[ref. ID; 4980 (Alastair G. B. Simpson, 2003)]

Excavate taxa
Some heterotrophic flagellates employ a longitudinal groove to collect suspended food particles from a current generated by the beating of one or more posteriorly directed flagella. Such organisms were recently characterized as 'excavate' (Patterson, 1999; Simpson & Patterson, 1999). Well-accepted monophyletic groups including such organisms are designated 'excavate taxa'; thus, some (potentially most) members of an excavate taxon can lack an excavate feeding groove. There are currently seven excavate taxa: Jakobida (core jakobids), Malawimonas, Trimastix, Carpediemonas, Retortamonadida, Diplomonadida and Heterolobosea.
The first four of these seven groups are composed exclusively of free-living, heterotrophic flagellates with conspicuous feeding grooves. These organisms have only been characterized within the last 15 years. The taxon Jakobida contains mitochondriate, biflagellate cells, including the free-swimming Jakoba (Patterson, 1990) and the sessile, loricate Histiona and Reclinomonas (Mylnikov, 1989; Flavin & Nerad, 1993). Stenocodon and Stomatochone are probably related closely to Reclinomonas and Histiona (Flavin & Nerad, 1993; Patterson et al., 2000). O'Kelly (1993) recognized that Jakoba, Reclinomonas and Histiona were morphologically similar (see also Flavin & Nerad, 1993) and called them 'jakobid flagellates', together with an unnamed, free-swimming, groove-bearing flagellate that was later described as Malawimonas jakobiformis (O'Kelly & Nerad, 1999). Further studies cast doubt as to whether Malawimonas was related particularly closely to other 'jakobid flagellates' (O'Kelly & Nerad, 1999; Simpson & Patterson, 1999) and the inclusiveness of this term became confused. For expediency, Jakoba, Reclinomonas and Histiona were referred to as 'core jakobids' (Simpson & Patterson, 1999, 2001). Hereafter, the taxon "Jakobida" and the term "jakobids' are held to be synonymous with 'core jakobids', i.e. Malawimonas is not a jakobid and is considered to be a separate taxon (Archibald et al., 2002; Cavalier-Smith, 2002). Trimastix and Carpediemonas are free-swimming cells that are usually encountered in oxygen-poor environments (Bernard et al., 2000). Both lack mitochondria, but possess double-membrane-bounded organelles that may be homologous (Brugerolle & Patterson, 1997; O'Kelly et al., 1999; Simpson & Patterson, 1999; Simpson et al., 2000). Trimastix has four flagella, whereas Carpediemonas is biflagellate, but has three basal bodies (Simpson & Patterson, 1999). Jakobids, Malawimonas, Trimastix, Carpediemonas and retortamonads (see below) are informally referred to as 'typical excavates, due to their similar cytoskeletal organization).
Retortamonads and diplomonads are the best known of the excavate taxa. These heterotrophic flagellates lack classical mitochondria and typically inhabit oxygen-poor environments, such as sediments and the intestinal tracts of vertebrates (Kulda & Nohynkova, 1978; Mylnikov, 1991; Fenchel & Finlay, 1995; Bernard et al., 2000). Retortamonads have four basal bodies, with either two (Retortamonas) or four (Chilomastix) emergent flagella and a conspicuous ventral groove (Brugerolle, 1991; Brugerolle & Muller, 2000). Most diplomonads are doubled cells with two nuclei, two kinetids (most have two sets of four flagella) and duplicate cytoskeletons (Brugerolle, 1991; Brugerolle & Muller, 2000). The most familiar diplomonad, the intestinal parasite Giardia, lacks feeding grooves. However, Trepomonas spp. and (arguably) Entermonas have feeding grooves that operate in conjunction with the posterior flagella (Brugerolle, 1975; Eyden & Vickerman, 1975). Many workers consider diplomonads and retortamonads together as a clade or as a phenetically united grade (e.g. Cavalier-Smith, 1987, 1993, 1999; Lipscomb, 1989; Siddall et al., 1992), but others, conservatively, consider them separately (e.g. Patterson, 1994, 1999).
Heterolobosea (= Tetramitea sensu Cavalier-Smith) was united as a taxon by Page & Blanton (1985), with the key organism Percolomonas cosmopolitus included by Fenchel & Patterson (1986). Heterolobosea are primarily amoebae or (acrasid) slime moulds, but many have alternative flagellate forms with two or four flagella and some (Lyromonas, Percolomonas) may exist only as flagellates (Patterson et al., 2000). Flagellates of Percolomonas, Lyromonas, Psalteriomonas and arguably some others (e.g. Tetramitus, Paratetramitus) have a broad ventral (or anterior) groove (Patterson et al., 2000). This is used for suspension-feeding, at least in Percolomonas (Fenchel & Patterson, 1986)
This list of excavate taxa is probably not exhaustive. For example, Ruinen (1938) described two free-living, groove-bearing flagellates with three flagella, Triflagellum diaphanum and Triflagellum hardyi. The groove of Triflagellum diaphanum is similar to those of Trimastix and Carpediemonas and is associated with a single posterior flagellum. Bernard et al. (2000) documented a small flagellate 'protist beta' with a ventral groove that contained a posterior flagellum. Feeding data are not available for these organisms, but suspension-feeding is plausible in each case. They are not immediately assignable to any established taxon, but neither electron microscopical, nor molecular, data are yet available.
Euglenozoans are unicellular (rarely colonial) flagellates. Best known are the photosynthetic 'green euglenids' (mostly uniflagellate) and the uniflagellate, parasitic trypanosomatids, but the bulk of euglenozoan diversity consists of free-living biflagellate phagotrophs (Simpson, 1997). Euglenozoans feed by using a tubular ingestion apparatus rather than a ventral groove. Most free-living taxa are raptorial feeders. The few suspension-feeders (e.g. Bodo saltans) use their anterior flagellum to generate the feeding current. The taxon Euglenozoa is usually considered to be related to Heterolobosea, based on some ultrastructural features (Patterson, 1988) and some molecular phylogenies (Baldauf et al., 2000; Edgcomb et al., 2001)

