Systematics

Protozoa, Rotifera, Oligochaeta, Nematoda
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
1.1 The Society of Protozoologists: 1964 version
1.2 The Society of Protozoologists: 1980 version (ref. ID; 923)
Systematic analysis; Mainly morphology

2. The Kingdom PROTOZOA
2.1 Thomas Cavalier-Smith: 1996/97 version (ref. ID; 4887)
2.2 Thomas Cavalier-Smith: 2003 version (ref. ID; 4924, 4979)
Systematic analysis; Molecular phylogenetics

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

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

Subphylum I. MASTIGOPHORA Diesing, 1866 (see: ref. ID; 3731)
One or more flagella typically present in trophozoites; asexual reproduction basically by intrakinetal (symmetrogenic) binary fission; sexual reproduction known in some groups.

Class 1. PHYTOMASTIGOPHOREA Calkins, 1909 (see: ref. ID; 7291)
Typically with chloroplasts; if chloroplasts lacking, relationship to pigmented forms clearly evident; mostly free-living.

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 (see: ref. ID; 4226)
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.

Suborder 1. EUTREPTIINA Leedale, 1967
Two highly mobile emergent flagella, one directed anteriorly and other laterally.
Genus: Distigma, Eutreptia

Suborder 2. EUGLENINA Butschli, 1884
Two flagella, one emergent from cell invagination, highly mobile, other short and non-emergent; one genus colonial, several with envelops.
Genus: Astasia, Euglena, Trachelmonas

Suborder 3. RHABDOMONADINA Leedale, 1967
Two flagella, one emergent from cell invagination, highly mobile during swimming, held straight when cell is stationary; cells colorless, rigid; pellicle composed of strips fused into single continuous structure; canal with intucking scrolls of skeletal material.
Genus: Menoidium

Suborder 4. SPHENOMONADINA Leedale, 1967
One or 2 emergent flagella, one always directed anteriorly, straight, not mobile; cells colorless, rigid, usually with pronounced keels or grooves.
Genus: Sphenomonas

Suborder 5. HETERONEMATINA Leedale, 1967
One or 2 emergent flagella, one directed anteriorly, straight, with coiling or flickering movement of tip only, causing characteristic gliding locomotion; with special ingestion organelles.
Genus: Peranema

Suborder 6. EUGLENAMORPHINA Leedale, 1967
Three or more emergent, homodynamic flagella; endozoic in digestive tracts of tadpoles.
Genus: Euglenamorpha

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

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.

Suborder 1. BODONINA Hollande, 1952 emend. Vickerman, 1976
Typically 2 heterodynamic flagella; typical, often large, adbasal kinetoplast (eukinetoplastic condition), or kDNA arranged in several discrete bodies (polykinetoplastic condition) or dispersed throughout mitochondrion (pankinetoplastic condition); free-living or parasitic.
Genus: Bodo, Cryptobia, Rhynchomonas

Suborder 2. TRYPAOSOMTATINA Kent, 1880
Single flagellum either free or attached to body by undulating membrane; kinetoplast relatively small and compact; parasitic.
Genus: Blastocrithidia, Leishmania, Trypanosoma

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.

Suborder 1. ENTEROMONADINA Brugerolle, 1975 emend. Kulda & Nohynkova, 1978
Single karyomastigont containing 1 to 4 flagella; in genera with more than single flagellum, one recurrent; frequent transitory forms with 2 karyomastigonts resulting from delayed cytokinesis; cysts in at least one genus; parasitic.
Genus: Enteromonas, Trimitus

Suborder 2. DIPLOMONADINA Wenyon, 1926 emend. Brugerolle, 1975
Two karyomastigonts; body with 2-fold rotational symmetry, or bilateral symmetry in one genus; each mastigont with 4 flagella, one of them recurrent; with variety of microtubular bands; cysts present; free-living or parasitic.
Genus: Giaridia, Hexamita, Trepomonas

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.

Suborder 1. LOPHOMONADINA Light, 1927
Extranuclear organelles arranged in one system; typical all old structures resorbed in division and daughter organelles formed de novo.
Genus: Lophomonas, Microjoenia

Suborder 2. TRICHONYMPHINA Poche, 1913
Two or occasionally 4 mastigont systems; symmetry basically 2- or 4-fold rotational; typically equal separation of mastigont systems in division, with total or partial retention of old structures when new systems are formed.
Genus: Barbulanympha, Spirotrichonympha, Trichonympha

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

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

Order 1. AMOEBIDA Ehrenberg, 1830 (see: ref. ID; 7594, 7615)
Typically uninucleate; mitochondria typically present; no flagellate stage.

Suborder 1. TUBULINA Bovee & Jahn, 1966
Body branched or unbranched cylinder; no bidirectional flow of cytoplasm; nuclear division mesomitotic.
Genus: Amoeba, Entamoeba, Saccamoeba

Suborder 2. THECINA Bovee & Jahn, 1966
Flattened, with more or less regular outline, often oblong, ovate, or flagellate; often with discernible pellicle-like layer, which may be distinctly wrinkled; rolling movement of surface; nuclear division patterns diverse.
Genus: Platyamoeba, Thecamoeba, Vannella

Suborder 3. FLABELLINA Page, 1976
Flattened, broad, sometimes discoid, with extensive hyaline zone but no obvious pellicle-like layer; locomotion often accompanied by gentle eruption; nuclear division, where known, mesomitotic.
Genus: Flabellula, Rosculus

Suborder 4. CONOPODINA Bovee & Jahn, 1966
Digitiform or mammilliform, usually blunt, normally unbranched hyaline sub-pseudopodia usually produced from a broad hyaline lobe; not discoid; cysts seldom formed; nuclear division typically mesomitotic.
Genus: Mayorella, Paramoeba

Suborder 5. ACANTHOPODINA Page, 1976
More or less finely tipped, sometimes filiform, often furcate hyaline sub-pseudopodia produced from a broad hyaline lobe; not regularly discoid; cysts usually formed; nuclear division mesomitotic or metamitotic.
Genus: Acanthamoeba, Echinamoeba

Order 2. SCHIZOPYRENIDA Singh, 1952 (see: ref. ID; 7594, *7755)
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.
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 (see: ref. ID; 6790, *7745)
Test, tectum, or other external membrane with single aperture and composed of either organic or inorganic material or both.
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 (see: ref. ID; 4224)
Hyaline, filiform pseudopodia, often branching, sometimes anastomosing; no spores or flagellate stage known.

