A higher level classification of all living organisms

PLoS ONE

Volumn 10, Issue 4, 2015, Pages

  Ruggiero, Michael A ^a   Gordon, Dennis P ^b   Orrell, Thomas M ^a   Bailly, Nicolas ^c   Bourgoin, Thierry ^d   Brusca, Richard C ^e   Cavalier Smith, Thomas ^f   Guiry, Michael D ^g   Kirk, Paul M ^h  

^a DEPARTMENT OF PALEOBIOLOGY   (United States)

^b NATIONAL INSTITUTE OF WATER AND ATMOSPHERIC RESEARCH   (New Zealand)

^c WORLDFISH   (Malaysia)

^d SORBONNE UNIVERSITÉ   (France)

^e University of Arizona   (United States)

^f UNIVERSITY OF OXFORD   (United Kingdom)

^g NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^h ROYAL BOTANIC GARDENS   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ARTICLE; BIODIVERSITY; CHROMALVEOLATA; CONSENSUS; EUKARYOTE; FUNGUS; INFORMATION SYSTEM; INFRASPECIFIC RANK; INTEGRATED TAXONOMIC INFORMATION SYSTEM; NONHUMAN; ORGANISMS; PLANT; PROCESS OPTIMIZATION; PROKARYOTE; PROTOZOON; REFERENCE DATABASE; TAXONOMIC IDENTIFICATION; COOPERATION; EVOLUTION; FACTUAL DATABASE; LIFE; PHYLOGENY;

BIODIVERSITY; BIOLOGICAL EVOLUTION; COOPERATIVE BEHAVIOR; DATABASES, FACTUAL; LIFE; PHYLOGENY;

EID: 84928745735     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0119248     Document Type: Article

References (100)

