View source for Biology:Excavata

{{short description|Supergroup of unicellular organisms belonging to the domain Eukaryota}}{{For|an explanation of very similar terms|Eukaryota}}{{Automatic taxobox
| fossil_range          = {{long fossil range|Neoproterozoic|present}}
| classification_status = obsolete as paraphyletic
| taxon                 = Excavata
| authority             = ([[Biography:Thomas Cavalier-Smith|Cavalier-Smith]]), 2002
| image                 = Giardia lamblia.jpg
| image_caption         = ''[[Biology:Giardia lamblia|Giardia lamblia]]'', a parasitic diplomonad
| subdivision_ranks     = Phyla and classes
| subdivision           = ''see text''
}}

[[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: Metamonada, 1-anterior flagella, 2-parabasal body, 3-undulating membrane, 4-posterior flagellum, 5-nucleus, 6-axostyle.]]

'''Excavata''' is an extensive and diverse but paraphyletic group of unicellular Eukaryota.<ref name="pmid19237557">{{cite journal |last1=Hampl |first1=Vladimir |last2=Hug |first2=Laura |last3=Leigh |first3=Jessica W. |last4=Dacks |first4=Joel B. |last5=Lang |first5=B. Franz |last6=Simpson |first6=Alastair G. B. |last7=Roger |first7=Andrew J. |display-authors=3 |title=Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups" |journal=PNAS |volume=106 |issue=10 |pages=3859–3864 |year=2009 |pmid=19237557 |doi=10.1073/pnas.0807880106 |pmc=2656170 |bibcode=2009PNAS..106.3859H |doi-access=free  }}</ref><ref name=simpson>{{Cite journal |last1=Simpson |first1=Alastair G. B. |last2=Inagaki |first2=Yuji |last3=Roger |first3=Andrew J. |doi=10.1093/molbev/msj068 |year=2006 |title=Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes |volume=23 |issue=3 |pages=615–625 |pmid=16308337 |journal=Molecular Biology and Evolution |doi-access=free  }}</ref> The group was first suggested by Simpson and Patterson in 1999<ref name="Simpson1999">{{Cite journal |date=December 1999 |title=The ultrastructure of Carpediemonas membranifera (Eukaryota) with reference to the 'excavate hypothesis' |journal=European Journal of Protistology |volume=35 |issue=4 |pages=353–370 |doi=10.1016/S0932-4739(99)80044-3 |last1=Simpson |first1=Alastair G.B. |last2=Patterson |first2=David J. }}</ref><ref name="Simpson2003">{{Cite journal |last=Simpson |first=Alastair G. B. |date= November 2003 |title=Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota) |journal=International Journal of Systematic and Evolutionary Microbiology |volume=53 |issue=6 |pages=1759–1777 |doi=10.1099/ijs.0.02578-0 |doi-access=free |pmid=14657103}}</ref> and the name latinized and assigned a rank by [[Biography:Thomas Cavalier-Smith|Thomas Cavalier-Smith]] in 2002. It contains a variety of free-living and symbiotic protists, and includes some important parasites of humans such as ''[[Biology:Giardia|Giardia]]'' and ''[[Biology:Trichomonas|Trichomonas]]''.<ref name="Ancestor">{{cite book |title=The Ancestor's Tale |isbn=978-0544859937 |last1=Dawkins  |first1=Richard |last2=Wong |first2=Yan |year=2016 |title-link=The Ancestor's Tale |publisher=Houghton Mifflin Harcourt |author1-link=Richard Dawkins }}</ref> Excavates were formerly considered to be included in the now obsolete Protista kingdom.<ref name="pmid11931142">{{cite journal|last1=Cavalier-Smith |first1=Thomas |title=The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa.|journal=International Journal of Systematic and Evolutionary Microbiology |year=2002 |volume=52 |issue=2 |pages=297–354 |doi=10.1099/00207713-52-2-297 |pmid=11931142 }}</ref> They were distinguished from other lineages based on electron-microscopic information about how the cells are arranged (they have a distinctive [[Biology:Ultrastructural identity|ultrastructural identity]]).<ref name="Simpson2003" /> They are considered to be a basal [[Biology:Flagellate|flagellate]] lineage.<ref>{{cite journal |last1=Dawson |first1=Scott C. |last2=Paredez |first2=Alexander R. |title=Alternative cytoskeletal landscapes: cytoskeletal novelty and evolution in basal excavate protists|journal=Current Opinion in Cell Biology |year=2013 |volume=25 |issue=1 |pages=134–141 |doi=10.1016/j.ceb.2012.11.005 |pmid=23312067 |pmc=4927265}}</ref> 