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.

Suborder 1. ALLOGROMIINA Hertog, 1906
Test membranous or tectinous, with ferruginous or, rarely, small quantities of agglutinated material.
Genus: Allogromia, Iridia, Myxotheca

Suborder 2. TEXTULARIINA Lankester, 1885
Test agglutinated, with foreign matter held together by various cements.
Genus: Saccammina, Textularia

Suborder 3. FUSULININA Wedekind, 1937
Test primitively of micro-granular calcite; 2 or more differentiated layers in test wall of more advanced forms.
Genus: Fusulina, Schwagerina

Suborder 4. MILIOLINA Lankester, 1885
Test porcellanous, perforate or imperforate.
Genus: Quinqueloculina, Triloculina

Suborder 5. ROTALIINA Lankester, 1885
Test hyaline, calcareous.
Genus: Ammonia, Elphidium, Rosalina

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.

Suborder 1. SPHAENACANTHINA Shewiakoff, 1926
Bases of spines without lateral wings.
Genus: Acanthometra, Dorataspis, Lithoptera

Suborder 2. PHYLLACANTHINA Schewiakoff, 1926
Bases of spines with lateral wings.

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.

Suborder 1. SPHAEROCOLLINA Brandt, 1902
Large, solitary cells, or cell colonies, skeleton absent or consisting of one or more isolated spicules or of usually single, perforated shell.
Genus: Collosphaera, Oroscena, Thalassicolla

Suborder 2. SPHAERELLARINA Haeckel, 1881
Small, solitary cells; skeleton always present, of one latticed piece, consisting of one shell, sometimes 2 or more concentric ones, more or less complete, with or without radial spines.
Genus: Coccodiscus, Lithelius, Octodendron

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

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 (see: ref. ID; 4884)
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.
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 (see: ref. ID; 1663, 4132)
[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".

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.

Suborder 1. ARCHISTOMATINA de Puytorac et al., 1974
Cytostome apical; simplest type of circumoral infraciliature (closely packed kinetosomes); somatic ciliature mostly in tufts or bands; concrement vacuoles; no toxicysts; all known species commensals, principally in equids.
Genus: Alloiozona, Blepharoprosthium, Bundleia, Didesmis

Suborder 2. PROSTOMATINA Schewiakoff, 1896
Cytostome apical, round; circumoral ciliature unspecialized; kineties bipolar, with axial-radial symmetry; no toxicysts.
Genus: Holophrya, Metacystis, Pelatractus

Suborder 3. PRORODONTINA Corliss, 1974
Cytostome apical or subapical, round or oval, sometimes in a shallow atrium; distinctive "brosse" typically present near oral area; toxicysts somatic; mostly carnivores or scavengers.
Genus: Coleps, Prododon, Urotricha

Suborder 4. HAPTORINA Corliss, 1974 (see: ref. ID; 3864, 4344, 4746)
[Notice] This taxon was considered an order by Corliss (1974, 1979). It is reduced here as a compromise with the French position in which both this group and the prorodontines are not even reorganized as separate suborders.
Cytostome apical or subapical, oval or slit-like; cytopharyngeal rhabdos complex; field of clavate "sensory" cilia prominent near anterior end of body; toxicysts in oral or cicumoral are or in proboscis or tentacles; rapacious carnivores.
Genus: Didinium, Dileptus, Lacrymaria, Spathidium

Order 2. PLEUROSTOMATIDA Schewiakoff, 1896 (see: ref. ID; 7355)
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.
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 (see: ref. ID; 4875)
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.
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.

Suborder 1. TRICHOSTOMATINA Butschli, 1889
Somatic ciliature not reduced.
Genus: Balantidium, Isotricha, Sonderia

Suborder 2. BLEPHAROCORYTHINA Wolska, 1971
Somatic ciliature markedly reduced; all species in herbivorous mammals, especially equids.
Genus: Blepharocorys, Ochoterenaia, Raabena

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 (see: ref. ID; 4692, 7466 (Grossglockneriids), 7537, *7706)
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.
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 (see: ref. ID; 7403)
Parts of generally extensive hypostomial frange more or less fused (= synhymenium); kineties bipolar; body often cylindrical, with complete ciliation; stomatogenesis parakinetal-like.
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.

Suborder 1. NASSULINA Jankowski, 1967
Frange of variable composition always distinct from suture line; body often large, cylindrical, fully ciliated; best-known forms from freshwater habitats, feeding on filamentous algae.
Genus: Furgasonia, Nassula, Paranassula
[Notice] Furgasonia (better known by its preoccupied name, Cyclogramma) has been considered by a number of workers (Grain et al. 1976, 1978) to belong in a new order, PARAHYMENOSTOMATIDA, of the subclass HYMENOSTOMATA and class OLIGOHYMENOPHORA. Principally because of its seemingly inexplicable possession of a cyrtos, Corliss (1977, 1979) (the present scheme) has retained it among the nassulids. Like other similar problems treated in these footnotes, the matter is perhaps best left unresolved until further comparative ultrastructural information becomes available.

Suborder 2. MICROTHORACINA Jankowski, 1967
Circumoral ciliature (frange) commonly reduced to 3 "pseudomembranelles"; somatic ciliation typically reduced; body often small and laterally flattened; unique kind of trichocyst characteristically present; cysts common; species freshwater or, often edaphic.
Genus: Leptopharynx, Microthorax, Pseudomicrothorax

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.

Suborder 1. CHLAMYDODONTINA Deroux, 1976
Ventral ciliature thigmotactic, without specialized glandular organelle; body broad and dorsoventrally flattened, with ventral surface in contact with substrate; macronucleus heteromerous; free-living or commensal, with some species parasitic, harmful to gills of freshwater fishes.
Genus: Chilodonella, Chlamydodon, Lynchella

Suborder 2. DYSTERIINA Deroux, 1976
Generally reduced ciliature and relatively narrow body, nematodesmata of cyrtos may be few in number and more conspicuous, sometimes with very prominent capitula ("teeth"); adhesive organelle well developed, often with protruding mobile appendix (podite); macronucleus heteromerous species numerous, mainly marine, free-living or commensal.
Genus: Dysteria, Hartmannula, Plesiotrichopus

Suborder 3. HYPOCOMATINA Deroux, 1976
Ventral surface quite densely ciliated; dorsal surface humped; cytopharyngeal tube, not surrounded by nematodesmata, may protrude from body; adhesive organelle inconspicuous in right-ventral pit or fosette; macronucleus not heteromerous; ecto- or endocommensals of marine hosts.
Genus: Crateristoma, Hypocoma, Parahypocoma

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.

