Diatomea

Girdle view of Corethron criophilum, copyright Wendy Kozlowski.

Belongs within: Ochrophyta.
Contains: Rhizosoleniaceae, Achnanthes, Cocconeis, Surirellaceae, Auliscus, Stephanodiscus, Eucentricophycidae, Actinodiscaceae, Melosiraceae, Bacillariophyceae, Mediophyceae.

The Diatomea, diatoms, are a group of mostly photosynthetic protists with a cell wall composed of a pair of siliceous valves.

Characters (from Adl et al. 2012): Vegetative cells cylindrical with a circular, elongate or multipolar cross-section, lacking any trace of cilia except as the sperm of centric lineages; cell wall complete, composed of tightly integrated silicified elements and comprised of two valves, one at each end of cell, with several girdle bands as hoops or segments covering cylindrical ‘girdle’ lying between valves; chloroplasts usually present, bounded by four membranes, and with lamellae of three thylakoids and a ring nucleoid (rarely multiple nucleoids); ciliated sperm cells bearing a single anterior cilium with a 9 + 0 axoneme and mastigonemes; life cycle diplontic and of unique pattern with slow size reduction over several years during the phase, caused by an unusual internal wall morphogenesis, alternating with rapid size restitution via a growth phase (auxospore) over several days.

<==Diatomea [Araphidineae, Bacillariophyta, Centricophyceae, Coscinophytina, Diatomeae, Discineae, Pennales] AS12
    |--+--Corethron [Corethrales, Corethrophycidae] C-SC06
    |  |    |--C. criophilum C-SC06
    |  |    `--C. valdiviae B26
    |  `--+--Eucentricophycidae C-SC06
    |     `--Actinodiscaceae C-SC06
    `--+--+--Aulacoseira distans C-SC06
       |  `--Melosiraceae C-SC06
       `--Bacillariophytina AS12
            |--Bacillariophyceae C-SC06
            `--Mediophyceae C-SC06

Diatomea incertae sedis:
  Rhizosoleniaceae RA05
  Streptotheca thamensis KI02
  Detonula DG01
    |--D. confervacea DG01
    `--D. cystifera B26
  Planothidium quadripunctatum (Oppenheim) Sabbe in Sabbe, Verleyen et al. 2003 (see below for synonymy) SV03
  Nanofrustulum shiloi (Lee, Reimer & McEnery) Round, Hallenstein & Paasche 1999 (see below for synonymy) SV03
  Sellaphora seminulum [=Navicula seminulum] SV03
  Chamaepinnularia krookii [=Pinnularia krookii] SV03
  Achnanthidium SV03
    |--A. kryophilum SV03
    |--A. lanceolatum TaJ06
    |--A. minutissimum TaJ06
    |--A. oblongella ThJ06
    `--A. reidensis TaJ06
  Eucocconeis austriaca [=Achnanthes austriaca] SV03
  Pseudostaurosira perminuta SV03
  Staurophora (nom. cons.) C03
  Alveus marinus P98
  Dictyopyxis Ehrenberg 1844 FT93
  Stauroforma SV03
    |--S. exiguiformis SV03
    `--S. inermis Flower, Jones & Round 1996 SV03
  Muelleria SV03
    |--M. gibbula [=Navicula gibbula] SV03
    `--M. peraustralis (West & West) Spaulding & Stoermer 1997 SV03
  Luticola SV03
    |--L. murrayi (West & West) Mann 1990 SV03
    |--L. muticopsis (van Heurck) Mann 1990 SV03
    `--L. palaearctica SV03
  Craspedostauros SV03
    |--C. britannicus SV03
    |--C. indubitabilis SV03
    `--C. laevissimus (West & West) Sabbe in Sabbe, Verleyen et al. 2003 (see below for synonymy) SV03
  Diadesmis SV03
    |--D. arcuata SV03
    |--D. contenta [=Navicula contenta] SV03
    |--D. gallica Smith 1857 SV03
    |--D. implicata SV03
    `--D. perpusilla (Grunow) Mann 1990 [=Navicula gallica var. perpusilla] SV03
  Achnanthaceae [Achnanthoideae, Monoraphidineae] W61b
    |--Achnanthes SV03
    |--Cocconeis W61b
    |--Campyloneis Grun. 1862 W61b
    |    `--C. grevillei (Smith) Grun. 1868 [=Cocconeis grevillei Smith 1853] W61a
    `--Rhoicosphenia Grunow 1860 W61b
         |--R. curvata (Kützing) Grun. 1860 [=Gomphonema curvatum Kützing 1844] W61a
         |--R. flexa Giffen 1970 G75
         `--R. marina [=R. curvata f. marina] G75
  Psammothidium SV03
    |--P. abundans (Manguin) Bukhtiyarova & Round 1996 SV03
    |--P. chlidanos SV03
    |--P. daonense SV03
    |--P. germainii (Manguin) Sabbe in Sabbe, Verleyen et al. 2003 [=Achnanthes germainii] SV03
    |--P. helveticum SV03
    |--P. marginulatum SV03
    |--P. metakryophilum (Lange-Bertalot & Schmidt) Sabbe in Sabbe, Verleyen et al. 2003 (see below for synonymy) SV03
    |--P. stauroneioides (Manguin) Bukhtiyarova 1996 [=P. stauroneioideum (l. c.)] SV03
    `--P. subatomoides SV03
  Brachysira ThJ06
    |--B. aponina TaJ06
    `--B. brebissonii ThJ06
  Camphylodiscus clypeus TaJ06
    |--C. c. var. clypeus TaJ06
    `--C. c. var. bicostata TaJ06
  Ctenophora pulchella TaJ06
  Entomoneis TaJ06
    |--E. alata TaJ06
    `--E. tenuistriata TaJ06
  Fallacia pygmaea TaJ06
  Surirellaceae W61b
  Tabularia tabulata TaJ06
  Tryblionella hungarica TaJ06
  Campylosira Grunow 1882 G75
    `--C. inane Giffen 1975 G75
  Anorthoneis Grunow 1867 G75
    `--A. eurystoma Cleve 1895 G75
  Odentella [Eupodiscaceae] RA05
    `--O. mobiliensis [=Biddulphia mobiliensis] RA05
  Auliscus W61b
  Eunotogramma Weisse 1854 G75
    |--E. marinum [=Smithiella marina] G75
    |--E. rostratum Hustedt 1955 G75
    `--E. weissii Ehr. 1854 CW59
         |--E. w. var. weissii CW59
         `--E. w. var. producta CW59
  Glyphodesmis Greville 1862 G75
    |--G. distans G75
    `--G. marginata CW59
  Opephora Petit 1888 G75
    |--O. gemmata (Grunow) Hustedt 1927-1964 G75
    |--O. martyi G75
    |--O. pacifica G75
    `--O. schwartzii G75
  Plagiotropis vitrea UPS98
  Cylindrotheca signata UPS98
  Scolioneis tumida UPS98
  Coscinosira polychorda B26
  Paralia sulcata B26
  Bacteriosira fragilis B26
  Cerataulina bergonii B26
  Leptocylindrus [Leptocylindraceae] RA05
    `--L. danicus RA05
  Stephanodiscus T92
  Anaulus Ehr. 1844 CW59
    `--A. mediterraneus CW59
  Rutilaria CW59
    |--R. epsilon Grev. 1863 CW59
    |--R. lanceolata CW59
    |--R. monile [=Pseudorutilaria monile] CW59
    |--R. pulchra A.S. 1893 CW59
    `--R. radiata CW59
  Stictodesmis Grev. 1863 CW59
    `--S. australis Grev. 1863 CW59
  Toxonidea Donk. 1858 CW59
    `--T. falcata Donk. 1858 CW59
  Denticella regia H04
  Asterolampra eximia H04
  Pyrgodiscus armatus H04
  Asteromphalus imbricatus H04
  Grovea pedalis H04
  Gephyria constricta H04
  Amphithetras elegans H04
  Arachnoidiscus AS12

