This cladogram shows the upper systematics of the whole biota with main emphasis on Eukaryota, or Unikonta respectively. It also shows some of the most widely used paraphyletic groups. The cladogram is mainly based on Cavalier-Smith (2010) and illustrates his recent concepts concerning the Prokaryota-Eukaryota-transition (Neomura-hypothesis) and the deep phylogeny of Eukaryota. For a different hypothesis about the Prokaryota-Eukaryota-transition please refer to Lake (2009). For a more conservative approach to the systematics of the Eukaryota please refer to Adl et al. (2005).

2. Notes to certain monophyletic groups

• Amoebozoa: Three subphyla, Protamoebae, Conosa and Lobosa (Cavalier-Smith 2009). Protamoebae consists of only one class, Breviatea.

• Animalia: The cladogram uses the name Animalia differently than the majority of the cited literature. There Animalia is used as a synonym to Metazoa. Unfortunately this leaves unnamed the node that comprises Metazoa with Choanoflagellata. However, in some instances the name Animalia is used the same way as here, for example Da Lage et al. (2007), page 3931. Furthermore, the concept to consider certain single-celled organisms as animals has a very long tradition and is still in use (Westheide/Rieger 2006).

• Apusozoa: Only one class, Thecomonadea with three orders, Ancyromonadida, Apusomonadida and Hemimastigida (Cavalier-Smith 2002).

• Choanoflagellata: Three clades that form two branches. The first branch is formed by Choanoflagellata-clade 1 and Choanoflagellata-clade 2, yet unnamed. The second branch is formed by the family Acanthoecidae, comprising Tectiformes and Nudiformes (Carr et al. 2008) [shown from the second file version onwards].

• Corticates: A name used by Cavalier-Smith (2010) to comprise a supposedly monophyletic group of eukaryotes that are not neozoans or unikonts.

• Cristidiscoidia: Only one class, Discicristoidea with two orders, Nucleariida and Fonticulida (Cavalier-Smith 2009) [shown from the second file version onwards].

• Filasterea: Only one order, Ministeriida (Shalchian-Tabrizi et al. 2008).

• Fungi: The cladogram mentions just kingdoms and phyla of the Fungi. For further information please refer to Hibbett et al. (2007).

• Mesomycetozoa: The cladogram uses the name Mesomycetozoa. Therefore it follows Adl et al. (2005) rather than Cavalier-Smith (2009). In Adl et al. (2005) the clade Mesomycetozoa comprised a few genera of which some were thereafter identified as Cristidiscoidia or Filasterea. The rest were genera of a class now called Ichthyosporea. What was further left was the genus ’Corallochytrium’. Thus recently Mesomycetozoa would comprise the class Ichthyosporea and the genus ’Corallochytrium’. Steenkamp et al. (2006) found out, that the left genera really form exactly such a monophyletic group. This result was considered by Cavalier-Smith (2009). However, he did not use the name Mesomycetozoa, but Ichthyosporea, which now should include ’Corallochytrium’ as the fourth genus: The clade Mesomycetozoa as used in this cladogram is synonymous with the clade Ichthyosporea as used by Cavalier-Smith (2009). In the cladogram the Mesomycetozoa comprises two classes. Ichthyosporea with the orders Aphelidida, Dermocystida and Ichthyophonida and Corallochytrea with the order Corallochytrida.

• Metazoa: Porifera and another, yet unnamed clade that comprises Placozoa and Eumetazoa (Philippe et al. 2009).

• Nucletmycea: Fungi and Cristidiscoidia (Brown et al. 2009).

• X, Y, Z: nodes yet unnamed.

3. Paraphyletic groups

• Bacteria: Negibacteria + Posibacteria
• Prokaryota: Bacteria + Archaea
• Eozoa: Euglenozoa + Excavata
• Bikonta: Eozoa + Corticates
• Choanofila: Mesomycetozoa + Filasterea + Choanoflagellata
• Choanozoa: Cristidiscoidia + Choanofila
• Sarcomastigota: Amoebozoa + Apusozoa + Choanozoa

4. Common taxonomic terms not used

• Archaebacteria - synonymous with Archaea
• Choanoflagellates - synonymous with Choanoflagellata
• Choanoflagellida - synonymous with Choanoflagellata
• Choanomonada - synonymous with Choanoflagellata
• DRIP - synonymous with a part of Ichthyosporea
• Eubacteria - synonymous with Bacteria
• Eukarya / Eukaryonta - synonymous with Eukaryota
• Eumycetes - synonymous with Fungi
• Monera - synonymous with Prokaryota
• Parazoa - paraphyletic group (Porifera + Placozoa)
• Prokarya / Prokaryonta - synonymous with Prokaryota
• Mesomycetozoea - synonymous with Ichthyosporea
• Mycetes - synonymous with Fungi
• Mycophyta - synonymous with Fungi
• Mycota - synonymous with Fungi

