DESCRIPTION OF THE SUPERGROUP EXCAVATA (CAVALIER-SMITH 2002)

EUKARYA> EXCAVATA

Excavata (eks-ka-VA-tuh) is formed from two Latin words that mean from (ex) and cavity (cavatum). The reference is to a depression in the cell called the excavate, which may be associated with one of the flagella and may function in feeding.

INTRODUCTION TO THE EXCAVATA The Excavata includes taxa that are photosynthetic, parasitic, symbiotic and heterotrophic. Many of the taxa lack mitochondria, and, therefore, seemed to conform to the requirements of an archaic premitochondrial ancestor of all eukaryotes. This theory, called the Archezoa Hypothesis, was created by Cavalier-Smith (1983). [Go to Domain Eukarya for an elaboration on the Archezoa Hypothesis.] The former archezoa began to find homes in interesting and unexpected places. Patterson (1999) and Simpson and Patterson (2001) defined a striking structural similarity that many of the former archezoan taxa possessed, a feeding groove called an excavate. The excavate was a groove that ran longitudinally on the cell surface and was associated with at least one recurrent flagellum, which set up currents in the groove that served to concentrate suspended particles and move them to a cytostome. Simpson (2003) identified seven such groups that had such an excavate apparatus: the Core Jakobids, Malawimonas, Trimastix, Carpediemonas, Retortomonads, Diplomonads, and the Heterolobosids (amoeboflagellates). Many of the excavate taxa were mitochondriate and had clear affinities with taxa that did not bear an excavate. So, by 2003 (Simpson 2003 and Cavalier-Smith 2003b) at least 10 groups (we interpret it as 11 groups) had been identified as excavate taxa (see Table 1). Burki et al. (2008) and Hampl et al. (2009) confirmed the monophyly of the excavates by phylogenomic analyses relative to members of the other supergroups. Furthermore, the excavates appear to be a very deep-rooting group, equivalent to the unikonts (Opisthokonta), and the bikonts (Chromalveolata + Rhizaria + Archaeplastida).

KINGDOMS OF THE EXCAVATA Earlier, Patterson (1999) had already shown the fundamental relationship between the kinetoplastids, euglenids, heteroloboseids, and acrasid cellular slime molds. He defined them on the basis of mitochondria with swollen or discoid cristae and similar flagellar structures. Even Margulis and Schwartz (1998) united these taxa into the same phylum. Cavalier-Smith (2002a) created the taxon Excavata (which he considered an infrakingdom) to house all of the taxa in Table 1. Supergroup analyses (e.g. Baldauf 2003a and Hampl et al. 2009) confirmed association of such taxa. However, the discicristate taxa still emerge as a coherent group, a clade that we interpret as the Kingdom Discicristatae. [We maintain that Animals and Fungi are separate kingdoms even though they occupy the same supergroup, Unikonta. We interpret the differences between the discicristates and euexcavates to be of the same magnitude and, therefore, retain their separation as kingdoms within the supergroup Excavata.] The remaining taxa occupy a different clade which we interpret as the Kingdom Euexcavatae. The Excavata still has some nagging problems. For example, the Jakobids, which we have placed in the Euexcavata, actually emerge in both lines, and therefore, form an artificial phylum. The affinities of Carpediemonas are unclear and need work. Also, the strange taxon, Stephanopogon, is one series of question marks. So, with these provisions, we introduce the Supergroup Excavata and its two kingdoms: Discicristatae and Euexcavatae.

TABLE 1. A list of excavate taxa taken from Simpson (2003) and Cavalier-Smith (2003b). We have indicated as to whether they have an excavate and mitochondria.
TAXA	EXCAVATE	MITOCHONDRIA
JAKOBIDS	+	+
MALAWAMONAS	+	+
CARPEDIEMONAS	+	–
TRIMASTIX	+	+
RETORTOMONADS	+	–
DIPLOMONADS	+	–
HETEROLOBOSEIDS (AMOEBOFLAGELLATES)	+	+
OXYMONADS	–	–
EUGLENIDS	-?	+
TRYPANOSOMATIDS	-?	+
PARABASALIDS	–	–

LITERATURE CITED Baldauf, S. L. 2003a. The deep roots of eukaryotes. Science. 300 (5626): 1701-1703. Burki, F., K. Shalchian-Tabrizi, and J. Pawlowski. 2008. Phylogenomics reveals a new ‘megagroup’ including most photosynthetic eukayotes. Biology Letters. 4: 366-369. Cavalier-Smith, T. 1983. A six-kingdom classification and a unified phylogeny. In: Schenk, H.E.A. and W.S. Schwemmler, eds. Endocytobiology II. de Gruyter , Berlin . pp. 1027-1034. Cavalier-Smith, T. 2002a. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa: International Journal of Systematic Evolutionary Microbiology. 52:297–354. Cavalier-Smith, T. 2003b. The excavate protozoan phyla Metamonada Grasse emend. (Anaeromonadea, Parabasalia, Carpediemonas, Eopharyngia) and Loukozoa emend. (Jakobea, Malawimonas): their evolutionary affinities and new higher taxa. International Journal of Systematic and Evolutionary Microbiology. 53:1741-1758. Hampl, V., L. Hug, J. W. Leigh, J. B. Dacks, B. F. Lang, A. G. B. Simpson, and A. J. Roger. 2009. Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”. Proceedings of the National Academy of Science. USA. 106(10): 3859-3864. Margulis, L. and K. Schwartz. 1998. Five kingdoms, an illustrated guide to the phyla of life on earth. 3rd Edition. W. H. Freeman and Company. New York. Patterson, D. J. 1999. The diversity of eukaryotes. American Naturalist. 154 (Suppl.): S96–S124. Simpson, A. G. 2003. Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota). International Journal of Systematic and Evolutionary Microbiology. 53: 1759-1777. Simpson, A.G. B., and D. J. Patterson. 2001. On core jakobids and excavate taxa: the ultrastructure of: Jakoba incarcerata. Journal of Eukaryotic Microbiology. 48: 480–492.

By Jack R. Holt. Last revised: 02/17/2014