Suborder 1. EXOGEMMINA Jankowski, 1972
External budding, often with single bud at a time; body relatively large, long, cylindrical, with well developed collar, but spines often absent; stalk almost universal; freshwater, brackish, and marine hosts, including alga.
Genus: Heliochona, Phyllochona, Spirochona

Suborder 2. CRYPTOGEMMINA Jankowski, 1975
Internal budding, with up to 8 tomites in brood pouch; body small, flattened, angular, with spines but reduced collar; stalk may be absent; marine crustacean/hosts (including "whale-lice").
Genus: Chonosaurus, Isochona, Stylochona

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.

Suborder 1. APOSTOMATINA Chatton & Lwoff, 1928
Cytostome present in both trophont and tomite stages, typically with rosette; palintomy usually within cysts; hosts mostly marine crustaceans, but a few species associated with polychaetes or freshwater crustaceans.
Genus: Foettingeria, Gymnodinioides, Hyalophysa

Suborder 2. ASTOMATOPHORINA Jankowski, 1966
Cytostome absent; remnants of oral ciliature present; body often elongate, vermiform; marked thigmotactism; strobilation type of budding producing catenoid colonies; life cycles incompletely known; some species in coelomic fluid of amphipods and isopods, others in organs of squid and octopus.
Genus: Chromidium, Collinia, Opalinopsis

Suborder 3. PILISUCTORINA Jankowski, 1966
Trophonts nonciliated, immobile, in cysts; some species impaled on setae of crustacean hosts; migrating tomites, produced by strobilation or budding, flattened and ciliated, but apparently mouthless; on marine crustaceans of various kinds and, perhaps, terrestrial mites.
Genus: Ascophrys, Askoella, Conidophrys

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.

Suborder 1. EXOGENINA Collin, 1912
Budding exogenous, without invagination of parental cortex; reproduction generally monogemmic, but polygemmy also occurring; some species with both prehensile and suctorial tentacles; larvae of some species long and vermiform, practically devoid of cilia and nonmotile; mostly large, solitary, and marine, free-living or ectocommensal; some species loricate and colonial.
Genus: Ephelota, Paracineta, Podophyra, Thecacineta

Suborder 2. ENDOGENINA Collin, 1912
Budding endogenous, with larvae free in pouch before emergence; reproduction monogemmic and polygemmic; some species stalkless; several with atypically huge ramified body; bundles of tentacles may be branched; migratory larvae often small; diverse habitats, with some species endocommensal in various hosts.
Genus: Acineta, Dendrosoma, Endosphaera, Tokophrya

Suborder 3. EVAGINOGENINA Jankowski, 1975
Budding involves evagination of enter pouch with bud still attached; large, single larva, flattened, with distinct patterns of ventral ciliature; some adults with branched tentacular bundles; common freshwater or marine symphorionts, with few endoparasitic species.
Genus: Cyathodinium, Dendrocometes, Discophrya, Heliophrya

Class 2. OLIGOHYMENOPHOREA de Puytorac et al., 1974 (see: ref. ID; 3915, 4125)
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.

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.

Suborder 1. TETRAHYMENINA Faure-Fremiet, in Corliss, 1956 *(see: ref. ID; 7733)
Uniformly ciliated; 3 oral membranelles on left and undulating or paroral membrane (stichodyad) on right; preoral but no postoral suture; seldom any thigmotactic ciliature, with even caudal cilia uncommon; no nematodesmata or trichocysts, but mucocysts common, stomatogenesis parakinetal; mostly free-living, freshwater microphagous forms, although few species faculative or even obligate endoparasites.
Genus: Colpidium, Glaucoma, Tetrahymena, Turaniella

Suborder 2. OPHRYOGLENINA Canella, 1964
Large, primarily freshwater, histophagous forms; life cycle polymorphic, with palintomic cyst stage; oral apparatus including 3 ciliary organelles on left and associated structure, enigmatic "watchglass organelle"; stomatogenesis parakinetal but complicated by life cycle; no nematodesmata or trichocysts; several species causing white spot disease in marine and freshwater fishes.
Genus: Ichthyophthirius, Ophryoglena

Suborder 3. PENICULINA Faure-Fremient, in Corliss, 1956
Large, free-living, monomorphic, predominantly freshwater microphagous forms; mucocysts uncommon; explosive fusiform trichocysts occurring widely throughout group; 3 peniculi, often located deep in buccal cavity; stomatogenesis buccokinetal; nematodesmata and pre- and postoral sutures often present, as is depression or oral groove leading to buccal cavity; many species with endosymbiotic algae or gram-negative bacteria; cysts known for only few groups.
Genus: Frontonia, Neobursaridium, Paramecium, Stokesia

Order 2. SCUTICOCILIATIDA Small, 1967 (see: ref. ID; 7213)
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.

Suborder 1. PHILASTERINA Small, 1967
Infraciliature of paroral membrane with reduced "a" and "c" segments; scutica very transient; mucocysts prominent, rod-shaped; director-meridian distinct; numerous species, especially in brackish or marine habitats, including sand; some inquilines of sea urchins, others endocommensals of molluscs, polychaetes, and other hosts.
Genus: Entodiscus, Loxocephalus, Philaster, Uronema

Suborder 2. PLEURONEMTINA Faure-Fremiet, in Corliss, 1956
Body commonly small or very small; paroral membrane often prominent (sometimes as stiff velum); cytostome equatorial to subequatorial; infraciliary base of paroral membrane clearly trisegmented, with segment "c" serving as permanent scutica; caudal cilia often conspicuous; mucocysts prominent; cytoproct typically present widely distributed mostly free-living, but some commensals.
Genus: Conchophthirus, Cyclidium, Pleuronema, Thigmocoma

Suborder 3. THIGMOTRICHINA Chatton & Lwoff, 1922
Prominent thigmotactic region, typically near anterior end, commonly present; cytostome often at or near posterior end; body usually heavily ciliated and laterally compressed; prominent sucker at anterior end in some groups; segment "c" of paroral; membrane may be indistinct "scutico-vestige"; director-meridian absent; cytoproct generally absent; all species parasitic, especially in lamellibranchs and oligochaetes.
Genus: Ancistrum, Boveria, Cheissinia, Ptychostomum

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.

