Nine additional lines of evidence for the root being between Euglenozoa and neokaryotes

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Supplementary material for Thomas Cavalier-Smith: Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree. Biology Letters.
This electronic supplement contains additional explanations for my conclusions, discussion of the drawbacks of alternative ideas in the literature, a summary of the revised classification of both kingdoms with nomenclatural details (Table 1), and further references, which severe space constraints did not allow including in the printed paper.
Since the final version of the paper was prepared I have found nine additional lines of evidence for the root being between Euglenozoa and neokaryotes. As space constraints did not allow their insertion into this paper I explain them elsewhere (Cavalier-Smith 2009d). They are: (1) absence of the centromeric histone H3 variant CENPA (crucial for neokaryote centromere assembly) in trypanosomatids and somewhat shorter N-terminal tails for histone H3 (with the segment embracing the key lysine for neokaryote acetylation labelling for heterochromatinization missing) and histone H4; (2) the RNase III dicer enzyme that generates small RNAs lacks two domains in trypanosomatids (like the ancestral prokaryotic RNase III) that were arguably added stepwise in neokaryotes and then neozoa; (3) absence in trypanosomatids (as in bacteria) of the PIWI paralogue of the Argonaute proteins that targets double-stranded RNA for digestion; (4) absence in trypanosomatids of RNA polymerase II transcription factors IIA, F, and H; (5) ER luminal quality control of nascent glycoproteins is simpler in trypanosomatids with two enzymes that Neozoa use to digest faulty ones (Mannosidase I and peptide-N-glycanase); (3) absence in trypanosomatids of kinesins 4-8 and 15; (6) absence in trypanosomatids of widespread tail domains from two of the three putatively ancestral myosins; (7) absence in trypanosomatids of the chromosomal cohesin Smc heterodimer Smc5/6; (8) absence in trypanosomatids of the ER calcium-binding protein calreticulin. (9) trypanosomatids have more primitive archaebacteria-like small nucleolar RNAs (snoRNAs) involved in prerRNA processing than do neokaryotes. All nine characters are most simply interpreted as the primitive condition for Euglenozoa (testable by studying them in bodonids, diplonemids, and euglenoids) and also for eukaryotes as a whole, rather than secondary simplifications of trypanosomatids alone.

Thus with ORC and TOM40 this makes at least 11 independent trypanosomatid characters best interpreted as the primitive state for all eukaryotes and supporting the primary eukaryotic dichotomy being between Euglenozoa and neokaryotes. The fact that these include such fundamental and diverse cell properties as mitochondrial protein import, nuclear DNA replication initiation, snoRNAs, and centromere biogenesis means that they cannot be dismissed as trivia and highlights the importance of studying all these features intensively in a phylogenetically broad spectrum of eukaryotes and carrying out genome projects for a similarly broad range of deep-branching Euglenozoa.

Furthermore, on the Polo-like paralogue-rooted aurora kinase tree Euglenozoa are the most divergent eukaryotes (Brown et al. 2004), as they are for each of the four paralogue subtrees of the giant chromatin protein SMC family (Gluenz et al. 2008); the latter may be especially significant as SMCs are extremely long and well-conserved proteins that seems to suffer much less from episodic quantum evolution in the stems of paralogue rooted trees than most other proteins and arguably give better single-gene trees than almost any other protein normally used for deep phylogeny.
‘Chromophyte’ here refers collectively to all algae with chlorophyll c so as to contrast them with non-photosynthetic Chromista such as Rhizaria, Ciliophora, Pseudofungi, and Heliozoa.
Throughout this paper ‘haem lyase’ refers always to the invariably nuclear-encoded monomolecular haem (=heme to Americans) lyase of neozoa only. Sometimes the unrelated non-homologous multigene Ccms of excavates and corticates (encoded in the mitochondrial genome in Loukozoa) are confusingly annotated in GenBank as haem or heme lyase, instead of by the more usual term ‘cytochrome c-type biogenesis protein’ normally used for their bacterial homologues); Allen et al. (2008) clearly explain all the different types of cytochrome c biogenesis enzymes currently known; the fourth method of cytochrome c-type biogenesis in eukaryotes is that chloroplasts use a second bacterial c-type biogenesis mechanism involving Res, probably introduced by their cyanobacterial ancestor and transferred to chromophytes by the secondary symbiogenetic red alga - but this was not discussed in this paper or shown on Fig. 1 as it is irrelevant to rooting the tree.

Table 1. Revised Classification of the Kingdoms Protozoa and Chromista

Kingdom Protozoa† Owen 1858 emend.

Subkingdom Eozoa†* Cavalier-Smith 1997 emend.

Infrakingdom and Phylum Euglenozoa Cavalier-Smith 1981 (Euglenoidea,

Diplonemea, Postgaardea**, Kinetoplastea)

Infrakingdom Excavata† Cavalier-Smith 2002 emend.

Phylum Percolozoa Cavalier-Smith 1991 (Pharyngomonadia and Tetramitia, i.e.

Lyromonadea, Heterolobosea, Percolatea)

Phylum Loukozoa† Cavalier-Smith 1999 (Jakobea, Malawimonadea, ?Diphyllatea)

Phylum Metamonada Cavalier-Smith 1981 emend. 2003 (Anaeromonadea, Eopharyngia, Parabasalia)

Subkingdom Sarcomastigota† Cavalier-Smith 1983 emend.

Phylum Amoebozoa Lühe 1913 emend. Cavalier-Smith 1998

Phylum Apusozoa Cavalier-Smith 1997 stat. n. 2003 emend. 2008

Phylum Choanozoa† Cavalier-Smith 1981

Kingdom Chromista Cavalier-Smith 1981 emend.

Subkingdom Harosa subk. n. Diagnosis: typically with cortical alveoli or tripartite

ciliary hairs or reticulose or filose pseudopods or ciliary gliding. Etymology: HAR the initials of Heterokonta (=stramenopiles) Alveolata and Rhizaria (= SAR group of Burki et al. 2007); plus meaningless suffix –osa as used in such names as Filosa (within the rhizarian Cercozoa), Lobosa (Amoebozoa) and Conosa (Amoebozoa) referring also to at least partially amoeboid groups.

Infrakingdom Heterokonta Cavalier-Smith 1986 (also known by the unnecessary junior (1989)

synonym ‘stramenopiles’)

Phylum Ochrophyta Cavalier-Smith 1986 (e.g. diatoms, brown algae, chrysophytes)

Phylum Pseudofungi Cavalier-Smith 1986 stat. n. 1989 (Oomycetes, Hyphochytrea, Developayella)

Phylum Bigyra Cavalier-Smith 1998 (Opalozoa, e.g. Actinophryida, Blastocystis; Bicoecea; Labyrinthulea)

Infrakingdom Alveolata Cavalier-Smith 1991

Phylum Myzozoa Cavalier-Smith 2004 (Dinozoa [dinoflagellates, ellobiopsids and

perkinsids]; Apicomplexa [apicomonads, Chromera, Sporozoa])

Phylum Ciliophora Doflein 1901 stat. n. Copeland 1956 (ciliates and suctorians)

Infrakingdom Rhizaria Cavalier-Smith 2002 emend.

Phylum Cercozoa Cavalier-Smith 1998

Phylum Retaria Cavalier-Smith 1999 (Foraminifera; Radiozoa)

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