalier-Smith, 2003)]

Emended diagnosis of phylum LOUKOZOA Cavalier-Smith 1999

Emended diagnosis; Ancestrally and typical aerobic zooflagellates with tubular, flat or discoid mitochondrial cristae; cristae rarely absent (only Jakoba incarcerata). Golgi dictyosome beside the kinetid. Nucleus attached by fibres to the two apical or subapical sharply diverging centrioles as a biciliate karyomastigont and with two main posterior roots of partially splayed microtubular bands supporting the edges of a longitudinal feeding groove associated with the posterior cilium and a third singlet microtubule root lying between them. Left root supported internally by a multilayered, striated C-fibre with internal offset vanes between the layers. Right root supported ventrally by a double-leaved, cross-striated B-fibre originating from the junction between the left root and the posterior centriole. Posterior cilium with a single lateral flange or vane. Ciliary transition zone without an axial sleeve around the central pair (in contrast to DIPHYLLEIDA). An anterior dorsal microtubular fan diverges from the kinetid.

Diagnosis of MALAWIMONADEA classis nov.

Diagnosis; Anisokont anaerobic biciliate zooflagellates with discoid mitochondrial cristae and a single ventral vane on the posterior cilium (Jakobea have a dorsal one instead) and two divergent centrioles. With curved, double-leaved I-fibre alongside anterior end of right root; the right root splits into a left and right half close to its origin. Left root supports only the left wall of the groove, unlike in jakobids, where it supports at least half the groove floor. With anterior microtubule band nucleating many of the fan microtubules. Mitochondrial cristae discoid.

Etymology; from the sole genus, Malawimonas (O'Kelly & Nerad, 1999)

Diagnosis of MALAWIMONADIDA ord. nov.

Diagnosis as for class MALAWIMONADEA.

Diagnosis of MALAWIMONADIDAE fam. nov.

Diagnosis as for class MALAWIMONADEA. (See: ref. ID; 7492)

Emended diagnosis of phylum METAMONADA Grasse 1952 stat. nov. Cavalier-Smith 1981

Emended diagnosis; Ancestrally anaerobic quadriciliate zooflagellates; with hydrogenosomes instead of mitochondria or without mitochondria or hydrogenesomes. Ancestrally with a nucleus attached by fibres to the four centrioles as a quadriciliate attached by fibres to the four centrioles as a quadriciliate karyomastiont with a posterior cilium bearing two vanes (not just a single one as in LOUKOZOA and the percolozoan Psalteriomonas) and with two posterior microtubular roots associated with a feeding groove [the groove was later lost (Parabasalia) or converted to/supplemented by a cytopharynx (Eopharyngia)]. With a strong evolutionary tendency to multiply karyomastigonts or sometimes secondarily to reduce the number of cilia. Golgi dictyosomes ancestrally present but independently suppressed in vegetative Eopharyngia and oxymonads.

Emended diagnosis of class ANAEROMONADEA Cavalier-Smith 1996/7

Emended diagnosis; Quadriciliate anaerobic zooflagellates without cristate mitochondria; with or without hydrogenosomes and Golgi dictyosome. Ancestrally with anterior microtubule band nucleating many of the fan microtubules (unlike JAKOBEA, but like MALAWIMONADEA). Golgi dictyosomes not attached to a striated parabasal filament.

Diagnosis of TRIMASTIGIDA ord. nov.

Diagnosis; Quadriciliate anaerobic zooflagellates with subapical, cruciately arranged centrioles, with anterior, posterior and two lateral cilia; posterior cilium with dorsal and ventral vane; hydrogenosome-like organelles.

Etymology; From the genus Trimastix (see Brugerolle & Patterson 1997; O'Kelly et al 1999; Simpson et al. 2000).

Emended diagnosis of subphylum TRICHOZOA Cavalier-Smith 1996/7

Emended diagnosis; Ancestrally with one posterior and three anterior cilia (the tetrakont arrangement), hydrogenosomes and Golgi dictyosomes, all secondarily lost in at least some groups; recurrent cilium with two or three ciliary vanes or smooth.

Diagnosis of TRICHONYMPHEA classis nov.

Diagnosis; Huge cells with a complex rostrum terminated by a hyaline mobile cap separated from the rest of the cell by a joint. Numerous longitudinal rows of cilia extending from a bare apical region along all sides of the cell. Cell posterior bare of cilia and used for phagotrophy and sex. Chromosomes with centromeric attachments to the nuclear envelope visible in interphase. Obligate symbionts of termites and the wood-eating cockroach Cryptocercus.

Etymology; After the included genus Trichonympha.

Diagnosis of CARPEDIEMONADEA classis nov.

Diagnosis; Biciliate zooflagellates with three centrioles; anaerobic with a hydrogenosome-like organelle. With curved, double-leaved I-fibre along side anterior end of right root; the right root splits into a left and right half close to its origin. Left root supports only the left wall of the groove, unlike in jakobids, where it supports at least half the groove floor. With anterior microtubule band nucleating many of the fan microtubules.

Etymology; After the sole genus, Carpediemonas (see Simpson & Patterson 1999)

Diagnosis of superclass 2. CARPEDIEMONADIA superclassis nov.

Diagnosis as for class CARPEDIEMONADEA.

Diagnosis of CARPEDIEMONADIDA ord. nov.

Diagnosis as for class CARPEDIEMONADEA.

Diagnosis of CARPEDIEMONADIDAE fam. nov.

Diagnosis as for order CARPEDIEMONADIDA.

Emended diagnosis of superphylum DISCICRISTATA Cavalier-Smith 1993

Emended diagnosis; Flagellates or amoeboflagellates or amoebae typically with flat, usually discoid mitocondrial cristae. Ancestrally with two (EUGLENOZOA) or four (PERCOLOZOA) subparallel centrioles bearing cilia and one anterior and two posterior microtubular roots.

Emended diagnosis of phylum PERCOLOZOA Cavalier-Smith 1991 emend. 2002

Emended diagnosis; Ancestrally aerobic quadriciliate zooflagellates with discoid mitochondrial cristae, sometimes secondarily anaerobic with hydrogenosomes instead of mitochondria. Ancestrally with a nucleus attached by fibres to the four parallel centrioles as a quadriciliate karyomastigont and with two posterior microtubular roots. Commonly alternate between a flagellate phase with a pellicle and a main trophic non-ciliate amoeboid phase with eruptive lobose pseudopods; Golgi dictyosome absent. The karyomastigont is sometimes multipled and, in amoeboid forms, the flagellate stage is sometimes absent. Kinetid rarely highly multiplied and reduced to a single centriole (Stephanopogon).

Diagnosis of class 2. PERCOLATEA classis nov.

Diagnosis; The new name PERCOLATEA is preferred to either of the existing class names PERCOLOMONADEA and PSEUDOCILIATEA, since, if either were retained with broadened circumscription. It could cause confusion with the similarly named included order. Flagellates with discoid mitochondrial cristae but no amoeboid phase; stacked Golgi dictyosomes absent; with single quadriciliate or numerous unikont kinetids.

Etymology; L. v. percolare to percolate, because Percolomonas is assumed to represent the ancestral phenotype and feeds by ciliary water currents.

The transfer of Stephanopogon to CERCOZOA, once suggested because its centriole cup resembles that of Spongomonas (Cavalier-Smith, 2002), overweighted one character of unclear homology compared with Golgi and mitochondrial characters responsible for originally including Stephanopogon in PERCOLOZOA (Cavalier-Smith, 1991, 1993); therefore, recent revision of cercozoan higher classification excluded it from CERCOZOA (Cavalier-Smith & Chao, 2003).

Diagnosis of DIPHYLLATEA classis nov.

Diagnosis; Zooflagellates with two (Diphylleia) or four (Collodictyon) anterior, equal-length, unvaned cilia with orthogonal centrioles liked by striated connectives. Deep ventral groove with rims supported by two broad, unsplayed microtubular centriolar roots with associated dense fibrous band, but cortical microtubules absent from the groove floor, unlike in LOUKOZOA. Ciliary transition region with a distal dense axial sleeve, a double-band axosome and indistinct proximal plate. Anterior microtubular root nucleates a dorsal microtubular fan. Sole order DIPHYLLEIDA Cavalier-Smith 1993 and family DIPHYLLEIDAE Cavalier-Smith 1993 (Diphylleia, Collodictyon).

