Excavata

This taxon is (or may be) paraphyletic

Superregnum: Eukaryota
Regnum: Protozoa
Subregnum: Eozoa
Infraregnum: Excavata
Phyla: Loukozoa – Metamonada – Percolozoa

Excavata Cavalier-Smith, 2002

• Cavalier-Smith, T. 2003. Protist phylogeny and the high-level classification of Protozoa, Europ. J. Protistol. 39, 338-348.
• Simpson, A.G.B.; Lang, B.F.; Dacks, J.B.; Leigh, J.W.; Hug, L.; Roger, A.J.; Hampl, V. 2009. Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups". PNAS, 106: 3859–3864.

• Excavata in the World Register of Marine Species

Simpson, A. G. B. & Patterson, D. J. 1999. The ultrastructure of Carpediemonas membranifera (Eukaryota) with reference to the excavate hypothesis. Europ. J. Protistol., 35:353-370, [1].

"excavate taxa"

• Heterolobosea
• diplomonads
• retortamonads
• core jakobids (Jakoba, Reclinomonas, Histiona )
• Malawimonas
• Trimastix
• Carpediemonas

Cavalier-Smith, T 2002: The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Syst Evol Microbiol, 52:297-354.

In Kingdom Protozoa, Subkingdom Corticata
Infrakingdom Excavata infraregnum nov.

• Superphylum Loukozoa
  • Phylum Loukozoa
• Superphylum Discicristata
  • Phylum Percolozoa
  • Phylum Euglenozoa
• Superphylum Archezoa
  • Phylum Metamonada
  • Phylum Parabasalia

Cavalier-Smith, T. (2003). The excavate protozoan phyla Metamonada Grassé emend. (Anaeromonadea, Parabasalia, Carpediemonas, Eopharyngia) and Loukozoa emend. (Jakobea, Malawimonas): their evolutionary affinities and new higher taxa. International Journal of Systematic and Evolutionary Microbiology, 53(6), 1741-1758, [2].