Craspedostauros laevissimus (West & West) Sabbe in Sabbe, Verleyen et al. 2003 [=Tropidoneis laevissima West & West 1911] SV03

Nanofrustulum shiloi (Lee, Reimer & McEnery) Round, Hallenstein & Paasche 1999 [=Fragilaria shiloi Lee, Reimer & McEnery 1980, Pseudostaurosira shiloi (Lee, Reimer & McEnery) Hallegraeff & Burford 1996; incl. Opephora krumbeinii Witkowski, Witak & Stachura 1999, Fragilaria sopotensis Witkowski 1994] SV03

Planothidium quadripunctatum (Oppenheim) Sabbe in Sabbe, Verleyen et al. 2003 [=Achnanthes quadripunctata Oppenheim 1994] SV03

Psammothidium metakryophilum (Lange-Bertalot & Schmidt) Sabbe in Sabbe, Verleyen et al. 2003 [=Achnanthes metakryophila Lange-Bertalot & Schmidt in Schmidt et al. 1990] SV03

*Type species of generic name indicated

REFERENCES

[AS12] Adl, S. M., A. G. B. Simpson, C. E. Lane, J. Lukeš, D. Bass, S. S. Bowser, M. W. Brown, F. Burki, M. Dunthorn, V. Hampl, A. Heiss, M. Hoppenrath, E. Lara, E. Le Gall, D. H. Lynn, H. McManus, E. A. D. Mitchell, S. E. Mozley-Stanridge, L. W. Parfrey, J. Pawlowski, S. Rueckert, L. Shadwick, C. L. Schoch, A. Smirnov & F. W. Spiegel. 2012. The revised classification of eukaryotes. Journal of Eukaryotic Microbiology 59 (5): 429–493.

[B26] Bigelow, H. B. 1926. Plankton of the offshore waters of the Gulf of Maine. Bulletin of the Bureau of Fisheries 40 (2): 1–509.

[C-SC06] Cavalier-Smith, T., & E. E.-Y. Chao. 2006. Phylogeny and megasystematics of phagotrophic heterokonts (kingdom Chromista). Journal of Molecular Evolution 62: 388–420.

[C03] Compère, P. 2003. Report of the Committee for Algae: 7. Taxon 52: 339–340.

[CW59] Crosby, L. H., & E. J. F. Wood. 1959. Studies on Australian and New Zealand diatoms. II.—Normally epontic and benthic genera. Transactions of the Royal Society of New Zealand 86 (1): 1–58, pls 51–59.

[DG01] Daugbjerg, N., & L. Guillou. 2001. Phylogenetic analyses of Bolidophyceae (Heterokontophyta) using rbcL gene sequences support their sister group relationship to diatoms. Phycologia 40 (2): 153–161.

[FT93] Fensome, R. A., F. J. R. Taylor, G. Norris, W. A. S. Sarjeant, D. I. Wharton & G. L. Williams. 1993. A classification of living and fossil dinoflagellates. Micropaleontology Special Publication 7: i–viii, 1–351.

[G75] Giffen, M. H. 1975. An account of the littoral diatoms from Langebaan, Saldanha Bay, Cape Province, South Africa. Botanica Marina 18: 71–95.

[H04] Haeckel, E. 1899–1904. Kunstformen der Natur. Bibliographisches Institut: Leipzig und Wien.

[KI02] Kawachi, M., I. Inouye, D. Honda, C. J. O’Kelly, J. C. Bailey, R. R. Bidigare & R. A. Andersen. 2002. The Pinguiophyceae classis nova, a new class of photosynthetic stramenopiles whose members produce large amounts of omega-3 fatty acids. Phycological Research 50: 31–47.

[P98] Prothero, D. R. 1998. Bringing Fossils to Life: An introduction to paleobiology. WCB McGraw-Hill: Boston.

[RA05] Rath, J., & S. P. Adhikary. 2005. A check list of algae from Chilika Lake, Orissa. Bulletin of the Botanical Survey of India 47 (1–4): 101–114.