Etymology; Gr. di- two; phyll- leaf, from the bilobed shape of the cells. The class name is not directly based on the generic name, as Diphylleia Michx. is unfortunately also the name of a flowering plant. Although Diphylla is a genus of vampire bats, Diphyllodes a bird of paradise, Diphyllidia a sea slug and Diphyllidea a group of tapeworms, none of these is sufficiently similar to cause of confusion. Collodictyonidae Brugerolle 2002 is an invalid junior synonym for Diphylleidae, if Collodictyon is included in the same family as Diphylleia.


3. Protist diversity

[ref. ID; 5694 (David J. Patterson, 1999)]

Defining Taxa

Taxa may be defined in a variety of different ways. Unless some effort is made to reflect on this, multiple types of definition may be used simultaneously. As these may be in conflict or may come into conflict after the acquisition of new data or insights, the result can be ambiguity or confusion. Some of the approaches that protistologists seem to have taken to defining taxa are listed below. Most groups are defined by an unspecified amalgam of these definitions.

Typified Definitions

Typified definitions are those definitions in which the concept of a group (and its name) is tied to the type genus. The name of the genus is driven by considerations of priority. This is a rather botanical tradition, an example is Prymnesiophyta (a synonym of Haptophyta). The Prymnesiophyta is then the division within which the genus Prymnesium finds itself. This approach stabilizes the name. However, changes in composition of the group may emerge from changed perceptions of relatedness or by arbitrary shifts in rank. In such cases, the defining concept survives even in the event of considerable change in composition, circumscription, or phylogenetic location. As phylogeny is appropriately becoming the dominating ethos in taxonomy, "typified definitions" tend not to be able to reflect phylogenetic insights and such definitions are here regared as undesirable.

Circumscriptive Definitions

Circumscriptive definitions seek to describe the appearance of all included taxa. Frequently they can include contrasting characters (e.g., 'possessing mitochondria and peroxisomes" and "when mitochondria and peroxisomes are both secondarily absent"), nondefining characters (e.g., "predominantly unicellular, plasmodial, or colonial"), or even to negative characters such as "haptonema absent" (examples from the diagnosis of Protozoa; Cavalier-Smith 1993). This is probably the most widespread approach to defining groups. These definitions may emphasize one or a few character. This approach may describe taxa but can fail to distinguish taxa. It is reactive in the sense that the definition does not determine membership, membership determines the definition. There is often no clear link between the name, definition, and composition. This approach allows more than one concept of the taxon to exist at the same time. Although circumscriptive definitions could easily be regarded as "bad", these less appetizing traits seem not to be an impediment to their continued use.

Definitions by Composition

These seek to define a group by the subordinate taxa included within it. Such an approach is precise at any one time, but any a changes in composition will cause a change in the concept. One name will have many meanings with the passage of time. The resulting ambiguity can only be dispelled by a detailed reference to the context in which the term is used. An alternative to allowing the meaning of the name to drift is to introduce a new name with every change in composition. This would be highly destabilizing and confusing. Compositional definitions foster ambiguity and are therefore not desirable.

Phylogenetic Definitions

Phylogenetic definitions were mentioned by Cavalier-Smith (1998). This approach seems to allow groups to be defined by one or more evolutionary events or hypotheses as to what evolutionary events might have taken place. One of these defining elements would define a monophyletic group, whereas others (which may or may not be used) may identify the evolutionary events associated with the emergence of subsets that are exclude the speculative element of these definitions and make the inclusion of paraphyletic taxa less likely.

Synapomorphic Definition

Taxa can be defined by reference to those evolutionary innovations (apomorphies) associated with the emergence of the group. Eukaryotes may be defined as living things with nuclei or derived from such organisms. Most characters appeared once in evolutionary lineages (there are exceptions caused by symbioses or other forms of lateral transfer). All characters therefore have the capacity to define monophyletic and holophyletic groups. Groups defined by these criteria include all descendants of the first common ancestor with the synapomorphic character, even if the synapomorphic feature has been lost. The advantages of using synapomorphic definitions were envisaged as being, first, that they clearly determine criteria for admission to the taxon; second, that they create monophyletic and holophyletic taxa that can be easily located within phylogenetic classification; third, that they are consistent with the dominant philosophy of phylogenetic reconstruction and classification; fourth, that the meaning of the name is independent of the composition of the grouping (the meaning of "the stramenopiles" is independent of whether the actinophryid heliozoa or opalines are included or excluded); and, fifth, that the resulting nomenclature is stable if the principle by which the name was defined is respected (but can be destabilized if it is equated with a circumscriptive or composition definition). The disadvantages of synapomorphic descriptions are that they give little indication of the contents of the group; that they may mislead or confuse those unversed in phylogenetic systematics in cases where synapomorphic characters are transformed or lost within a group; and that they cannot be used universally because synapomorphies for many taxa are unknown and may indeed be nonexistent. A taxon defined by reference to synapomorphy is destabilized (falsified?) only by agreement that the defining character is homoplasious. This would indicate that the group so defined is polyphyletic. The synapomorphic definition can be made more utilitarian by adding a "binomial" dimension to place it within the context of a broader phylogeny. This can be done by defining the in-group with reference to the next most extensive group of organisms that includes the in-group. This ideally will link the in-group to the sister group. This next most inclusive cluster is here referred to as the "extended in-group." As an example, we might define the ciliates as the alveolates with nuclear dimorphism. In this case, the ciliates are the in-group, the alveolates are the next most inclusive (resolved) clade, and nuclear dimorphism is the synapomorphy of the in-group. Because the relationship between sister group and the in-group may change as phylogenetic insights develop, stability can only be protected by recognizing that the extended in-group is not part of the synapomorphic definition but an adjunct to it.

Synapomorphic definitions have been applied to the stramenopiles and to the minimal group containing the euglenids and kinetoplastids (Simpson 1997). The latter group (Euglenozoa) has also been defined in other ways. The approach has yet to be universally applied to all major types of eukaryotes listed elsewhere (Patterson 1994). The term "stramenopiles" was introduced as a test case for the use of synapomorphic definitions among protists. The concept has been widely used by protistologists, especially in the context of phylogenetic schemes to which it is well suited (e.g., Sogin et al. 1996; Beakes 1998). Alternative concepts (heterokonts, chromists, etc.) are also widely used. The "stramenopiles" has survived compositional adjustments - as it was designed to. The concept therefore appears robust and utilitarian but not persuasive. It has been confused somewhat by being regarded as equal or equivalent to traditional concepts (e.g., Lipscomb et al. 1998).

The "Archezoa" was initially defined as "containing those protozoan phyla that totally lack mitochondria (i.e., the Parabasalia, Metamonadina, the Microspora" (Cavalier-Smith 1983, p. 1028) and by the statement that "I suggest also that the various amoebae such as Entamoeba and Pelomyxa palustris which lack mitochondria be removed from the phylum Sarcodina to form a further phylum of Archezoa called Archamoebae" (Cavalier-Smith 1983, p.1029). Largely on the basis of the use of the "i.e." in the original definition, this was interpreted to mean that the Archezoa was defined by composition (Patterson 1988). This has been disputed (Cavalier-Smith 1998) with the suggestion that the definition is "phylogenetic". The group is paraphyletic and defined by two evolutionary events - the first being the emergence of eukaryotes and the second being the appearance of mitochondria. The group was defined as a subset of the "Protozoa", but this too is confusing because during the life of the Archezoa, the same author has conceived of the protozoa as excluding Archezoa (e.g., Cavalier-Smith 1990). The composition and rank of the group has been unstable. Despite the ambiguities, this term is in fairly wide use within evolutionary protistology.

Ultimately, the use of ranks, definitions, and hierarchy should serve to add value to concepts and to the redue ambiguity. What debate currently exists tends to defend past practices rather than to concentrate on the needs of the future. A progressive debate is still needed to identify weaker practices and replace them with better practices. At this time, and in the absence of agreement, I have segregated the major different approaches of defining taxa and applied then independently, and in a summary form, to all grouping for which sister groups are not widely accepted.

Eukaryotic Taxa without Known Sister Groups

Acantharea

Circumscription

One of several groups of "radiolaria" - large marine unicells with radiating axopodia and an inorganic skeleton (in the case of Acantharea composed of 10/20 spicules made of strontium sulphate). Cell with central endoplasm and peripheral ectoplasm separated by a fibrous capsular wall, outside face of cytoplasm coated with a fibrous cortex that is joined to spicules by contractile myonemes. Often with symbionts. No propulsive organelles in trophic form but may have flagellated stage and/or amoebas and/or cysts in life cycle.