Suborder 1. SESSILINA Kahl, 1933 (see: ref. ID; 4335)
Sedentary and sessile, with rare exceptions; body characteristically bell- or goblet-shaped, with stalk at tapered end; mouthless telotroch with locomotory posterior ciliary girdle; many species colonial, some loricate; scopulary kinetosomes typically producing aboral stalk or thigmotactic (adhesive) disc; adults generally filter-feeding bactivores, attached to various substrates in wide range of habitats.
Genus: Carchesium, Epistylis, Opercularia, Vaginicola, Vorticella, Zoothamnium

Suborder 2. MOBILINA Kahl, 1933
Mobile forms, usually conical or cylindrical (or discoidal and orally-aborally flattened), with permanently ciliated trochal band (ciliary girdle); complex thigmotactic apparatus at aboral end, often with highly distinctive denticulate ring; all species ecto- and endoparasites of freshwater or marine vertebrates and invertebrates; forms on gills of fishes pathogenic.
Genus: Polycycla, Trichodina, Urceolaria

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

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.

Suborder 1. HETEROTRICHINA Stein, 1859
Somatic ciliature well developed; body very contractile, often with simple axis of symmetry; single, conspicuous contractile vacuole at posterior end; peristomial ciliature comprised of numerous paramembranelles and paroral membranes of diplostichomonad type or with pairs of basal bodies; no loricae cyst common; stomatogenesis either parakinetal or apokinetal; free-living forms large, widely distributed.
Genus: Blepharisma, Metopus, Spirostomum, Stentor

Suborder 2. CLEVELANDELLINA de Puytorac & Grain, 1976
Somatic ciliature well developed, sometimes separated into distinct areas by well defined suture lines ("systemes secants"); buccal ciliature composed of heteromembranelles and diplostichomonad paroral line(s); several specialized unique fibers associated with kinetosomes; macronuclear karyophore and/or conspicuous dorsoanterior sucker characteristic of many species; endoparasitic in digestive tract of insects (and related arthropods) or lower vertebrates, occasionally in oligochaetes or molluscs.
Genus: Clevelandella, Nyctotherus, Sicuophora

Suborder 3. ARMOPHORINA Jankowski, 1964
AZM commonly encircling body, spiraling posterior; cytostome near antapical end; somatic ciliature absent except for caudal tuft, several anterior cirri, and "ciliary stripe" accompanying AZM; pellicle rigid, armor-like, with 2 or 2 posterior spines; few species, small, all polysaprobic.
Genus: Caenomorpha, Cirranter, Ludio

Suborder 4. COLIPHORINA Jankowski, 1967
AZM borne on pair of prominent "peristomial wings" extending out from lorica-encased body; somatic ciliation uniform and holotrichous stomatogenesis parakinetal; in division, proter becoming vermiform migratory stage in life cycle; adult attached (by lorica) to various substrates; all but very few species marine.
Genus: Ascobius, Folliculina, Lagotia

Suborder 5. PLAGIOTOMINA Albart, 1974
Body laterally flattened, with extensive AZM and 2 diplostichomonad paroral lines on right side; cytostome subequatorial; stomatogenesis parakinetal; no macronuclear karyophore; body uniformly ciliated, with groups of cilia highly reminiscent of cirri of primitive hypotrichs; few species, all endocommensals in oligochaetes.
Genus: Plagiotoma

Suborder 6. LICNOPHORINA Corliss, 1957
Hourglass-like shape; prominent oral disc bearing massive wreath of membranelles; conspicuous basal disc at antapical pole, later disc with particularly complex substructure, serving as attachment organelle; body proper without cilia, possibly with infraciliature several ectocommensal species associated with variety of marine invertebrates, with one species on alga.
Genus: Licnophora

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 (see: ref. ID; 4356)
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.

Suborder 1. OLIGOTRICHINA Butschli, 1887
Somatic ciliature commonly, but not universally, reduced of few short rows of cirrus-like bristles; prominent bipartite AZM (forming open or closed ring), with perioral region used in locomotion; body seldom loricate; endoskeletal "trichites" and polysaccharide platelets may be present; mostly marine, but several widely distributed freshwater species and at least one strongly edaphic.
Genus: Halteria, Strombilidium, Strombidium

Suborder 2. TINTINNINA Kofoid & Campbell, 1929
Ciliature dominated by AZM, always forming closed ring; somatic ciliation reduced; body cylindrical or cone-shaped, highly contractile; loricae universally present; tentaculoids sometimes located between adjacent paramembranelles; great majority of species pelagic, some neritic, with a few abundant in freshwater habitats; fossil forms known.
Genus: Codonella, Dictyocysta, Epiplocylis, Tintinnopsis

Order 4. HYPOTRICHIDA Stein, 1859 (see: ref. ID; 3630, 4386, 4889, 7307, 7354, 7590, *7679)
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.

Suborder 1. STICHOTRICHINA Faure-Fremiet, 1961
Body generally elongate; cirri often small and quite inconspicuous, typically in 3 to 12 longitudinal, sometimes spiraled, rows on ventral surface; stomatogenesis presumably parakinetal in more primitive forms; predominantly free-living, but one species ectocommensal on hydras.
Genus: Holosticha, Hypotrichidium, Kerona, Urostyla

Suborder 2. SPORADOTRICHINA Faure-Fremiet, 1961 (see: ref. ID; 4894, 7423)
Body often oval to elliptical, cirri, non-aligned, typically heavy and conspicuous, in isolated groups in specific regions of ventral surface; stomatogenesis apokinetal; most species free-living in widely diverse habitats (freshwater, edaphic, interstitial, marine, etc.), but few inquilines of echinoids or ectocommensals associated with several invertebrate groups.
Genus: Aspidisca, Euplotes, Oxytricha, Stylonychia


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.

Subphylum ANAEROMONADA Cavalier-Smith 1996
Golgi dictyosome without striated parabasal fibre. Sole class ANAEROMONADEA Cavalier-Smith 1996 and order ANAEROMONADIDA Cavalier-Smith 1996, with diagnoses as for subphylum ANAEROMONADA.