On the basis of phylogenomic analyses, the group was shown to contain three widely separated eukaryote groups, the discobids, metamonads, and malawimonads.<ref name="pmid31606140">{{cite journal | last1 = Burki | first1 = Fabien | last2 = Roger | first2 = Andrew J. | last3 = Brown | first3 = Matthew W. | last4 = Simpson | first4 = Alastair G.B. |display-authors=3 | title = The New Tree of Eukaryotes | journal = Trends in Ecology & Evolution | volume = 35 | issue = 1 | pages = 43–55 | date = January 2020 | pmid = 31606140 | doi = 10.1016/j.tree.2019.08.008  | s2cid = 204545629 | doi-access = free }}</ref><ref name = "Brown_2018" /><ref>{{cite journal |last1=Heiss |first1=Aaron A. |last2=Kolisko |first2=Martin |last3=Ekelund |first3=Fleming |last4=Brown |first4=Matthew W. |last5=Roger |first5=Andrew J. |last6=Simpson |first6=Alastair G. B. |display-authors=3 |title=Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes |journal=Royal Society Open Science |date=4 April 2018 |volume=5 |issue=4 |pages=171707 |doi=10.1098/rsos.171707 |pmid=29765641 |pmc=5936906 |bibcode=2018RSOS....571707H }}</ref><ref>{{cite journal |last1=Keeling |first1= Patrick J. |last2=Burki |first2= Fabien |title=Progress towards the Tree of Eukaryotes |journal=Current Biology |date=19 August 2019 |volume=29 |issue=16 |pages=R808–R817 |doi=10.1016/j.cub.2019.07.031 |pmid=31430481 |doi-access=free }}</ref> A current view of the composition of the excavates is given below, indicating that the group is paraphyletic. Except for some [[Biology:Euglenozoa|Euglenozoa]],  all are non-[[Earth:Photosynthesis|photosynthetic]].

==Characteristics==

Most excavates are unicellular, heterotrophic flagellates. Only some [[Biology:Euglenozoa|Euglenozoa]] are photosynthetic. In some (particularly anaerobic intestinal parasites), the mitochondria have been greatly reduced.<ref name=Ancestor/> Some excavates lack "classical" [[Biology:Mitochondria|mitochondria]], and are called "amitochondriate", although most retain a mitochondrial organelle in greatly modified form (e.g. a [[Biology:Hydrogenosome|hydrogenosome]] or [[Biology:Mitosome|mitosome]]). Among those with mitochondria, the mitochondrial [[Biology:Crista|crista]]e may be tubular, discoidal, or in some cases, laminar. Most excavates have two, four, or more [[Biology:Flagellum|flagella]].<ref name="Simpson2003" /> Many have a conspicuous ventral feeding groove with a characteristic [[Physics:Ultrastructure|ultrastructure]], supported by [[Biology:Microtubule|microtubule]]s—the "excavated" appearance of this groove giving the organisms their name.<ref name="Simpson1999" /><ref name="pmid11931142" /> However, various groups that lack these traits are considered to be derived excavates based on genetic evidence (primarily phylogenetic trees of molecular sequences).<ref name="pmid11931142"/>

The [[Biology:Acrasidae|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.