• Infrakingdom Excavata
  • Superphylum 1. Eozoa Cavalier-Smith 1996/7 emend. 1999 stat. nov.
    • Phylum 1. Loukozoa* Cavalier-Smith 1999 emend.
      • Class 1. Jakobea Cavalier-Smith 1999 [Once also included Discocelida (Cavalier-Smith, 1997), but molecular data are needed to determine whether this is correct.]
        • Order Jakobida Cavalier-Smith 1993
          • Families Histionidae Flavin & Nerad 1993 (Reclinomonas, Histiona), Jakobidae Patterson 1990 (Jakoba)
      • Class 2. Malawimonadea classis nov.
        • Order Malawimonadida ord. nov. (Malawimonas)
    • Phylum 2. Metamonada Grassé 1952 stat. nov. emend.
      • Subphylum 1. Anaeromonada Cavalier-Smith 1996/7
        • Class Anaeromonadea Cavalier-Smith 1996/7 emend. 1999
          • Order 1. Trimastigida ord. nov. (Trimastix)
          • Order 2. Oxymonadida Grassé 1952 emend. auct. (e.g. Pyrsonympha, Dinenympha)
      • Subphylum 2. Trichozoa Cavalier-Smith 1996/7 stat. nov. emend.
        • Superclass 1. Parabasalia Honigberg 1973 stat. nov.
          • Class 1. Trichomonadea Kirby 1947 stat. nov. Margulis 1974 emend.
            • Order 1. Trichomonadida Kirby 1947 (e.g. Trichomonas, Calonympha)
            • Order 2. Lophomonadida Light 1927 (e.g. Lophomonas, Microjoenia)
            • Order 3. Spirotrichonymphida Grassé 1952 (e.g. Spirotrichonympha, Holomastigoides)
          • Class 2. Trichonymphea classis nov.
            • Order Trichonymphida Poche 1913 (e.g. Trichonympha)
        • Superclass 2. Carpediemonadia superclassis nov.
          • Class Carpediemonadea classis nov.
            • Order Carpediemonadida ord. nov. (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)
              • Order 1. Distomatida Klebs 1892 (Trepomonas, Hexamita, Spironucleus)
              • Order 2. Giardiida Cavalier-Smith 1996 (Giardia, Octomitus)
            • Subclass 2. Enteromonadia (enteromonads) Cavalier-Smith 1996
              • Order Enteromonadida Brugerolle 1975 stat. nov. Cavalier-Smith 1993 (Enteromonas)
          • Class 2. Retortamonadea Cavalier-Smith 1993
            • Order Retortamonadida Grassé 1952 (e.g. Retortamonas, Chilomastix)
  • Superphylum 2. Discicristata Cavalier-Smith 1993
    • Phylum 1. Percolozoa Cavalier-Smith 1991
      • Class 1. Heterolobosea Page & Blanton 1985
        • Order 1. Schizopyrenida Singh 1952 (e.g. Naegleria, Tetramitus, Vahlkampfia)
        • Order 2. Acrasida Shröter 1886 emend. Page & Blanton 1985 (e.g. Acrasis)
        • Order 3. Lyromonadida Cavalier-Smith 1993 (Lyromonas, Psalteriomonas)
      • Class 2. Percolatea classis nov.
        • Order 1. Percolomonadida Cavalier-Smith 1993 (Percolomonas)
        • Order 2. Pseudociliatida Corliss & Lipscomb 1982 (Stephanopogon)
    • Phylum 2. Euglenozoa Cavalier-Smith 1981
      • Subphylum 1. Plicostoma Cavalier-Smith 1998
        • Class 1. Euglenoidea Bütschli 1884
          • Order 1. Petalomonadida Cavalier-Smith 1993 (bacteria-eaters, e.g. Petalomonas, Calycimonas)
          • Order 2. Peranemida Bütschli 1884 (eukaryote-eaters with complex vane/rod ingestion apparatus, e.g. Peranema, Entosiphon)
          • Order 3. Rhabdomonadida Leedale 1967 emend. (saprotrophs, e.g. Menoidium, Rhabdomonas, Distigma)
          • Order 4. Euglenida Bütschli 1884 (plastid-bearing, mostly photosynthetic, e.g. Euglena, Astasia, Eutreptia, Phacus, Trachelomonas)
        • Class 2. Diplonemea Cavalier-Smith 1993
          • Order Diplonemida Cavalier-Smith 1993 (Diplonema, Rhynchopus)
      • Subphylum 2. Saccostoma Cavalier-Smith 1998
        • Class 1. Kinetoplastea Honigberg 1963 stat. nov. Margulis 1974
          • Order 1. Bodonida* Hollande 1952 (e.g. Bodo, Rhynchomonas, Cryptobia, Dimastigella, Ichthyobodo, Trypanoplasma)
          • Order 2. Trypanosomatida Kent 1880 stat. nov. Hollande 1952 (e.g. Trypanosoma, Crithidia, Leishmania, Herpetomonas)
        • Class 2. Postgaardea Cavalier-Smith 1998
          • Order Postgaardida ord. nov. Diagnosis: mitochondria without kinetoplast or cristae (Postgaardi, Calkinsia)
• Protozoa incertae sedis
  • Phylum Apusozoa Cavalier-Smith 1996/7 stat nov. 2003 emend.
    • Class 1. Diphyllatea classis nov.
      • Order Diphylleida Cavalier-Smith 1993 (Diphylleia, Collodictyon)
    • Class 2. Thecomonadea Cavalier-Smith 1993 stat. nov. 1995
      • Order 1. Apusomonadida Karpov & Mylnikov 1989 (Amastigomonas, Apusomonas)
      • Order 2. Ancyromonadida Cavalier-Smith 1998 (Ancyromonas)
      • Order 3. Hemimastigida Foissner, Blatterer & Foissner 1988 (e.g. Hemimastix, Spironema)

[*Probably paraphyletic.]

Simpson A.G.B. 2003: Cytoskeletal organization, phylogenetic affinities, and systematics in the contentious taxon Excavata (Eukaryota). Int J Syst Evol Micr 53: 1759–1777, [3].

In Eukaryota

• Clade Excavata
  • Preaxostyla
    • Oxymonadida
    • Trimastix
  • Malawimonas
  • Fornicata
    • Carpediemonas
    • Eopharyngia
      • Retortamonadida
      • Diplomonadida
  • Parabasalia
  • Jakobida
  • Heterolobosea
  • Euglenozoa

• Adl, S.M., Simpson, A.G.B., Lane, C.E., Lukeš, J., Bass, D., Bowser, S.S., Brown, M.W., Burki, F., Dunthorn, M., Hampl, V., Heiss, A., Hoppenrath, M., Lara, E., Le Gall, L., Lynn, D.H., McManus, H., Mitchell, E.A.D., Mozley-Stanridge, S.E., Parfrey, L.W., Pawlowski, J., Rueckert, S., Shadwick, L., Schoch, C.L., Smirnow, A. & Spiegel, F.W. 2012. The revised classification of eukaryotes. Journal of Eukaryotic Microbiology 59(5): 429–514. DOI: 10.1111/j.1550-7408.2012.00644.x . [Erratum: 60(3): 321. DOI: 10.1111/jeu.12033 .] Reference page. 