1. Hennig W. Phylogenetic systematics, translated by Davis D & Zangerl R. Champaign-Urbana: University of Illinois; 1966.
2. Mayr E, Bock WJ. Classifications and other ordering systems. J Zoolog Syst Evol Res. 2002; 40: 169-194.
3. Stuessy TF, Hoerandl E. The importance of comprehensive phylogenetic (evolutionary) classification - a response to Schmidt-Lebuhn's commentary on paraphyletic taxa. Cladistics. 2014; 30: 291-293.
4. Schmidt-Lebuhn AN. "Evolutionary" classifications do not have any information content - a reply to Stuessy and Hoerandl. Cladistics. 2014; 30: 229-231.
5. Chapman AD. Numbers of living species in Australia and the world, second edition. Australian Biodiversity Information Services, Toowoomba, Australia. A Report for the Australian Biological Resources Study; 2009.
6. Roskov Y, Kunze T, Orrell T, Abucay L, Paglinawan L, Culham A, et al., editors. Species 2000 & ITIS Catalogue of Life, 2014 Annual Checklist [DVD]. 2014; Naturalis, Leiden, the Netherlands: Species 2000.
7. Parker SP, editor. Synopsis and classification of living organisms, volumes 1 & 2. New York: McGraw Hill; 1982.
8. Vences M, Guayasamin JM, Miralles A, De la Riva I. To name or not to name: criteria to promote economy of change in Linnaean classification schemes. Zootaxa. 2013; 3636: 201-244.
9. Linnaeus C. Species plantarum, exhibentes plantas rite cognitas, ad genera relatas, cum differentiis specificis, nominus trivialibus, synonymis selectis, locis natalibus, secundum systema sexuale digestas. Stockholm: Laurentius Salvius; 1753.
10. Linnaeus C. Systema naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis (10th edition). Stockholm: Laurentius Salvius; 1758.
11. David J, Garrity GM, Greuter W, Hawksworth D, Jahn R, Kirk P et al. Biological nomenclature terms for facilitating communication in the naming of organisms. ZooKeys. 2012; 192: 67-72. doi: 10.3897/zookeys.192.3347 PMID: 22639540
12. Adl SM, Simpson AGB, Farmer MA, Andersen RA, Anderson OR, Barta JR, et al. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol. 2005; 52: 399-451. PMID: 16248873
13. Baldauf SL. The deep roots of eukaryotes. Science. 2003; 300: 1703-1706. PMID: 12805537
14. Simpson AGB, Roger AJ. The real 'kingdoms' of eukaryotes. Curr Biol. 2004; 14: R693-R696. PMID: 15341755
15. Keeling PJ, Burger G, Durnford DG, Lang BF, Lee RW, Pearlman RE, et al. The tree of eukaryotes. Trends Ecol Evol. 2005; 20: 670-676. PMID: 16701456
16. Wegener Parfrey L, Barbero E, Lasser E, Dunthorn M, Bhattacharya D, Patterson D, et al. Evaluating support for the current classification of eukaryotic diversity. PLoS Genet 2. 2006; (e220:): 2062-2073.
17. Lane CE, Archibald JM. The eukaryotic tree of life: endosymbiosis takes its TOL. Trends Ecol Evol. 2008; 23: 268-275. doi: 10.1016/j.tree.2008.02.004 PMID: 18378040
18. Adl SM, Simpson AGB, Lane CE, Lukeš J, Bass D, Bowser SS, et al. The revised classification of eukaryotes. J. Eukaryot Microbiol. 2012; 59: 429-493. doi: 10.1111/j.1550-7408.2012.00644.x PMID: 23020233
19. Cavalier-Smith T. A revised six-kingdom system of life. Biol Rev. 1998; 73: 203-266. PMID: 9809012
20. Mayr E, Ashlock PD. Principles of systematic zoology, 2nd edition. New York: McGraw Hill; 1991.
21. Cavalier-Smith T. Deep phylogeny, ancestral groups, and the four ages of life. Philos Trans R Soc Lond B Biol Sci. 2010; 365: 111-132. doi: 10.1098/rstb.2009.0161 PMID: 20008390
22. Keeling PJ, Palmer JD. Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet. 2008; 9: 605-618. doi: 10.1038/nrg2386 PMID: 18591983
23. Liu R, editor. Checklist of marine biota of Chinese seas. Beijing: Science Press, Academia Sinica; 2008.
24. Gordon DP, editor. New Zealand inventory of biodiversity, volume one, Kingdom Animalia: Radiata, Lophotrochozoa, Deuterostomia. Christchurch: Canterbury University Press. 2009.
25. Gordon DP, editor. New Zealand inventory of biodiversity, volume two, Kingdom Animalia: Chaetognatha, Ecdysozoa, Ichnofossils. Christchurch: Canterbury University Press. 2010.
26. Gordon DP, editor. New Zealand inventory of biodiversity, volume three, Kingdoms Bacteria, Protozoa, Chromista, Plantae, Fungi. Christchurch: Canterbury University Press. 2012.
27. Woese CR, Fox GE. Phylogenetic structure of the prokaryote domain: the primary kingdoms. Proc Natl Acad Sci USA. 1977; 74(11): 5088-5090. PMID: 270744
28. Margulis L, Schwartz KV. Five kingdoms: an illustrated guide to the phyla of life on earth, third edition. New York: WH Freeman and Company; 2001.
29. Cavalier-Smith T. The neomuran revolution and phagotrophic origin of eukaryotes in the light of intracellular coevolution and a revised tree of life. In: The origin and evolution of eukaryotes. Keeling PJ, Koonin EV, editors. Cold Spring Harb Perspect Biol; 2014. doi: 10.1101/cshperspect.a016006
30. LPSN - list of prokaryotic names with standing in nomenclature; 2013. Available: http://www.bacterio.net. Accessed 21 October 2014.
31. Garrity GM, Lilburn TG, Cole JR, Harrison SH, Euzéby J, Tindall BJ. Taxonomic Outline of Bacteria and Archaea (TOBA) Release 7.7; 2007. Available: http://www.taxonomicoutline.org/index.php/toba/issue/view/3. Accessed 2012 October 23.