[SV03] Sabbe, K., E. Verleyen, D. A. Hodgson, K. Vanhoutte & W. Vyverman. 2003. Benthic diatom flora of freshwater and saline lakes in the Larsemann Hills and Rauer Islands, East Antarctica. Antarctic Science 15 (2): 227–248.

[TaJ06] Taukulis, F. E., & J. John. 2006. Diatoms as ecological indicators in lakes and streams of varying salinity from the wheatbelt region of Western Australia. Journal of the Royal Society of Western Australia 89 (1): 17–25.

[T92] Theriot, E. 1992. Clusters, species concepts, and morphological evolution of diatoms. Systematic Biology 41 (2): 141–157.

[ThJ06] Thomas, E. J., & J. John. 2006. Diatoms and macroinvertebrates as biomonitors of mine-lakes in Collie, Western Australia. Journal of the Royal Society of Western Australia 89 (3): 109–117.

[UPS98] Underwood, G. J. C., J. Phillips & K. Saunders. 1998. Distribution of estuarine benthic diatom species along salinity and nutrient gradients. European Journal of Phycology 33: 173–183.

[W61a] Wood, E. J. F. 1961a. Studies on Australian and New Zealand diatoms. IV.—Descriptions of further sedentary species. Transactions of the Royal Society of New Zealand 88 (4): 669–698.

[W61b] Wood, E. J. F. 1961b. Studies on Australian and New Zealand diatoms. V.—The Rawson Collection of recent diatoms. Transactions of the Royal Society of New Zealand 88 (4): 699–712.

Oodiniaceae

Parasitic trophonts of Oodinium attached to fish skin, from here.

Belongs within: Thoracosphaeraceae.

The Oodiniaceae are a group of dinoflagellates exhibiting an invasive parasitic stage (Fensome et al. 1993).

Characters (from Fensome et al. 1993): Parasitic trophont generally suboval to fusiform in outline, not exhibiting a typical dinoflagellate form; invasive organelle consisting of complex rhizoid-like absorptive structure; amphiesma usually pelliculate, occasionally tabulate. Reproduction by palintomic sporogenesis, with trophont detaching and its cytoplasm retracting from cell wall, dividing to produce numerous dinospores. Chromosomes decondensing during feeding stage, recondensing during palintomic sporogenesis. Cyst stage absent. Plastids occasionally present.

<==Oodiniaceae [Oodinidae]
    |--Crepidoodinium Lom & Lawlor in Lom 1981 FT93
    |--Amyloodinium Brown & Hovasse 1946 FT93
    |    `--A. ocellatum C-SC04
    |--Piscinoodinium Lom 1981 FT93
    |    `--P. pillulare (Schäperclaus 1954) Lom 1981 FT93
    |--Bargoniella Loeblich & Tappan 1961 (see below for synonymy) FT93
    |    `--*B. amylacea FT93 (see below for synonymy)
    `--Oodinium Chatton 1912 [incl. Branchiophilus Schäperclaus 1935] FT93
         |--O. cyprinodinium Lawler 1967 FT93
         |--O. fritillariae Chatton 1912 FT93
         |--O. ocellatum K-M02
         `--O. pouchetii (Lemmermann 1899) Chatton 1912 FT93

Bargoniella Loeblich & Tappan 1961 [=Salpicola Bargoni 1894 non Richiardi 1880 (ICZN)/Bargoni ex Farr et al. 1979 (ICBN)] FT93

*Bargoniella amylacea FT93 [=*Salpicola amylacea Bargoni 1894 LT64, Amyloodinium amylaceum FT93, Oodinium amylaceum (Bargoni) Chatton 1920 FT93]

*Type species of generic name indicated

REFERENCES

[C-SC04] Cavalier-Smith, T., & E. E. Chao. 2004. Protalveolate phylogeny and systematics and the origins of Sporozoa and dinoflagellates (phylum Myzozoa nom. nov.) European Journal of Protistology 40: 185–212.

[FT93] Fensome, R. A., F. J. R. Taylor, G. Norris, W. A. S. Sarjeant, D. I. Wharton & G. L. Williams. 1993. A classification of living and fossil dinoflagellates. Micropaleontology Special Publication 7: i–viii, 1–351.

[K-M02] Klein-MacPhee, G. 2002. Porcupinefishes. Family Diodontidae. In: Collette, B. B., & G. Klein-MacPhee (eds) Bigelow and Schroeder’s Fishes of the Gulf of Maine 3^rd ed. pp. 601–602. Smithsonian Institute Press: Washington.

[LT64] Loeblich, A. R., Jr & H. Tappan. 1964. Sarcodina: chiefly “thecamoebians” and Foraminiferida. In: Moore, R. C. (ed.) Treatise on Invertebrate Paleontology pt C. Protista 2 vol. 1. The Geological Society of America and The University of Kansas Press.

Gromiidae

2 mm individual of Gromia oviformis, copyright Gary McDonald.

Belongs within: Cercozoa.

The Gromiidae are a group of amoeboid protists with an organic test (note that Loeblich & Tappan, 1964, included a number of taxa in Gromiidae that are no longer regarded as closely related to the type genus Gromia; it is possible that other genera listed below are similarly misplaced).

Characters (from Loeblich & Tappan 1964): Test membranous or pseudochitinous, rigid or slightly flexible, without distinct plates or scales, but with some siliceous elements, and commonly with foreign material.