Ultrastructural identity

Not well established because of difficulty of good preservation. Mitochondria with tubular cristae. Axopodia arising from unspecified sites in the cytoplasm but having an open hexagonal or larger polygonal arrays of microtubules; periplasmic cortex axopodia details, extrusomes and so forth. With concentric extrusomes. Mitosis involves an eccentric spindle located inside an intact nuclear envelope.

Synapomorphy

Tubulocristae protists with strontium sulphate skeleton with symmetry based on 20 radial elements.

Composition

About 150 species in 50 genera in four or five major subtaxa defined by skeletal characteristics.

Reference

Febvre 1990.

Actinophryids

Circumscription

One of several groups of organisms previously placed together as the heliozoa; round bodies with radiating stiff arms (axopodia); cell surface naked, no flagellated stage known. With one or many nuclei; siliceous plates or other siliceous aggregates form one layer of an encysted state. Affinities not known; possibly related to the pedinellids, a group of stramenopiles.

Ultrastructural identity

Mitocondria with bleblike (tubular) cristae. Axopodia supported by axonemes with microtubules in double polygonal spiral and nucleating on nucleus or amorphous material. Two types of extrusomes: one larger homogeneous andosmiophilic, the other smaller and more heterogeneous. Dictyosomes typically associated with nuclei. Mitosis with microtubules penetrating from the cytoplasm, nuclear envelope mostly fragments.

Synapomorphy

Tubulocristate protists with double polygonal spiral arrangement of microtubules in axopodia.

Composition

Probably with only two genera, Actinophrys and Actinosphaerium (the latter probably having Echinosphaerium and Camptonema) as synonyms.

Reference

Smith and Patterson 1986.

Alveolates

Circumscription

A significant group containing many species of "algae" and "protozoa" - both free-living and parasitic. Grouping suggested initially by the presence of the alveoli (see "synapomorphy"). Began to appear in discussions in the early 1980s; the grouping was confirmed by Gajadhar et al. (1991); the colloquial name was formally introduced into the literature by Cavalier-Smith. With three major subsets, the ciliates distinguished by nuclear dimorphism and cilia arranged in kineties. The dinoflagellates mostly with nuclei with unusual condensed chromosomes, and the apicomplexa - a group dominated by intracellular and extracelluar parasites but including the agent for malaria. Structurally very complex.

Ultrastructural identity

Mitochondria tubulocristate, cell surface underlain by a system of abutting sacs - the alveoli. Dictyosomes often reduced. Contains several lineages each with discrete ultrastructural identities (i.e., ciliates, apicomplexa, and dinoflagellates). Group has various idiosyncrasies such as eyes, ingestion devices, cytoproct, and extrusomes. Flagella when present (whether as flagella or cilia) typically with at least one cross-striated fibrous root.

Synapomorphy

Tubulocristate protists with cortical alveoli (cortical alveoli defined as abutting sacs without attached ribosomes and not continuous with other membranous systems and that form a continuous layer under the plasma membrane broken only by penetration of ingestion and egestion organelles, extrusomes, etc.).

Composition

Includes the Apicomplexa (inclusive of the predatory flagellates Acrocoelus, Colpodella, and the parastitic Perkinsus, which get from one host to another as swimming forms), the ciliates (Ciliophora), and the dinoflagellates. Some consider affinities with one other flagellate, Colponema. However, the identity of this genus and the alveolate nature of the subsurface sacs in this genus still need to be clarified. Haplosporidia also excluded as structural evidence does not support molecular insights of an affinity between these and the alveolates.

References

Mignot and Brugerolle 1975; Gajadhar et al. 1991; Patterson and Zolffel 1991; Cavalier-Smith 1993.

Apusomonads

Circumscription

Glinding biflagellated heterotrophic protists with organic dorsal sheath. One flagellum projecting anteriorly, ventral side is naked and may produce pseudopodia. Probably consume bacteria. Argued by Cavalier-Smith and Chao (1995) to be related to the opisthokonts = (animal + choanoflagellate) + (fungi + chytrid) clade; a conclusion that seems to be permature.

Ultrastructural identity

Mitochondria tubulocristate, dorsal face of cell supported by an organic and intracellular theca. Flagella with two basal bodies located almost orthogonally and giving rise to microtubular roots, two of which seem to determine the margins of the ventral face of the cell.

Synapomorphy

Not specified but probably with refer to internal dorsal organic sheath.

Composition

Two genera: Apusomonas and Amastigomonas.

References

Patterson and Larsen 1991; Cavalier-Smith and Chao 1995.

Centroheliozoa

Circumscription

The centrohelids, one of several groups previously assigned to the Heliozoa that are now regarded as polyphyletic. Round bodied with stiff radiating arms (axopodia) supported internally by microtubules and with extrusomes that are quite easy to see. Cell surface naked or with organic or siliceous spines and/or scales. Some species it symbiotic algae. No flagellated stages known, may form cysts.

Ultrastructural identity

Mitochondria with lamellate flat cristate. Microtubules of radiating axonemes in hexagon with triangle arrangement and arising from a multilamellate microtubule organizing center, extrusomes with ball-and-cone organization. Radiating system of lacunae near cell surface. Many conventional dictyosomes dispersed in cytoplasm. Siliceous elements of periplast created within silicon deposition vesicles.

Synapomorphy

Platycristate heliozoa with multilamellate microtubule organizing center faced with hemispherical structures giving rise to axonemes of microtubules arranged in hexagons and triangles.

Composition

About 85 species; Family Heterophryidae (Cienkowskya, Oxnerella, Sphaerastrum, Heterophrys), Family Raphidiophryidae (Parasphaerastrum, Polyplacocystis, Raphidiophrys, Raphidocystis), Family Acanthocystidae (Pseudoraphidocystis, Pseudoraphidiophrys, Pterocystis, Echinocystis, Choanocystis, Acanthocystis).

References

Smith and Patterson 1986; Mikrjukov 1996.

Cercomonads

Circumscription

Biflagellated gliding protists, anterior flagellum beating stiffly, posterior flagellum trailing, body more or less capable of producing pseudopodia, may be amoeboid. Argued by some to be related to Chlorarachnion but both probably belong to a more extensive group (including cercomonads, Chlorarachnion, some slime molds, thaumatomonads, Hyperamoeba) of tubulocristate flagellates with a tendency to an amoeboid body form, but which has yet to be properly defined. Common and widespread.

Ultrastructural identity

With tubular cristae in mitochondria. Dictyosomes. Two flagella without excrescences or paraxonemal structures; basal bodies inserting almost at right angles, interconnected with nonmicrotubular material and giving rise to several microtubular roots (Massisteria excepted). With darkly staining membrane-bound paranuclear body. With electron-dense or concentric extrusomes. Nuclear envelope breaks down during mitosis, spindle microtubules arise at basal bodies.

Synapomorphy

Tubulocristate protists with paranuclear body.

Composition

Several genera: Cercomonas, Massisteria, Bodomorpha, Heteromita.

References

Patterson and Zolffel 1991; Karpov 1997.

Chlorarachniophytes

Circumscription

Reticulate amoeboid organisms with cytoplasmic strands linking cell bodies, uniflagellated dispersal stage, with photosynthetic compartment formed from a eukaryotic algal symbiont probably derived from green algae. Recent molecular work suggests close relationship with the euglyphid filose testate amoebas but in the absence of a synapomorphy and the ramicristate nature of the mitochondrial cristae; they are here kept separated, ranked up to level of division. Also, see cercomonads.

Ultrastructural identity

Mitochondria with tubular cristae. Dictyosomes present. With concentric extrusomes. Flagella of flagellated stage without hairs, scales, or other excrescences, also without paraxonemal structures. Basal bodies anchored by microtubular roots. Plastids with variable number of thylakoids per lamella and with associated nucleomorpha and with pyrenoids.

Synapomorphy

None known but may be definable by the plastid symbiosis.

Composition

Four genera, six species.

References

Bhattacharya et al. 1995; McFadden et al. 1997.

Copromyxids

Circumscription

Cellular slime molds, spores released from treelike structures (sorocarps), which form from aggregation of encysting cells with or without a pseudoplasmodium - a coordinated mass of motile aggregated cells.

Ultrastructural identity

Mitochondria with tubular cristae. Other details not available.

Synapomorphy

Not specified - currently tubulocristate protist behaving as cellular slime mold.

Composition

Two genera, Copromyxa and Copromyxella.

Reference

Blanton 1990.

