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Protistology 6 (1), 3—13 (2009)
Protistology
Systems Naturae or the outline of living world classification
Alexey B. Shipunov
Marine Biological Laboratory, Woods Hole, Massachusetts, USA
Summary
Here we present the short outline of the classification of living things (to the level of classes), given with two main goals: to provide a compact, synthetic overview of the biological diversity; and to supply users with up-todate information of latest taxonomic achievements. The latter is especially important in the recent epoch of “molecular revolution” in the taxonomy.
Key words: living organisms classification, kingdoms, phyla, classes
The era of fundamental works with the depth and breadth of “Systema Naturae” almost ended with the last edition of this great book (Linnaeus, 1767). However, oveviews of the diversity of living things, both collective (Adl et al., 2005, Hibbett et al., 2007) and individual (Corliss, 1984, 1994; Cavalier-Smith, 1998, 2004 and many others) continued to appear regularly until the recent time. Here we present the similar work.
Features
1) Coverage. The classification cover all indisputable living things. This means that viruses, virus-like forms and prions are not included. Author believes that classification should be a “slice” of the recent diversity, therefore fossil taxa also are not listed. We restricted the level of classification with classes.
2) Currentness. The classification presented here is very changeable: when new data (any suggestions about closeness of particular groups) be-
come available, classification is also changed. To approach changeability, we use simple versioning (RCS-based) system. The version presented here has number 5.8020, more recent versions periodically appear on the Web page http://herba.msu.ru/ shipunov/os/os-en.htm, older versions are also stored there.
3) Synthesis. The classification is fully synthetic: it is compiling from numerous sources treated as multiple opinions. Any suggestion addresses any triplet of relevant taxa (which could be represented like “A,(B,C)”) is taking into account with no selection between scientific sources. Weighting of the opinions is also a major component of classification construction.
4) Concepts. Kingdoms as highest taxa have a special treatment. We use a holistic approach to designate kingdoms according to the three levels of organization: (1) prokaryotic cells, (2) eukaryotic cells, (3) tissues/ organs (multitissued organisms sensu Corliss, 1989). On the third level, two kindoms
© 2009 by Russia, Protistology
(Animalia and Vegetabilia) designated, because their tissue/organ systems of them are not homologous (Ivanov, 1968; Kaiser, 1985a).
5) Lumping. We are holding with large taxa: if the aggregation of taxa is feasible on the given rank level, we treat them as one taxon. This approach follows the simple Occam razor (Swinburne, 1997).
6) Traditions. The classification is traditional from many points of view: (1) it is fully hierarchical, (2) uses only habitual ranks, (3) suggestions based on the morphological material are using with same extent as “molecular”, (4) retains traditional names, even in cases where underlying concepts are (slightly) different.
7) Order. Classification presented here is in a form of hierarchical list. The order ofsub-taxa within the super-taxon group is important. For example, sub-taxa designated as “peripheral” (Ljubarskij, 1996), are usually placing at the beginning or at the end of their part of list.
8) Fuzziness. To represent multiple opinions in one classification, we are using the extended traditional marks:
sed. m. (sedis mutabilis) given if there is a possibility to move the taxon “horizontally” either within super-taxon, or between supertaxa;
stat. m. (status mutabilis) is for the possibility to move the taxon downwards (“stat. m. i.”), or upwards (“stat. m. s.”) in the hierarchy;
i. s. (incertae sedis) used here only for cases where both previous states are simultaneously applicable;
sed. p. (sedis possibilis) designates the possible alternative location of “sed. m.” taxon;
s. str. (sensu stricto) marks “sticky” taxa where the aggregation with neighbor taxa is the alternative;
s. a. (sensu amplo) used here for “fragile” taxa which can be easily split;
s. aggr. (sensu aggregato) when both previous states are applicable;
(z) used in case of hemiohomonyms (Kluge, 2000) for ICZN names;
MY (dagger) for “traditional” names introduced here (see below);
“quotes” are for environmental groups which have only DNA sequencebased descriptions; here we list the most prominent of them, but usually not as separate items of the classification list;
* (asterisk) used for paraphyletic taxa; in general, our intention is to eliminate paraphyly, but some high taxa here are paraphyletic;
/ (slash) used for marginal notes designating domains (see below).
9) Nomenclature. Double nomenclature is used here:
Traditional names which are largely circumscription- and/or volumebased names (Kluge, 2000). We removed the authorship from all names because most of names for higher taxa have been used in various senses (it is especially frequent in protists), therefore, designation an authorship will make situation even less clear. In that regard, we are generally agree with recent proposal of Dubois (2007) abut non-citing authors. In some cases, new names have been created, mostly with changed endings to avoid inter-rank homonymy. These names are marked with dagger (f).
Typified names as simple genus-like uninomi-als without endings but with rank designated by left-hand superscript (i.e., “Phylum Arthropoda” becomes “Araneus”.). The designator is a number with optional decimal part, ranged from 0 (individual) to 7 (kingdom). All intermediate ranks received the unique fraction part: —0.2 (0.8) for sub-, 0.5 for infra-, and 0.2 for super-groups. We hope that from this attempt the list of typified names will finally emerge and become an essential part of higher taxa nomenclature. Types have been chosen types mostly in the accordance with the original descriptions, but for the few taxa we introduced new types. In particular, we chose several type names which sounds similar to the traditional name of taxon (Tatarinov and Shimanskij, 1984).
Kingdoms
Ifwe accept that the highest divisions of organic world should be as broad as possible, we may end up with two different conceptions. We call them “kingdoms” and “domains” (Blackwell, 2004). The first concept is the logical derivate of symbiogenetic theory (Merezhkovsky, 1909) and based on the idea of levels of organization. These levels correspond with four kingdoms: Monera (or Prokaryota), Protista, Vegetabilia (or Plantae) and Animalia (or Metazoa). The third, multi-tissued level is the least stable: it corresponds with two kingdoms and several groups of protists which also reached this level of organization, notably lichenized fungi and higher brown algae like Fucales and Laminariales (Smith, 1939; Kaiser, 1985b; Buedel and Scheidegger, 2008). These latter groups are usually not considered as kingdoms because of lesser gap between them and their non-multitissued relatives. The other problem of “kingdoms” concept is the absence of positive description for protists. It is possible, however, to
define protists as “eukaryotic organisms with cells forming a homogeneous assemblages or developing independently after the division”, but it will not improve our understanding of protists as a paraphyletic group. Monera also have problems with paraphyly and non-negative description, which may be at least partly solved (Martin and Koonin, 2006).