Gromiidae (see below for synonymy)
    |--Micramphoraeopsis Sudzuki 1979 G86
    |    `--M. pinangensis Sudzuki 1979 G86
    |--Amoebogromia Giard 1900 LT64
    |    `--*A. cinnabarina Giard 1900 LT64
    |--Lagunculina Rhumbler 1904 (see below for synonymy) LT64
    |    `--*L. urnula (Gruber 1884) [=*Ovulina urnula, *Arlagunculum urnulum] LT64
    |--Urnulina Gruber 1884 [=Arurnulum Rhumbler 1913] LT64
    |    |--*U. difflugiaeformis Gruber 1884 [=*Arurnulum difflugiaeforme] LT64
    |    `--U. compressa C40
    `--Gromia Dujardin 1835 [incl. Arcellina DuPleiss 1876 non Carter 1856, Hyalopus Schaudinn 1894] LT64
         |--*G. oviformis Dujardin 1835 LT64
         |--G. dujardinii Schultze 1854 [=*Hyalopus dujardinii] LT64
         |--G. fluvialis Dujardin 1837 [=Allogromia fluvialis] LT64
         |--‘*Arcellina’ marina DuPleiss 1876 LT64
         `--G. sphaerica C-SCL15

Gromiidae [Gromiacea, Gromiada, Gromidae, Gromiida, Gromiidea, Gromiina, Gromiinae, Grominae, Nuditestiidae, Pseudogromiinae]

Lagunculina Rhumbler 1904 [=Arlagunculum Rhumbler 1913, Ovulina Gruber 1884 nec Ehrenberg 1845 nec Schultze 1854] LT64

*Type species of generic name indicated

REFERENCES

[C-SCL15] Cavalier-Smith, T., E. E. Chao & R. Lewis. 2015. Multiple origins of Heliozoa from flagellate ancestors: new cryptist subphylum Corbihelia, superclass Corbistoma, and monophyly of Haptista, Cryptista, Hacrobia and Chromista. Molecular Phylogenetics and Evolution 93: 331–362.

[C40] Cushman, J. A. 1940. Foraminifera: Their classification and economic use 3^rd ed. Harvard University Press: Cambridge (Massachusetts).

[G86] Golemansky, V. G. 1986. Rhizopoda: Testacea. In: Botosaneanu, L. (ed.) Stygofauna Mundi: A Faunistic, Distributional, and Ecological Synthesis of the World Fauna inhabiting Subterranean Waters (including the Marine Interstitial) pp. 5–16. E. J. Brill/Dr. W. Backhuys: Leiden.

[LT64] Loeblich, A. R., Jr & H. Tappan. 1964. Sarcodina: chiefly “thecamoebians” and Foraminiferida. In: Moore, R. C. (ed.) Treatise on Invertebrate Paleontology pt C. Protista 2 vol. 1. The Geological Society of America and The University of Kansas Press.

Labyrinthulomycetes

Vegetative cells of Thraustochytrium, copyright Celeste Leander.

Belongs within: Heterokonta.

The Labyrinthulomycetes, slime nets, are a group of mostly aquatic protists producing a network of anastomosing filaments.

See also: Slime nets: another group of not-fungi; Return of the slime-nets.

Characters (from Adl et al. 2012): Producing an ectoplasmic network of branched, anastomosing, wall-less filaments via a specialized organelle known as the bothrosome; Golgi-derived scales; biciliate zoospores with lateral insertion in many species.

Labyrinthulomycetes (see below for synonymy)
    |--+--‘Thraustochytrium’ multirudimentale C-SC06
    |  `--Schizochytrium minutum C-SC06
    `--+--+--Labyrinthula Cienkowski 1867 C-SC06, AS12 [Labyrinthulaceae]
       |  `--+--Aplanochytrium kerguelense C-SC06
       |     |--Diplophrys Barker 1868 C-SC06, LT64 [Diplophryidae]
       |     |    |--*D. archeri Barker 1868 LT64
       |     |    `--D. marina C-SC06
       |     `--Labyrinthuloides C-SC06
       |          |--L. minuta [=Labyrinthula minuta] AC97
       |          |--L. saliens AC97
       |          |--L. schizochytrops AC97
       |          `--L. yorkensis AC97
       `--Thraustochytrium C-SC06
            |  i. s.: T. kinnei MNI02
            |--T. pachydermum C-SC06
            `--+--T. aggregatum C-SC06
               `--+--T. striatum C-SC06
                  `--Ulkenia C-SC06
                       |  i. s.: U. profunda MNI02
                       |--+--U. visurgensis C-SC06
                       |  `--Japonochytrium C-SC06
                       `--+--‘Labyrinthuloides’ haliotidis C-SC06
                          `--+--U. radiata C-SC06
                             `--‘Thraustochytrium’ aureum C-SC06

Labyrinthulomycetes incertae sedis:
  Sorodiplophrys C-S98
  Althornia AC97
  Elnia AS12
  Amphitremidae [Amphitrematidae, Amphitreminae] AS12
    |--Paramphitrema Valkanov 1970 G86
    |    `--P. pontica Valkanov 1970 G86
    |--Amphitrema Archer 1867 LT64
    |    `--*A. wrightianum Archer 1869 LT64
    `--Archerella Loeblich & Tappan 1961 (see below for synonymy) LT64
         `--*A. flavum (Archer 1877) [=*Ditrema flavum] LT64

Archerella Loeblich & Tappan 1961 [=Ditrema Archer 1877 non Temminck & Schlegel in von Siebold 1844] LT64

Labyrinthulomycetes [Labyrinthista, Labyrinthulales, Labyrinthulea, Labyrinthulia, Labyrinthulida, Labyrinthulidae, Labyrinthulomorpha, Labyrinthulomycota, Thraustochytriaceae, Thraustochytriales, Thraustochytridae]

*Type species of generic name indicated

REFERENCES

[AS12] Adl, S. M., A. G. B. Simpson, C. E. Lane, J. Lukeš, D. Bass, S. S. Bowser, M. W. Brown, F. Burki, M. Dunthorn, V. Hampl, A. Heiss, M. Hoppenrath, E. Lara, E. Le Gall, D. H. Lynn, H. McManus, E. A. D. Mitchell, S. E. Mozley-Stanridge, L. W. Parfrey, J. Pawlowski, S. Rueckert, L. Shadwick, C. L. Schoch, A. Smirnov & F. W. Spiegel. 2012. The revised classification of eukaryotes. Journal of Eukaryotic Microbiology 59 (5): 429–493.