Cryptomonads

Circumscription

Biflagellated autotrophic, mixotropic and heterotrophic flagellates, flagella inserting in an anterior groove/channel lines with refractile ejectisomes. Variously colored photosynthetic compartments, in some taxa at least, formed from secondary symbioses with eukaryotes, the symbiont being located in a membrane-bound compartment and provided with a reduced nucleus (the nucleomorph). Two genera of heterotrophs, one (Goniomonas) possibly primitively so.

Ultrastructural identity

Mitochondria cristae flattened, mitochondrion often extensive. Coiled ribbon extrusomes (ejectisomes) associated with flagellar pocket (gullet) and with cell surface. Geometrically positioned plates of fibrous cytoskeletal material underlie the membrane. Pastidic taxa with prastid inside a fold of the nuclear envelope and with nucleomorph were studied. No eyespot. Both flagella with stiff bipartite hairs. Small scales may be attached to cell body. Flagella insert into near parallel basal bodies, usually with multilamellate root structure (rhizostyle) in addition to several microtubular roots. Nuclear division with spindle developing from basal bodies and penetrating the dividing nucleus, the membrane of which completely breaks down.

Synapomorphy

Flagellar groove/channel with associated ejectisomes and/or double row of flagellar hairs on both flagella and/or cortical plates.

Composition

With about 25 genera, two of which are heterotrophic.

References

Roberts 1984; Gillott 1990.

Desmothoracids

Circumscription

One subset of the group previously referred to as heliozoa. Amoeboid body giving rise to stiff pseudopodia (the heliozoan stage) located in an organic lorica, often stalked. Heliozoan stage produces biflagellated motile stage, which can then give rise to an amoeboid form with stiff but motile pseudopodia. Heterotrophic.

Ultrastructural identity

Mitochondria with tubular cristae, microtubules in support of pseudopodia not in organized geometric arrays or in open hexagons, and no microtubule organizing center is known. Many dictyosomes. Extrusomes concentric core and girdle (kinetocysts). Flagellated stage not studied in any detail.

Synapomorphy

Tubulocristate protists with a heliozoan stage located in a fenestrated organic lorica.

Composition

Three genera; Clathrulina (= Elaster?), Hedriocystis, and Cienkowskya (= Monomastigocystis).

References

Bardele 1972; Smith and Patterson 1986.

Dimorphids

Circumscription

Helioflagellates, with two or four similar flagella, very elongate kinetosomes. Flagellates in trophic stage with axopodia radiating from an amorphous microtubule organizing center located between kinetosomes and nucleus. Microtubules tending to be in square packing. With tubular mitochondrial cristae.

Ultrastructural identity

Mitochondria with tubular cristae possibly ramicristate. With concentric extrusomes. Dictyosomes present. Microtubules supporting pseudopodia in clusters, tightly packed sometimes in square pattern, arising from an amorphous structure associated with flagellar basal body. Flagella with hairs, scales, or other excrescences also without paraoxnemal structures. Basal bodies very long, with fibrous and nonmicrotubular anchorage materials and linked to nucleating site of pseudopodial axonemes.

Synapomorphy

Tubulocristate protists with axopodial axonemes nucleating on an amorphous site linked to kinetosomes.

Composition

Two genera, Dimorpha and Tetradimorpha.

Reference

Brugerolle and Mignot 1984.

Diplomonads

Circumscription

Amitochondriate flagellates with nuclei associated with a group of four kinetosomes, giving rise to two to four flagella each. Most with two nuclei and two sets of flagella. Flagella sometimes arising at anterior end of feeding groove (i.e., the taxa are excavate), others with cytoskeletal suckers for attachment to surfaces, some (Octomitus) with neither groove nor suckers. All heterotrophs, free-living or parasitic.

Ultrastructural identity

Without mitochondria, kinetid with four basal bodies giving rise to two or three major microtubular roots. Cell surface naked, no dictyosomes. Nuclear envelope largely intact during mitosis but spindle penetrates from the cytoplasm.

Synapomorphy

None specified, unless the duplex nucleo/kinetid structure is ancestral, but this hypothesis needs to be assessed.

Composition

About nine genera.

Reference

Vickerman 1990.

Ebriids

Circumscription

Biflagellated protists, with internal solid siliceous, branching or fenestrated, skeleton. Heterotrophic, able to produce pseudopodia. Marine. Considered by some to be a dinoflagellate, but there is no strong case for this. Few species living but with a good fossil record.

Ultrastructural identity

Few ultrastructural data are available, identity attributable to siliceous inclusion.

Synapomorphy

Flagellated protist with internal soild siliceous skeleton with branching of fenestrated appearance.

Composition

About three extant species in two genera.

Reference

Taylor 1990.

Ellobiopsids

Circumscription

Parasites of marine invertebrates, attached externally. Multicellular with trophic and generative sections. Release of biflagellated distributive stages follows multiple fission.

Ultrastructural identity

With very limited ultrastructural information, identity based largely on life history. Miotochondria with tubular cristae, trophic form with internal thick pellicle penetrated by membranous invaginations. Flagella without paraxonemal structures or hairs. Centriolar complexes embedded within folds of the nuclear envelope.

Synapomorphy

Not specified.

Composition

Ellobiopsis and Thalassomyces, possibly also Parallobiopsis, Rhizellobiopsis and Ellobiocystis.

Reference

Whisler 1990.

Entamoebidae

Circumscription

Amitochondriate parasitic amoebas with pseudopodia as clear semieruptive bulges from anterior of cell. Forms cysts. Amitochondriate status probably secondary.

Ultrastructural identity

Mitochondria absent, disctyosomes present. Small osmiophilic bodies sometimes adhering to inner surface of cell membrane. Cytoplasm with helical arrays (said to be of ribosomes), mitosis with entirely intranulear spindle with amorphous intranuclear microtubule organizing center.

Synapomorphy

Amitohondriate amoebas with intrenuclear spindle.

Composition

Entamoeba (three species); possibly also Endolimax (monotypic), Iodamoeba (monotypic).

References

Albach and Booden 1978; Espinosa-Cantellano et al. 1998.

Euglenoza

Circumscription

Flagellates with two flagella inserting into an anterior pocket. Two basal bodies giving rise to three microtubular rootlets, free living or parasitic, autotrophs, heterotrophs, and mixotrophs. Mostly with discicristate mitochondria and possibly distantly related to other taxa (Stephanopogon, Hemimastigophora, nucleariids, and Heterolobosea) with discicristate mitochondria.

Ultrastructural identity

Well studied, with two flagella, flagella typically inserting parallel or nearly so, giving rise to three microtubular ribbons, one or which associated with actual or presumptive ingestion device. Flagella with paraoxnemal rod, and the ventral (recurrent) flagellum with a paraxonemal rod with a lattice structure. Flagella often with fine hairs. Extrusomes with lattice walls when extruded and a cruciate pattern when not. Mitochondrial cristae typically disc shaped with short pedicel; some (kinetoplastids) with aggregates of DNA. Cell surface naked or with strips or cytoskeletal material (euglenids). Nuclear envelope intact during mitosis, spindle microtubules internal.

Synapomorphy

Discristate protists with heteromorphic paraxonemal rods (dorsal flagellum with tubular rod, ventral with lattice structure).

Composition

Four subtaxa: euglenids; kinetoplastids, including Hemistasia (and its probable synonym Entomosigma), and Rhynchobodo (and its synonym Cryptaulax); Postagaardi; and diplonemids.

References

Simpson 1997; Bernard et al. 1999.

Eumycetozoa - see ramicristates

Glaucophytes

Circumscription

Eukaryotes with cyanelles (reduced cyanobacteria) but with a wide array of trophic forms (flagellates, nonmotile coccoid organisms, palmelloid). Presence or absence of a cellulosic cell wall, presence or absence of a mucilage sheath. Given the variation, monophyly, which is largely based on the cyanelles, requires confirmation.

Ultrastructural identity

Considerable variation, mitochondria with flat cristae. With flattened sacs under cell membrane, which in some species may produce scales. Dictyosomes present and may be associated with the nucleus or with the flagellar apparatus, cyanelles present with or without a surrounding wall. Differing numbers of multilayered structures associated with the flagellar anchorage system if flagella are present. Flagella if present may have fine hairs. Nuclear envelope breaks down during mitosis, basal bodies/centrioles not used to nucleate spindle microtubules.

Synapomorphy

None available but probably platycristate protists with cyanelles with subsurface layer of sacs.