5. Literature

Adl SM, Simpson AGB, Farmer MA, Andersen RA, Anderson OR, Barta JA, Bowser SS, Bragerolle G, Fensome RA, Fredericq S, James TY, Karpov S, Kugrens P, Krug J, Lane CE, Lewis LA, Lodge J, Lynn DH, Mann DG, McCourt RM, Mendoza L, Moestrup Ø, Mozley-Standridge SE, Nerad TA, Shearer CA, Smirnov AV, Spiegel FW, Taylor MFJR: ’The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists’. In: ’Journal of Eukaryotic Microbiology’ 52 (2005): 399 - 451

Brown MW, Spiegel FW, Silberman JD: ’Phylogeny of the "forgotten" cellular slime mold, Fonticula alba, reveals a key evolutionary branch within Opisthokonta’. In: ’Mol Biol Evol.’ 26 (2009): 2699 - 2709

Carr M, Leadbeater BSC, Hassan R, Nelson M, Baldauf SL: ’Molecular phylogeny of choanoflagellates, the sister group to Metazoa’. In: ’PNAS’ 105 (2008): 16641 - 16646

Cavalier-Smith T: ’ The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa’. In: ‘International Journal of Systematic and Evolutionary Microbiology’ 52 (2002): 297 - 354

Cavalier-Smith T: ’Megaphylogeny, Cell Body Plans, Adaptive Zones: Causes and Timing of Eukaryote Basal Radiations’. In: ’J. Eukaryot. Microbiol’ 56 (2009): 26 - 33

Cavalier-Smith T: ’Deep phylogeny, ancestral groups and the four ages of life’. In: ‘Phil. Trans. R. Soc. B’ 365 (2010): 111 - 132

Da Lage J-L, Danchin EGJ, Casane D: ’Where do animal a-amylases come from? An interkingdom trip’. In: ’FEBS Letters’ 581 (2007): 3927 - 3935

Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, Eriksson OE, Huhndorf S, James T, Kirk PM, Lücking R, Thorsten Lumbsch H, Lutzoni F, Matheny PB, McLaughlin DJ, Powell MJ, Redhead S, Schoch CL, Spatafora JW, Stalpers JA, Vilgalys R, Aime MC, Aptroot A, Bauer R, Begerow D, Benny GL, Castlebury LA, Crous PW, Dai YC, Gams W, Geiser DM, Griffith GW, Gueidan C, Hawksworth DL, Hestmark G, Hosaka K, Humber RA, Hyde KD, Ironside JE, Kõljalg U, Kurtzman CP, Larsson KH, Lichtwardt R, Longcore J, Miadlikowska J, Miller A, Moncalvo JM, Mozley-Standridge S, Oberwinkler F, Parmasto E, Reeb V, Rogers JD, Roux C, Ryvarden L, Sampaio JP, Schüssler A, Sugiyama J, Thorn RG, Tibell L, Untereiner WA, Walker C, Wang Z, Weir A, Weiss M, White MM, Winka K, Yao YJ, Zhang N: 'A higher-level phylogenetic classification of the Fungi'. In: 'mycological research' 111 (2007): 509 - 47

Lake JA: ‘Evidence for an early prokaryotic endosymbiosis’. In: ’Nature’ 460 (2009): 967 - 971

Philippe H, Derelle R, Lopez P, Pick K, Borchiellini C, Boury-Esnault N, Vacelet J, Renard E, Houliston E, Quéinnec E, Da Silva C, Wincker P, Le Guyader H, Leys S, Jackson DJ, Schreiber F, Erpenbeck D, Morgenstern, Wörheide G, Manuel M: ‘’Phylogenomics Revives Traditional Views on Deep Animal Relationships’’. In: ‘Current Biology’ 19 (2009): 706 - 12

Shalchian-Tabrizi K, Minge MA, Espelund M, Orr R, Ruden T, Jakobsen KS, Cavalier-Smith T: ’Multigene phylogeny of Choanozoa and the origin of animals’. In: ‘’PLoS ONE’’ 3 (2008): e2098

Steenkamp ET, Wright J, Baldauf SL: ‘The protistan origins of animals and fungi’. In: ’Molecular biology and evolution’ 23 (2006): 93 - 106