[AC97] Azevedo, C., & L. Corral. 1997. Some ultrastructural observations of a thraustochytrid (Protoctista, Labyrinthulomycota) from the clam Ruditapes decussatus (Mollusca, Bivalvia). Diseases of Aquatic Organisms 31: 73–78.

[C-S98] Cavalier-Smith, T. 1998. A revised six-kingdom system of life. Biological Reviews 73: 203–266.

[C-SC06] Cavalier-Smith, T., & E. E.-Y. Chao. 2006. Phylogeny and megasystematics of phagotrophic heterokonts (kingdom Chromista). Journal of Molecular Evolution 62: 388–420.

[G86] Golemansky, V. G. 1986. Rhizopoda: Testacea. In: Botosaneanu, L. (ed.) Stygofauna Mundi: A Faunistic, Distributional, and Ecological Synthesis of the World Fauna inhabiting Subterranean Waters (including the Marine Interstitial) pp. 5–16. E. J. Brill/Dr. W. Backhuys: Leiden.

[LT64] Loeblich, A. R., Jr & H. Tappan. 1964. Sarcodina: chiefly “thecamoebians” and Foraminiferida. In: Moore, R. C. (ed.) Treatise on Invertebrate Paleontology pt C. Protista 2 vol. 1. The Geological Society of America and The University of Kansas Press.

[MNI02] Moriya, M., T. Nakayama & I. Inouye. 2002. A new class of the stramenopiles, Placididea classis nova: description of Placidia cafeteriopsis gen. et sp. nov. Protist 153: 143–156.

Thecofilosea

Difflugiella oviformis, copyright Ralf Meisterfeld.

Belongs within: Monadofilosa.
Contains: Ebriacea, Phaeodarea.

The Thecofilosea are a lineage of mostly amoeboid protists, ancestrally with a robust extracellular theca (Adl et al. 2012).

Characters (from Adl et al. 2012): Usually with robust organic extracellular theca; ventral filose pseudopodia emerging from ventral groove; two cilia with divergent kinetosomes, may be secondarily lost or restricted to zoospores; ancestrally benthic gliding on posterior cilium only, but some secondarily planktonic swimmers which may have lost pseudopodia; theca with perforations for cilia and for pseudopodia; silica scales absent, but hollow silica endoskeleton sometimes present.

Thecofilosea
    |  i. s.: Ventricleftida AS12
    |           |--Ventrifissura AS12
    |           `--Verrucomonas AS12
    |         Ebriacea AS12
    |         Botuliforma AS12
    |         Mataza AS12
    |--Cryomonadida BM05
    |    |--Cryothecomonadidae [Protaspidae] BM05
    |    |    |--Cryothecomonas BM05
    |    |    |    |--C. aestivalis BM05
    |    |    |    `--C. longipes BM05
    |    |    `--Protaspa AS12 [incl. Protaspis Skuja 1939 (preoc. ICZN) AS12, C-S93]
    |    |         |--‘Protaspis’ glans Skuja 1939 S73
    |    |         `--‘Protaspis’ tanyopsis Norris 1961 S73
    |    `--Rhizaspididae AS12
    |         |--Rhizaspis Skuja 1948 C-S93
    |         `--Rhogostoma Bělař 1921 AS12, LT64
    |              `--*R. schuessleri Bělař 1921 [=Capsellina schuessleri] LT64
    `--Tectofilosida BM05
         |  i. s.: Volutellidae AS12
         |           |--Volutella Sudzuki 1979 C-SC03, G86
         |           |    `--V. cochlea Sudzuki 1979 G86
         |           `--Pseudovolutella Sudzuki 1979 AS12, G86
         |                `--P. iriomotensis Sudzuki 1979 G86
         |--Pseudodifflugiidae [Pseudodifflugiinae] C-SC03
         |    |--Pseudowailesella Sudzuki 1979 G86
         |    |    `--P. japonica Sudzuki 1979 G86
         |    |--Petalopella Loeblich & Tappan 1961 (see below for synonymy) LT64
         |    |    `--*P. diffluens (Claparède & Lachmann 1859) [=*Petalopus diffluens] LT64
         |    |--Pseudodifflugia Schlumberger 1845 G86
         |    |    |--*P. gracilis Schlumberger 1845 LT64 [incl. P. gracilis var. terricola LB90]
         |    |    `--P. andreevi Golemansky 1976 G86
         |    `--Difflugiella Cash 1904 G86
         |         |--*D. apiculata Cash 1904 LT64
         |         |--D. collum Chardez 1971 G86
         |         |--D. lamingerae Chardez 1977 G86
         |         |--D. oviformis [incl. D. oviformis var. fusca] LB90
         |         `--D. psammophila Golemansky 1970 G86
         `--+--Chlamydophryidae NB04
            |    |--Chlamydophrys Cienkowski 1876 LT64 [Chlamydophryinae]
            |    |    `--*C. stercorea Cienkowski 1876 LT64
            |    |--Capsellina Penard 1909 AS12, LT64
            |    |    `--*C. bryorum Penard 1909 LT64
            |    |--Lecythium Hertwig & Lesser 1874 AS12, LT64 (see below for synonymy)
            |    |    |--*L. hyalinum (Ehrenberg 1838) (see below for synonymy) LT64
            |    |    |--‘*Pamphagus’ mutabilis Bailey 1853 [=*Baileya mutabilis] LT64
            |    |    |--‘*Phonergates’ vorax Buck 1878 LT64
            |    |    `--‘*Troglodytes’ zoster Gabriel 1876 LT64
            |    |--Clypeolina Penard 1902 AS12, LT64
            |    |    `--*C. marginata Penard 1902 LT64
            |    |--Diaphorodon Archer 1869 AS12, LT64
            |    |    `--*D. mobile Archer 1869 LT64
            |    |--Leptochlamydophrys AS12
            |    `--Penardeugenia Deflandre in Deflandre-Rigaud 1958 AS12, LT64 (see below for synonymy)
            |         `--*P. bathybiotica (Penard 1904) [=Pamphagus bathybioticus, *Eugenia bathybiotica] LT64
            `--Phaeodarea NB04