Phylogenetic (apomorphy-based) diagnoses of taxa
Analysis method; Small-subunit rRNA (SSU-rRNA) gene sequence

Excavata (Cavalier-Smith 2002, emend.)
Apomorphy: suspension-feeding groove, homologous to that in Jakoba libera.

Fornicata taxon nov.
Apomorphy: B fibre ('arched fibre') origin against R2, homologous to the organization in Chilomastix cuspidata.

Preaxostyla taxon nov.
Apomorphy: I fibre with preaxostylar substructure (double-cross matrix, with a single fine outer sheet), homologous to that in Pyrsonympha vertens.

Unquesitonably, it has been the rapid growth of molecular phylogenetics (Taylor, 1994, 1999; Cavalier-Smith, 1995; Patterson, 2000) that has kept the interest in eukaryotic macro-evolution strong and the evolutionary protistan pot simmering; molecular sequencing continues to provide new insights, cement protistan relationships and raise new debates, particularly as different molecules and different methods yield differing results. 5S rDNA trees obviously had anomalous features, attributed to the small size of the molecule and the correspondingly small amount of usale nucleotide sequence variation. LSU rRNA genes are so large and hypervariable in multiple regions that the latter need to be selectively removed in order to study group-level relationships (e.g. Ben Ali et al., 2001). In the 1980s and 1990s, SSU rDNA seemed to be 'just right' in size and information content for the latter purpose. In broad features, the trees it generated corresponded well with the main features of the TEM data (Sogin, 1994; Sogin et al., 1996; Taylor, 1994). Now, finally, it seemed that there was a molecule that could be used to resolve which of the 'absence/loss' choices was actually a primary absence. Some of the amitochondriate groups, such as the diplomonads and parabasalians and microsporidia, were basal in SSU rDNA trees. However, they were long branches and therefore .