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.
Phylum RETICULOSA Carpenter 1862 emend. stat. nov. De Saedeleer 1934
Phylum MYCETOZOA De Bary 1873 stat. nov. Engler & Prantl 1888

Superphylum HAPLOSPORIDA Cavalier-Smith 1996
Diagnosis as for sole constituent phylum HAPLOSPORIDIA Caullery and Mesnil, 1899 (Cavalier-Smith 1993)
Phylum HAPLOSPORIDIA Caullery and Mesnil, 1899 stat. nov. Corliss 1984

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.

Subphylum PHYTOMYXA Cavalier-Smith 1996
Diagnosis as for sole class PHYTOMYXEA Engler & Prantl, 1897 (Cavalier-Smith 1993)
Class PHYTOMYXEA Engler & Prantl, 1897 orthog. emend. Cavalier-Smith 1993
Order 1. PHAGOMYXIDA Cavalier-Smith 1993 (e.g. Phagomyxa)
Order 2. PLASMODIOPHORIDA Cook 1928 (e.g. Plasmodiophora)

Subphylum RETICULOFILOSA subphy. nov. Cavalier-Smith 1996
Amoeboflagellates typically with a long-lived amoeboid trophic phase with reticulopodia or filopodia and a short-lived flagellate dispersal phase with one or two cilia; with or without plastids.
Class 1. CHLORARACHNEA Hibberd & Norris 1984 orthog. emend. Cavalier-Smith 1993
Order CHLORARACHNIDA Hibberd & Norris 1984 orthog. emend. (e.g. Chlorarachnion, Cryptochlora)

Class 2. PROTEOMYXIDEA Lankester 1885 emend. Cavalier-Smith 1993
Order 1. PSEUDOSPORIDA Cavalier-Smith 1993 (e.g. Pseudospora)
Order 2. LEUCODICTYIDA Cavalier-Smith 1993 (e.g. Leucodictyon)

Subphylum MONADOFILOSA subphy. nov. Cavalier-Smith 1996
Trophic phase either flagellates with two anisokont cilia, usually having a marked tendency to produce pseudopods of varying form, or filose amoebae lacking a flagellate stage; plastids absent (unless the cyanelle of Paulinella is really a plastid).
Class 1. SARCOMONADEA Cavalier-Smith 1993 stat. nov. 1995 emend.
Order 1. CERCOMONADIDA Poche 1913 emend. Vickerman in Honigberg 1983 (e.g. Cercomonas, Heteromita, Massisteria) (see: ref. ID; 6794)
Order 2. THAUMATOMONADIDA Shirkina 1987 (e.g. Thaumatomonas, Thaumatomastix)

Class 2. FILOSEA Leidy 1879 emend. Cavalier-Smith 1993
Subclass 1. CRISTIDISCOIDIA Page 1987 stat. nov. Cavalier-Smith 1993
Order 1. NUCLEARIIDA Cavalier-Smith 1993 (e.g. Nuclearia)
Order 2. FONTICULIDA Cavalier-Smith 1993 (Fonticula)
Order 3. MINISTERIIDA ord. nov. Cavalier-Smith 1996
Protozoa with sparse, slender, radiating, semi-rigid, and very regularly arranged filopodia with inflated distal ends; mitochondrial cristae discoid; flagellate stage unknown. Sole genus Ministeria Patterson 1993.
Subclass 2. CRISTIVESICULATIA Page, 1987 stat. nov. Cavalier-Smith 1993
Order VAMPYRELLIDA Starobogatov ex Krylov et al. 1980 (e.g. Vampyrella)
Subclass 3. TESTACEFILOSA De Saedeleer, 1934
Order 1. GROMIIDA Claparede & Lachmann 1856 (e.g. Gromia)
Order 2. EUGLYPHIDA stat. nov. Cavalier-Smith 1996 (e.g. Euglypha, Paulinella) (see: ref. ID; 6795)

Phylum AMOEBOZOA Luhe 1913 stat. nov. Corliss 1984 emend. Cavalier-Smith 1995 (see: ref. ID; 4944, 6789)
Emended diagnosis: Non-ciliate amoebae with lobose pseudopodia, multiciliated amoebae, or uniciliate amoebae; mitochondrial cristae tubular or mitochondria and peroxisomes absent; extrusomes absent.

Subphylum ARCHAMOEBAE Cavalier-Smith 1983 stat. nov.
Class 1. PELOBIONTEA Page 1976 stat. nov. Cavalier-Smith 1981 emend. 1991 (see: ref. ID; 7078)
Order 1. MASTIGAMOEBIA Frenzel 1892 (syn. RHIZOFLAGELLATA Kent 1880) (e.g. Mastigina, Mastigamoeba, Mastigella, Pelomyxa)
Order 2. PHREATAMOEBIDA Cavalier-Smith 1991 (Phreatamoeba)

Class 2. ENTAMOEBEA Cavalier-Smith 1991
Order ENTAMOEBIDA Cavalier-Smith 1993 (e.g. Entamoeba)

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
Class 1. AMOEBAEA Ehrenberg 1830 stat. nov. (syn. GYMNAMOEBAE Haeckel 1862) Cavalier-Smith 1993 (see: ref. ID; 7077)
Naked lobose amoebae with mitochondria.
Order 1. EUAMOEBIDA Lepsi 1960 (e.g. Amoeba)
Order 2. LEPTOMYXIDA Pussard & Pons 1976 emend. Page 1987 (e.g. Leptomyxa)
Order 3. COPROMYXIDA Cavalier-Smith 1993 (Copromyxa)
Order 4. ACANTHOPODIDA Page 1976 (e.g. Acanthamoeba, Hartmanella)
Order 5. LOBORETICULATIDA Page 1987 (Corallomyxa)

Class 2. TESTACEALOBOSEA De Saedeleer 1934 stat. nov.
Testate lobose amoebae.
Order 1. ARCELLINIDA Kent 1880 (e.g. Arcella, Difflugia)
Order 2. TRICHOSIDA Mobius 1889 (Trichospharium)
Order 3. HIMATISMENIDA Page 1987 (e.g. Cochliopodium)

Infrakingdom ALVEOLATA Cavalier-Smith 1991
Superphylum MIOZOA Cavalier-Smith 1987
Phylum DINOZOA Cavalier-Smith 1981 emend. 1991
Phylum APICOMPLEXA Levine 1970 emend.