Lecythium Hertwig & Lesser 1874 AS12, LT64 [incl. Baileya Averintsev in Schouteden 1906 LT64, Pamphagus Bailey 1853 non Thunberg 1815 LT64, Phonergates Buck 1878 non Stål 1853 LT64, Troglodytes Gabriel 1876 nec Vieillot 1807 nec Geoffroy 1812 LT64]

*Lecythium hyalinum (Ehrenberg 1838) [=Arcella hyalina, Pamphagus hyalinus; incl. Plagiophrys spherica] LT64

Penardeugenia Deflandre in Deflandre-Rigaud 1958 AS12, LT64 [=Eugenia Averintsev 1906 nec Gould 1855 nec Martens 1860 nec Robineau-Desvoidy 1863 nec Hall 1867 LT64]

Petalopella Loeblich & Tappan 1961 [=Petalopus Claparède & Lachmann 1859 nec Kirby & Spence 1828 nec Motschoulsky 1845] LT64

*Type species of generic name indicated

REFERENCES

[AS12] Adl, S. M., A. G. B. Simpson, C. E. Lane, J. Lukeš, D. Bass, S. S. Bowser, M. W. Brown, F. Burki, M. Dunthorn, V. Hampl, A. Heiss, M. Hoppenrath, E. Lara, E. Le Gall, D. H. Lynn, H. McManus, E. A. D. Mitchell, S. E. Mozley-Stanridge, L. W. Parfrey, J. Pawlowski, S. Rueckert, L. Shadwick, C. L. Schoch, A. Smirnov & F. W. Spiegel. 2012. The revised classification of eukaryotes. Journal of Eukaryotic Microbiology 59 (5): 429–493.

[BM05] Bass, D., D. Moreira, P. López-García, S. Polet, E. E. Chao, S. von der Heyden, J. Pawlowski & T. Cavalier-Smith. 2005. Polyubiquitin insertions and the phylogeny of Cercozoa and Rhizaria. Protist 156: 149–161.

[C-S93] Cavalier-Smith, T. 1993. The protozoan phylum Opalozoa. Journal of Eukaryotic Microbiology 40 (5): 609–615.

[C-SC03] Cavalier-Smith, T., & E. E.-Y. Chao. 2003. Phylogeny and classification of phylum Cercozoa. Protist 154: 341–358.

[G86] Golemansky, V. G. 1986. Rhizopoda: Testacea. In: Botosaneanu, L. (ed.) Stygofauna Mundi: A Faunistic, Distributional, and Ecological Synthesis of the World Fauna inhabiting Subterranean Waters (including the Marine Interstitial) pp. 5–16. E. J. Brill/Dr. W. Backhuys: Leiden.

[LT64] Loeblich, A. R., Jr & H. Tappan. 1964. Sarcodina: chiefly “thecamoebians” and Foraminiferida. In: Moore, R. C. (ed.) Treatise on Invertebrate Paleontology pt C. Protista 2 vol. 1. The Geological Society of America and The University of Kansas Press.

[LB90] Lousier, J. D., & S. S. Bamforth. 1990. Soil protozoa. In: Dindal, D. L. (ed.) Soil Biology Guide pp. 97–136. John Wiley & Sones: New York.

[NB04] Nikolaev, S. I., C. Berney, J. F. Fahrni, I. Bolivar, S. Polet, A. P. Mylnikov, V. V. Aleshin, N. B. Petrov & J. Pawlowski. 2004. The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proceedings of the National Academy of Sciences of the USA 101 (21): 8066–8071.

[S73] Sournia, A. 1973. Catalogue des espèces et taxons infraspécifiques de Dinoflagellés marins actuels publiés depuis la révision de J. Schiller. I. Dinoflagellés libres. Beihefte zur Nova Hedwigia 48: 1–92.

Granofilosea

Hedriocystis pellucida, copyright Proyecto Agua.

Belongs within: Cercozoa.

The Granofilosea are a group of amoeboid protists bearing granular reticulopodia.

Characters (from Adl et al. 2012): With very fine branching or unbranched granuloreticulopodia bearing obvious extrusomes as granules at frequent rather regular intervals, or with radiating, sometimes branched, axopodia with similar granules; pseudopodia supported by internal microtubules and typically appressed to substratum during feeding, in semi-immobile state; pseudopodia usually not anastomosing; occasionally with biciliated swimming or gliding stage.

Granofilosea [Proteomyxidea]
    |  i. s.: Pseudosporidae [Pseudosporida] C-SC03b
    |           |--Pseudospora Cienkowski 1865 C-S93
    |           |--Protomonas G00
    |           |--Pseudosporopsis G00
    |           `--Barbetia G00
    |         Limnofila borokensis AS12, C-SCL15
    |         Mesofila AS12
    |         Minimassisteria diva AS12, C-SCL15
    |         Nanofila AS12
    |--+--Leucodictyida C-SC03b
    |  |    |--Massisteria Patterson & Fenchel 1990 C-S93 [Massisteriidae C-SC03b]
    |  |    |    `--M. marina M00b
    |  |    `--Leucodictyidae C-SC03b
    |  |         |--Leucodictyon Grell 1991 C-S93
    |  |         `--Reticulamoeba C-SC03b
    |  `--Gymnophryidae [Araudia, Biomyxida, Gymnophrea, Reticulosida] C-SC03b
    |       |--Gymnophrys cometa NB04
    |       |--Borkovia desaedeleeri C-SC03b, M00a
    |       `--Biomyxa Leidy 1875 C-SC03b, LT64 [Biomyxidae]
    |            `--*B. vagans Leidy 1875 LT64
    `--+--Gymnosphaerida C-SC03a
       |    |--Actinocoryne contractilis M00b
       |    |--Gymnosphaera M00b
       |    `--Hedraiophrys AS12
       `--Clathrulinidae [Desmothoracida] AS12
            |--Clathrulina elegans BM05
            |--Hedriocystis BM05
            |    |--H. pellucida M00b
            |    |--H. reticulata BM05
            |    `--H. spinifera NB04
            |--Cienkowskia AS12
            `--Servetia AS12

