Excavate

This article is about the protist group. For the process of digging, see Excavation (disambiguation).

Excavates
Giardia lamblia, a parasitic diplomonad
Scientific classification
Domain:	Eukaryota
(unranked):	Bikonta
Kingdom:	Excavata (Cavalier-Smith) Simpson, 2003
Phyla
Metamonada Loukozoa Euglenozoa Percolozoa

The excavates are a major kingdom of unicellular^[1] eukaryotes,^[2] often known as Excavata. The phylogenetic category Excavata, proposed by Cavalier-Smith in 2002, contains a variety of free-living and symbiotic forms, and also includes some important parasites of humans.

Characteristics

Many excavates lack 'classical' mitochondria - these organisms are often referred to as 'amitochondriate', although most, perhaps all, retain a mitochondrial organelle in greatly modified form. Others have mitochondria with tubular, discoidal, or in some cases, laminar cristae. Most excavates have two, four, or more flagella^[3] and many have a conspicuous ventral feeding groove with a characteristic ultrastructure, supported by microtubules.^[4] However, various groups that lack these traits may be considered excavates based on genetic evidence (primarily phylogenetic trees of molecular sequences).

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.

Subgroups

Excavates are classified into four major subgroups at the phylum/superphylum level. These are shown in the table below.

Superphylum	Phylum	Representative genera	Description
Discoba	Euglenozoa	e.g. Euglena, Trypanosoma	Many important parasites, one large group with plastids (chloroplasts)
	Percolozoa (Heterolobosea)	e.g. Naegleria, Acrasis	Most alternate between flagellate and amoeboid forms
	Jakobida (see also Loukozoa)	e.g. Jakoba, Reclinomonas	Free-living, sometimes loricate flagellates, with very gene-rich mitochondrial genomes
Metamonada	Preaxostyla	e.g. Oxymonads, Trimastix	Amitochontriate flagellates, either free-living (Trimastix) or living in the hindguts of insects
	Fornicata	e.g. Giardia, Carpediemonas	Amitochondriate, mostly symbiotes and parasites of animals.
	Parabasalia	e.g. Trichomonas	Amitochondriate flagellates, generally intestinal commensals of insects. Some human pathogens.

Heterolobosea (Percolozoa) and Euglenozoa 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.^[5] Most jakobids have tubular cristae, like most other protists, while the metamonads are unusual in having lost classical mitochondria—instead they have 'hydrogenosomes', 'mitosomes' or uncharacterised organelles. In addition to the groups mentioned in the table above, the genus Malawimonas is generally considered to be a member of Excavata owing to its typical excavate morphology, and phylogenetic affinity to excavate groups in some molecular phylogenies. However, its position among excavates remains elusive.

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 which are monophyletic.^[6]

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.

See also: Eukaryote#Phylogeny

References

1. ^ Simpson, Ag; Inagaki, Y; Roger, Aj (Mar 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. http://mbe.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=16308337 
2. ^ Hampl V, Hug L, Leigh JW, et al (March 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 2656170. PMID 19237557. http://www.pnas.org/cgi/pmidlookup?view=long&pmid=19237557. 
3. ^ Simpson AG (November 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. http://ijs.sgmjournals.org/cgi/pmidlookup?view=long&pmid=14657103. 
4. ^ Cavalier-Smith T (March 2002). "The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa". Int. J. Syst. Evol. Microbiol. 52 (Pt 2): 297–354. PMID 11931142. http://ijs.sgmjournals.org/cgi/pmidlookup?view=long&pmid=11931142. 
5. ^ Naiara Rodríguez-Ezpeleta, Henner Brinkmann, Gertraud Burger, Andrew J. Roger, Michael W. Gray, Hervé Philippe, and B. Franz Lang (August 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. http://www.cell.com/current-biology/retrieve/pii/S0960982207017162. 
6. ^ Laura Wegener Parfrey, Erika Barbero, Elyse Lasser, Micah Dunthorn, Debashish Bhattacharya, David J Patterson, and Laura A Katz (December 2006). "Evaluating Support for the Current Classification of Eukaryotic Diversity". PLoS Genet. 2 (12): e220. doi:10.1371/journal.pgen.0020220. PMC 1713255. PMID 17194223. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1713255. 

External links

• Tree of Life Eukaryotes
• Tree of Life: Jakobida
• Tree of Life: Fornicata