Superphylum HETEROKARYOTA Hickson 1903 stat. nov. Cavalier-Smith 1993
Phylum CILIOPHORA Doflein 1901 stat. nov. Copeland 1956 emend. auct.

Infrakingdom ACTINOPODA Calkins 1902 stat. nov. Cavalier-Smith 1996
Phylum HELIOZOA Haeckel 1886 stat. nov. Margulis 1974
Phylum RADIOZOA Cavalier-Smith 1987

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.

Subphylum APUSOZOA Cavalier-Smith 1996
Non-amoeboid aerobic flagellates with peroxisomes and usually tubular mitochondrial cristae, but no cortical alveoli or tubular ciliary hairs; with two anisokont cilia or on trailing cilium; cilia not surrounded by a collar of discrete microvilli; extrusomes isodiametric, elongated or absent, never of the scroll ejectisome type; axopodia and pseudopodia absent.
Classes: THECOMONADEA, JAKOBEA, KINETOMONADEA, ANISOMONADEA, EBRIDEA

Infraphylum EXTRUMONADA Cavalier-Smith 1996
Apusozoans with extrusomes.
Class THECOMONADEA Cavalier-Smith 1993 (as subclass) stat. nov. 1995
Order 1. APUSOMONADIDA Karpov & Mylnikov 1989 (Apusomonas)
Order 2. CRYOMONADIDA Cavalier-Smith 1993 (Cryothecomonas)

Class JAKOBEA Cavalier-Smith 1996 (see: ref. ID; 7295)
Anisokont biciliate zooflagellates with tubular or irregularly flattened mitochondrial cristae; three asymmetric microtubular ciliary roots, but lacking an extensive pelicular array of microtubules; heterodynamic cilia emerging from a lateral groove; ciliary transition sheath absent; silicious endoskeleton absent; extrusomes isodiametric.
Order: JAKOBIDA Cavalier-Smith 1993 (Jakoba)
Order: DISCOCELIDA Cavalier-Smith 1996
Flattened discoid gliding biflagellates with tubular mitochondrial cristae. Sole genus Discocelis Vors 1988

Class KINETOMONADEA
Subclass: VARICISTIA Cavalier-Smith 1996
Kinetomonads with unbranched tubular or with irregularly flattened mitochondrial cristae. Sole order HISTIONIDA
Order: HISTIONIDA Cavalier-Smith 1993 (e.g. Histiona, Reclinomonas, Ancyromonas)

Subclass RAMICRISTIA Cavalier-Smith 1996
Kinetomonads with branched tubular cristae. Orders HELIOMONADIDA and COMMATIIDA.
Order: HELIOMONADIDA Cavalier-Smith 1993 (Dimorpha, Tetradimorpha)
Order: COMMATIIDA Cavalier-Smith 1996 Biflagellates with branched tubular cristae, kinetocyst-like extrusomes but, unlike HELIOMONADIDA, without axopodia.
Sole genus: Commation Thomsen & Larsen 1993

Infraphylum EURYMONADA Cavalier-Smith 1996
Apusozoans without extrusomes. Classes ANISOMONADEA, EBRIDEA
Class: ANISOMONADEA Cavalier-Smith 1993 emend.
Order: DIPHYLLEIDA Cavalier-Smith 1993 (Diphyllea)
Order: PHAGODINIDA Cavalier-Smith 1993 (Phagodinium)
Order: CAECITELLIDA Cavalier-Smith 1996
Anisokont biflagellates with unbranched tubular cristae and no extrusomes; cilia without basal sheath around central pair (distinction from Diphylleida); without starch (distinction from PHAGODINIDA).
Sole genus: Caecitellus Patterson

Class EBRIDEA Lemmermann 1901 emend. Deflandre 1936 stat. nov. Loeblich III 1970
Order: EBRIIDA Deflandre 1936 (e.g. Ebria, Hermesinum)

Subphylum ISOMITA Cavalier-Smith 1996
Non-amoeboid aerobic flagellates with peroxisomes and tubular mitochondrial cristae, but no cortical alveoli or tubular ciliary hairs; with two isokont cilia or one anterior cilium; cilia not surrounded by a collar of discrete microvilli; extrusomes absent or of the single scroll ejectisome type; axopodia and pseudopodia absent.
Classes: CYATHOBODONEA Cavalier-Smith 1993 and TELONEMEA Cavalier-Smith 1993
Class: CYATHOBODONEA Cavalier-Smith 1993
Order: PSEUDODENDROMONADIDA Hibberd 1985 (Cyathobodo, Pseudodendromonas)
Order: SPONGOMONADIDA Hibberd 1983 emend. Karpov 1990 *(see: ref. ID; 5731 (Spongomonas, Rhipidodendron, Phalansterium)
Order: KATHABLEPHARIDA Cavalier-Smith 1993 (Kathablepharis)
Class: TELONEMEA Cavalier-Smith 1993
Order: TELONEMIDA Cavalier-Smith 1993 (Telonema)
Order: NEPHROMYCIDA Cavalier-Smith 1993 (Nephromyces)

Subphylum HEMIMASTIGOPHORA Foissner, Blatterer & Foissner 1988 stat. nov. Cavalier-Smith 1993 (see: ref. ID; 4898, 5727)
Class: HEMIMASTIGEA Foissner, Blatterer & Foissner 1988
Order: HEMIMASTIGIDA Foissner, Blatterer & Foissner 1988 (e.g. Spironema, Hemimastix)

Subphylum CHOANOZOA Cavalier-Smith 1981 stat. nov. emend. 1983 stat. nov.
Uniciliate or secondarily non-ciliate unicellular or colonial protozoa with flat non-discoidal cristae; cilia when present surrounded by collar or actin-supported microvilli and with a symmetric cone of microtubules as a ciliary root.
Classes: CHOANOFLAGELLEA and CORALLOCHYTREA.
Class: CHOANOFLAGELLEA Kent 1880 (as order CHOANOFLAGELLIDA) stat. nov. (syn. CHOANOMONADEA Krylov et al. 1980)

Order: CRASPEDIDA Cavalier-Smith 1996 (e.g. Monosiga)
Choanoflagellates without a silicious lorica. Families CODOSIGIDAE, SALPINGOECIDAE.