== Proposed group ==

{{anchor|Discoba}}

Excavate relationships were always uncertain, suggesting that they are not a [[Biology:Monophyletic|monophyletic]] group.<ref>{{cite Q|Q21090155|doi-access=free}}</ref> Phylogenetic analyses often do not place malawimonads on the same branch as the other Excavata.<ref>{{Cite journal |last1=Tice |first1=Alexander K. |last2=Žihala |first2=David |last3=Pánek |first3=Tomáš |last4=Jones |first4=Robert E. |last5=Salomaki |first5=Eric D. |last6=Nenarokov |first6=Serafim |last7=Burki |first7=Fabien |last8=Eliáš |first8=Marek |last9=Eme |first9=Laura |last10=Roger |first10=Andrew J. |last11=Rokas |first11=Antonis |last12=Shen |first12=Xing-Xing |last13=Strassert |first13=Jürgen F. H. |last14=Kolísko |first14=Martin |last15=Brown |first15=Matthew W. | display-authors = 3 |date=2021 |title=PhyloFisher: A phylogenomic package for resolving eukaryotic relationships |journal=PLOS Biology |volume=19 |issue=8 |pages=e3001365 |doi=10.1371/journal.pbio.3001365 |pmc=8345874 |pmid=34358228 |doi-access=free }}</ref>

Excavates were thought to include multiple groups: 

{| class=wikitable
! Kingdom/Superphylum !! Included taxa !! Representative genera (examples) !! Description
|-
| rowspan="4" | '''Discoba&nbsp;or&nbsp;JEH or Eozoa'''||Tsukubea||''Tsukubamonas''||
|-
|[[Biology:Euglenozoa|Euglenozoa]]
|''[[Biology:Euglena|Euglena]]'',&nbsp;''[[Biology:Trypanosoma|Trypanosoma]]''
|Many important parasites, one large group with plastids (chloroplasts)
|-
|Heterolobosea&nbsp;(Percolozoa) || ''[[Biology:Naegleria|Naegleria]]'', ''Acrasis'' || Most alternate between flagellate and amoeboid forms
|-
|Jakobea || ''[[Biology:Jakoba|Jakoba]]'', ''[[Biology:Reclinomonas|Reclinomonas]]'' || Free-living, sometimes loricate flagellates, with very gene-rich mitochondrial genomes
|-
|rowspan=4|Metamonada&nbsp;or&nbsp;POD||Preaxostyla || Oxymonads, ''[[Biology:Trimastix|Trimastix]]'' || Amitochondriate flagellates, either free-living (''[[Biology:Trimastix|Trimastix]]'', ''Paratrimastix'') or living in the hindguts of insects
|-
|Fornicata|| ''[[Biology:Giardia|Giardia]]'', ''[[Biology:Carpediemonas|Carpediemonas]]'' || Amitochondriate, mostly symbiotes and parasites of animals.
|-
|Parabasalia|| ''[[Biology:Trichomonas|Trichomonas]]'' || Amitochondriate flagellates, generally intestinal [[Biology:Commensalism|commensals]] of insects. Some human pathogens.
|-
|[[Biology:Anaeramoeba|Anaeramoeba]]|| ''Anaeramoeba ignava'' ||Anaerobic protists with [[Biology:Hydrogenosome|hydrogenosome]]s instead of mitochondria.
|-
|Neolouka
|Malawimonadida|| ''[[Biology:Malawimonas|Malawimonas]]'' 
|
|}

