Excavata

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Excavata
Temporal range: Neoproterozoic–present
Giardia lamblia.jpg
Giardia lamblia, a parasitic diplomonad
Scientific classification e
Domain: Eukaryota
(unranked): Excavata
(Cavalier-Smith), 2002
Phyla
Three types of excavate cells. Top: Jakobida, 1-nucleus, 2-anterior flagellum, 3-ventral/posterior flagellum, 4-ventral feeding groove. Middle: Euglenozoa, 1-nucleus, 2-flagellar pocket/reservoir, 3-dorsal/anterior flagellum, 4-ventral/posterior flagellum, 5-cytostome/feeding apparatus. Bottom: Metamonada, 1-anterior flagella, 2-parabasal body, 3-undulating membrane, 4-posterior flagellum, 5-nucleus, 6-axostyle.

Excavata is a major supergroup of unicellular organisms belonging to the domain Eukaryota.[1][2][3] Introduced by Thomas Cavalier-Smith in 2002 as a new phylogenetic category, it contains a variety of free-living and symbiotic forms, and also includes some important parasites of humans. Excavates were formerly considered to be included in the now obsolete Protista kingdom.[4] They are classified based on their flagellar structures,[5] and they are considered to be the most basal Flagellate lineage.[6]

The Discobaean excavata (Euglenozoa, Percolozoa, Tsukubea, Jakobea) now appear to be basal Eukaryotes, while the Metamonadaean and Malawimonaen excavata now appear to be sister clades of the Podiata. The Discoba may be highly paraphyletic.[7]

Characteristics[edit]

Many excavates lack "classical" mitochondria—these organisms are often referred to as "amitochondriate", although most retain a mitochondrial organelle in greatly modified form (e.g. a hydrogenosome or mitosome). Among those with mitochondria, the mitochondrial cristae may be tubular, discoidal, or in some cases, laminar. Most excavates have two, four, or more flagella[8] and many have a conspicuous ventral feeding groove with a characteristic ultrastructure, supported by microtubules (with the term "excavate" deriving from the organisms showing clear evidence of this "excavated" feeding groove).[9][4] However, various groups that lack these traits may be considered excavates based on genetic evidence (primarily phylogenetic trees of molecular sequences).[4]

The closest that the excavates come to multicellularity are the Acrasidae slime molds. Like other cellular slime molds, they live most of their life as single cells, but will sometimes assemble into a larger cluster.

Classification[edit]

Excavates are classified into six major subdivisions at the phylum/class level. These are shown in the table below. An additional organism, Malawimonas, may also be included amongst excavates, though phylogenetic evidence is equivocal.

Kingdom/Superphylum Phylum/Class Representative genera (examples) Description
Discoba or JEH or Eozoa Tsukubea T. globosa
Euglenozoa EuglenaTrypanosoma Many important parasites, one large group with plastids (chloroplasts)
Heterolobosea (Percolozoa) Naegleria, Acrasis Most alternate between flagellate and amoeboid forms
Jakobea Jakoba, Reclinomonas Free-living, sometimes loricate flagellates, with very gene-rich mitochondrial genomes
Metamonada or POD Preaxostyla Oxymonads, Trimastix Amitochondriate flagellates, either free-living (Trimastix, Paratrimastix) or living in the hindguts of insects
Fornicata Giardia, Carpediemonas Amitochondriate, mostly symbiotes and parasites of animals.
Parabasalia Trichomonas Amitochondriate flagellates, generally intestinal commensals of insects. Some human pathogens.
Neolouka Malawimonas
Ancyromonadida

Discoba or JEH clade[edit]

Euglenozoa and Heterolobosea (Percolozoa) or Eozoa (Cavalier-Smith) appear to be particularly close relatives, and are united by the presence of discoid cristae within the mitochondria (Superphylum Discicristata). More recently a close relationship has been shown between Discicristata and Jakobida,[10] the latter having tubular cristae like most other protists, and hence were united under the taxon name Discoba, which was proposed for this apparently monophyletic group.[2]

Metamonads[edit]

Metamonads are unusual in having lost classical mitochondria—instead they have hydrogenosomes, mitosomes or uncharacterised organelles. The oxymonad Monocercomonoides is reported to have completely lost homologous organelles.

Monophyly[edit]

Excavate relationships are still uncertain; it is possible that they are not a monophyletic group. The monophyly of the excavates is far from clear, although it seems like there are several clades within the excavates that are monophyletic.[11]

Certain excavates are often considered among the most primitive eukaryotes, based partly on their placement in many evolutionary trees. This could encourage proposals that excavates are a paraphyletic grade that includes the ancestors of other living eukaryotes. However, the placement of certain excavates as 'early branches' may be an analysis artifact caused by long branch attraction, as has been seen with some other groups, for example, microsporidia.