Order: ACANTHOECIDA Cavalier-Smith 1996 (e.g. Diaphanoeca)
Choanoflagellates with a silicious lorica. Family ACANTHOECIDAE.

Class: CORALLOCHYTREA Cavalier-Smith 1995
Order: CORALLOCHYTRIDA Cavalier-Smith 1995 (Corallochytrium)

[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
Class 1: BREVIATEA+ Cavalier-Smith 2004 (e.g. 'Mastigamoeba invertens')
Class 2: LOBOSEA Carpenter 1861 emend. *(see: ref. ID; 7755) (e.g. Amoeba, Chaos, Saccamoeba, Hartmannella, Echinamoeba, Leptomyxa, Rhizamoeba, Copromyxa, Arcella)
Class 3: Discosea+ Cavalier-Smith 2004 (e.g. Vannella, Platyamoeba, Multicilia, Vexillifera, Paramoeba, Mayorella, Cochliopodium, Thecamoeba)
Class 4: VARIOSEA+ Cavalier-Smith 2004 (e.g. Phalansterium, Acanthamoeba, Balamuthia, Gephyramoeba, Filamoeba, Stereomyxa)

Subphylum 2: CONOSA Cavalier-Smith 1998
Infraphylum 1: ARCHAMOEBAE Cavalier-Smith 1983 stat. nov. 1998
Class: ARCHAMOEBA Cavalier-Smith 1983 stat. nov. (e.g. Pelomyxa, Mastigina, Entamoeba, Mastigamoeba, Phreatamoeba, Endolimax)
Infraphylum 2: MYCETOZOA De Bary stat. nov.
Class 1: STELAMOEBEA+ Cavalier-Smith 2004 (e.g. Protostelium, Schizoplasmodium, Cavostelium, Planoprotostelium, Acytostelium, Dictyostelium)
Class 2: MYXOGASTREA Fries 1829 stat. nov. Cavalier-Smith 1993 emend. (e.g. Hyperamoeba, Ceratiomyxa, Stemonitis, Physarum, Didymium)

Phylum 2: CHOANOZOA Cavalier-Smith 1981 emend. 1998
Class 1: CHOANOFLAGELLATEA Kent 1880 stat. nov. Cavalier-Smith 1998 (e.g. Monosiga)
Class 2: CORALLOCHYTREA Cavalier-Smith 1995 (Corallochytrium)
Class 3: ICHTHYOSPOREA Cavalier-Smith 1998 (e.g. Dermocystidium, Ichthyophonus)
Class 4: CRISTIDISCOIDEA Page 1987 stat. nov. Cavalier-Smith 1997 (e.g. Ministeria, Nuclearia)

Subkingdom BICILIATA subkingd. nov.
Diagnosis: 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
Superclass 1: RETICULOFILOSA Cavalier-Smith 1997 stat. nov. 2003
Class 1: CHLORARACHNEA Hibberd and Norris 1984 (e.g. Chlorarachnion, Bigelowiella, Lotharella, Cryptochlora, Gymnochlora)
Class 2: PROTEOMYXIDEA Lankester 1885 em. Cavalier-Smith 2003 (e.g. Pseudospora, Leucodictyon, Reticulamoeba, Massisteria, Dimorpha, Gymnophrys, Borkovia)
Superclass 2: MONADOFILOSA Cavalier-Smith 1997 stat. nov. 2003
Class 1: SARCOMONADEA Cavalier-Smith 1993 emend. 2003 (e.g. Cercomonas, Heteromita, Bodomorpha, Proleptomonas, Allantion)
Class 2: THECOFILOSEA Cavalier-Smith 2003 (e.g. Cryptodifflugia, Cryothecomonas)
Class 3: SPONGOMONADEA Cavalier-Smith 2000 (e.g. Spongomonas, Rhipidodendron)
Class 4: IMBRICATEA Cavalier-Smith 2003 (e.g. Thaumatomonas, Thaumatomastix, Allas, Gyromitus, Euglypha, Trinema, Paulinella)
Subphylum 2: ENDOMYXA Cavalier-Smith 2002 emend.
Class 1: PHYTOMYXEA Engler and Prantl 1897 (e.g. Phagomyxa, Plasmodiophora)
Class 2: ASCETOSPOREA Sprague 1979 stat. nov. Cavalier-Smith 2002 (e.g. Minchinia, Haplosporidium, Urosporidium, Bonamia, Marteilia, Paramyxa, Paramarteilia, Claustrosporidium, Microcytos)
Class 3: GROMIIDEA Cavalier-Smith 2003 (Gromia)
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)
Class 1: ACANTHAREA Haeckel 1881 stat. nov. Cavalier-Smith 1993 (e.g. Acanthometra)
Class 2: STICHOLONCHEA Poche 1913 stat. nov. Petrushevskaya 1977 (Sticholonche)
Class 3: POLYCYSTINEA Ehrenberg 1838 stat. nov. Cavalier-Smith 1993 (e.g. Collozoum)
Subphylum 2: FORAMINIFERA (D'Orbigny 1826) Eichwald 1830 stat. nov. Mikhalevich 1980
Class 1: ATHALAMEA Haeckel, 1862 (Reticulomyxa)
Class 2: POLYTHALAMEA Ehrenberg 1838 stat. nov. Mikhalevich 1980 (e.g. Allogromia, Textularia, Globigerina, Miliola)
Class 3: XENOPHYOPHOREA Schulze 1904 (e.g. Psammina). Possibly also class SCHIZOCLADEA Cedhagen and Mattson 1992 (Schizocladus)
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
Class 1: JAKOBEA Cavalier-Smith 1999 (Reclinomonas, Histiona, Jakoba)
Class 2: MALAWIMONADEA Cavalier-Smith 2003 (Malawimonas)
Phylum 2: METAMONADA Grasse 1952 stat. nov. emend. Cavalier-Smith 2003
Subphylum 1: ANAEROMONADA Cavalier-Smith 1996/7
Class: ANAEROMONADEA Cavalier-Smith 1996/7 emend. 1999 (Trimastix; Oxymonadida e.g. Pyrsonympha, Dinenympha)
Subphylum 2: TRICHOZOA Cavalier-Smith 1996/7 stat. nov. emend. 2003
Superclass 1: PARABASALIA Honigberg 1973 stat. nov. Cavalier-Smith 2003
Class 1: TRICHOMONADEA Kirby 1947 stat. nov. Margulis 1974 emend. Cavalier-Smith 2003 (e.g. Trichomonas, Lophomonas, Microjoenia, Spirotrichonympha)
Class 2: TRICHONYMPHEA Cavalier-Smith 2003 (e.g. Trichonympha)
Superclass 2: CARPEDIEMONADIA Cavalier-Smith 2003
Class: CARPEDIEMONADEA Cavalier-Smith 2003 (Carpediemonas)
Superclass 3: EOPHARYNGIA Cavalier-Smith 1993 stat. nov.
Class 1: TREPOMONADEA Cavalier-Smith 1993
Subclass 1: DIPLOZOA Dangeard 1910 stat. nov. Cavalier-Smith 1996 (diplomonads: Trepomonas, Hexamita, Spironucleus, Giardia, Octomitus)
Subclass 2: ENTEROMONADIA Cavalier-Smith 1996 (Enteromonas)
Class 2: RETORTAMONADEA Cavalier-Smith 1993 (e.g. Retortamonas, Chilomastix)
Superphylum 1: DISCICRISTATA Cavalier-Smith 1993
Phylum 1: PERCOLOZOA Cavalier-Smith 1991 stat. nov.
Class 1: HETEROLOBOSEA Page and Blanton 1985 (e.g. Naegleria, Tetramitus, Vahlkampfia, Lyromonas, Psalteriomonas)
Class 2: PERCOLATEA Cavalier-Smith 2003 (Percolomonas, Stephanopogon)
Phylum 2: EUGLENOZOA Cavalier-Smith 1981 (see: ref. ID; 4898)
Subphylum 1: PLICOSTOMA Cavalier-Smith 1998
Class 1: EUGLENOIDEA Butschli 1884 (e.g. Petalomonas, Peranema, Rhabdomonas, Euglena, Astasia, Eutreptia, Trachelomonas)
Class 2: DIPLONEMEA Cavalier-Smith 1993 (Diplonema, Rhynchopus)
Subphylum 2: SACCOSTOMA Cavalier-Smith 1998
Class 1: KINETOPLASTEA Honinberg 1963 stat. nov. Margulis 1974 (e.g. Bodo, Rhynchomonas, Ichthyobodo, Trypanosoma, Crithidia, Leishmania)
Class 2: POSTGAARDEA Cavalier-Smith 1998 (Postgaardi, Calkinsia)

