Excavata

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Excavata
Temporal range: Neoproterozoic–present
Giardia lamblia.jpg
Giardia lamblia , a parasitic diplomonad
Scientific classification OOjs UI icon edit-ltr.svg
(obsolete as paraphyletic)
Domain: Eukaryota
(unranked): Excavata
(Cavalier-Smith), 2002
Phyla and classes

see text

Cladistically included but traditionally excluded taxa
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 cell schemes.svg
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. [1] [2] The group was first suggested by Simpson and Patterson in 1999 [3] [4] and the name latinized and assigned a rank by Thomas Cavalier-Smith in 2002. It contains a variety of free-living and symbiotic protists, and includes some important parasites of humans such as Giardia and Trichomonas . [5] Excavates were formerly considered to be included in the now obsolete Protista kingdom. [6] They were distinguished from other lineages based on electron-microscopic information about how the cells are arranged (they have a distinctive ultrastructural identity). [4] They are considered to be a basal flagellate lineage. [7]

Contents

On the basis of phylogenomic analyses, the group was shown to contain three widely separated eukaryote groups, the discobids, metamonads, and malawimonads. [8] [9] [10] [11] A current view of the composition of the excavates is given below, indicating that the group is paraphyletic. Except for some Euglenozoa, all are non-photosynthetic.

Characteristics

Most excavates are unicellular, heterotrophic flagellates. Only some Euglenozoa are photosynthetic. In some (particularly anaerobic intestinal parasites), the mitochondria have been greatly reduced. [5] 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. [4] 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. [3] [6] However, various groups that lack these traits are considered to be derived excavates based on genetic evidence (primarily phylogenetic trees of molecular sequences). [6]

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.

Proposed group

Excavate relationships were always uncertain, suggesting that they are not a monophyletic group. [12] Phylogenetic analyses often do not place malawimonads on the same branch as the other Excavata. [13]

Excavates were thought to include multiple groups:

Kingdom/SuperphylumIncluded taxaRepresentative genera (examples)Description
Discoba  or JEH or Eozoa Tsukubea Tsukubamonas
Euglenozoa Euglena , Trypanosoma 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.
Anaeramoeba Anaeramoeba ignavaAnaerobic protists with hydrogenosomes instead of mitochondria.
Neolouka Malawimonadida Malawimonas

Discoba or JEH clade

Euglenozoa and Heterolobosea (Percolozoa) or Eozoa (as named by Cavalier-Smith [14] ) 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, [15] 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. [1] Alternatively, the clade has been termed the jakobid, euglenazoan and heterolobosean group JEH. [16]

Metamonads

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. [17] [18]

Malawimonads

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. [2]

Ancyromonads

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. [9]

Evolution

Origin of the Eukaryotes

The conventional explanation for the origin of the Eukaryotes is that a heimdallarchaeian or another Archaea acquired an alphaproteobacterium [19] as an endosymbiont, and that this became the mitochondrion, the organelle providing oxidative respiration to the eukaryotic cell. [20]

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. [18]

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 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. [18]

Hodarchaeales [20]

Eukaryota

Parabasalia

Fornicata

Preaxostyla

Discoba
Neokaryotes

Amorphea (inc. animals, fungi)

SAR

Archaeplastida (inc. plants)

+ α‑proteobacterium
+ δ/γ‑proteobacterium
"Excavata"

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. [21]