Composition

Cyanophora (two species), Glaucocystis (10 species), Gloeochaete (probably monotypic), and (?) Glaucosphaera (one species). Cyanidium and relatives included by some are assinged to the red algae.

References

Mignot et al. 1969; Kies and Bremer 1990.

Granuloreticulosa

Circumscription

Amoeboid organisms, mostly marine. With pseudopodia, which extend from the cell body as a series of strands which divide and anastomose. The structure of the net is always changing, and granular cytoplasm moves actively in both directions along the strands, which internally have microtubules. The appearance and behavior of the pseudopodial network is held by many to be synapomorphic. The group is dominated by the foraminifera, the trophic cells of which occupy multichambered or agglutinated tests. Some organisms that live in a single chambered test (the Monothalamida) and some without tests (Athalamids) may be included. Because branching dynamic pseudopodial networks may be found in some taxa that may not be granuloreticulosea (such as Microcometes, a flagellate, Biomyxa, gymnophreids, Gymnophrydium, Vampyrellids leptomyxids, various slime molds, etc.), the monophyly of the group is still uncertain. Consequently, some taxa assigned by others to this group, such as the Komokiacea and Biomyxa, are excluded here - even though there are undoubtedly some monothalamid and athalamid relatives of the foraminifera. The foraminifera includes taxa with complex life cycles (phases involving production of gametes separated by phases involving asexual reproduction); with or without flagellated swarmers; with or without nuclear dimorphism. Many species with endosymbiotic algae.

Ultrastructural identity

Mitochondria with tubular cristae. Nuclear envelope may be supported by fibrous sheath. Pseudopodia containing microtubules but not in geometric arrays, also with dark osmiophilic bodies. Flagellated stage generally unstudied, but it is now generally agreed that the flagella are without tripartite hairs (cf. Patterson 1989). Wall of testate forms variable in composition and make-up.

Synapomorphy

Usually said to be branching/anastomosing dynamic filamentous pseudopodial system, but this needs to be confirmed.

Composition

About 40,000 species; most are foraminifera.

Reference

Lee 1990.

Gymnophrea

Circumscription

Small- to medium-sized amoebas with branching bodies from which extend the fine pseudopodia with extrusomes and which may branch and anastomose. Cytoplasmic movements not strongly noticeable. Heterotrophic. Two short flagella. Flagellated zoospores may be produced.

Ultrastructural identity

Mitochondria with flat cristae. Perinuclear dictyosomes. With two short flagella, basal bodies parallel, anchorage not well characterized With concentric extrusomes. Microtubules occur in the pseudopodia.

Synapomorphy

None defined.

Composition

Two genera: Gymnophrys and Borkowia.

Reference

Mikrjukov and Mylnikov 1998.

Gymnosphaerida

Circumscription

Heliozoa with axonemes arising from a central nucleating site; uninucleate or multinucleate, naked or with adhering siliceous spicules. Cell may be differentiated into a stalk and head. With extrusomes and tubulocristate mitochondria.

Synapomorphy

Tubulocristate heliozoa with axopodial axonemes having hexagonal packing arrangements and arising from an amorphus nucleating structure.

Composition

Gymnosphaera, Hedraiophrys, and Actinocoryne - all monotypic.

References

Febvre-Chevalier 1980; Jones 1980.

Haplosporids

Circumscription

Sporozoan parasites of mostly marine invertebrates. Trophic cells uninucleate or multinucleate, intracellular, and no flagella. Spore walls develop intracellularly from haplosporosomes, and the spore has a distinctive lid and often extraneous filaments. Held by some to be related to the alveolates, but there is no evidence of alveoli.

Ultrastructural identity

Mitochondria with tubular cristae. Dividing nucleus with internal spindle and the nuclear envelope remains intact. There is residuum of parallel microtubules from the mitotic spindle, and this "kernstab" persists through interphase.

Synapomorphy

Tubulocristate protists with lidded spore and/or persistent spindle (Kernstab) in nondividing nucleus.

Composition

Three genera with about 35 nominal species. Proliferative kidney disease organism X (pkx) is included, though some regard this as being allied to myxospora.

References

Seagrave et al. 1980; Perkins 1990; Siddall et al. 1995.

Haptophytes

Circumscription

Marine flagellates, almost all with plastids with chlorophylls a and c, with two flagella done additional locomotor/feeding organelle, the haptonema. Some mixotrophic, one species exclusively heterotrophic. Many with inorganic (calcareous) scales (coccoliths). Some with polymorphic life cycles. Cytological organization similar in many respects to stramenopiles with chloroplasts, and they have been classified with that group by some. They lack the synapomorphy of stramenopiles, and at this time molecular evidence does not support derivation from that group.

Ultrastructural identity

Mitochondria with tubular cristae. Dictyosomes present. Plastids with lamellae comprised of three thylakloids, no stigma; plastid in an extension of endoplasmic reticulum - the periplastidial endoplasmic reticulum. Haptonema with enclosed microtubules not in 9+2 arrangement. Two flagella, without hairs, scales, or other excrescences, with up to four major microtubular roots and some nonmicrotubular materials. Mitosis with spindle nucleating in cytoplasm and nuclear envelope breaking down.

Synapomorphy

Tubulocristate flagellates with haptonema.

Composition

Several hundred species, with some dispute as to the status of one subset, the Pavlovales.

References

Hibberd 1976; Bhattacharya et al. 1993; Green and Leadbeater 1994.

Heterolobosea

Circumscription

Heterotrophic amoebas, amoebo-flagellates (collectively the vahlkampfiids or schizopyrenids), flagellates (Percolomonas), and slime molds (the acrasids). Two genera have no flagellated stage, but the majority of species have the capacity to convert from amoebas to flagellates or to encyst. Flagellates have two to four flagella and usually in ingestion region with an adjacent ridge supported by microtubules. Amoebas move with eruptive pseudopodia. Common in soils, but the group contains a facultative pathogen of the human central nervous systems (Naegleria). The acrasid slime molds are one of two types of cellular slime molds in which resistant spores are released from an aggregated mass of cells and in which differentiation may occur.

Ultrastructural identity

Mitochondrial cristae discoidal (i.e., with pedicel) or sacculate, mitochondria may be partly enclosed by an extensin of endoplasmic reticulum. Basal bodies parallel or nearly so, giving rise to several microtubular roots and sometimes a cross-striated non-microtubular root. Without dictyosomes with stacks of sacs, usually no extrusomes, cell surface naked. Nuclear envelope intact during mitosis, spindle microtubules internal.

Synapomorphy

To be resolved but either discicristate protists forming eruptive pseudopodia or discicristate protists with parallel basal bodies inserting on an electron-dense pad, possibly with a substantial cross-striated root.

Composition

Schizopyrenida, Acrasida, Percolomonas.

References

Page and Blanton 1985; Patterson and Zolffel 1991.

Jakobids

Circumscription

Flagellates with two flagella located at the anterior end of a ventral feeding groove (i.e., are excavate), with mitochondria, freely swimming or loricate.

Ultrastructural identity

Mitochondria with flat or tubular cristae, flagellar apparatus with two basal bodies giving rise to two major microtubular roots, which support the margins of the ventral groove. Other cytoskeletal microtubules arise directly or indirectly from the basal bodies, no extrusomes. Mitosis not described.

Synapomorphy

Excavate mitochondriates with two basal bodies.

Composition

Jakoba, Reclinomonas, and Histiona.

Reference

O'Kelly 1993. (See: ref. ID; 7295)

Kathablepharids

Circumscription

Relatively large biflagellated flagellates, heterotrophic, ingesting larger food particles (other protists) often by means of anteriorly located mouth, with long flagella that appear thicker than most flagella because they (and the body) are covered with a layer of organic matter structured as if comprised of tiny scales in regular arrays. Cells typically with extrusomes in a line along one face of body.

Ultrastructural identity

Mitochondria tubulocristate, dictyosomes are well developed. Two flagella, acutely inclined or near parallel basal bodies give rise to microtubular and microfibrillar structures, with regularly arrayed organic material attached to flagellar membrane and to cell membrane. Microtubules also underlie cell surface, extrusomes rolled ribbon type, with anterior ingestion device being an expanded cone of microtubules, the wall of which may incorporate a cylinder of microtubular ribbons. The nuclear envelope disperses during mitosis, and microtubules of the spindle arise in the cytoplasm. Discrete microtubule organizing centers have not been observed.

Synapomorphy

Tubulocristate protists with body and flagella coated in an organic layer appearently formed of fine scales in regular arrays.

Composition

Kathablepharis (= Katablepharis), Leucocryptos, and Platychilomonas.