Infrakingdom ALVEOLATA Cavalier-Smith 1991
Phylum 1: MIOZOA Cavalier-Smith 1987 stat. nov. 1999
Subphylum 1: PROTALVELATA Cavalier-Smith 1991 em.
Class 1: COLPONEMEA Cavalier-Smith 1993 (Colponema)
Class 2: PERKINSEA Levine 1978 (Perkinsus)
Subphylum 2: DINOZOA Cavalier-Smith 1981 em.

Infraphylum 1: ELLOBIOPSA infraph. nov.
Diagnosis as the for class ELLOBIOPSEA
Class: ELLOBIOPSEA Loeblich III 1970 (e.g. Ellobiopsis, Thalassomyces)

Infraphylum 2: DINOFLAGELLATA Butschli 1885 stat. nov. Cavalier-Smith 1999
Superclass 1: SYNDINA Cavalier-Smith 1993
Class: SYNDINEA Chatton 1920 stat. nov. Loeblich 1976 (e.g. Amoebophrya)
Superclass 2: DINOKARYOTA Fensome et al. 1993
Class 1: NOCTILUCEA Haeckel 1866 stat. nov. Cavalier-Smith 1993 (e.g. Noctiluca)
Class 2: PERIDINEA Ehrenberg, 1830 stat. nov. Wettstein (e.g. Peridinium, Prorocentrum, Haplozoon, Dinophysis, Ceratium, Crypthecodinium, Symbiodinium, Polarella, Oxyrrhis)
Subphylum 3: APICOMPLEXA Levine 1970 emend. stat. nov.

Infraphylum 1: APICOMONADA Cavalier-Smith 1993 stat. nov.
Class 1: APICOMONADEA Cavalier-Smith 1993 (e.g. Acrocoelus, Parvilucifera, Colpodella)

Infraphylum 2: SPOROZOA Leuckart 1879 stat. nov. Cavalier-Smith 1999
Class 1: COCCIDEA Leuckart 1879 (e.g. Hepatozoon, Cryptosporidium, Toxoplasma)
Class 2: GREGARINEA Dufour 1828 (e.g. Monocystis, Ophriocystis)
Class 3: HEMATOZOA Vivier 1982 (e.g. Plasmodium, Babesia, Theileria)

Phylum 2: CILIOPHORA Doflein 1901 (ciliates and suctorians) (see: ref. ID; 4926)
Subphylum 1: POSTCILIODESMATOPHORA Gerassimova and Seravin 1976
Class 1: KARYORELICTEA Corliss 1974 (e.g. Kentrophoros, Tracheloraphis, Loxodes)
Class 2: HETEROTRICHEA Stein, 1859 (e.g. Stentor, Folliculina, Blepharisma)
Subphylum 2: INTRAMACORNUCLEATA Lynn, 1996
Class 1: SPIROTRICHEA (e.g. Oxytricha, Euplotes, Tintinnus, Metopus)
Class 2: LITOSTOMATEA (e.g. Didinium, Lacrymaria, Entodinium)
Class 3: PHYLLOPHARYNGEA (e.g. Dysteria, Podophrya)
Class 4: COLPODEA (e.g. Colpoda)
Class 5: NASSOPHOREA (e.g. Nassula)
Class 6: PROSTOMATEA (e.g. Coleps)
Class 7: PLAGIOPHYLEA
Class 8: OLIGOHYMENOPHOREA (e.g. Tetrahymena, Paramecium, Vorticella)

BICILIATA incertae sedes
1. Phylum APUSOZOA Cavalier-Smith 1996/7 stat. nov. 2003 emend.
Class 1: DIPHYLLATEA Cavalier-Smith 2003 (Diphylleia, Collodictyon)
Class 2: THECOMONADEA Cavalier-Smith 1993 stat. nov. 1995 (e.g. Amastigomonas, Apusomonas, Ancyromonas, Hemimastix, Spironema)
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. (see: ref. ID; 7492)
Diagnosis as for class MALAWIMONADEA.

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.


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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