See also

Metakaryota

References

  1. 1 2 Hampl, Vladimir; Hug, Laura; Leigh, Jessica W.; et al. (2009). "Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups"". PNAS. 106 (10): 3859–3864. Bibcode:2009PNAS..106.3859H. doi: 10.1073/pnas.0807880106 . PMC   2656170 . PMID   19237557.
  2. 1 2 Simpson, Alastair G. B.; Inagaki, Yuji; Roger, Andrew J. (2006). "Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes". Molecular Biology and Evolution. 23 (3): 615–625. doi: 10.1093/molbev/msj068 . PMID   16308337.
  3. 1 2 Simpson, Alastair G.B.; Patterson, David J. (December 1999). "The ultrastructure of Carpediemonas membranifera (Eukaryota) with reference to the 'excavate hypothesis'". European Journal of Protistology. 35 (4): 353–370. doi:10.1016/S0932-4739(99)80044-3.
  4. 1 2 3 Simpson, Alastair G. B. (November 2003). "Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota)". International Journal of Systematic and Evolutionary Microbiology. 53 (6): 1759–1777. doi: 10.1099/ijs.0.02578-0 . PMID   14657103.
  5. 1 2 Dawkins, Richard; Wong, Yan (2016). The Ancestor's Tale. Houghton Mifflin Harcourt. ISBN   978-0544859937.
  6. 1 2 3 Cavalier-Smith, Thomas (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.
  7. ↑ 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   4927265 . PMID   23312067.
  8. ↑ Burki, Fabien; Roger, Andrew J.; Brown, Matthew W.; et al. (January 2020). "The New Tree of Eukaryotes". Trends in Ecology & Evolution. 35 (1): 43–55. doi: 10.1016/j.tree.2019.08.008 . PMID   31606140. S2CID   204545629.
  9. 1 2 Brown, Matthew W.; Heiss, Aaron A.; Kamikawa, Ryoma; et al. (2018-01-19). "Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group". Genome Biology and Evolution. 10 (2): 427–433. doi:10.1093/gbe/evy014. PMC   5793813 . PMID   29360967.
  10. ↑ Heiss, Aaron A.; Kolisko, Martin; Ekelund, Fleming; et al. (4 April 2018). "Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes". Royal Society Open Science. 5 (4): 171707. Bibcode:2018RSOS....571707H. doi:10.1098/rsos.171707. PMC   5936906 . PMID   29765641.
  11. ↑ Keeling, Patrick J.; Burki, Fabien (19 August 2019). "Progress towards the Tree of Eukaryotes". Current Biology. 29 (16): R808 –R817. Bibcode:2019CBio...29.R808K. doi: 10.1016/j.cub.2019.07.031 . PMID   31430481.
  12. ↑ Laura Wegener Parfrey; Erika Barbero; Elyse Lasser; Micah Dunthorn; Debashish Bhattacharya; David J Patterson; Laura A Katz (December 2006). "Evaluating support for the current classification of eukaryotic diversity". PLOS Genetics . 2 (12): e220. doi: 10.1371/JOURNAL.PGEN.0020220 . ISSN   1553-7390. PMC   1713255 . PMID   17194223. Wikidata   Q21090155.
  13. ↑ Tice, Alexander K.; Žihala, David; Pánek, Tomáš; et al. (2021). "PhyloFisher: A phylogenomic package for resolving eukaryotic relationships". PLOS Biology. 19 (8): e3001365. doi: 10.1371/journal.pbio.3001365 . PMC   8345874 . PMID   34358228.
  14. ↑ Cavalier-Smith, Thomas (23 December 2009). "Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree". Biology Letters. 6 (3). The Royal Society: 342–345. doi:10.1098/rsbl.2009.0948. ISSN   1744-9561. PMC   2880060 . PMID   20031978.
  15. ↑ Rodríguez-Ezpeleta, Naiara; Brinkmann, Henner; Burger, Gertraud; et al. (2007). "Toward Resolving the Eukaryotic Tree: The Phylogenetic Positions of Jakobids and Cercozoans". Current Biology. 17 (16): 1420–1425. Bibcode:2007CBio...17.1420R. doi: 10.1016/j.cub.2007.07.036 . PMID   17689961.
  16. ↑ Rodríguez-Ezpeleta N, Brinkmann H, Burger G, Roger AJ, Gray MW, Philippe H, Franz Lang B (2007). "Toward Resolving the Eukaryotic Tree: The Phylogenetic Positions of Jakobids and Cercozoans". Current Biology. 17 (16): 1420–1425. doi: 10.1016/j.cub.2007.07.036 . PMID   17689961.
  17. ↑ Bui, Elisabeth T.; Bradley, Peter J.; Johnson, Patricia J. (3 September 1996). "A common evolutionary origin for mitochondria and hydrogenosomes". Proceedings of the National Academy of Sciences. 93 (18): 9651–9656. Bibcode:1996PNAS...93.9651B. doi: 10.1073/pnas.93.18.9651 . ISSN   0027-8424. PMC   38483 . PMID   8790385.
  18. 1 2 3 Al Jewari, Caesar; Baldauf, Sandra L. (2023-04-28). "An excavate root for the eukaryote tree of life". Science Advances. 9 (17): eade4973. Bibcode:2023SciA....9E4973A. doi:10.1126/sciadv.ade4973. ISSN   2375-2548. PMC   10146883 . PMID   37115919.
  19. ↑ Tria, F.D.K.; Brueckner, J.; Skejo, J.; Xavier, J.C.; Kapust, N.; Knopp, M.; et al. (7 May 2021). "Gene Duplications Trace Mitochondria to the Onset of Eukaryote Complexity". Genome Biology and Evolution. 13 (5). doi:10.1093/gbe/evab055. PMC   8175051 . PMID   33739376.
  20. 1 2 Eme, Laura; Tamarit, Daniel; Caceres, Eva F.; et al. (2023-03-09). "Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes". Nature. 618 (7967): 992–999. bioRxiv   10.1101/2023.03.07.531504 . doi:10.1038/s41586-023-06186-2. PMC   10307638 . PMID   37316666.
  21. ↑ Stairs, Courtney W.; Táborský, Petr; Salomaki, Eric D.; et al. (December 2021). "Anaeramoebae are a divergent lineage of eukaryotes that shed light on the transition from anaerobic mitochondria to hydrogenosomes". Current Biology. 31 (24): 5605–5612.e5. Bibcode:2021CBio...31E5605S. doi: 10.1016/j.cub.2021.10.010 . ISSN   0960-9822. PMID   34710348. S2CID   240054026.
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