*Type species of generic name indicated

REFERENCES

[AS12] Adl, S. M., A. G. B. Simpson, C. E. Lane, J. Lukeš, D. Bass, S. S. Bowser, M. W. Brown, F. Burki, M. Dunthorn, V. Hampl, A. Heiss, M. Hoppenrath, E. Lara, E. Le Gall, D. H. Lynn, H. McManus, E. A. D. Mitchell, S. E. Mozley-Stanridge, L. W. Parfrey, J. Pawlowski, S. Rueckert, L. Shadwick, C. L. Schoch, A. Smirnov & F. W. Spiegel. 2012. The revised classification of eukaryotes. Journal of Eukaryotic Microbiology 59 (5): 429–493.

[BM05] Bass, D., D. Moreira, P. López-García, S. Polet, E. E. Chao, S. von der Heyden, J. Pawlowski & T. Cavalier-Smith. 2005. Polyubiquitin insertions and the phylogeny of Cercozoa and Rhizaria. Protist 156: 149–161.

[C-S93] Cavalier-Smith, T. 1993. The protozoan phylum Opalozoa. Journal of Eukaryotic Microbiology 40 (5): 609–615.

[C-SC03a] Cavalier-Smith, T., & E. E.-Y. Chao. 2003a. Molecular phylogeny of centrohelid heliozoa, a novel lineage of bikont eukaryotes that arose by ciliary loss. Journal of Molecular Evolution 56: 387–396.

[C-SC03b] Cavalier-Smith, T., & E. E.-Y. Chao. 2003b. Phylogeny and classification of phylum Cercozoa. Protist 154: 341–358.

[C-SCL15] Cavalier-Smith, T., E. E. Chao & R. Lewis. 2015. Multiple origins of Heliozoa from flagellate ancestors: new cryptist subphylum Corbihelia, superclass Corbistoma, and monophyly of Haptista, Cryptista, Hacrobia and Chromista. Molecular Phylogenetics and Evolution 93: 331–362.

[G00] Gromov, B. V. 2000. Algal parasites of the genera Aphelidium, Amoeboaphelidium, and Pseudaphelidium from Cienkovski’s “Monadinea” group as representatives of a new class. Zoologicheskii Zhurnal 79 (5): 517–525 (transl. Entomological Review 80 (Suppl. 1): S26–S34).

[LT64] Loeblich, A. R., Jr & H. Tappan. 1964. Sarcodina: chiefly “thecamoebians” and Foraminiferida. In: Moore, R. C. (ed.) Treatise on Invertebrate Paleontology pt C. Protista 2 vol. 1. The Geological Society of America and The University of Kansas Press.

[M00a] Mikrjukov, K. A. 2000a. Taxonomy and phylogeny of Heliozoa: Should this taxon exist in modern classification of Protista? Zoologicheskii Zhurnal 79 (8): 883–897 (transl. Entomological Review 80 (Suppl. 1): S35–S50).

[M00b] Mikrjukov, K. A. 2000b. Taxonomy and phylogeny of Heliozoa. II. The order Dimorphida Siemensma, 1991 (Cercomonadea classis n.): diversity and relatedness with cercomonads. Acta Protozoologica 39: 99–115.

[NB04] Nikolaev, S. I., C. Berney, J. F. Fahrni, I. Bolivar, S. Polet, A. P. Mylnikov, V. V. Aleshin, N. B. Petrov & J. Pawlowski. 2004. The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proceedings of the National Academy of Sciences of the USA 101 (21): 8066–8071.

Euglyphida

Cyphoderia ampulla, copyright Picturepest.

Belongs within: Monadofilosa.
Contains: Psammonobiotidae, Euglyphidae.

The Euglyphida are a group of testate amoeboids, often with a covering of silica scales (Adl et al. 2012).

Characters (from Adl et al. 2012): Test of organic material; usually with secreted silica scales held together by organic cement; tubular mitochondrial cristae.

