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Excavata
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{{short description|Supergroup of unicellular organisms belonging to the domain Eukaryota}}{{Automatic taxobox|Euglenozoa|EuglenaTrypanosoma|Many important parasites, one large group with plastids (chloroplasts)|Neolouka|Malawimonas|||Ancyromonadida|||
Neoproterozoic|present}}| taxon = ExcavataThomas Cavalier-Smith>Cavalier-Smith), 2002| image = Giardia lamblia.jpg| image_caption = Giardia lamblia, a parasitic diplomonad| subdivision_ranks = Phyla| subdivision = }}File:Excavata cell schemes.svg|thumb|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: MetamonadaMetamonadaExcavata is a major supergroup of unicellular organisms belonging to the domain Eukaryota.JOURNAL, Hampl, V., Hug, L., Leigh, J. W., Dacks, J. B., Lang, B. F., Simpson, A. G. B., Roger, A. J., Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups", Proceedings of the National Academy of Sciences, 2009, 106, 10, 3859–3864, 10.1073/pnas.0807880106, 19237557, 2656170, 2009PNAS..106.3859H, JOURNAL, Hampl V, Hug L, Leigh JW, Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups", Proc. Natl. Acad. Sci. U.S.A., 106, 10, 3859–64, 2009, 19237557, 10.1073/pnas.0807880106, 2656170, 2009PNAS..106.3859H, etal, JOURNAL, 10.1093/molbev/msj068, 2006, Simpson, Ag, Inagaki, Y, Roger, Aj, Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes, 23, 3, 615–25, 16308337, Molecular Biology and Evolution,weblink Free full text, 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, including Giardia and Trichomonas.BOOK, The Ancestor's Tale, 978-0544859937, Richard Dawkins, Dawkins, Richard, Wong, Yan, 2016, The Ancestor's Tale, Excavates were formerly considered to be included in the now obsolete Protista kingdom.JOURNAL, Cavalier-Smith, T, The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa., International Journal of Systematic and Evolutionary Microbiology, 2002, 52, 2, 297–354, 10.1099/00207713-52-2-297, 11931142, They are classified based on their flagellar structures,JOURNAL, Simpson, AG, Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota), International Journal of Systematic and Evolutionary Microbiology, 2003, 53, Pt 6, 1759–1777, 10.1099/ijs.0.02578-0, 14657103, and they are considered to be the most basal Flagellate lineage.JOURNAL, Dawson, Scott C, Paredez, Alexander R, Alternative cytoskeletal landscapes: cytoskeletal novelty and evolution in basal excavate protists, Current Opinion in Cell Biology, 2013, 25, 1, 134–141, 10.1016/j.ceb.2012.11.005, 23312067, 4927265, Except for Euglenozoa, they are all non-photosynthetic.

Characteristics

Most excavates are unicellular, heterotrophic flagellates. Only the Euglenozoa are photosynthetic. In some (particularly anaerobic intestinal parasites), the mitochondria have been greatly reduced. They often 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 flagellaJOURNAL, Simpson AG, Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota), Int. J. Syst. Evol. Microbiol., 53, Pt 6, 1759–77, 2003, 14657103, 10.1099/ijs.0.02578-0,weblink {{Dead link|date=August 2019 |bot=InternetArchiveBot |fix-attempted=yes }} 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).JOURNAL, Simpson, A. G. B., Patterson, D. J., The ultrastructure of Carpediemonas membranifera (Eukaryota) with reference to the 'excavate hypothesis', Eur J Protistol, 1999, 35, 4, 353–370, 10.1016/s0932-4739(99)80044-3, However, various groups that lack these traits may be considered excavates based on genetic evidence (primarily phylogenetic trees of molecular sequences).The Acrasidae slime molds are the only excavates to exhibit limited multicellularity. Like other cellular slime molds, they live most of their life as single cells, but will sometimes assemble into larger clusters.

Classification

{{See also|Eukaryote#Phylogeny|wikispecies:Excavata}}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.{| class=wikitable! Kingdom/Superphylum !! Phylum/Class !! Representative genera (examples) !! Description
Discoba or JEH or EozoaTsukubeaTsukubea''>|
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 PODPreaxostyla 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 >Commensalism>commensals of insects. Some human pathogens.

Discoba or JEH clade

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,JOURNAL, Toward Resolving the Eukaryotic Tree: The Phylogenetic Positions of Jakobids and Cercozoans, Naiara Rodríguez-Ezpeleta, Henner Brinkmann, Gertraud Burger, Andrew J. Roger, Michael W. Gray, Hervé Philippe, B. Franz Lang, yes, 10.1016/j.cub.2007.07.036, Curr. Biol., 2007, 17, 16, 1420–1425, 17689961, 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.

Metamonads

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

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 there seem to be several clades within the excavates that are monophyletic.JOURNAL, Evaluating Support for the Current Classification of Eukaryotic Diversity, Laura Wegener Parfrey, Erika Barbero, Elyse Lasser, Micah Dunthorn, Debashish Bhattacharya, David J Patterson, Laura A Katz, 10.1371/journal.pgen.0020220, PLoS Genet., 2006, 2, 12, e220, 17194223, 1713255, 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

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.