Malawimonas and Ancyromonads[edit]

In addition to the groups mentioned in the table above, the genus Malawimonas and the Ancyromonads are generally considered to be members of Excavata owing to their typical excavate morphology, and phylogenetic affinity to excavate groups in some molecular phylogenies. However, their position among excavates remains elusive.[3]

Cladogram[edit]

Here is a proposed cladogram for the positioning of the Excavata, with the Eukaryote root in the excavates, mainly following Cavalier-Smith.[7][12][13][14][15][16][17][18][19]

Eukaryota

Tsukubea

Discicristata

Euglenozoa

Percolozoa

Orthokaryotes

Jakobea

Neokaryotes
Scotokaryotes/Opimoda/Neozoa

Metamonada

Malawimonas

Sulcozoa/Podiata/

Planomonadida

Mantamonadida

Diphyllatea

Amorphea/

Amoebozoa

Obazoa

Breviata

Apusomonadida

Opisthokonta/Choanozoa

Unikont
Sarcomastigota
Corticata/

Archaeplastida

Chromista

Hacrobia

SAR

Bikont/Diaphoretickes

In this view, excavata is highly paraphyletic, and is proposed to be abandoned.[20] In alternative view, the Discoba are sister to the rest of the Diphoda.[12][21]

Eukaryota
Opimoda

Metamonada

Malawimonas

Podiata

Varisulca

Amorphea

Amoebozoa

Obazoa

Breviata

Apusomonadida

Opisthokonta

Diphoda
Discoba

Jakobea

Tsukubea

Discicristata

Heterolobosa

Euglenozoa

Archaeplastida

Cryptomonadida

Haptophyta

SAR

Gallery[edit]

References[edit]