Euglyphida [Euglyphacea]
    |  i. s.: Deharvengia AS12
    |         Matsakision AS12
    |         Psammonobiotidae AS12
    |--+--Paulinellidae AS12
    |  |    |--Paulinella Lauterborn 1895 BM05, MM05 [incl. Cyanospira Chodat 1920 LT64; Paulinellinae]
    |  |    |    |--*P. chromatophora Lauterborn 1895 MM05
    |  |    |    |--‘*Cyanospira’ aeruginosa Chodat 1920 LT64
    |  |    |    `--P. ovalis MM05
    |  |    `--Ovulinata AS12
    |  `--Cyphoderiidae [Revolventiidae] N03
    |       |--Messemvriella Golemansky 1973 N03, G86
    |       |    `--M. filosa Golemansky 1973 G86
    |       |--Pseudocyphoderia Sudzuki 1979 G86
    |       |    `--P. orientalis Sudzuki 1979 G86
    |       |--Corythionella Golemansky 1970 N03, G86
    |       |    |--C. acolla Golemansky 1970 G86
    |       |    |--C. anteroplanata Chardez 1977 G86
    |       |    |--C. minima Golemansky 1970 [incl. C. minima var. nipponica Sudzuki 1979] G86
    |       |    |--C. pontica Golemansky 1970 G86
    |       |    `--C. sudzukii Chardez 1977 G86
    |       |--Pseudocorythion Valkanov 1970 N03, G86
    |       |    |--P. acutum (Wailes 1927) [incl. P. acutum var. nipponicum Sudzuki 1979] G86
    |       |    |--P. mannei Chardez 1971 G86
    |       |    |--P. nipponicum Sudzuki 1976 G86
    |       |    |--P. undulacollis Chardez & Thomas 1980 G86
    |       |    `--P. wailesi Golemansky 1971 G86
    |       |--Cyphoderia Schlumberger 1845 G86 (see below for synonymy)
    |       |    |--C. ampulla (Ehrenberg 1840) (see below for synonymy) LT64
    |       |    |    |--C. a. ampulla N03
    |       |    |    `--C. a. bicornis N03
    |       |    |--C. compressa Golemansky 1979 G86
    |       |    |--C. laevis N03
    |       |    |--‘Difflugia’ lagena Ehrenberg 1843 [=*Allodictya lagena, D. (Reticella) lagena] LT64
    |       |    |--C. littoralis Golemansky 1973 [incl. C. littoralis var. simodensis Sudzuki 1979] G86
    |       |    `--C. lunata Štĕpánek 1967 N03
    |       `--Schaudinnula Averintsev 1906 AS12, LT64
    |            `--*S. arcelloides Averintsev 1906 [=Cyphoderia arcelloides] LT64
    `--+--Tracheleuglypha Deflandre 1928 C-SC03, LT64
       |    |--*T. dentata (Vejdovský 1882) [=Euglypha dentata] LT64
       |    `--T. acolla LNB03
       `--+--Assulinidae AS12
          |    |--Assulina Ehrenberg 1872 C-SC03, LT64
          |    |    |--*A. seminulum (Ehrenberg 1848) [=Difflugia seminulum, Sphenoderia seminulum] LT64
          |    |    `--A. muscorum C-SC03
          |    |--Placocista Leidy 1879 AS12, LT64 [=Placocysta Blochmann 1886 LT64]
          |    |    `--*P. spinosa (Carter 1865) [=Euglypha spinosa, *Placocysta spinosa] LT64
          |    `--Valkanovia AS12
          `--+--Trinematidae [Trinematinae, Trinemidae, Trineminae] LT64
             |    |--Corythion Taránek 1882 LT64
             |    |    |--*C. dubium Taránek 1882 LT64
             |    |    `--C. delmarei LB90
             |    |--Trinema Dujardin 1841 BM05, LT64 [incl. Homoeochlamys Ehrenberg 1872 LT64]
             |    |    |--T. enchelys (Ehrenberg 1838) (see below for synonymy) LT64
             |    |    |--T. complanatum [incl. T. complanatum var. inaequalis] LNB03
             |    |    `--T. lineare G86
             |    |--Playfairina AS12
             |    `--Puytoracia AS12
             `--+--Trachelocorythion pulchellum C-SC03
                `--Euglyphidae BM05

Cyphoderia Schlumberger 1845 G86 [incl. Allodictya Ehrenberg 1872 LT64, Ampullaria Werneck in Ehrenberg 1872 non Lamarck 1799 LT64]

Cyphoderia ampulla (Ehrenberg 1840) [=Difflugia ampulla, *Ampullaria ampulla; incl. *Cyphoderia margaritacea Schlumberger 1845] LT64

‘Difflugia’ laevigata Ehrenberg 1842 [=*Crossopyxis laevigata, D. (Exassula) laevigata] LT64

Trinema enchelys (Ehrenberg 1838) [=Difflugia enchelys, Arcella (*Homoeochlamys) enchelys; incl. *Trinema acinus Dujardin 1841] LT64

*Type species of generic name indicated

REFERENCES

[AS12] Adl, S. M., A. G. B. Simpson, C. E. Lane, J. Lukeš, D. Bass, S. S. Bowser, M. W. Brown, F. Burki, M. Dunthorn, V. Hampl, A. Heiss, M. Hoppenrath, E. Lara, E. Le Gall, D. H. Lynn, H. McManus, E. A. D. Mitchell, S. E. Mozley-Stanridge, L. W. Parfrey, J. Pawlowski, S. Rueckert, L. Shadwick, C. L. Schoch, A. Smirnov & F. W. Spiegel. 2012. The revised classification of eukaryotes. Journal of Eukaryotic Microbiology 59 (5): 429–493.

[BM05] Bass, D., D. Moreira, P. López-García, S. Polet, E. E. Chao, S. von der Heyden, J. Pawlowski & T. Cavalier-Smith. 2005. Polyubiquitin insertions and the phylogeny of Cercozoa and Rhizaria. Protist 156: 149–161.

[C-SC03] Cavalier-Smith, T., & E. E.-Y. Chao. 2003. Phylogeny and classification of phylum Cercozoa. Protist 154: 341–358.

[G86] Golemansky, V. G. 1986. Rhizopoda: Testacea. In: Botosaneanu, L. (ed.) Stygofauna Mundi: A Faunistic, Distributional, and Ecological Synthesis of the World Fauna inhabiting Subterranean Waters (including the Marine Interstitial) pp. 5–16. E. J. Brill/Dr. W. Backhuys: Leiden.

[LNB03] Ledeganck, P., I. Nijs & L. Beyens. 2003. Plant functional group diversity promotes soil protist diversity. Protist 154 (2): 239–249.

[LT64] Loeblich, A. R., Jr & H. Tappan. 1964. Sarcodina: chiefly “thecamoebians” and Foraminiferida. In: Moore, R. C. (ed.) Treatise on Invertebrate Paleontology pt C. Protista 2 vol. 1. The Geological Society of America and The University of Kansas Press.

[LB90] Lousier, J. D., & S. S. Bamforth. 1990. Soil protozoa. In: Dindal, D. L. (ed.) Soil Biology Guide pp. 97–136. John Wiley & Sones: New York.

[MM05] Melkonian, M., & D. Mollenhauer. 2005. Robert Lauterborn (1869–1952) and his Paulinella chromatophora. Protist 156: 253–262.

[N03] Nicholls, K. H. 2003. Form variation in Campascus minutus and a description of Campascus simcoei sp. n. (Testaceafilosea, Psammonobiotidae). European Journal of Protistology 39 (1): 103–112.