The reductionist “domains” conception takes into account mostly molecular characters and better coincides with cladistic way of thought. Bacteria, Archaea and Eukarya are usually considered as “primary” domains, Panplantae (aka “bikonts”) and Pananimalia (“unikonts”) may also belong here. In many publications, they are monophyletic, and primary domains appear in every analysis of the environmental DNA. However, recent genomic findings such as “tree of1%” (Dagan and Martin, 2006) became less supportive for domains; genome-wide data of prokaryotes is also in favor to the Monera, then to domains (Koonin and Wolf, 2008). There are also some concerns about strict monophyly of Archaea (Cox et al., 2008; Yutin et al., 2009) and even Bacteria (Lake et al., 2008). In addition, this conception simply ignores morphological diversity of higher groups whereas it is well known that different taxonomic characters may play different roles in the classification of distant taxa (Ljubarskij, 1996).
It is not an easy task to interbreed these conceptions together (see Table 1). We are accepting here more traditional “kingdoms” conception as having more explanatory power, and also as a better interscience communication tool. However, we designate domains as marginal notes in the outline, and also as “girts” in the classification scheme (Fig. 1). There are the list of accepted kingdoms:
Monera This kingdom corresponds with two domains: Bacteria and Archaea, which are treated here as subkingdoms (Fig. 1). The classification based mostly on the results of sequence comparisons and wholegenome analyses. During the widespread HGT events (Koonin and Wolf, 2008), the stability of higher taxa is lower than for other kingdoms.
Protista This is a good example of paraphyletic but integral (according to the level of organization) taxon. Since the idea (Stechmann and Cavalier-Smith, 2002) about two major eukaryotic branches (here we use names Pananimalia and Panplantae reflecting the their cross-kingdom nature) is obtaining more support (Hampl et al., 2009), we marked them as domains. Infrakingdom Apusobionta may finally appear as non-natural because the support for the position and unity of this group is quite moderate (Cavalier-Smith et al., 2008). Fungi in our classification belong to protists since they generally lack organ/tissue systems.
Table 1. Two concepts of highest taxonomic categories.
Monera Vegetabilia Protista Animalia
Bacteria Archaea Panplantae Pananimalia
Vegetabilia Only three phyla reflecting the major features of the life cycle (with gametophyte dominance; with sporophyte dominance and free gametophyte; and with a seed) are accepted here. On the Fig. 1, the “girt” shows that with the domain approach this kingdom should be treated as a part of Panplantae.
Animalia Historically, animal phyla reflect the traditional idea of “bauplan”. However, since sponges, coelenterates, placozoans and acoels are now the “hot spots” of animal classification, groups here should be considered as generally unstable. The position of the latter group in Deuterostomia is based on the recent publications (Deutsch, 2008 and others). The volume of phylum Platyzoa is also discussable. With the domain approach, the kingdom will become a part of Pananimalia (“unikonts”).
The outline
Regnum Monera [ 1 Bacillus j /Bacteria
Subregnum Bacteria [ 6 8Bacillus j*1 Superphylum Terrabacteria [ 62Bacillus j s.a. Phylum 1. Thermobacteria^ [ 6Deinococcusj s.a. Classis 1(1). Aquificae [ 5Aquifex j sed.m.2
2(2). Thermotogae [ 5Thermotoga j sed.m. 3(3). Deinococci [ 5Demococcus j3 Phylum 2. Actinobacteres f [ 6Actynomyces j Classis 1(4). Actinobacteria [ 5Actinomyces j Phylum 3. Firmicutes [ 6Bacillus j s.a., sed.m.4 Classis 1(5). Clostridia [ 5 Clostridium j5 2(6). Bacilli [ 5Bacillus j 3(7). Erysipelotrichi [ 5Erysipelothrix j 4(8). Mollicutes [ 5Mycoplasma j6 5(9). Dictyoglomia [ 5Dictyoglomus j sed.m. 6(10). Fusobacteria [ 5Fusobacterium j sed.m. Phylum 4. OBSCUROBACTERESf 7
1Incl. “Nanobacteria” i.s. et dubitativa
2Incl. Desulfurobacteriaceae, Thermodesulfobacteriaceae, Hydrogenothermaceae.
3Incl. Thermales.
4Incl. “OP9” and probably other environmental groups.
5Incl. Symbiobacteria, Thermolithobacteria stat.m., Sulfoba-cillus i.s., Thermaerobacter i.s.
6Incl. Lumbricincola.
7“TM7”—“OP11” group, one of the largest and best delineated environmental groups. Probably includes “TM7”, “OD1”, “OP11”, “WS6”, “WWE3” and some other lineages.
Fig. 1. The schematic view of the classification. This scheme is a variant of nested treemap, a compact alternative to the tree-like presentations (Johnson and Shneiderman, 1991). The most outer squares designate kingdoms, text strings represent phyla, all other squares represent taxa of the intermediate ranks. To make the scheme even more compact, all names of taxa higher than phyla, and squares for the phyla are omitted. “Channels” between squares designate cases of accepted paraphyly on the level of kingdoms.
Phylum 5. Chloroflexes [ бChloroflexus j8 Classis 1(11). Thermomicrobia [ 5 Thermomicrobium j 2(12). Chloroflexi [ 5Chloroflexus j 3(13). Dehalococcoidetes [ 5Dehalococcoidesj 4(14). Anaerolineae [ 5Anaerolinea j9 5(15). Ktedonobacteria [ 5Ktedonobacter j Phylum б. Cyanobacteria [ 6Nostoc j sed.m. Classis 1(1б). Gloeobacteria [ 5Gloeobacter j 2(11). Oscillatorineae* [ 5 Oscillatoria j10 3(18). Nostocineae [ 5Nostoc j Superphylum Gracilicutes [ б.2Шodospirillum\ s.a. Phylum 1. Spirochaetae [ (sSpirochaeta j sed.m. Classis 1(19). Spirochaetes [ 5Spirochaeta j s.a.11
8Incl. Thermobaculum i.s.
9Incl. Caldilineae.
10Incl. Synechococcineae stat.m., ‘Prochlorophyceae’, Acaryochloris.
11Incl. Leptospira.
Phylum 8. Endomicrobest [ бEndomicrobium j sed.m.
Classis 1(20). Endomicrobia [ 5Endomicrobium j12 Phylum 9. Bacteroidetes [ 6Bacteroides j s.a.13 Classis 1(21). Gemmatimonadetes [ 5Gemmatimonas j sed.m.
2(22). Fibrobacteria [ 5Fibrobacter j 3(23). Chlorobia [ 5Chlorobium j 4(24). Bacteroidia [ 5Bacteroides j14 5(25). Salinibacteriay [ 5Salinibacter ]
stat.m.s.
Phylum 10. Planctobacteria [ 6Planctomyces j15 Classis 1(2б). Planctomycea [ 5Planctomycesj 2(21). “Poribacteria” [ 5“Poribacter” j
12= “TG1”.
13Incl. “TG3”.