Cladogram

Here is a proposed cladogram for the positioning of the Excavata, with the Eukaryote root in the excavates, mainly following Cavalier-Smith.JOURNAL, 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, 10.1016/j.ympev.2016.03.023, 27001604, JOURNAL, 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, en, 112, 7, E693–E699, 10.1073/pnas.1420657112, 0027-8424, 4343179, 25646484, 2015PNAS..112E.693D, JOURNAL, 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, 10.1016/j.ympev.2014.08.012, 25152275, Cavalier-Smith, T., JOURNAL, Cavalier-Smith, Thomas, 2010-06-23, Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree, Biology Letters, en, 6, 3, 342–345, 10.1098/rsbl.2009.0948, 1744-9561, 2880060, 20031978, JOURNAL, He, Ding, Fiz-Palacios, Omar, Fu, Cheng-Jie, Fehling, Johanna, Tsai, Chun-Chieh, Baldauf, Sandra L., An Alternative Root for the Eukaryote Tree of Life, Current Biology, 24, 4, 465–470, 10.1016/j.cub.2014.01.036, 24508168, 2014, 1996CBio....6.1213A, JOURNAL, Cavelier Smith, 2013, Early evolution of eukaryote feeding modes, cell structural diversity, and classification of the protozoan phyla Loukozoa, Sulcozoa, and Choanozoa, European Journal of Protistology, 115–178, 10.1016/j.ejop.2012.06.001, 23085100, 49, 2, JOURNAL, 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, en, 1, 5, 10.1038/nmicrobiol.2016.48, 27572647, 2058-5276, 16048, JOURNAL, 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, en, 297–357, 10.1007/s00709-017-1147-3, 28875267, 5756292, 0033-183X, 255, 1, JOURNAL, Cavalier-Smith, Thomas, 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, 10.1016/j.ejop.2017.09.002, 29073503, 61, Pt A, 2017, 137–179, {hide}clade|{{Clade
|1=Tsukubea
|2={{Clade
|label1=Discicristata
|1={{Clade
|1=Euglenozoa
|2=Percolozoa
{edih}
|label2=Orthokaryotes
|2={hide}Clade
|1=Jakobea
|label2=Neokaryotes
|2={{Clade
|label1=Scotokaryotes/|sublabel1=Opimoda/Neozoa
|1={{Clade
|state1=dashed
|1=Metamonada
|2={{Clade
|state1=dashed
|1=Malawimonas
|label2=Sulcozoa/Podiata/|sublabel2=Sarcomastigota
|2={{Clade
|1=Planomonadida
|2={{Clade
|1=CRuMs

|label2=Amorphea/
|sublabel2=Unikont
|2={{Clade
|1=Amoebozoa
|label2=Obazoa
|2={{Clade

|1=Breviata
|2={{Clade
|1=Apusomonadida
|2=Opisthokonta/Choanozoa
{edih}}}}}}}}}}}}}
|label2=Corticata/
|sublabel2=Bikont/Diaphoretickes
|2={{Clade
|1=Archaeplastida
|label2=Chromista
|2={{Clade
|1=Hacrobia
|2=SAR}}}}}}}}}}
}}|label1=Eukaryota|style=font-size:80%;line-height:80%}}In this view, excavata is highly paraphyletic, and is proposed to be abandoned.JOURNAL, Cavalier-Smith, Thomas, 2016-10-01, Higher classification and phylogeny of Euglenozoa, European Journal of Protistology, 56, 250–276, 10.1016/j.ejop.2016.09.003, 27889663, In alternative view, the Discoba are sister to the rest of the Diphoda.JOURNAL, 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, en, 4, 1, 4641, 10.1038/srep04641, 24717814, 3982174, 2045-2322, 2014NatSR...4E4641Y, {hide}clade|{{Clade
|label1=Opimoda
|1={{Clade
|state1=dashed
|1=Metamonada
|2={{Clade
|state1=dashed
|1=Malawimonas
|label2=Podiata
|2={{Clade

|1=CRuMs
|label2=Amorphea
|2={{Clade
|1=Amoebozoa
|label2=Obazoa
|2={{Clade
|1=Breviata
|2={{Clade
|1=Apusomonadida
|2=Opisthokonta{edih}}}}}}}}}}}
|label2=Diphoda
|2={{Clade
|label1=Discoba
|1={{Clade
|1=Jakobea
|2={{Clade
|1=Tsukubea
|label2=Discicristata
|2={{Clade
|1=Heterolobosa
|2=Euglenozoa
}}
}}
}}
|2={{Clade
|1={{Clade
|1=Archaeplastida
|2=Cryptomonadida}}
|2={{Clade
|state1=dashed
|1=Haptophyta
|2=SAR}}}}
}}}}|label1=Eukaryota|style1=font-size:80%;line-height:80%}}

Gallery

File:Two Euglena.jpg|Euglena (Euglenozoa: Euglenoida)File:TrypanosomaBrucei ProcyclicTrypomastigote SEM.jpg|Trypanosoma brucei (Euglenozoa: Kinetoplastida)File:Bodo_saltans_-_400x_(13895749563).jpg|Bodo sp. (Euglenozoa: Kinetoplastida)File:Percolomonas_sp.jpg|Percolomonas sp. (Percolozoa)File:Stephanopogon_sp.jpg|Stephanopogon sp. (Percolozoa)File:Naegleria_(formes).png|Stages of Naegleria sp. (Percolozoa: Heterolobosea)File:Acrasis_rosea_31095.jpg|Acrasis rosea (Percolozoa: Heterolobosea)File:Jakobida.svg|Jakobids (Jakobida)File:Trichomonas Giemsa DPDx.JPG|Trichomonas vaginalis (Metamonada: Parabasalia)File:Metamonada_retortamonas_hexamita_giardia.svg|Retortamonas sp., left (Metamonada: Fornicata: Retortamonadida)File:Giardia_1.jpg|Giardia sp. (Metamonada: Fornicata: Diplomonadida)

References

{{Reflist|30em}}

External links

{{Excavata}}{{Protozoal diseases}}{{Life}}{{Taxonbar|from=Q691551}}

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