Most excavates are unicellular, heterotrophic flagellates. Only the 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 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.
Excavates are classified into six major subdivisions at the phylum/class level. These are shown in the table below. An additional group, Malawimonadida (e.g. Malawimonas), may also be included amongst excavates, though phylogenetic evidence is equivocal.
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). A close relationship has been shown between Discicristata and Jakobida, 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 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.
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.
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.
The malawimonads are generally considered 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. Consequently, it is possible that ancyromonads are relevant for understand the evolution of 'true' excavates.
^ abSimpson, Ag; Inagaki, Y; Roger, Aj (2006). "Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes". Molecular Biology and Evolution. 23 (3): 615-25. doi:10.1093/molbev/msj068. PMID16308337.
^ abSimpson, Alastair G.B.; Patterson, David J. (Dec 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.
^ abcSimpson, Alastair G.B. (2003-11-01). "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. ISSN1466-5026. PMID14657103.
^ abcCavalier-Smith, T (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. PMID11931142.
^Naiara Rodríguez-Ezpeleta; Henner Brinkmann; Gertraud Burger; Andrew J. Roger; Michael W. Gray; Hervé Philippe & B. Franz Lang (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. PMID17689961.
^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. doi:10.1016/j.ympev.2016.03.023. PMID27001604.
^Cavalier-Smith, T.; 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. doi:10.1016/j.ympev.2014.08.012. PMID25152275.
^He, Ding; Fiz-Palacios, Omar; Fu, Cheng-Jie; Fehling, Johanna; Tsai, Chun-Chieh; Baldauf, Sandra L. (2014). "An Alternative Root for the Eukaryote Tree of Life". Current Biology. 24 (4): 465-470. doi:10.1016/j.cub.2014.01.036. PMID24508168.
^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. 49 (2): 115-178. doi:10.1016/j.ejop.2012.06.001. PMID23085100.
^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. 1 (5): 16048. doi:10.1038/nmicrobiol.2016.48. ISSN2058-5276. PMID27572647.
^Cavalier-Smith, Thomas (2017). "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. 61 (Pt A): 137-179. doi:10.1016/j.ejop.2017.09.002. PMID29073503.