14Incl. Flavobacteria, Sphingobacteria, Cytophagia.
15= “PVC”, incl. “OP3”.
3(28). Chlamydiae [ 5 Chlamydia j 4(29). Lentisphaeria [ 5Lentisphaera j 5(30). Verrucomicrobiae [5Verrucomicrobi-
umj16
Phylum 11. Proteobacteria [ 6Rhodospirillum ] s.a. Classis 1(31). Caldiseria' [ 5Caldisericum j i.s.11 2(32). Aminanaerobia [ 5Deferribacter j i.s. et s.a.18 3(33). Acidobacteria [ 5Acidobacterium j sed.m.19 4(34). Desulfobacteria [ 5Desulfobacter j s.a.20 5(35). Rhodobacteria [ 5Rhodobacter j21 Subregnum Archaebacteria [ 6.8Methanobac-terum j* /Archaea
Phylum 12. Nanoarchaeota [ 6Nanoarchaeum ] stat.m.
Classis 1(3б). Nanoarchea [ 5Nanoarchaeum j Phylum 13. Euryarchaeota [ 6Methanobacte-rium j
Classis 1(31). Thermococci [ 5 Thermococcus j
2(38). Methanobacteria [ 5Methanobacterium j
s.a.22
3(39). Thermoplasmata [ 5Thermoplasma j 4(40). Archaeoglobi [ 5Archaeoglobus j 5(41). Halomebacteria [ 5Halobacterium j23 Phylum 14. Korarchaeota [ 6Korarchaeum ] stat.m.
Classis 1(42). Korarchaea [ 5Korarchaeum j Phylum 15. Thaumarcheota [ 6Cenarchaeum ] stat.m.
Classis 1(43). Cenarchaea [ 5 Cenarchaeum j Phylum 1б. Crenarchaeota [ 6Sulfolobus ] Classis 1(44). Thermoprotei [ 5 Thermoproteus j 2(45). Sulfolobea [ 5Sulfolobus j24
Regnum Protista [ JEuglena j*
Infraregnum Panmycota' [ б5Agaricus j*
/Pananimalia Superphylum Myconta' [ 62Agaricus ]* s.a. Phylum 11. Choanozoa [ 6Codosiga ] s.a.
Classis 1(4б). Filasterea [ 5Capsaspora j25
16Incl. Opitutae, Spartobacteria.
11=“OP5”, the formal name is not yet published.
18Incl. Synergistetes, Chrysiogenetes i.s., Nitrospira i.s.,
Calditrix i.s.
19Incl. Halophagae, Solibacteres.
20Incl. Deltaproteobacteria, Epsilonproteobacteria.
21Incl. Alphaproteobacteria, Betaproteobacteria, Gamm-aproteobacteria.
22Incl. Methanobacteriales, Methanococcales stat.m., Meth-anopyrales i.s.
23Incl. Methanomicrobiales, Methanosrcinales, Halobacte-riales.
24Incl. Desulfurococcales, Caldisphaerales.
25Incl. Ministeria.
2(41). Choanomonadea [ 5Codosiga j 3(48). Ichthyosporea [ 5Ichthyophonus j26 4(49). Cristidiscoidia [ 5Nuclearia j21 Phylum 18. Eomycotay [ 6Mucor ]* s.a.
Classis 1(50). Chytridiomycetes [ 5 Chytridiopsis j28 2(51). Blastocladiomycetes [ 5Blastocladium j 3(52). Rozellomycetes [ 5Rozella j29 4(53). Kickxellomycetes [ 5Kickxella j30 5(54). Mucoromycetes [ 5Mucor j*31 б(55). Glomeromycetes [ 5Glomus j Phylum 19. Microsporidia [ (,Microsporidium ] Classis 1(5б). Microsporea [ 5Microsporidium j32 Phylum 20. Basidiomycota [ бAgaricus ] Subphylum Ustilagomycotina [ 5 8 Ustilago ] Classis 1(51). Exobasidiomycetes [ 5Exobasidium j 2(58). Ustilaginomycetes [ 5 Ustilago j Subphylum Pucciniomycotina [ 5 8 Uredo ] Classis 3(59). Pucciniomycetes [ 5 Uredo j
4(б0). Atractiellomycetes [ 5Atractiella j 5(б1). Cystobasidiomycetes [ 5 Cystobasidium j б(б2). Agaricostilbomycetes [ 5Agaricostilbum j 1(б3). Microbotryomycetes [ 5Microbotryum j33 8(б4). Mixiomycetes [ 5Mixia j Subphylum Agaricomycotina [ 5 8Agaricus ] Classis 9(б5). Wallemiomycetes [ 5Wallemia j sed.m.34
10(бб). Bartheletiomycetesy [ 5Bartheletia j 11(б1). Tremellomycetes [ 5Tremella j 12(б8). Dacrymycetes [ 5Dacrymyces j 13(б9). Agaricomycetes [ 5Agaricus j Phylum 21. Ascomycota [ ^comyces ]35 Subphylum Taphrinomycotina [ 5.8Ascomyces j*36 Classis 1(10). Taphrinomycetes [ 5Ascomyces j31
2(11). Schizosaccharomycetes [ 5Schizosac-
caromyces j38
3(12). Saccharomycetes [ 5Saccaromyces j 4(13). Neolectomycetes [ 5Neolecta j Subphylum Pezizomycotina [ 5 8 Tuber ]
2l5Incl. Amoebidium, Eccrinales, Aphelidea sed.m., Coral-
lochytrium.
21
Incl. Nucleariidae, Pompholyxophryidae sed.m.
28Incl. Neocallimastigales, Thalassochytrium sed.m.
29Incl. Olpidium et Caulochytrium sed.m.
30Incl. Basidiobolaceae, Harpellales, Asellariales, Zoopagales, Entomophthorales, Nephridiophaga.
31Incl. Endogonales, Mortierellales.
32Incl. Metchnikovellidea sed.m., Mikrocytos mackinised.m.
33Incl. Cryptomycocolacales, Classiculales.
34Incl. Entorrhiza stat.m.i.
35Incl. Spirogyromyces i.s.
36іш1. “SCGI” group.
31Incl. Saitoella.
38Incl. Pneumocystis.
