Joined: May 2002
New TCS article gives us the short version of current euk. phylogeny & who may and may not be primitively non-ciliated:
J Mol Evol 2003 Apr;56(4):387-96
Molecular phylogeny of centrohelid heliozoa, a novel lineage of bikont eukaryotes that arose by ciliary loss.
Cavalier-Smith T, Chao EE.
Recent molecular and cellular evidence indicates that eukaryotes comprise three major lineages: the probably ancestrally uniciliate protozoan phylum Amoebozoa; the ancestrally posteriorly uniciliate opisthokont clade (animals, Choanozoa, and fungi); and a very diverse ancestrally biciliate clade, the bikonts-plants, chromalveolates, and excavate and rhizarian Protozoa. As Heliozoa are the only eukaryote phylum not yet placed on molecular sequence trees, we have sequenced the 18S rRNA genes of three centrohelid heliozoa, Raphidiophrys ambigua, Heterophrys marina, and Chlamydaster sterni, to investigate their phylogenetic position. Phylogenetic analysis by distance and maximum likelihood methods allowing for intersite rate variation and invariable sites confirms that centrohelid heliozoa are a robust clade that does not fall within any other phyla. In particular, they are decisively very distant from the heterokont pedinellid chromists, at one time thought to be related to heliozoa, and lack the unique heterokont signature sequence. They also appear not to be specifically related to either Amoebozoa or Radiolaria, with which they have sometimes been classified, so it is desirable to retain Heliozoa as a separate protozoan phylum. Even though centrohelids have no cilia or centrioles, the centrohelid clade branches among the bikont eukaryotes, but there is no strong bootstrap support for any particular position. Distance trees usually place centrohelids as sisters to haptophytes, whereas parsimony puts them as sisters to red algae, but there is no reason to think that either position is correct; both have very low bootstrap support. Quartet puzzling places them with fairly low support as sisters to the apusozoan zooflagellate Ancyromonas. As Ancyromonas is the only other eukaryote that shares the character combination of flat plate-like mitochondrial cristae and kinetocyst-type extrusomes with centrohelids, this position is biologically plausible, but because of weak support and conflict between trees it might not be correct. Irrespective of their precise position, our trees (together with previous evidence that Chlamydaster sterni has the derived dihydrofolate reductase/thymidylate synthetase gene fusion unique to bikonts) indicate that centrohelid heliozoa are ancestrally derived from a bikont flagellate by the loss of cilia. The centroplast that nucleates their axonemal microtubules is therefore almost certainly homologous with the centrosome of ciliated eukaryotes and should simply be called a centrosome.
Recent reappraisal of the basal radiation of eukaryotes argues that all eukaryotes belong to one of three major lineages: Amoebozoa, opisthokonts, and bikonts (Cavalier-Smith 2002a). Opisthokonts comprise the kingdoms Animalia and Fungi and the protozoan phylum Choanozoa (Cavalier-Smith 1987) and are the best-established multikingdom clade on the eukaryotic tree (Baldauf 1999; Baldauf et al. 2000; Cavalier-Smith 1998b, 2002a; Cavalier-Smith and Chao 2003; Patterson 1999; Stechmann and Cavalier-Smith 2002). Opisthokonts are characterized by a single posterior cilium with two centrioles, radiating singlet centrosomal microtubules, flat mitochondrial cristae, an insertion in EF-1, characteristic indels in enolase, and a very rare base-pair change in 18S rRNA (Cavalier-Smith and Chao 2003). Bikonts have only recently been recognized as a clade ancestrally with two divergent centrioles and cilia, at least two dissimilar microtubular centriolar roots, and often ciliary and centriolar root transformation spread over two cell cycles (Cavalier-Smith 2002a). The probable holophyly of the bikonts has been strikingly supported by the discovery that they share a derived gene fusion between dihydrofolate reductase and thymidylate synthetase (Stechmann and Cavalier-Smith 2002). The demonstration that the centrohelid heliozoan Chlamydaster sterni also has this fusion (Stechmann and Cavalier-Smith 2002) strongly indicates that it must have had a biciliate ancestry also and lost both cilia and centrioles. In agreement with this, we find no evidence for a grouping of Heliozoa with Amoebozoa, the only protozoan phylum for which a nonciliated ancestry remains open, given our present understanding of the position of the eukaryote root (Stechmann and Cavalier-Smith 2002).