References

Lee and Kugrens 1991; Vors 1992; Lee et al. 1993; Clay and Kugrens 1999.

Komokiacea

Circumscription

Large marine benthic organisms with a cytoplasmic mass surrounded by agglutinated material. Only known as large amoeboid organisms producing branching pseudopodial strings with which detritus and food is collected. Mostly reported from deep-sea habitats. Very few observations have been made on live cells. Initially classified within the foraminifera, but there is no evidence of a single-chambered or multichambered test. Assigned to the Granuloreticulosea on the basis of one observation of "granulo-reticulate" pseudopodia - but as pointed out under Granuloreticulosea, this character is not restricted to that group.

Ultrastructural identity

No clear ultrastructural identity, this group is distinguished by unusual gross morphology only.

Synapomorphy

None known.

Composition

About 12 genera in two families (Komokiacea and Baculellidae).

References

Tendal and Hessler 1977; Cedhagen and Mattson 1991.

Microsporida

Circumscription

Intracellular parasitic protozoa, heterotrophic, minute, no flagella, no mitochondria, no dictyosomes. Infect animals and other protozoa. Trophic stages are uninucleate or multinucleate plasmodia, may be diplokaryotic (i.e. nuclei are paired). There is evidence for meiosis. Distinguished from other sporotza by the distinctive spores that contain a coiled filament that everts to infectious organisms into host cells. Argued by some to be the most primitive eukaryotes, byothers to be allied to the true fungi.

Ultrastructural identity

No mitochondria, dictyosomes, or flagella. Spores with coiled introverted filaments through which the infectious cell is injected into hosts, spores also with layered system of sacs - the polaroplast also involved in discharge of infectious organism. Nucleus intact during mitosis, microtubules of mitotic spindle lie within the nucleus but nucleate on amorphous structures external or attached to nuclear envelope.

Synapomorphy

Spore with introverted polar filament.

Composition

Fairly large group containing the rudimicrosporidia and the true microsporidia (chytridiopsids, and the microsporida with about 20 families).

References

Larsson 1986; Canning 1990.

Myxospora - see opisthokonts

Nephridiophagids

Circumscription

Parasitic organisms associated with the malpighian tubules of insects; early development exracellular, later development involves plasmodia, which may bud. Spores are produced by parts of plasmodium and are concave or biconcave with a banded appearance when viewed by light microscopy. Previously linked with Coelosporidium but life cycle and ultrastructural differences now indicate that association is not appropriate.

Ultrastructural identity

Shape of mitochondrial cristae not established. Dictyosomes present. Nuclear envelope remains intact during nuclear division. Mitotic microtubules nucleating from amorphous materials external to nucleus. No centrioles reported as associated with spindle during mitosis.

Synapomorphy

None specified.

Composition

About 12 species previously assigned to five nominal genera.

Reference

Lange 1993.

Nucleariidae

Circumscription

Amoeboid organisms, with fine pseudopodia unsupported by microtubules, with or without hollow siliceous plates or spheres or spine, the walls of which are a meshwork. Uninucleate or multinucleate. No flagellated stages known. Mostly described from soils or freshwater.

Ultrastructural identity

Mitochondria with discoidal cristae. With dictyosomes. Pseudopodia without microtubules, supported by microfibrillar material. During mitosis, tne nuclear envelope remains intact and microtubules lie within the nucleus. One species reported with a microfibrillar cytoskeletal sheath. No extrusomes.

Synapomorphy

None known, distinguished at this time as filose amoebas with discoid mitochondrial cristae.

Composition

Nuclearia, Pompholyxophrys, Pinaciophora, Rabdiophrys, and Vampyrellidium.

References

Patterson 1983; Patterson et al. 1999.

"Opisthokonts"

Circumscription

This group contains the true fungi and thier protist relatives (the chytrids) and the animals and their protist relatives (the choanoflagellates). The close relationship of the multicellular taxa was initially indicated by molecular means. The group contains uniflagellated solitary and colonial protists with one flagellum at some stage in their life history, phagotrophs, saprophytes, mycelial organisms with spore-forming bodies but no flagella, multicelluar hetorotrophs formed from layers of cells (epithelia), and the sponges with a less structured arrangement of cells. Collagen, one of the components of the exracellular matrix of the animals has also been reported from some fungi. All of the flagellated taxa and flagellated cells swim with a single flagellum beating behind the cell. The term "opisthokonta" has been applied to this grouping (Cavalier-Smith and Chao 1995; Cavalier-Smith 1996). However, Cavalier-Smith and Chao do not use the term as a formal taxon because it would require that more "important" taxa are suboridinated to less "important" taxa. Here, the opisthokonts is a taxon with the composition as indicated below on an interim basis. Unfortunately, the name should be revisited as the term Opisthokonta has previously been used by Copeland (1956) for the chytrids. Some other permanently or temporarily "opisthokont" protists- such as several nominal pelobionts or the unassigned Phalansterium or Pseudaphelidium - are not included, and it is not yet known if they form part of this group.

Ultrastructural identity

The diversity of organization within this group is great, extending from uniflagellated protists with or without the ability to make siliceous products to multicelluar mycelial or epitheliate organisms. Apart from having platycristate mitochondria and being dictyosomate, this group has few discriminating characters that extend throughout this group. Nuclear division is variable within the fungi but in the animals, the envelope breaks down during mitosis.

Synapomorphy

Unspecified but probably may relate to the radiating and arcing anchorage structures associated with the single flagellum. Very few studies of the protistan (ancestral) members have been conducted, and until more detailed ultrastructural studies are carried out, such a determinatin would probably be premature. Most included taxa have secondarily lost this character.

Composition

The largest of the major eukaryote lineages with probably in excess of 1,000,000 species, in two major clusters: (chytrids + true fungi) + (choanoflagellates + Metazoa). These two clusters themselves require appopriately defined names. This taxon includes the Myxospora (previously thought of as a group of protozoa) as a subset of the Cnidaria. Some argue that the opisthokonts should include the Microspora.

References

Copeland 1956; Morris 1993; Wainright et al. 1993, 1994; Cavalier-Smith and Chao 1995; Cavalier-Smith 1998; Muller 1998.

Oxymonads

Circumscription

Mostly flagellates, all known species are commensals usually in intestines of termites, typically with four flagella in two pairs, and basal bodies giving rise to an organelle, the axostyle, which may be able to undulate.

Ultrastructural identity

No mitochondria, four basal bodies arranged in two separated pairs and giving rise to several major microtubular roots, some with associated nonmicrotubular roots. Axostyle, comprised of parallel sheets of microtubules, which in some species slide relative to each other and may have associated additional material. No extrusomes nor dictyosomes, cell surface naked.

Synapomorphy

Amitochondriate protists with axostyle constituted of multiple sheets of microtubules.

Composition

Fewer than 100 species located in several families (polymastigids, pyrsonymphids, and oxymonads).

Reference

Brugerolle and Koning 1997.

Parabasalids

Circumscription

Mostly flagellated protozoa, mostly commensals in insects or parasites. Some (hypermastigids) may have very large numbers of flagella and are usually symbionts in the intestines of wood-eating insects, others (trichomonads) may have an undulating membrane. An axostyle may be visible. A few species are free living.

Ultrastructural identity

No mitochondria. All cells (excepting aflagellated taxa) with at least one cluster of four basal bodies, which are the source of microtubular roots. Dictyosomes are well developed, often numerous, and may be associated with a nonmicrotubular rootlet, the parabasal fiber. Cell surface naked, no extrusomes. Mitosis with intact nuclear envelope and with spindle microtubules lying external to the nucleus.

Synapomorphy

Flagellated protists with a parabasal apparatus of dictyosomes anchored to a striated root.

Composition

Trichomondas, hypermastigids, and Cochlosoma.

References

Lee et al. 1985; Pecka et al. 1996.

Paramyxea

Circumscription

Parasitic heterotrophic protists typically found in the digestive system of marine invertebrates where they feed by osmotrophy. Initial infectious cell is amoeboid. Paramyxeids are regarded as multicellular because the daughter cells formed by division of the infectious cell may be contained within the initial cell; these continue to develop into multicellular spores. With a complex process of nuclear and cellular division.

Ultrastructural identity

Shape of mitochondria not confirmed. With a reduced (nine single microtubules) centriolar structure associated with the microtubules of the mitotic spindle; nuclear envelope disrupts during division.

Synapomorphy

Tubulocristate protists, during spore development endogenous budding accompanies cell division.