Classis 5(14). Orbiliomycetes [ 5Orbilia j 6(15). Pezizomycetes [ 5Tuber j 1(16). Dothideomycetes [ 5Dothidea j39 8(11). Eurotiomycetes [ 5Penicillium j 9(18). Lecanoromycetes [ 5Lecanora j40 10(19). Laboulbeniomycetes [ 5Laboulbenia j 11(80). Leotiomycetes [ 5Leotia j 12(81). Sordariomycetes [ 5Sordaria j Superphylum Sarcobionta' [ 6 2Amoeba ]
Phylum 22. Amoebozoa [ 6Amoeba ]41 Subphylum Lobosea [ 5 8Amoeba ]42 Classis 1(82). Tubulinea [ 5Amoeba j 2(83). Flabellinea [ 5Vannella j 3(84). Acanthopodida [ 5Acanthamoeba j43 4(85). Thecamoebida i.s.[ 5Thecamoeba j 5(86). Mayorellida' [ 5Mayorella j i.s.44 Subphylum Conosea [ 5 8Physarum ]
Classis 6(81). Variosea [ 5Filamoeba j sed.m.45
1(88). Mastigamoebidae [ 5Mastigamoeba j46 8(89). Mycetozoa [ 5Physarum j41 Phylum 23. Breviatozoa' [ 6Breviata ] i.s. Classis 1(90). Breviatea [ 5Breviata j InfTaregnum Apusobionta' [ 65Apusomonas j i.s.
/Panplantae Phylum 24. Apusozoa [ 6Apusomonas ]
Classis 1(91). Apusomonadea [ 5Apusomonas j48
2(92). Planomonadea [ 5Planomonas j sed.m.49 Infraregnum Excavata [ 6 5Euglena j
Phylum 25. Metamonada [ 6Trichomonas ] s.a. Classis 1(93). Preaxostyla [ 5Oxymonas j50
2(94). Parabasalea [ 5 Trichomonas j51 3(95). Fornicata [ 5Hexamita j52 Phylum 26. Discoba [ 6Euglena ] s.a. Subphylum Jakobozoay [ 5.8Jacoba j
39Incl. Arthoniales.
40Incl. Lichniales.
41Incl. ‘X-cells’ i.s.
42Incl. Trichosphaerium i.s., Vermistella i.s., Cochliopodium i.s., Corallomyxa i.s, Stereomyxa i.s.
43Incl. Balamuthia.
44Incl. Dermamoeba.
45Incl. [ 5Phalansterium j, Acramoeba, Multicilia, ‘Arachnula’ sensu Tekle et al., 2008.
46Incl. Pelomyxa, Entamoeba, Endolimax, Endamoeba.
41Dictyostelia, Protostelia, Copromyxidae sed.m., Ceratiomyxa sed.m., Semimorula.
48Incl. Amastigomonas, Apusomonas.
49Incl. “Ancyromonas” = Planomonas, Micronuclearia sed.m.
50Incl. oxymonadida, Trimastix.
51Incl. Trichomonadida, Hypermastigida.
52Incl. Carpediemonas, Hicanonectes, Dysnectes, Retortamona-
dida, Diplomonadida.
Classis 1(96). Anisomonadea [ 5Collodictyon j i.s.53 2(91). Malawimonadea [ 5Malawimonas j
sed.m.
3(98). Jakobea [ 5Jakoba j54 4(99). Heterolobosea [ 5Naegleria j55 5(100). Hemimastigea [ 5Spironematella j i.s.56 Subphylum Euglenozoa [ 5 8Euglena ]
Classis 6(101). Euglenophyceae [ 5Euglena j* s.a.51 1(102). Kinetoplastea [ 5Bodo j Infraregnum Chlorobionta [ 65 Volvox j* Superphylum Rhizaria [ 6 2 Cercomonas ]
Phylum 21. Cercozoa [ 6Cercomonas ] s.a.58 Subphylum Monadofilosea [ 5 8 Cercomonas ] Classis 1(103). Chlorarachniophyceae [ 5Chlorar-achnion j
2(104). Metromonadea [ 5Metromonas j stat.m. 3(105). Granofilosea [ 5Heliomorpha j59 4(106). Sarcomonadea [ 5Cercomonas j* s.a60 5(101). Thecofilosea [ 5 Coelodendrum j s.a.61 Subphylum Endomyxa [ 5 8 Gromia ]
Classis 6(108). Foraminifera [ 5Rotalia j62 1(109). Gromiidea [ 5 Gromia j 8(110). Proteomyxidea [ 5Filoreta j63 9(111). Plasmodiophorea [ 5Plasmodiophora j64 10(112). Ascetosporea [ 5Haplosporidium j65 Phylum 28. Radiolaria [ 6Acanthometra ] Classis 1(113). Acantharia [ 5Acanthometra j
53Incl. Diphylleia (z), Collodictyon, Sulcomonas.
54Incl. Andalucia.
55Incl. Pleurostomum, Acrasis, Guttulinopsis sed.m., Fonticula sed.m., Stephanopogon stat.m.i.
56Sed.p. juxta Thecofilosea; incl. Hemimastix, Stereonema, Paramastix sed.m.
51Incl. Diplonemea (= Diplosonematea) stat.m., Symbiontida stat.m. (Calkinsia, Postgaardi), Notosolenus, Petalomonas.
58Incl. Meteora i.s.
59Incl. Massisteria, Limnofila, Nanofila, Mesofila, Desmotho-racida, Gymnosphaeridae sed.m., Heliomonadida, Microcometes sed.m., Boveemonas sed.m., Pseudodimorpha sed.m., Kibisdytes sed.m.
60Incl. Cercomopnadida sed.m., Glissomonadida, Pansomon-adida, Metopion sed.m., Allantion sed.m.
61Incl. Cryomonadida, Phaeodarea, Ebriida, Protaspis, Pseu-dodifflugia, Spongomonadida, Thaumatomonadida, Pseudopir-sonia, Auranticordis, Euglyphida.
62Incl. Xenophyophorea, Reticulomyxa, Komokiacea, Schizo-cladus.
63Incl. Vampyrellidae sed.m., Biomyxidae sed.m., Pseudospora sed.m., Rhizoplasmidae s.aggr., Leucodictyon sed.m., Reticu-loamoeba sed.m.
64Incl. Phagomyxa.
65Incl. Paramyxidia, Bonamia, Claustrosporidium, Paradin-ium.
2(114). Taxopodida [ 5Sticholonche j 66 3(115). Polycystinea [ 5Collosphaera j Superphylum Heteroconta [ 6 2Fucus ]
Phylum 29. Bicosoecozoa [ 6Bicosoeca ]
Classis 1(116). Bicoecea [ 5Bicosoeca j61 Phylum 30. Labyrinthomorpha [ 6Labyrinthula ] Classis 1(111). Labyrinthulea [ 5Labyrinthula j68 Phylum 31. Opalinomorpha' [ 6Opalina ] Classis 1(118). Blastocystea [ 5Blastocystis j 2(119). Opalinea [ 5Opalina j69 3(120). Actinophryida [ 5Actinophrys j sed.m.10 Phylum 32. Oomycota [ 6Saprolegnia ]
Classis 1(121). Oomycetes [ 5Saprolegnia j 11 Phylum 33. Chromophyta [ 6Fucus ] 12 Classis 1(122). Bacillariophyceae [ 5Diatoma j s.a.13 2(123). Dictyochophyceae [ 5Dictyocha j 14 3(124). Pelagophyceae [ 5Pelagomonas j 15 4(125). Eustigmatophyceae [ 5Eustigmatos j 5(126). Chrysophyceae [ 5 Chrysococcus j s.a.16 6(121). Pinguiophyceae [ 5Pinguiochrysis j 1(128). Raphidophyceae [ 5Rhaphidomonas j 8(129). Phaeophyceae [ 5Fucus j s.a.11 Superphylum Alveolata [ 6.2Paramecium ] Phylum 34. Myzozoa [ 6Peridinium ] Subphylum Apicomplexa [ 5.8Plasmodium ]
s.a.