  1. ^ Hampl, V.; Hug, L.; Leigh, J. W.; Dacks, J. B.; Lang, B. F.; Simpson, A. G. B.; Roger, A. J. (2009). "Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups"". Proceedings of the National Academy of Sciences. 106 (10): 3859–3864. Bibcode:2009PNAS..106.3859H. doi:10.1073/pnas.0807880106. PMC 2656170Freely accessible. PMID 19237557. 
  2. ^ a b Hampl V, Hug L, Leigh JW, et al. (2009). "Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups"". Proc. Natl. Acad. Sci. U.S.A. 106 (10): 3859–64. Bibcode:2009PNAS..106.3859H. doi:10.1073/pnas.0807880106. PMC 2656170Freely accessible. PMID 19237557. 
  3. ^ a b Simpson, Ag; Inagaki, Y; Roger, Aj (2006). "Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes" (Free full text). Molecular Biology and Evolution. 23 (3): 615–25. doi:10.1093/molbev/msj068. PMID 16308337. 
  4. ^ a b c Cavalier-Smith, T (2002). "The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa". International Journal of Systematic and Evolutionary Microbiology. 52 (2): 297–354. doi:10.1099/00207713-52-2-297. PMID 11931142. 
  5. ^ Simpson, AG (2003). "Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota)". International Journal of Systematic and Evolutionary Microbiology. 53 (Pt 6): 1759–1777. doi:10.1099/ijs.0.02578-0. PMID 14657103. 
  6. ^ Dawson, Scott C; Paredez, Alexander R (2013). "Alternative cytoskeletal landscapes: cytoskeletal novelty and evolution in basal excavate protists". Current Opinion in Cell Biology. 25 (1): 134–141. doi:10.1016/j.ceb.2012.11.005. PMC 4927265Freely accessible. PMID 23312067. 
  7. ^ a b Cavalier-Smith, Thomas; Chao, Ema E.; Lewis, Rhodri (2016-06-01). "187-gene phylogeny of protozoan phylum Amoebozoa reveals a new class (Cutosea) of deep-branching, ultrastructurally unique, enveloped marine Lobosa and clarifies amoeba evolution". Molecular Phylogenetics and Evolution. 99: 275–296. doi:10.1016/j.ympev.2016.03.023. 
  8. ^ Simpson AG (2003). "Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota)". Int. J. Syst. Evol. Microbiol. 53 (Pt 6): 1759–77. doi:10.1099/ijs.0.02578-0. PMID 14657103. 
  9. ^ Simpson, A. G. B.; Patterson, D. J. (1999). "The ultrastructure of Carpediemonas membranifera (Eukaryota) with reference to the `excavate hypothesis'". Eur J Protistol. 35: 353–370. doi:10.1016/s0932-4739(99)80044-3. 
  10. ^ Naiara Rodríguez-Ezpeleta; Henner Brinkmann; Gertraud Burger; Andrew J. Roger; Michael W. Gray; Hervé Philippe & B. Franz Lang (2007). "Toward Resolving the Eukaryotic Tree: The Phylogenetic Positions of Jakobids and Cercozoans". Curr. Biol. 17 (16): 1420–1425. doi:10.1016/j.cub.2007.07.036. PMID 17689961. 
  11. ^ Laura Wegener Parfrey; Erika Barbero; Elyse Lasser; Micah Dunthorn; Debashish Bhattacharya; David J Patterson; Laura A Katz (2006). "Evaluating Support for the Current Classification of Eukaryotic Diversity". PLoS Genet. 2 (12): e220. doi:10.1371/journal.pgen.0020220. PMC 1713255Freely accessible. PMID 17194223. 
  12. ^ a b Derelle, Romain; Torruella, Guifré; Klimeš, Vladimír; Brinkmann, Henner; Kim, Eunsoo; Vlček, Čestmír; Lang, B. Franz; Eliáš, Marek (2015-02-17). "Bacterial proteins pinpoint a single eukaryotic root". Proceedings of the National Academy of Sciences. 112 (7): E693–E699. Bibcode:2015PNAS..112E.693D. doi:10.1073/pnas.1420657112. ISSN 0027-8424. PMC 4343179Freely accessible. PMID 25646484. 
  13. ^ Cavalier-Smith, T.; Chao, E. E.; Snell, E. A.; Berney, C.; Fiore-Donno, A. M.; Lewis, R. (2014). "Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa". Molecular Phylogenetics & Evolution. 81: 71–85. doi:10.1016/j.ympev.2014.08.012. 
  14. ^ Cavalier-Smith, Thomas (2010-06-23). "Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree". Biology Letters. 6 (3): 342–345. doi:10.1098/rsbl.2009.0948. ISSN 1744-9561. PMC 2880060Freely accessible. PMID 20031978. 
  15. ^ He, Ding; Fiz-Palacios, Omar; Fu, Cheng-Jie; Fehling, Johanna; Tsai, Chun-Chieh; Baldauf, Sandra L. (2014). "An Alternative Root for the Eukaryote Tree of Life". Current Biology. 24 (4): 465–470. doi:10.1016/j.cub.2014.01.036. 
  16. ^ Cavelier Smith (2013). "Early evolution of eukaryote ...". Elsevier. 49: 115–178. doi:10.1016/j.ejop.2012.06.001. 
  17. ^ Hug, Laura A.; Baker, Brett J.; Anantharaman, Karthik; Brown, Christopher T.; Probst, Alexander J.; Castelle, Cindy J.; Butterfield, Cristina N.; Hernsdorf, Alex W.; Amano, Yuki (2016-04-11). "A new view of the tree of life". Nature Microbiology. 1 (5): 16048. doi:10.1038/nmicrobiol.2016.48. ISSN 2058-5276. 
  18. ^ Cavalier-Smith, Thomas (2017-09-05). "Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences". Protoplasma. 255: 1–61. doi:10.1007/s00709-017-1147-3. ISSN 0033-183X. 
  19. ^ Cavalier-Smith, Thomas (2017). "Euglenoid pellicle morphogenesis and evolution in light of comparative ultrastructure and trypanosomatid biology: semi-conservative microtubule/strip duplication, strip shaping and transformation". European Journal of Protistology. 61: 137–179. doi:10.1016/j.ejop.2017.09.002. 
  20. ^ Cavalier-Smith, Thomas (2016-10-01). "Higher classification and phylogeny of Euglenozoa". European Journal of Protistology. 56: 250–276. doi:10.1016/j.ejop.2016.09.003. 
  21. ^ Yabuki, Akinori; Kamikawa, Ryoma; Ishikawa, Sohta A.; Kolisko, Martin; Kim, Eunsoo; Tanabe, Akifumi S.; Kume, Keitaro; Ishida, Ken-ichiro; Inagki, Yuji (2014-04-10). "Palpitomonas bilix represents a basal cryptist lineage: insight into the character evolution in Cryptista". Scientific Reports. 4 (1). Bibcode:2014NatSR...4E4641Y. doi:10.1038/srep04641. ISSN 2045-2322. 

External links[edit]