Composition

Several genera.

Reference

Desportes and Perkins 1990.

Pelobionts

Circumscription

Four genera of about 200 nominal species, mostly uniflagellated, without mitochondria or dictyosomes. Ribosomal RNA sequences places pelobionts away from the base of the tree, one other molecule and structural evidence suggest a more basal location. Phreatamoeba has been synonymized with Mastigamoeba.

Ultrastructural identity

Without mitochondria, dictyosomes, or fibrous cytoskeletal structures. Basal bodies are not paired and are supported by a cone of microtubules and, excepting taxa with nonmotile flagella, with a single radiating ribbon of microtubules. Flagella without paraxial structures. No extrusomes and no ingestion device. Some taxa with non- "9+2" arrangement of microtubules in axonemes and without nine X triplet organization of microtubules in basal bodies.

Synapomorphy

(Primitively?) amitochondriate protists with unpaired basal bodies anchored with cone and ribbon of microtubules.

Composition

Pelomyxa, Mastigamoeba, Mastigella, and Mastigina.

References

Hinkle et al. 1994; Simpson et al. 1997; Stiller et al. 1998.

Phaeodarea

Circumscription

A group of marine radiolaria (protists with axopodia, skeletons, and no flagella in the trophic state). Most have a skeleton of amorphous silica with associated organic matter, cytoplasm separated into an inner area by a thick capsule, and an inner layer that is further divided by a cape of vesicles - the cape having three openings: an apical astropyle that seems to be associated with the formation of feeding pseudopodia and two parapyles from which axonemal microtubules arise. Contain aggregates of waste material: the phaeodium. Life cycle may be complex, and flagellated distributive stages are produced.

Ultrastructural identity

Little studied, mitochondria probably tubulocristate.

Synapomorphy

Radiolaria with central capsule with three openings: and apical astropyle and two parapyles.

Composition

About 100 genera.

References

Cachon and Cachon 1985; Cachon et al. 1990.

Plasmodiophorids

Circumscription

Mostly parasitic, some phagotrophic consumers of cell contents of plants and oomycetes. Some with a highly unusual extrusome (stachel) used for penetrating food cells. Feeding cell may or may not be plasmodial, giving rise to multiple "zoospores" with two or four flagella; flagella without hairs, hence excluded from Oomycetes (stramenopiles) with which they are normally allied. With long-lived cysts with chitin in their walls.

Ultrastructural identity

Form of mitochondrial cristae is ambiguous, appearing either flat or sacculate (molecular evidence suggests plasmodiophorids are allied to tubulocristate eukaryotes). With a distinctive cruciate appearance of nucleus during mitosis of vegetative cells. Flagellar basal bodies long. May have complex extrusomes.

Synapomorphy

Eukaryotes with cruciate mitotic profiles in dividing vegetative cells.

Composition

About 40 species in 10 genera.

References

Barr 1983; Dylewski and Miller 1983; Beakes 1998.

Polycystinea

Circumscription

A group of marine radiolaria (protists with axopodia, skeletons, and no flagella in trophic state), usually with a skeleton of hydrated amorphous silica, developing from a four pornged spicule which may be dissolved by at least some species. Cytoplasm separated into an inner area by a capsule having differentiated regions (the fusules) through which the axopodia pass. Frequently with symbiotic dinoflagellates. Distributive stages have two flagella and some have strontium sulphate crystals, suggesting relationship with Acantharea.

Ultrastructural identity

Mitochondria with tubular cristae. Microtubules of axopodia form brancing arrays or wide hexagons. Capsule a discrete organic structure with fusules as a pore with electron-dense material enveloping the microtubules of the axoneme. Microtubule organizing center amorphous/fibrous/granular. Mitosis with spindle inside nucleus but microtubule nucleating material external to nuclear envelope.

Synapomorphy

Tubulocristate eukaryotes, with capsule with fusules separating endoplasm and ectoplasm.

Composition

Spumellarids (fusules distributed over entire capsule) and nasellarids (fusules located at one apex).

References

Cachon and Cachon 1985; Cachon et al. 1990.

Pseudodendromonads

Circumscription

Heterotrophic flagellates with two flagella and discrete ingestion area formed by loop of two microtubular roots, rather like bicosoecid stramenopiles to which - it is argued by some - they are related. May be solitary and swimming, attached by a stalk, or colonial and attached. May or may not have surface scales.

Ultrastructural identity

Mitocondria with tubular cristae, two flagella arising from two inclined basal bodies. Flagella with associated microtubular roots, one of which forms a hairpin structure that wraps around the cytopharyngeal region. Flagella without hairs or scales or other excrescences. Dictyosome usually associated with the nucleus. Nuclear envelope fragments during mitosis. Spindle microtubules arise within the cytoplasm. Some species with structures believed to be extrusomes. May be related to bicosoecids (stramenopiles) and Caecitellus.

Synapomorphy

Tubulocristate protist with hairpin rootlet of microtubules surrounding an ingestion region.

Composition

Adriamonas, Pseudodendromonas, and Cyathobodo.

References

Mignot 1984; Verhagen et al. 1994; Struder-Kypke and Hausmann 1998.

Ramicristates

Circumscription

Amoeboid organisms with tubular cristae that branch. Amoebas are distinguished by moving and/or acquiring food by means of pseudopodia, which can be filose, lobose, branching, conical, or with subpseudopodia. This group contains the bulk of the naked lobose amoebas of previous classifications, the lobose and filose testate amoebas. Three groups - stereomyxids, dictyostelids (a type of cellular slime mold), and acanthamoebids have a lamellate microtubule organizing center. Dictyostelids and acanthamoebids use cellulose, the former in the stalks, which support spores and in the cysts of the latter. The true slime molds (the eumycetozoa = protostelid and myxomycetes) are included. In these, the individual cells aggregate into a syncitial plasmodium that moves with an ebb and flow pattern. The syncitium produces a fruiting body from which are released resistant distributive cysts (spores). The eumycetozoa have a biflagellated stage in life cycle - one of the few types of ramicristates with flagellated forms. Leucodictyon is another plasmodial organism with flagellated distributive stage.

Ultrastructural identity

Mitochondria with irregular tubular and branching cristae. Mitosis variable but typically with nuclear envelope either breaking down at poles or breaking down entirely. Spindle microtubules arising from amorphous material near the nucleus or from basal bodies if flagella are present.

Synapomorphy

Mitochondriate eukaryotes with branched tubular mitochondrial cristae.

Composition

The euamoebae (corresponding broadly with the naked lobose amoebas); centramoebae (i.e., with lamellate microtubule organizing center; Acanthamoebae, Stereomyxidae and Dictyosteliidae), the leptomyxids, Trichosphaerium, lobose testate amoebas (Testacealobosea), filose testate amoebas (Testaceafilosea), and Gromia, protostelids, and myxomycetes. This group contains the bulk of the naked lobose amoebas of previous classifications, the lobose and filose testate amoebas.

References

Roos 1975; Frederick 1990; Spiegel 1990, 1991; Grell 1991; Grell and Schuller 1991; Patterson 1994; Patterson et al. 1999.

Red algae

Circumscription

The red algae, unicellular to multicellular (up to 1 m) mostly free-living but some parasitic or symbiotic, with chloroplasts containing phycobilins. Cell walls made of cellulose with mucopolysaccharides penetrated in many red algae by pores partially blocked by proteins (complex referred to as pit connections). Usually with separated phases of vegetative growth and sexual reproduction. Common and widespread, ecologically important, economically important (source of agar). No flagella.

Ultrastructural identity

Mitochondria with flat cristae, sometimes associated with forming faces of dictyosomes. Thylakoids single, with phycobilisomes, plastids with peripheral thylakoid. During mitosis, nuclear envelope mostly remains intact but some microtubules of spindle extend from noncentriolar polar bodies through polar gaps in the nuclear envelope.

Synapomorphy

No clear-cut feature available; possibly pit connections.

Composition

About 4,000 species, usually divided into two subclasses; The Bangiophyceae and the Floridophyceae.

References

Gabrielson et al. 1990; Ragan and Guttell 1995; Saunders and Kraft 1997.

Retortamonads

Circumscription

Heterotrophic flagellates, typically with two or four flagella, mostly commensal or parasitic but at least one free-living taxon known. Excavate, in the sense that the flagella sit at the head of a ventral feeding groove with ingestion occurring at the base of the groove.