===Discoba or JEH clade===

Euglenozoa and Heterolobosea (Percolozoa) or Eozoa (as named by Cavalier-Smith<ref name="Cavalier-Smith 2009">{{cite journal |last=Cavalier-Smith |first=Thomas |title=Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree |journal=Biology Letters |publisher=The Royal Society |volume=6 |issue=3 |date=23 December 2009 |issn=1744-9561 |doi=10.1098/rsbl.2009.0948 |pages=342–345|pmid=20031978 |pmc=2880060 }}</ref>) appear to be particularly close relatives, and are united by the presence of discoid [[Biology:Crista|crista]]e within the [[Biology:Mitochondrion|mitochondria]] (Superphylum [[Biology:Discicristata|Discicristata]]). A close relationship has been shown between Discicristata and Jakobida,<ref>{{cite journal |title=Toward Resolving the Eukaryotic Tree: The Phylogenetic Positions of Jakobids and Cercozoans |last1=Rodríguez-Ezpeleta |first1=Naiara |last2=Brinkmann |first2=Henner |last3=Burger |first3=Gertraud |last4=Roger |first4=Andrew J. |last5=Gray |first5=Michael W. |last6=Philippe |first6=Hervé |last7=Lang |first7=B. Franz |display-authors=3 |doi=10.1016/j.cub.2007.07.036 |journal=Current Biology |year=2007 |volume=17 |issue=16 |pages=1420–1425 |pmid=17689961 |doi-access=free  }}</ref> 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.<ref name="pmid19237557" />

===Metamonads===

Metamonads are unusual in not having classical mitochondria—instead they have [[Biology:Hydrogenosome|hydrogenosome]]s, [[Biology:Mitosome|mitosome]]s or uncharacterised organelles. The oxymonad ''[[Biology:Monocercomonoides|Monocercomonoides]]'' is reported to have completely lost homologous organelles. There are competing explanations.<ref>{{Cite journal |date=3 September 1996 |title=A common evolutionary origin for mitochondria and hydrogenosomes |journal=Proceedings of the National Academy of Sciences |volume=93 |issue=18 |pages=9651–9656 |doi=10.1073/pnas.93.18.9651 |issn=0027-8424 |pmc=38483 |pmid=8790385 |bibcode=1996PNAS...93.9651B |doi-access=free |last1=Bui |first1= Elisabeth T. |last2=Bradley |first2=Peter J. |last3=Johnson |first3=Patricia J. }}</ref><ref name="Al Jewari Baldauf 2023" />

===Malawimonads===

The [[Biology:Malawimonas|malawimonads]] have been proposed to be members of Excavata owing to their typical excavate morphology, and phylogenetic affinity to other excavate groups in some molecular phylogenies. However, their position among eukaryotes remains elusive.<ref name=simpson/>

===Ancyromonads===

[[Biology:Ancyromonadida|Ancyromonads]] are small free-living cells with a narrow longitudinal groove down one side of the cell.  The ancyromonad groove is not used for "suspension feeding", unlike in "typical excavates" (e.g. malawimonads, jakobids, ''Trimastix'', ''Carpediemonas'', ''Kiperferlia'', etc).  Ancyromonads instead capture prokaryotes attached to surfaces. The phylogenetic placement of ancyromonads is poorly understood (in 2020), however some phylogenetic analyses place them as close relatives of malawimonads.<ref name = "Brown_2018">{{Cite journal |last1=Brown |first1=Matthew W. |last2=Heiss |first2=Aaron A. |last3=Kamikawa |first3=Ryoma |last4=Inagaki |first4=Yuji |last5=Yabuki |first5=Akinori |last6=Tice |first6=Alexander K. |last7=Shiratori |first7=Takash i|last8=Ishida |first8=Ken-Ichiro |last9=Hashimoto |first9=Tetsuo |last10=Simpson |first10=Alastair |last11=Roger |first11=Andrew |display-authors=3 |date=2018-01-19|title=Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group |journal=Genome Biology and Evolution |volume=10 |issue=2 |pages=427–433 |doi=10.1093/gbe/evy014 |pmc=5793813 |pmid=29360967}}</ref>

