Excavata

TaxonavigationEdit

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

NameEdit

Excavata Cavalier-Smith, 2002

Vernacular namesEdit

English: Excavate
français: Excavates, excavés
中文: 古虫下界

ReferencesEdit

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.

LinksEdit

Excavata in the World Register of Marine Species

Alternative classificationsEdit

Simpson & Patterson (1999)Edit

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 (2002)Edit

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 (2003)Edit

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 (2003)Edit

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 et al. (2012)Edit

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., Smirnov, A. and Spiegel, F. W. (2012), The Revised Classification of Eukaryotes. Journal of Eukaryotic Microbiology, 59: 429–514. doi: 10.1111/j.1550-7408.2012.00644.x, [4].

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 et al. (2015)Edit

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, [5].

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