Classis 1(130). Apicomonadea [ 5 Colpodella j18 2(131). Chromerida [ 5 Chromera j 3(132). Gregarinea [ 5Gregarina j 19
66Incl. Larcopyle.
61Incl. Placidiales (incl. Wobbia), Borokales, Anoecales (incl. Cafeteria, Caecitellus), Bicoecales, Commation sed.m., Discocelis sed.m.
68Incl. Diplophrys, Sorodiplophrys, Thraustochytridiales, Labyrinthuloideales.
69Incl. Proteromonadida.
10Sed.p. juxta Pedinellales.
11Incl. Developayella, Pirsonia, Hyphochitriomycetales, “MAST-4, 1, 8” groups.
12Incl. Leukarachnion.
13= Khakista, incl. Bolidomonas stat.m.
14Incl. Pedinellales, Rhizochromulinales.
15Incl. Sarcinochrysidales.
16Incl. Picophagus, Synchroma, Chlamydomyxa, Leukara-chnion, Oikomonas, Paraphysomonas, “MAST-1, 2, 3, б” groups sed.m.
11= Fucistia, incl. Chrysomeridophyceae stat.m., Schizo-cladiophyceae, Xanthophyceae stat.m., Phaeothamniales, Aurearenophyceae.
18Incl. Colponema sed.m. Algovora, Voromonas, Aplphamonas, Chilovora, Colpodella, Acrocoelus.
19Incl. Rhytidocystisstat.m., Cryptosporidium sed.m., Selenidium.
4(133). Sporozoa [ 5Plasmodium j s.s.80
Subphylum Dinozoa [ 5 8Peridinium ]
Classis 5(134). Perkinsida [ 5Perkinsus j81 6(135). Ellobiopsea [ 5Ellobiopsis j82 1(136). Syndinea [ 5Syndinium j83 8(131). Oxyrridea [ 5Oxyrris j 9(138). Dinoflagellata [ 5Peridinium j84 Phylum 35. Ciliophora [ 6Paramecium ]
Subphylum Postciliodesmatophora [ 5 8Spirosto-mum j
Classis 1(139). Karyorelictea [ 5Trachelocerca j 2(140). Heterotrichea [ 5Spirostomum j
Subphylum Intramacronucleata [ 5 8Parame-cium j
Classis 3(141). Spirotrichea [ 5Oxytricha j85 4(142). Armophorea [ 5Clevelandella j 5(143). Litostomatea [ 5Spathidium j 6(144). Phyllopharyngea [ 5Podophrya j86 1(145). Nassophorea [ 5Nassula j81 8(146). Colpodea [ 5Colpoda j 9(141). Prostomatea [ 5Prorodon j 10(148). Plagiopylea [ 5Plagiopyla j 11(149). Oligohymenophorea [ 5Paramecium j Superphylum Cryptobionta [ 6 2 Cryptomonas ] Phylum 36. Cryptista [ 6Cryptomonas ] s.a.88
Classis 1(150). Cryptophyceae [ 5Cryptomonas j89
2(151). Katablepharidea [ 5Katablepharis j
sed.m.90
3(152). “Biliphyta” [ 5“Biliphyta” j91 4(153). Telonemia [ 5Telonema j stat.m. Phylum 31. Centrohelida [ 6Acanthocystis ] sed.m.
Classis 1(154). Holosea [ 5Luffisphaera j i.s.92
2(155). Centrohelea [ 5Acanthocystis j93 Phylum 38. Haptophyta [ 6Prymnesium ]
80Incl. Coccidia sed.m., Piroplasmida, Haemosporidia, Ne-phromyces.
81Incl. Perkinsus, Parvilucifera, Rastrimonas, Phagodinium sed.m.
82Incl. Ellobiocystis, Parallobiopsis, Rhizellobiopsis, Thalas-somyces.
83Incl. “Marine Alveolate Groups I and II”.
84Incl. Noctiluca.
85Incl. Protocruzia, Phacodinium, Lycnophora.
86Incl. Suctoria, Synchimeniida.
81Incl. Nassulina, Microthoracina.
88Incl. Palpitomonas sed.m.
89Incl. Goniomonas, Tetragonidium, Bjornbergiella.
90Incl. Leucocryptos, Platychilomonas, Hatena.
91Incl. “Picobiliphyta”
92Incl. Paraluffisphaera.
93Incl. ‘Microheliozoan’.
Classis 1(156). Prymnesiophyceae [ 5Prymnesium j94 Superphylum Archaeplastida [ 6 2 Volvox ]
Phylum 39. Glaucophyta [ 6Glaucocystis ] Classis 1(151). Glaucophyceae [ 5Glaucocystis j Phylum 40. Rhodophyta [ 6Bangia ]
Classis 1(158). Cyanidiophyceae [ 5Cyanidium j95 2(159). Rhodellophyceae s.a.[ 5Rhodella j96 3(160). Compsogonophyceae [ 5Compsopogon j 4(161). Bangiophyceae [ 5Bangia j 5(162). Florideophyceae [ 5Palmaria j Phylum 41. Chlorophyta [ 6 Volvox ]* s.a. Subphylum Chlorophytina [ 5 8 Volvox ]
Classis 1(163). Prasinococcophyceae [ 5Prasinococ-cus j stat.m.s.
2(164). Nephroselmidophyceae [ 5Nephrosel-
mis j*91
3(165). Tetraphyceaey [ 5Tetraselmis j 4(166). Pedinophyceae [ 5Pedinomonas j
stat.m.s.