Ultrastructural identity

Without mitochondria, flagella associated with four basal bodies arranged in a cruciate pattern or in separated pairs, giving rise to two major microtubular roots, which support the margins of the ventral feeding groove and are associated with some non-microtubular strands. Microtubules, which underlie the dorsal cells surface, arise from a band (lapel) of dense material near the basal bodies. Extrusomes not reported, no dictyosomes.

Synapomorphy

None known, possibly a cytoskeletal lapel dorsal to flagellar anchorage, or hook-shape of anterior part of right microtubular root.

Composition

Two known genera, Chilomastix and Retrotamonas.

Reference

Bernard et al. 1997.

Rosette agent

Circumscription

Obligate intracellular parasite from spleen and kidneys of farmed chinook salmon, with multilayered cellulose-containing wall within host cells, and with distinctive transverse plates developing at fission. Sequences studies suggest affinity with several other parasites such as Dermocystidium and Ichthyophonus, and a colloquial name (DRIPS) is emerging for this clauster, although it currently lacks a structural synapomorphy.

Ultrastructural identity

Ultrastructural studies not detailed, mitochondria present. Cristal form not known, with a multilayered wall. No flagellum or discernible cytoskeleton.

Synapomorphy

None specified.

Composition

Currently monotypic.

References

Harrell et al. 1986; Kerk et al. 1995.

Spironemidae

Circumscription

Multiflagellated heterotrophic protists, usually elongate body. Flagella arranged in a small number of longitudinal rows (kineties). Body surface underlain by one large dorsal organic plate and one large ventral organic plate.

Ultrastructural identity

Mitochondria cristal form ambiguous but probably tubular or sacculate. With flagella arising from short basal bodies and anchored by longitudinal fibrous and microtubular elements. With dictyosomes. Cell surface folded, underlain by microtubules and organic layers. Concentric extrusomes.

Synapomorphy

Mitochondriate protist with flagella in kineties and with two subsurface organic plates.

Composition

Three genera: Stereonema, Spironea, and Hemimastix.

Reference

Foissner and Foissner 1993.

Spongomonads

Circumscription

Heterotrophic flagellates, two flagella inserting at the apex of cells, which are embedded in a matrix of iron-rich mucoid globules, some forming large colonies.

Ultrastructural identity

Mitochondria with tubular cristae. With two flagella inserting in near parallel basal bodies, basal bodies with radiating fibrous anchorage structures and radiating microtubules, as well as cross-striated fibers running between and away from the basal bodies. Dictyosomes located adjacent to nucleus and basal bodies.

Synapomorphy

Tubulocristate flagellates embedded in globular mucoid iron-rich matrix.

Composition

Two genera, few species.

References

Hibberd 1976, 1984; Struder-Krypke and Hausmann 1998.

Stramenopiles

(See: ref. ID; 5772)

Circumscription

A major assemblage of tubulocristate protists, including taxa with and without chloroplasts. Plastids if present with chlorophylls a and c. Most flagellated taxa with one short and one long flagellum but some with only one flagellum. The long flagellum usually carrying tripartite tubular hairs that reverse the thrust from the flagellum. In few cells the hairs are absent and in one lineage they may be attached to the body surface. Cells may also be aflagellated, amoeboid, or mycelial, may be extremely large (some brown algal kelps). Cells may have scales, organic walls, or inorganic walls. Includes parasites, saprophytes, autotrophs, and heterotrophs; includes some taxa with great species diversity (e.g., diatoms).

Ultrastructural identity

This group has considerable diversity, with few features common to all species. Mitochondria have tubular cristae, usually with two flagella but one group of lineages have a single flagellum, and another lineage has many flagella arranged in rows (kineties). If two basal bodies are present, they are typically anchored by four microtubular roots. Plastids are present in many species, with three thylakoids per lamellae and with a stigma usually included within the plastid. Dictyosomes present. Extrusomes may be present or absent. Mitosis typically with fragmenting membrane and microtubules arising from external to the nucleus, most usually from the base of the flagella.

Synapomorphy

Tubulocristate protists with tripartite tubular hairs, but there has been secondary loss of this character in some subsents.

Composition

Aureococcus, Bicosoecids, Blastocystis, brown algae, Chlamydomyxa, chromulinids, Chrysomeridales, Commation, diatoms, Developayella, Diplophrys, eustigmatophytes, Hibberdiales, Hydrurales, labyrinthulids and thraustochytrids, Ollicola, Oomycetes, Parmales, pedinellids, pelagophytes, Pendulomonas, phaeothamniids, Pirsonia, proteromonads, raphidophytes, Reticulosphaera, Rhizochromulina, silicoflgaellates, slopalines, synurids, xanthophytes (inter alia).

References

Patterson 1989; Andersen 1991; Leipe et al. 1994; Saunders et al. 1995; Schnepf and Schweikert 1996; Silberman et al. 1996.

Thaumatomonads

Circumscription

Heterotrophic flagellates, two flagella; glide or swim; able to produce pseudopodia with which food is ingested. All species studied ultrastructurally have inorganic external scales and perhaps spines. Some syncitial.

Ultrastructural identity

Ultrastructural studies more or less restricted to whole mount preparations and details of the scales. Spines appear hollow and have symmetrical extensions from the base, scales tend to have margins that are rolled over. In those species that have been studied in more detail, the scales from in association with tubulocristate mitochondria.

Synapomorphy

Probably formation of surface scales in association with mitochondria of all scaley species (but apparently naked species have yet to be examined).

Composition

Seven genera.

References

Swale and Belcher 1974; Beech and Moestrup 1986; Patterson and Zolffel 1991.

Vampyrellids

Circumscription

Amoebas with filose/tapering pseudopodia usually finely granular cytoplasm, pseudopodia rarely anastomosing. Mostly ingest the contents of algal and fungal cells, which they gain access to by perforating the cell walls. Feeding amoebas alternating with digestive cysts, cytoplasm frequently orange. Freshwater and marine. Cells uninucleate or multinucleate.

Ultrastructural identity

Mitochondria with tubular cristae. Dictyosomes present. No flagella or centrioles known. Cytoplasm with helical arrays (of ribosomes?) Mitotic nuclei with intact nuclear envelopes and intranuclear spindles.

Synapomorphy

Tubulocristate filose amoebas with alternation of motile amoebas and digestive cysts.

Composition

Arachnula, Gobiella, Hyalodiscus, Leptomyxa, Vampyrella, and Vampyrelloides.

Reference

Ropstorf et al. 1994.

Viridaeplantae

The green algae and plants, distinguished as platycristate taxa with or without flagella with chloroplast containing chlorophylls a and b, eyespot when present in plastid, basal bodies anchored by cruciate system of rootlets. Coccoid, filamentous, palmelloid, amoeboid, or multicellular, most with cellulosic cells walls (prasinophytes are an exception). A major group and includes the multicellular plants. "Chlorophyta" is usually the term used or refer to nonplant elements of the clade.

Ultrastructural identity

Mitochondria with flat cristate, plastids in cells with thylakoids arranged in granae (stacks), two bounding membranes around the plastids; stigma if present within the plastid. With flagella typically anchored by cruciate array of microtubular roots and or a multilayered structure or derived from such structures; transition region with star and "H-piece". Mitosis may or may not involve loss of the nuclear envelope. Microtubules usually assist in controlling the orientation of new walls. The cell walls of "multicellular" species may or may not have pores called plasmodesmata.

Synapomorphy

Platycristate taxa with plastid thylakoids bearing chlorophylls a and b in stacks.

Composition

Typically about 11 categories (Classes?) of algae, one being the prasinophytes; plus (the Kingdom including) all green metaphyta.

Reference

van den Hoek et al. 1991.

Xenophyophores

Circumscription

Generally large (>1 cm) marine amoebas with an agglutinated test. Cell multinucleated; waste material (stercomata) accumulate around cell within test. Cytoplasm contains barite crystals. Very little information on cell organization, pseudopodia said to be filopodial or granuloreticulopodial. Widespread and possibly significant in deep sea sediments.

Ultrastructural identity

No information, identity based on gross morphology, stercomata, and barite crystals.

Synapomorphy

Large marine amoebas containing barite (BaSO4) crystals, and with adhering stercomata.

Composition

Two subsets (psamminids and stannomoids); 50 species in about 15 genera.

Reference

Tendal 1972.

Scientists list


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ref. ID; 4887, 4898, 4924, 4944, 4978, 4979, 4980, 5695, 5731, 5753, 6790, 6795, 6796, 7130, 7292, 7295, 7403, 7423, 7590, 7594, 7615, 7679