Eukaryota

• Excavata Cavalier-Smith 2002, emend. Simpson 2003
  • Metamonada Cavalier-Smith 1987 (= Metamonadina Grassé 1952), emend. Cavalier-Smith 2003
    • Fornicata Simpson 2003
      • Diplomonadida Wenyon 1926, emend. Brugerolle et al. 1975
        • Hexamitinae Kent 1880, emend. Brugerolle et al. 1975
          • Enteromonas, Hexamita, Spironucleus, Trepomonas, Trimitus
        • Giardiinae Kulda and Nohýnková 1978
          • Giardia, Octomitus
      • Retortamonadida Grassé 1952
        • Chilomastix, Retortamonas
      • ‘Carpediemonas-like organisms’ (Kolísko et al. 2010) (P)
        • Carpediemonas, Dysnectes, Ergobibamus, Hicanonectes, Kipferlia
    • Parabasalia Honigberg 1973
      • Trichomonadea Kirby 1947, sensu Margulis 1974, emend. Čepička et al. 2010 (P?)
        • Hexamastix, Pentatrichomonas, Pseudotrichomonas, Tricercomitus, Trichomonas
      • Hypotrichomonadea Čepička et al. 2010
        • Hypotrichomonas, Trichomitus
      • Tritrichomonadea Čepička et al. 2010 (P?)
        • Dientamoeba, Histomonas, Monocercomonas, Tritrichomonas
      • Cristamonadea Brugerolle & Patterson 2001, sensu Čepička et al. 2010
        • Coronympha, Deltotrichonympha, Devescovina, Foaina, Joenia, Mixotricha
      • Trichonymphea Poche 1913, sensu Cavalier-Smith 2003
        • Barbulanympha, Hoplonympha, Staurojoenia [Staurojoenina], Trichonympha
      • Spirotrichonymphea Grassé 1952, sensu Čepička et al. 2010
        • Holomastigotes, Holomastigotoides, Microjoenia, Spirotrichonympha
    • Preaxostyla Simpson 2003
      • Oxymonadida Grassé 1952
        • Dinenympha, Monocercomonoides, Oxymonas, Polymastix, Pyrsonympha, Saccinobaculus, Streblomastix
      • Trimastix Kent 1880
  • Malawimonas O’Kelly & Nerad 1999
  • Discoba Simpson in Hampl et al. 2009 (R)
    • Jakobida Cavalier-Smith 1993, emend. Adl et al. 2005
      • Jakoba Patterson 1990 (M)
      • Histionidae Flavin & Nerad 1993
        • Histiona, Reclinomonas
        • Incertae sedis Histionidae: Stenocodon, Stomatochone
      • Andalucia Lara et al. 2006
      • Incertae sedis Jakobida: Seculamonas nomen nudum
    • Discicristata Cavalier-Smith 1998
      • Heterolobosea Page & Blanton 1985
        • Pharyngomonadidae Cavalier-Smith in Cavalier-Smith & Nikolaev 2008
          • Pharyngomonas
        • Tetramitia Cavalier-Smith 1993, emend. Cavalier-Smith in Cavalier-Smith & Nikolaev 2008 (= Vahlkampfiidae Jollos 1917)
          • Acrasis, Heteramoeba, Naegleria, Percolomonas, Pocheina, Psalteriomonas, Stephanopogon, Tetramitus, Vahlkampfia
      • Euglenozoa Cavalier-Smith 1981, emend. Simpson 1997
        • Euglenida Bütschli 1884, emend. Simpson 1997
          • Heteronematina Leedale 1967 (P)
            • Anisonema, Dinema, Entosiphon, Heteronema, Lentomonas, Metanema, Notosolenus, Peranema, Petalomonas, Ploeotia
            • [Alternative classification of Heteronematina:
              • Ploeotiida (Ploeotia, Entosiphon, Lentomonas, ?Keelungia)
              • Petalomonadida (Petalomonas, Notosolenus, Calycimonas, ?Sphenomonas)]
          • Euglenophyceae Schoenichen 1925, emend. Marin & Melkonian 2003 (= Euglenea Bütschli 1884, emend. Busse & Preisfeld 2002)
            • Rapaza Yamaguchi et al. 2012 (M)
            • Eutreptiales Leedale 1967, emend. Marin & Melkonian 2003
              • Eutreptia, Eutreptiella
            • Euglenea Bütschli 1884, emend. Busse & Preisfeld 2002 [emend. Adl et al. 2012?] (= Euglenales Leedale 1967, emend. Marin & Melkonian 2003)
              • Phacaceae Kim et al. 2010
                • Discoplastis, Lepocinclis, Phacus
              • Euglenaceae Dujardin 1841, emend. Kim et al. 2010
                • Ascoglena, Colacium, Cryptoglena, Cyclidiopsis, Euglena, Euglenaria, Euglenopsis, Monomorphina, Strombomonas, Trachelomonas
          • Aphagea Cavalier-Smith 1993, emend. Busse & Preisfeld 2002
            • Astasia sensu stricto, Distigma, Distigmopsis, Menoidium, Rhabdomonas
        • Diplonemea Cavalier-Smith 1993, emend. Simpson 1997
          • Diplonema, Rhynchopus
        • Symbiontida Yubuki et al. 2009
          • Bihospites, Calkinsia, Postgaardi
        • Kinetoplastea Honigberg 1963
          • Prokinetoplastina Vickerman in Moreira et al. 2004 (R)
            • Ichthyobodo, Perkinsela
          • Metakinetoplastina Vickerman in Moreira et al. 2004 (R)
            • Neobodonida Vickerman in Moreira et al. 2004 (R)
              • Node: Cruzella, Dimastigella, Neobodo, Rhynchobodo, Rhynchomonas. Other included genera: Actuariola.
            • Parabodonida Vickerman in Moreira et al. 2004 (R)
              • Node: Cryptobia, Parabodo, Procryptobia, Trypanoplasma
            • Eubodonida Vickerman in Moreira et al. 2004 (R)
              • Bodo
            • Trypanosomatida Kent 1880, emend. Vickerman in Moreira et al. 2004
              • Node: Blastocrithidia, Crithidia, Herpetomonas, Leishmania, Leptomonas, Phytomonas, Rhynchoidomonas, Trypanosoma, Wallaceina. Other included genera: Angomonas, Sergeia, Strigomonas.
          • Incertae sedis Kinetoplastea: Bordnamonas, Cephalothamnium, Hemistasia
    • Tsukubamonas Yabuki et al. 2011