5(161). Chlorophyceae [ 5 Volvox j 6(168). Trebouxiophyceae [ 5Chlorella j98 1(169). Ulvophyceae [ 5U?va j Subphylum Charophytina [ 5 8 Chara ]*
Classis 8(110). Mesostigmatophyceae [ 5Mesostigma j 9(111). Charophyceae [ 5Chara j*99 Regnum Vegetabilia [ 1 Magnolia j Phylum 42. Bryophyta [ 6Bryum ]*
Subphylum Hepaticae [ 5.8Marchantia j Classis 1(112). Haplomitriopsida [ 5Haplomitrium j100 2(113). Marchantiopsida [ 5Marchantia j101 3(114). Jungermanniopsida [ 5Jungerman-
nia j102
Subphylum Bryophytina [ 5.8Bryum j Classis 4(115). Takakiopsida [ 5Takakia j
5(116). Sphagnopsida [ 5Sphagnum j103 6(111). Andreaeopsida [ 5Andreaea j104 1(118). Polytrichopsida [ 5Polytrichum j*105 8(119). Bryopsida [ 5Bryum j106 Subphylum Anthocerotophytina [ 5 8Anthoceros ]
94Incl. Pavlovophyceae.
95Incl. Cyanidium, Galdieria, Glaucosphaera.
96Incl. Stylonematophyceae, Porphyridiophyceae.
91Incl. Pyraminomonadales, Mamiellales, Nephroselmidales, Picocystis.
98Incl. Helicosporidium, Geminella and Microspora i.s.
99Incl. Conjugatophyceae.
100Incl. Treubiales.
101Incl. Blasiales, Sphaerocarpales, Monocleales.
102Incl. Pelliales, Fossombroniales, Pallaviciniales.
103Incl. Ambuchanania.
104Incl. Andreaeobryum stat.m.i.
105Incl. Oedipodiales stat.m.i., Tetraphidales stat.m.i.
106Incl. Buxbaumiales sed.m., Diphysciales, Timmiales.
Classis 9(180). Anthocerotopsida [ 5Anthoceros j101 Phylum 43. Pteridophyta [ 6Pteris ]* Subphylum Lycopodiophytina [ 5 8Lycopodium ] Classis 1(181). Lycopodiopsida [ 5Lycopodium j108 Subphylum Pteridophytina [ 5 8Pteris ]
Classis 2(182). Psilotopsida [ 5Psilotum j
3(183). Ophioglossopsida [ 5Ophioglossum j 4(184). Equisetopsida [ 5Equisetum j 5(185). Marattiopsida [ 5Marattia j 6(186). Pteridopsida [ 5Pteris j Phylum 44. Spermatophyta [ 6Magnolia ] s.a. Classis 1(181). Cycadopsida [ 5Cycas j 2(188). Ginkgoopsida [ 5Ginkgo j 3(189). Gnetopsida [ 5Gnetum j 4(190). Pinopsida [ 5Pinus j109 5(191). Angiospermae [ 5Magnolia j Regnum Animalia [ 1Araneus j 110 /Pananimalia Subregnum Spongia [ 68 Spongia ]
Phylum 45. Silicea [ 6Spongia ] stat.m.s.
Classis 1(192). Hexactinellea [ 5Euplectella j
2(193). Demospongia [ 5Spongia j s.aggr. Phylum 46. Calcispongia [ 6Sycetta ] stat.m.s. Classis 1(194). Calcarea [ 5Sycetta j Phylum 41. Homosclerea [ 6Oscarella ] stat.m.s. Classis 1(195). Homoscleromorpha [ 5Oscarella j Subregnum Phagocytellozoa [ 6 8 Trichoplax ] Phylum 48. Placozoa [ 6 Trichoplax ]
Classis 1(196). Trichoplacoidea [ 5 Trichoplax j Subregnum Ctenophora [ 6 8 Ctenoplana ]
Phylum 49. Ctenophora [ 6 Ctenoplana ]
Classis 1(191). Ctenophoroidea [ 5Ctenoplana j111 Subregnum Cnidaria [ 6 8Hydra ]
Phylum 50. Anthozoa [ 6Actinia ]
Classis 1(198). Zoantharia [ 5Actinia j
2(199). Alcyonaria [ 5Alcyonium j Phylum 51. Medusozoa [ 6Hydra ]*
Classis 1(200). Staurozoa [ 5Lucernaria j 2(201). Cubozoa [ 5Carybdea j 3(202). Scyphozoa [ 5Aurelia j 4(203). Hydrozoa [ sHydra j 5(204). Polypodiozoa [ 5Polypodium j stat.m. Phylum 52. Myxozoa [ 6Myxidium ]
Classis 1(205). Malacosporea [ 5Tetracapsula j112 2(206). Myxosporea [ 5Myxidium j113 Subregnum Bilateria [ 6 8Araneus ]
Infraregnum Deuterostomia [ 65 Felis ] s.a.
101Incl. Leiosporocerotales. 108Incl. Isoetopsida stat.m.
109Incl. Cupressopsida.
110Incl. Salinella i.s. et dubitativa. 111Incl. Tentaculifera, Nuda.
112= Tetracapsula, Buddenbrockia. 113= Actinomyxidia.
Phylum 53. Acoelomorpha [ 6Convoluta ] sed.m. Classis 1(201). Acoela [ 5Convoluta j
2(208). Nemertodermatida [ 5Nemertoderma j 3(209). Xenoturbelloidea [ 5Xenoturbella j
stat.m.
Phylum 54. Echinodermata [ 6 Echinus ]
Classis 1(210). Crinoidea [ 5Metacrinus j 2(211). Ophiuroidea [ 5Ophiura j 3(212). Asteroidea [ 5Asterias j114 4(213). Echinoidea [ 5Echinus j 5(214). Holothurioidea [ 5Holothuria j Phylum 55. Hemichordata [ 6Balanoglossus ] Classis 1(215). Enteropneusta [ 5Balanoglossus j* 115 2(216). Pterobranchia [ 5Rhabdopleura j Phylum 56. Chordata [ 6Felis ] s.a.
Subphylum Cephalochordata [ 58Branchiostoma ] Classis 1(211). Leptocardii [ 5Branchiostoma j Subphylum Vertebrata [ 5 8Felis ]
Classis 2(218). Cyclostomata [ 5Myxine j 3(219). Chondrichtyes [ 5Squalus j 4(220). Actinopterygii [ 5Perca j 5(221). Dipnoi [ 5Protopterus j116 6(222). Amphibia [ 5Rana j 1(223). Reptilia [ 5Gecko j*
8(224). Aves [ 5Gallus j stat.m.s.
9(225). Mammalia [ 5Felis j Subphylum Tunicata [ 5 8Ascidia ] stat.m.i. Classis 10(226). Ascidiacea [ 5Ascidia j111 Infraregnum Protostomia [ 65Araneus j Superphylum Chaetozoa' [ 6 2Sagitta ]
Phylum 51. Chaetognatha [ 6Sagitta ]
Classis 1(221). Sagittoidea [ 5Sagitta j Superphylum Spiralia [ 62Nereis ]
Phylum 58. Rhombozoa [ 6Dicyema ] sed.m. Classis 1(228). Dicyemida [ 5Dicyema j Phylum 59. Platyzoa [ 6Fasciola ] s.a. Subphylum Gastrotricha [ 5 8Macrodasys ] stat.m.i.