== Evolution ==

=== Origin of the Eukaryotes ===

{{further|Biology:Eukaryogenesis}}

The conventional explanation for the origin of the Eukaryotes is that a heimdallarchaeian or another Archaea acquired an [[Biology:Alphaproteobacteria|alphaproteobacterium]] as an endosymbiont, and that this became the [[Biology:Mitochondrion|mitochondrion]], the [[Biology:Organelle|organelle]] providing [[Biology:Citric acid cycle|oxidative respiration]] to the eukaryotic cell.<ref name="Eme 2023">{{Cite journal |last1=Eme |first1=Laura |last2=Tamarit |first2=Daniel |last3=Caceres |first3=Eva F. |last4=Stairs |first4=Courtney W. |last5=Anda |first5=Valerie De |last6=Schön |first6=Max E. |last7=Seitz |first7=Kiley W. |last8=Dombrowski |first8=Nina |last9=Lewis |first9=William H. |last10=Homa |first10=Felix |last11=Saw |first11=Jimmy H. |last12=Lombard |first12=Jonathan |last13=Nunoura |first13=Takuro |last14=Li |first14=Wen-Jun |last15=Hua |first15=Zheng-Shuang |display-authors=3 |date=2023-03-09 |title=Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes |journal=Nature |volume=618 |issue=7967 |url=https://www.biorxiv.org/content/10.1101/2023.03.07.531504v1 |pages=992–999 |doi=10.1101/2023.03.07.531504|pmid=37316666 |pmc=10307638 }}</ref>

Caesar al Jewari and Sandra Baldauf argue instead that the Eukaryotes possibly started with an endosymbiosis event of a Deltaproteobacterium or Aammaproteobacterium, accounting for the otherwise unexplained presence of anaerobic bacterial enzymes in Metamonada. The sister of the Preaxostyla within Metamonada represents the rest of the Eukaryotes which acquired an Alphaproteobacterium. In their scenario, the [[Biology:Hydrogenosome|hydrogenosome]] and [[Biology:Mitosome|mitosome]], both conventionally considered "mitochondrion-derived organelles", would predate the mitochondrion, and instead be derived from the earlier symbiotic bacterium.<ref name="Al Jewari Baldauf 2023">{{Cite journal |last1=Al Jewari |first1=Caesar |last2=Baldauf |first2=Sandra L. |date=2023-04-28 |title=An excavate root for the eukaryote tree of life |journal=Science Advances |volume=9 |issue=17 |pages=eade4973 |doi=10.1126/sciadv.ade4973 |issn=2375-2548 |pmc=10146883 |pmid=37115919 |bibcode=2023SciA....9E4973A }}</ref>

=== Phylogeny ===

In 2023, using molecular phylogenetic analysis of 186 taxa, Al Jewari and Baldauf proposed a phylogenetic tree with the metamonad Parabasalia as basal Eukaryotes. Discoba and the rest of the Eukaryota appear to have emerged as [[Biology:Sister group|sister taxon]] to the Preaxostyla, incorporating a single alphaproteobacterium as mitochondria by endosymbiosis. Thus the Fornicata are more closely related to e.g. animals than to Parabasalia. The rest of the Eukaryotes emerged within the Excavata as sister of the Discoba; as they are within the same clade but are not cladistically considered part of the Excavata yet, the Excavata are in this analysis highly paraphyletic.<ref name="Al Jewari Baldauf 2023"/>

{{clade
|grouplabel1={{clade labels|label1="Excavata"|top=32%}}
|1={{clade
|1=Hodarchaeales<ref name="Eme 2023"/>
|label2=Eukaryota
|2={{clade
   |1=Parabasalia |barbegin1=red
   |2={{clade
      |1=Fornicata |bar1=red
      |2={{clade
         |1=Preaxostyla |bar1=red
         |2={{clade
            |label1=Discoba |barend1=red
            |1={{clade
               |1=[[Biology:Jakoba|Jakobida]]
               |2={{clade
                  |1=[[Biology:Percolozoa|Heterolobosea]]
                  |2=[[Biology:Euglenozoa|Euglenozoa]] and allies
                  }}
               }}
            |label2=Neokaryotes
            |2={{clade
               |1=[[Biology:Amorphea|Amorphea]] (inc. animals, fungi)
               |2={{clade
                  |1=[[Biology:SAR supergroup|SAR]]
                  |2=[[Biology:Archaeplastida|Archaeplastida]] (inc. plants)
                  }}   
               }}
            }}
         }}
      }}
   }}}}
}}