[Notes: M, monotypic group with only one described species; P, paraphyletic group; R, ribogroup assembled from phylogenetic studies.]

Ruggiero, M.A., Gordon, D.P., Orrell, T.M., Bailly, N., Bourgoin, T., Brusca, R.C., Cavalier-Smith, T., Guiry, M. D. & Kirk, P. M. (2015). A Higher Level Classification of All Living Organisms. PLoS ONE 10(4): e0119248, [4].

• Superkingdom Prokaryota
  • Kingdom Archaea [= Archaebacteria]
  • Kingdom Bacteria [= Eubacteria]
• Superkingdom Eukaryota
  • Kingdom Protozoa
    • Subkingdom Eozoa
      • Infrakingdom Euglenozoa
      • Infrakingdom Excavata
        • Phylum Loukozoa
          • Subphylum Eolouka
            • Class Jakobea
              • Order Jakobida
            • Class Tsukubea
              • Order Tsukubamonadida
          • Subphylum Neolouka
            • Class Malawimonadea
              • Order Malawimonadida
        • Phylum Metamonada
          • Class Anaeromonadea
            • Order Oxymonadida
            • Order Trimastigida
          • Class Carpomonadea
            • Order Carpediemonadida
            • Order Chilomastigida
            • Order Dysnectida
          • Class Eopharyngea
            • Order Diplomonadida
            • Order Retortamonadida
          • Class Trichomonadea
            • Order Cristamonadida
            • Order Spirotrichonymphida
            • Order Trichomonadida
            • Order Tritrichomonadida
          • Class Trichonymphea
            • Order Lophomonadida
            • Order Trichonymphida
        • Phylum Percolozoa
          • Subphylum Pharyngomonada
            • Class Pharyngomonadea
              • Order Pharyngomonadida
          • Subphylum Tetramitia
            • Class Heterolobosea
              • Order Acrasida
              • Order Schizopyrenida
            • Class Lyromonadea
              • Order Lyromonadida
            • Class Percolatea
              • Order Percolomonadida
              • Order Pseudociliatida
    • Subkingdom Sarcomastigota
      • Phylum Amoebozoa
      • Phylum Choanozoa [with Microsporidia, Animalia, and Fungi constitutes "Supergroup Opisthokonta"]
      • Phylum Microsporidia [with Choanozoa, Animalia, and Fungi constitutes "Supergroup Opisthokonta"]
      • Phylum Sulcozoa
  • Kingdom Chromista
    • Subkingdom Hacrobia
    • Subkingdom Harosa [= "Supergroup SAR"]
      • Infrakingdom Halvaria
        • Superphylum Alveolata
        • Superphylum Heterokonta [= "Supergroup Stramenopiles"]
      • Infrakingdom Rhizaria
  • Kingdom Fungi
  • Kingdom Plantae [= Archaeplastida]
  • Kingdom Animalia