Classis 1(229). Gastrotrichoidea [ 5Macrodasys j Subphylum Gnathostomulea' [ 5 8 Gnathostomula ] stat.m.i.
Classis 2(230). Gnathostomulida [ 5Gnathostomula j118 Subphylum Gnathifera [ 5 8Rotifer ] s.s.
Classis 3(231). Micrognathozoa [ 5Limnognathia j 4(232). Diurodrilidae [ 5Diurodrilus j sed.m.119 5(233). Syndermata [ 5Rotifer j120
114Incl. Xyloplax.
115Incl. Planctosphaera.
116Incl. Latimeria sed.m.
111
Incl. Thaliacea, Larvacea stat.m.
118Incl. Filospermoidea, Bursovaginoidea.
119Sed.poss. juxta Polychaeta.
120Incl. Hemirotifera stat.m. (Seison, Acanthocephala et Bdel-loidea), Monogononta.
Subphylum Platyhelminthes [ 5 8Fasciola ] Classis 6(234). Catenulida [ 5Catenula j
1(235). Rhabditophora [ 5Planaria j*121 8(236). Neodermata [ 5Fasciola j122 Phylum 60. Kamptozoa [ 6Pedicellina ]
Classis 1(231). Cycliophora [ 5Symbion j stat.m.
2(238). Entoprocta [ 5Pedicellina j sed.m. Phylum 61. Mollusca [ 6Limax ]
Classis 1(239). Aplacophora [ 5Neomenia j s.a.123 2(240). Polyplacophora [ 5Chiton j 3(241). Monoplacophora [ 5Monoplacophorus j 4(242). Bivalvia [ 5Mytilus j 5(243). Scaphopoda [ 5Dentalium j 6(244). Gastropoda [ 5Limax j 1(245). Cephalopoda [ 5 Octopus j Phylum 62. Tentaculata [ 6Lingula ] s.aggr. Classis 1(246). Gymnolaemata [ 5Flustra j stat.m.124 2(241). Phylactolaemata [ 5Plumatella j 3(248). Phoronida [ 5Phoronis j 4(249). Linguliformea [ 5Lingula j 5(250). Craniiformea [ 5Craniscus j 6(251). Rhynchonelliformea [ 5Rhynchonella j Phylum 63. Nemertea [ 6Nemertes ]
Classis 1(252). Archynchocoela [ 5Archynchonemertes j 2(253). Nemertini [ 5Nemertes j125 Phylum 64. Annelida [ 6Nereis ]
Classis 1(254). Myzostomida [ 5Myzostoma j sed.m. 2(255). Sipunculida [ 5Sipunculus j stat.m.126 3(256). Polychaeta [ 5Nereis j s.a.121 Phylum 65. Orthonecta [ 6Rhopalura ] sed.m. Classis 1(251). Orthonectida [ 5Rhopalura j Superphylum Ecdysozoa [ 6 2Araneus ]
Phylum 66. Cycloneuralia [ 6Ascaris ] s.a. Subphylum Scalidomorpha [ 5 8Priapulus ] s.s. Classis 1(258). Kinorhyncha [ 5Kinorhynchus j 2(259). Priapulida [ 5Priapulus j Subphylum Nematoidea [ 5 8As,caris ]
Classis 3(260). Nematoda [ 5Ascaris j128
4(261). Nematomorpha [ 5Gordius j 5(262). Loricifera [ 5Nanaloricus j Phylum 61. Tardigrada [ 6Macrobiotus ]
Classis 1(263). Tardigradoidea [ 5Macrobiotus j129 Phylum 68. Arthropoda [ 6Araneus ] s.a.
121Incl. Macrostomida, Polycladida, Neoophora s.s.
122Incl. Monogenea, Trematoda, Cestoda.
123Incl. Caudofoveata stat.m.i.
124Incl. Stenolaemata.
125Incl. Anopla, Enopla.
126Incl. Sipunculoidea, Phascolosomatidea.
121Incl. Lobatocerebrum sed.m., Jennaria sed.m., Aelosomata, Clitellata, Echiura stat.m., Sibolginida (Pogonophora et Vesti-mentifera).
128Incl. Adenophorea, Secernentea.
129Incl. Heterotardigrada, Mesotardigrada i.s., Eutardigrada.
Subphylum Lobopoda [ 58Peripatus ] stat.m. Classis 1(264). Onychophora [ 5Peripatus ] Subphylum Cheliceromorpha [ 5 8Araneus ] Classis 2(265). Chelicerata [ 5Araneus ]130 3(266). Pantopoda [ 5Pycnogonum ] Subphylum Myriapoda [ 5.8Scolopendra ]
Classis 4(267). Chilopoda [ 5Scolopendra ]
5(268). Pauropoda [ 5Pauropus ]
6(269). Diplopoda [ 5Julus ]
7(270). Symphyla [ 5Symphylella ] Subphylum Pancrustacea [ 5.8Scarabaeus ] Classis 8(271). Branchiura [ 5Argulus ] stat.m.
9(272). Pentastomida [ 5Cephalobaena ] i.s. 10(273). Ostracoda [ 5Cypris ]
11(274). Cephalocarida [ 5Hutchinsoniella ] 12(275). Hexapoda [ 5Scarabaeus ] s.a.131 13(276). Branchiopoda [ 5Daphnia ]
14(277). Copepodoidea [ 5Cyclops ] 132 15(278). Thecostraca [ 5Lepax ] 133 16(279). Remipedia [ 5Speleonectes ]
17(280). Malacostraca [ 5Cancer]134
Acknowledgments
Author is very grateful to books which initiated his child-born interest ofglobal taxonomy, first of all to “Homunculus” of N. Plavilschikov, and famous Russian popular encyclopedias “Zhizn’ rastenij” and “Zhizn’ zhivotnykh”. There were many fruitful discussions with A. Aleshin, I. Mirabdullaev, A. Mylnikov, K. Mikrjukov, Th. Cavalier-Smith, L. Margulis, D. Patterson, S. Glagolev, A. Rautian, N. Kluge, A. Chernyshev, V. Filin, D. Sokoloff, anonymous reviewer and many others which were the sources of significant improvement of the classification.
Selected References
Nearly 1700 references (mostly articles from 1980s, but also some important books and older works) have been used for the construction of classification. Here we list only references cited directly in the introductory text; the full list is available for
130Incl. Xiphosura.
131Incl. Entognatha stat.m.
132Incl. Mystacorarida.
133Incl. Tantulocarida, Facetotecta, Ascothoracida.
134Incl. Leptostraca.
download as a BibTEX file from http://herba.msu. ru/shipunov/os/current/synat.bib.