The [[Biology:Anaeramoeba|Anaeramoeba]] are associated with Parabasalia, but could turn out to be more basal as the root of a tree is often difficult to pinpoint.<ref>{{Cite journal |last1=Stairs |first1=Courtney W. |last2=Táborský |first2=Petr |last3=Salomaki |first3=Eric D. |last4=Kolisko |first4=Martin |last5=Pánek |first5=Tomáš |last6=Eme |first6=Laura |last7=Hradilová |first7=Miluše |last8=Vlček |first8=Čestmír |last9=Jerlström-Hultqvist |first9=Jon |last10=Roger |first10=Andrew J. |last11=Čepička |first11=Ivan |display-authors=3 |date=December 2021 |title=Anaeramoebae are a divergent lineage of eukaryotes that shed light on the transition from anaerobic mitochondria to hydrogenosomes |journal=Current Biology |volume=31 |issue=24 |pages=5605–5612.e5 |doi=10.1016/j.cub.2021.10.010 |pmid=34710348 |s2cid=240054026 |issn=0960-9822|doi-access=free }}</ref>

== See also ==
Metakaryota

==Gallery==
<gallery class="center" mode="nolines">
File:Two Euglena.jpg|''[[Biology:Euglena|Euglena]]'' ([[Biology:Euglenozoa|Euglenozoa]]: Euglenoida)
File:TrypanosomaBrucei ProcyclicTrypomastigote SEM.jpg|''[[Biology:Trypanosoma brucei|Trypanosoma brucei]]'' (Euglenozoa: Kinetoplastida)
File:Bodo_saltans_-_400x_(13895749563).jpg|''Bodo'' sp. (Euglenozoa: Kinetoplastida)
File:Percolomonas_sp.jpg|''[[Biology:Percolomonas|Percolomonas]]'' sp. (Percolozoa)
File:Stephanopogon_sp.jpg|''[[Biology:Stephanopogon|Stephanopogon]]'' sp. (Percolozoa)
File:Naegleria (formes) en.png|Stages of ''[[Biology:Naegleria|Naegleria]]'' sp. ([[Biology:Percolozoa|Percolozoa]]: Heterolobosea)
File:Acrasis_rosea_31095.jpg|''[[Biology:Acrasis rosea|Acrasis rosea]]'' (Percolozoa: Heterolobosea)
File:Jakobida.svg|Jakobids (Jakobida)
File:Trichomonas Giemsa DPDx.JPG|''Trichomonas vaginalis'' (Metamonada: Parabasalia)
File:Metamonada_retortamonas_hexamita_giardia.svg|''[[Biology:Retortamonas|Retortamonas]]'' sp., left (Metamonada: Fornicata: Retortamonadida)
File:Giardia_1.jpg|''[[Biology:Giardia|Giardia]]'' sp. (Metamonada: Fornicata: Diplomonadida)
</gallery>

== References ==
{{Reflist|30em}}

== External links ==
* [https://tree.opentreeoflife.org/opentree/argus/ottol@2927065/Excavata Open Tree of Life]
* [http://taxonomicon.taxonomy.nl/TaxonName.aspx?id=199102&src=0 Taxonomicon]
* [http://tolweb.org/Eukaryotes/3 Tree of Life Eukaryotes]
* [http://tolweb.org/Jakobida/97407 Tree of Life: Jakobida]
* [http://tolweb.org/Fornicata/121182 Tree of Life: Fornicata]

{{Protozoal diseases}}
{{Eukaryota}}
{{Taxonbar|from=Q691551}}

[[Category:Excavata| ]]

{{Sourceattribution|Excavata}}