Excavata#Discobids or JEH clade

Most excavates are unicellular, heterotrophic flagellates. Only some Euglenozoa are photosynthetic. In some (particularly anaerobic intestinal parasites), the mitochondria have been greatly reduced. Some excavates lack "classical" mitochondria, and are called "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. Many have a conspicuous ventral feeding groove with a characteristic ultrastructure, supported by microtubules—the "excavated" appearance of this groove giving the organisms their name. However, various groups that lack these traits are considered to be derived 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.

{{See also|Eukaryote#Phylogeny|wikispecies:Excavata}}

{{anchor|Discoba}}

Excavate relationships were always uncertain, suggesting that they are not a monophyletic group.{{cite Q|Q21090155|doi-access=free}} Phylogenetic analyses often do not place malawimonads on the same branch as the other Excavata.{{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 }}

Excavates were thought to include multiple groups:

Euglenozoa and Heterolobosea (Percolozoa) or Eozoa (as named by Cavalier-Smith{{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 }}) appear to be particularly close relatives, and are united by the presence of discoid cristae within the mitochondria (superphylum Discicristata). A close relationship has been shown between Discicristata and Jakobida,{{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 |bibcode=2007CBio...17.1420R }} the latter having tubular cristae like most other protists, and hence were united under the taxon name Discoba, which was proposed for this supposedly monophyletic group. This clade was defined as a node-based clade, receiving the definition "The least inclusive clade containing Jakoba libera (Ruinen, 1938) Patterson, 1990; Andalucia godoyi, Lara et al., 2006; Euglena gracilis Klebs 1883; and Naegleria gruberi (Schardinger, 1899) Alexeieff, 1912." Alternatively, the clade has been termed the jakobid, euglenazoan and heterolobosean group JEH.{{cite journal|vauthors=Rodríguez-Ezpeleta N, Brinkmann H, Burger G, Roger AJ, Gray MW, Philippe H, Franz Lang B|title=Toward Resolving the Eukaryotic Tree: The Phylogenetic Positions of Jakobids and Cercozoans|journal=Current Biology|volume=17|issue=16|pages=1420-1425|doi=10.1016/j.cub.2007.07.036|year=2007|doi-access=free|pmid=17689961}}

Metamonads are unusual in not having classical mitochondria—instead they have hydrogenosomes, mitosomes or uncharacterised organelles. The oxymonad Monocercomonoides is reported to have completely lost homologous organelles. There are competing explanations.{{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. }}

The 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.

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.{{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}}

{{further|Eukaryogenesis}}

The conventional explanation for the origin of the eukaryotes is that a heimdallarchaeian or another Archaea acquired an alphaproteobacterium{{cite journal |last1=Tria |first1=F.D.K. |last2=Brueckner |first2=J. |last3=Skejo |first3=J. |last4=Xavier |first4=J.C. |last5=Kapust |first5=N. |last6=Knopp |first6=M. |last7=Wimmer |first7=J.L.E. |last8=Nagies |first8=F.S.P. |last9=Zimorski |first9=V. |last10=Gould |first10=S.B. |last11=Garg |first11=S.G. |last12=Martin |first12=W.F. |display-authors=6 |title=Gene Duplications Trace Mitochondria to the Onset of Eukaryote Complexity. |journal=Genome Biology and Evolution |date=7 May 2021 |volume=13 |issue=5 |doi=10.1093/gbe/evab055 |pmid=33739376|pmc=8175051 }} as an endosymbiont, and that this became the mitochondrion, the organelle providing oxidative respiration to the eukaryotic cell.{{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 |pages=992–999 |doi=10.1038/s41586-023-06186-2|biorxiv=10.1101/2023.03.07.531504|pmid=37316666 |pmc=10307638 }}

Caesar al Jewari and Sandra Baldauf argue instead that the eukaryotes possibly started with an endosymbiosis event of a Deltaproteobacterium or Gammaproteobacterium, 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 hydrogenosome and mitosome, both conventionally considered "mitochondrion-derived organelles", would predate the mitochondrion, and instead be derived from the earlier symbiotic bacterium.{{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 }}

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 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 in this analysis is highly paraphyletic.

{{clade

|grouplabel1={{clade labels|label1="Excavata"|top=32%}}

|1={{clade

|1=Hodarchaeales

|label2=Eukaryota

|sublabel2=+ δ/γ-proteobacterium

|2={{clade

|1=Parabasalia |barbegin1=red

|2={{clade

|1=Fornicata |bar1=red

|2={{clade

|1=Preaxostyla |bar1=red

|sublabel2=+ α-proteobacterium

|2={{clade

|label1=Discoba |barend1=red

|1={{clade

|1=Jakobida

|2={{clade

|1=Heterolobosea

|2=Euglenozoa and allies

}}

}}

|label2=Neokaryotes

|2={{clade

|1=Amorphea (inc. animals, fungi)

|2={{clade

|1=SAR

|2=Archaeplastida (inc. plants)

}}

}}

}}

}}

}}

}}}}

}}

The Anaeramoeba are associated with Parabasalia, but could turn out to be more basal as the root of a tree is often difficult to pinpoint.{{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 |bibcode=2021CBio...31E5605S }}

Metakaryota

{{gallery |width=125 |mode=nolines |align=center|

|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) en.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)

}}

{{Reflist|30em}}

• [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]

{{Eukaryota}}

{{Excavata}}

{{Protozoal diseases}}

{{Taxonbar|from=Q691551}}

Category:Infrakingdoms

Category:Taxa named by Thomas Cavalier-Smith

Category:2002 introductions