Adl S.M., Simpson A.G.B., Farmer M.A., Andersen R.A., Anderson O.R., Barta J.R., Bowser
S.S., Brugerolle G., Fensome R.A., Fredericq S., James T.Y., Karpov S., Kugrens P., Krug J., Lane C.E., Lewis L.A., Lodge J., Lynn D.H., Mann D.G., Mccourt R.M., Mendoza L., Moestrup J., Mozley-Standridge S.E., Nerad T.A., Shearer C.A., Smirnov A.V., Spiegel F.W. and Taylor M.F.J.R. 2005. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J. Euk. Microbiol. 52 (5), 399-451.
Blackwell W.H. 2004. Is It Kingdoms or Domains? Confusion and Solutions. The American Biology Teacher. 66 (4), 268-276.
Buedel B. and Scheidegger C. 2008. Thallus morphology and anatomy. In: Lichen Biology. 2nd ed. (Ed. T.H. Nash). Cambridge University Press, Cambridge. pp.40-69.
Cavalier-Smith T. 1998. A revised six-kingdom system of life. Biol. Rev. 73 (2), 203-266.
Cavalier-Smith T. 2004. Only six kingdoms of life. Proc. R. Soc. B. 271, 1251-1262.
Cavalier-Smith T., Chao E.E., Stechmann A., Oates B. and Nikolaev S. 2008. Planomonadida ord. nov. (Apusozoa): ultrastructural affinity with Micro-nuclearia podoventralis and deep divergences within Planomonas gen. nov. Protist. 159 (4), 535-562.
Corliss J.O. 1984. The kingdom Protista and its 45 phyla. BioSystems. 17 (2), 87-126.
Corliss J.O. 1989. Protistan diversity and origin ofmulticellular/ multitissued organisms. Boll. Zool. 56, 227-234.
Corliss J.O. 1994. An iterim utilitation [“user-friendly”] hierarchial classification and characterization of protists. Acta Protozool. 33 (1), 1-51.
Cox C.J., Foster P.G., Hirt R.P., Harris S.R. and Embley T.M. 2008. The archaebacterial origin of eukaryotes. Proc. Natl. Acad. Sci. USA 105, 20356-20361.
Dagan T. and Martin W. 2006. The tree of one percent. Genome Biol . 7 (10), 118.
Deutsch J.S. 2008. Do acoels climb up the “Scale of Beings”? Evol. Devel. 10, 135-140.
Dubois A. 2007. A partial but radical solution to the problem of nomenclatural taxonomic inflation and synonymy load. Biol. J. Linn. Soc. 93, 857-863.
Hampl V., Hug L., Leigh J.W., Dacks J.B., Lang B.F., Simpson A.G.B. and Roger A.J. 2009. Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryo-
tic “supergroups”. Proc. Natl. Acad. Sci. USA. 106 (10), 3859-3864.
Hibbett D.S., Binder M., Bischoff J.F., Blackwell M., Cannon P.F., Eriksson O.E., Huhndorf
S., James T., Kirk P.M., Luecking R., Lumbsch T., Lutzoni F., Matheny P.B., Mclaughlin D.J., Powell M.J., Redhead S., Schoch C.L., Spatafora J.W., Stalpers J.A., Vilgalys R., Aime M.C., Aptroot A., Bauer R., Begerow D., Benny G.L., Castlebury L.A., Crous P.W., Dai Y.C., Gams W., Geiser D.M., Griffith G.W., Gueidan C., Hawksworth D.L., Hestmark G., Hosaka K., Humber R.A., Hyde K., Ironside J.E., Koljalg U., Kurtzman C.P., Larsson K.H., Lichtwardt R., Longcore J., Miadlikowska J., Miller A., Moncalvo J.M., Mozley-Standridge S., Oberwinkler F., Parmasto E., Reeb V., Rogers J.D., Roux C., Ryvarden L., Sampaio J.P., Schuessler A., Sugiyama J., Thorn R.G., Tibell L., Untereiner W.A., Walker C., Wang Z., Weir A., Weiss M., White M.M., Winka K., Yao Y.J. and Zhang N. 2007. A higher-level phylogenetic classification of the Fungi. Mycol. Res. 111 (5), 509-547.
Ivanov A.V. 1968. The origin of multicellular animals. Nauka, Leningrad (in Russian).
Johnson B. and Shneiderman B. 1991. Treem-aps: a space-filling approach to the visualization of hierarchical information structures. In: Proc. 2nd Intern. IEEE Visualization Conf. pp.284-291.
Kaiser H.E. 1985a. Functional comparative histology. 2. Communication: organismic taxonomy (plant and animal taxonomy). Gegenbaurs Morphol Jahrb. 131, 643-699.
Kaiser H.E. 1985b. Functional comparative histology. 3. Communication: distribution of or-ganismic tissues. Gegenbaurs Morphol. Jahrb. 131, 701-716.
Kluge N.J. 2000. Modern systematics ofinsects. Part I. Principles of systematics of living organisms
and general system of insects, with classification of primary wingless and paleopterous insects. Lan’, St.Petersburg.
Koonin E.V. and Wolf Y.I. 2008. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res. 36 (21), 6688-6719.
Lake J.A., Servin J.A., Herbold C.W. and Sko-phammer R.G. 2008. Evidence for a new root of the tree of life. Syst. Biol. 57 (6), 835-843.
Linnaeus C. 1767. Systema naturae, per regna tria naturae, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Typis Ioannis Thomae.
Ljubarskij G.J. 1996. Arhetype, style and rank in the biological systematics. KMK Ltd., Moscow (in Russian).
Martin W. and Koonin E.V. 2006. A positive definition of prokaryotes. Nature. 441, 868.
Merezhkovsky K.S. 1909. The Theory of Two Plasms as the Basis of Symbiogenesis, a New Study or the Origins of Organisms. Proc. Studies Imperial Kazan Univer. (in Russian).
Smith A.I. 1939. The comparative histology of some ofthe Laminariales. Am. J. Bot. 26, 571-585.
Stechmann A. and Cavalier-Smith T. 2002. Rooting the eukaryote tree by using a derived gene fusion. Science. 297, 89-91.
Swinburne R. 1997. Simplicity as evidence of truth (Aquinas Lecture). Marquette Univ Pr.
Tatarinov L.P. and Shimanskij V.P. (Eds.) 1984. Handbook of systematics of fossil organisms (taxa of the ordinal and higher groups). Nauka, Moscow (in Russian).
Yutin N., WolfM.Y., WolfY.I. and Koonin E.V. 2009. The origins of phagocytosis and eukaryogen-esis. Biol. Direct. 4, 9.
Address for correspondence: Alexey Shipunov. Marine Biological Laboratory,Woods Hole, Massachusetts, USA 02543, e-mail: [email protected]
