Sunday Protist - A sampling of Cercozoa Part I

This post grew out of proportion, so I'm splitting it into two or three parts, to cater to our ever-shortening attention spans (mine included)...

[Warning: Taxonomy. Of the harshest kind: involves Cavalier-Smith]

At the moment, among my favourite supergroups is Rhizaria (tree). Rhizaria is generally where all the obscure, interesting, and outright weird eukaryotes get sent by molecular data these days. The group itself is fairly recent, having been formally spewed out declared by Cavalier-Smith in 2002, as a fusion of Cercozoa and Retaria(=forams and 'radiolarians'), as well as Heliozoa and Apusozoa, apparently because they had "a centrosomal core or radiating microtubules and two microtubular roots and soft surface, typically with reticulopodia." (TC-S 2002 IJSEM:297) Don't worry, I don't really know what that means either. That is, those are fairly common traits in many non-Rhizarians, even according to the TC-S 2002 classification.

The name derives from the group's inclusion of many members of the then-defunct "Rhizopods" ('root-feet' - members typically had thin, branchy pseudopodia). Since then, Heliozoa died a horrible death with its limbs strewn all over the tree (Nikolaev et al. 2004 PNAS) and [many] Apusozoa now seem to enjoy their privileged life as the putative basal Opisthokonts (or their sisters). Ironically, many of the "Heliozoa" did return to Cercozoa later. Obligatory TC-S Diagram:

The birth of Rhizaria. As the young supergroup struggles to open its eyes to the world for the first time, it is confronted by the glaring faces of frustrated readers threatening to ban the author from ever birthing another taxon, for the sake of global sanity. Yet, despite its weak, fragile synapomorphies, the newborn supergroup, heavily-medicated by state-of-the-art molecular phylogenies, rises to become a bona fide citizen of the taxonomic world. For now. As all other life forms on earth, the higher taxa themselves are mortal. (diagram slightly modified (red box added) from Cavalier-Smith 2002 IJSEM)

"Radiolarians" (Acantharians+Taxopodids+Polycystines) and Forams (more generally, Granuloreticulosea) are massively diverse, complicated and awesome, but Cercozoa are more obscure to non-protistologists, and are a rather weird assemblage of stuff. I think the Amoebozoan taxon "Variosea" would have been quite fitting for them, were it not taken by amoebae instead. Cercozoa is older than Rhizaria, but not by much - it was formally established by Cavalier-Smith in 1998 (Biol Rev) as a modified successor of Rhizopoda:

"The recently revised phylum Rhizopoda is modified further by adding more flagellates and removing some ‘ rhizopods ’ and is therefore renamed Cercozoa" (TC-S 1998 BiolRev:203)

Of course, that was Tom's version of Rhizopoda to begin with. Taxonomy gets very fun when different people at different times mean different things by the same name. Can't seem to find the etymology of Cercozoa, but the formal description reads pretty much like 'miscellaneous eukaryotes with thin pseudopodia'. And that they are.

While Cercozoa was initially based loosely on morphology and sketchy data from the dawn of molecular phylogenetics, it mostly survived intact over the years, and grew further (with various things shaved off too, of course). The original members were Phytomyxids (incl. the plant pathogen Plasmodiophora), Reticulofilosa (basically, Chlorarachniophytes) and Monadofilosa (Cercomonas, Gymnophrys, Euglypha and Spongomonas are given as original examples). Curiously, all of them survived the onslaught of molecular reality (or so we hope...). Stuff has been added, like Ascetosporea (paramyxids and haplosporidia; added in TC-S 2002 IJSEM) and the gromiids, as well as various obscure incertae sedis orphans and a few refugees from 'Heliozoa'.

Eventually, the Cercozoa got 'sistered' to the forams (Keeling 2001 MBE) by ACTIN phylogenies, which got taxonomically recognised in the TC-S 2002 IJSEM revision of The Book of Tom by declaring the holy union of Retaria (forams and rads) and Cercozoa as Rhizaria. Going overboard as usual by adding in Heliozoa and Apusozoa, of course. We're talking about the mad taxonomist here ;-) (now someone needs to make that into a pop culture phenomenon to rival mad scientists..."And along comes the evil mad taxonomist...and RENAMES EVERYTHING!" *cue spooky music*) The group still lacks any solid synapomorphies (shared derived characters); the situation is such that even the use of obscure ultrastructural elements has been attempted, such as Cavalier-Smith's "transitional nonagonal fibre" (TC-S 2008 Protist) – even one of his own past students has no idea what he meant there!

And a whole bunch of other stuff happened but I think that was enough Historical Taxonomy (would make the most popular course evar, srsly) for...the month. Ok, so have we lost everyone yet? Or have the wiser ones employed the high art of The Scrollbar and skimmed accordingly? In any case, I'd like to very briefly and shallowly run over a few of the major cercozoans to give you a taste of the phylum, and just how diverse and varied it is. Things will be skipped, including, quite possibly, The Most Interesting Thing Ever Because You Studied it for the Past Ten Years. Apologies in advance. TMITEBYSiftPTY will get its chance, someday.

Some phylogeny and taxonomy sources: TC-S & Chao 2003; Bass & TC-S 2004; Bass et al. 2005; Pawlowski & Burki 2009; Chantangsi et al. 2010.

(L: Pawlowski & Burki 2009; R: Chantangsi et al. 2010)

To be continued in Part II – Endomyxa.

References
Bass D, & Cavalier-Smith T (2004). Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa). International journal of systematic and evolutionary microbiology, 54 (Pt 6), 2393-404 PMID: 15545489

BASS, D. (2005). Polyubiquitin Insertions and the Phylogeny of Cercozoa and Rhizaria Protist, 156 (2), 149-161 DOI: 10.1016/j.protis.2005.03.001

CAVALIER-SMITH, T. (1998). A revised six-kingdom system of life Biological Reviews of the Cambridge Philosophical Society, 73 (3), 203-266 DOI: 10.1017/S0006323198005167

Cavalier-Smith T (2002). The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. International journal of systematic and evolutionary microbiology, 52 (Pt 2), 297-354 PMID: 11931142

Cavalier-Smith, T., & Chao, E. (2003). Phylogeny of Choanozoa, Apusozoa, and Other Protozoa and Early Eukaryote Megaevolution Journal of Molecular Evolution, 56 (5), 540-563 DOI: 10.1007/s00239-002-2424-z

CAVALIERSMITH, T., LEWIS, R., CHAO, E., OATES, B., & BASS, D. (2008). Morphology and Phylogeny of Sainouron acronematica sp. n. and the Ultrastructural Unity of Cercozoa Protist, 159 (4), 591-620 DOI: 10.1016/j.protis.2008.04.002

Chantangsi, C., Hoppenrath, M., & Leander, B. (2010). Evolutionary relationships among marine cercozoans as inferred from combined SSU and LSU rDNA sequences and polyubiquitin insertions Molecular Phylogenetics and Evolution, 57 (2), 518-527 DOI: 10.1016/j.ympev.2010.07.007

Keeling PJ (2001). Foraminifera and Cercozoa are related in actin phylogeny: two orphans find a home? Molecular biology and evolution, 18 (8), 1551-7 PMID: 11470846

Nikolaev, S. (2004). From the Cover: The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes Proceedings of the National Academy of Sciences, 101 (21), 8066-8071 DOI: 10.1073/pnas.0308602101

PAWLOWSKI, J., & BURKI, F. (2009). Untangling the Phylogeny of Amoeboid Protists Journal of Eukaryotic Microbiology, 56 (1), 16-25 DOI: 10.1111/j.1550-7408.2008.00379.x