32. Parte AC. LPSN - list of prokaryotic names with standing in nomenclature. Nucleic Acids Research. 2014; 42, Database issue D613-D616, doi: 10.1093/nar/gkt1111 PMID: 24243842
33. Cavalier-Smith T. What are Fungi? In: McLaughlin DJ, McLaughlin EJ, Lemke P, editors. The Mycota, volume VII Part A. Berlin: Springer-Verlag; 2000.
34. James TY, Pelin A, Bonen L, Ahrendt S, Sain D, Corradi N, et al. Shared signatures of parasitism and phylogenomics unite Cryptomycota and Microsporidia. Curr Biol. 2013; 23: 1548-1553. doi: 10.1016/j.cub.2013.06.057 PMID: 23932404
35. Cavalier-Smith T. Eukaryote kingdoms: seven or nine? Biosystems. 1981; 14: 461-481. PMID: 7337818
36. Burki F, Inagaki Y, Br åte J, Archibald JM, Keeling PJ, Cavalier-Smith T, et al. Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, Telonemia and Centroheliozoa, are related to photosynthetic chromalveolates. Genome Biol Evol. 2009; 1: 231-238. doi: 10.1093/gbe/evp022 PMID: 20333193
37. Burki F, Okamoto N, Pombert JF, Keeling PJ. The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins. Proc R Soc Lond B Biol Sci. 2012; 279: 2246-2254.
38. Cavalier-Smith T. Early evolution of eukaryote feeding modes, cell structural diversity, and classification of the protozoan phyla Loukozoa, Sulcozoa, and Choanozoa. Eur J Protistol. 2013; 49: 115-178. doi: 10.1016/j.ejop.2012.06.001 PMID: 23085100
39. Cavalier-Smith T, Chao EE, Snell EA, Berney C, Fiore-Donno AM, Lewis R. Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa. Mol Phylogen Evol. 2014; 81: 71-85. doi: 10.1016/j.ympev.2014.08.012 PMID: 25152275
40. Kirk PM, Cannon PF, Minter DM, Stalpers JA. Dictionary of Fungi, 10th Edition. Oxon, UK: CAB International; 2008.
41. Jeffrey C. Thallophytes and kingdoms - a critique. Kew Bull. 1971; 25: 291-299.
42. Cavalier-Smith T. The origin, losses and gains of chloroplasts. In: Lewin RA, editor. Origin of plastids: Symbiogenesis, prochlorophytes and the origins of chloroplasts. Chapman & Hall, New York; 1993.
43. Bremer K. Summary of green plant phylogeny and classification. Cladistics. 1985; 1(4): 369-385.
44. Chase MW, Reveal JL. A phylogenetic classification of the land plants to accompany APG III. Bot J Linn Soc. 2009; 161: 122-127.
45. Stech M, Frey W. A morpho-molecular classification of the mosses (Bryophyta). Nova Hedwigia. 2008; 86: 1-21.
46. Villarreal JC, Cargill C, Hagborg A, Söderström L, Renzaglia KS. A synthesis of hornwort diversity: patterns, causes and future work. Phytotaxa. 2010; 9: 150-166.
47. Mabberley DJ. Mabberley's plant-book: A portable dictionary of plants, their classifications, and uses. Cambridge, UK: Cambridge University Press; 2008.
48. Stevens PF. Angiosperm phylogeny website, Version 12; 2014. Available: http://www.mobot.org/MOBOT/research/APweb. Accessed 18 November 2014.
49. Zrzavý J, Mihulka S, Kepka P, Bezdk A. Phylogeny of the Metazoa based on morphological and 18S ribosomal DNA evidence. Cladistics. 1998; 14: 249-285.
50. Giribet G. Relationships among metazoan phyla as inferred from 18S rRNA sequence data: a methodological approach. In: Desalle R, Giribet G, Wheeler WC, editors. Molecular systematics and evolution: theory and practice. Basel: Birkhauser Verlag; 2002.
51. Mallatt J, Winchell CJ. Testing the new animal phylogeny: first use of combined large-subunit and small-subunit rRNA gene sequences to classify the protostomes. Mol Biol Evol. 2002; 19: 289-301. PMID: 11861888
52. Halanych KM. The new view of animal phylogeny. Annu Rev Ecol Evol Syst. 2004; 35: 229-256.
53. Jenner RA. Towards a phylogeny of the Metazoa: evaluating alternative phylogenetic positions of Platyhelminthes, Nemertea, and Gnathostomulida, with a critical appraisal of cladistics characters. Contrib Zool. 2004; 73: 3-163.
54. Giribet G, Dunn CW, Edgecombe GD, Rouse GW. A modern look at the animal tree of life. Zootaxa. 2007; 1668: 61-79.
55. Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, et al. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature. 2008; 452: 745-749. doi: 10.1038/nature06614 PMID: 18322464
56. Paps J, Baguñà J, Riutort M. Lophotrochozoa internal phylogeny: new insights from an up-to-date analysis of nuclear ribosomal genes. Proc R Soc Lond B Biol Sci. 2009; 276: 1245-1254.
57. Hejnol A, Obst M, Stamatakis A, Ott M, Rouse GW, Edgecombe GD, et al. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc R Soc Lond B Biol Sci. 2009; 276: 4261-4270.
58. Pick KS, Philippe H, Schreiber F, Erpenbeck D, Jackson DJ, Wrede P, et al. Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol Biol Evol. 2010; 27: 1983-1987. doi: 10.1093/molbev/msq089 PMID: 20378579
59. Edgecombe GD, Giribet G, Dunn CW, Hejnol A, Kristensen RM, Neves RC, et al. Higher-level metazoan relationships: recent progress and remaining questions. Org Divers Evol. 2011; 11: 151-172.
60. Zhang Z-Q. Animal diversity: an introduction to higher-level classification and taxonomic richness. Zootaxa. 2011; 3148: 7-12.
61. Zhang Z-Q. Animal biodiversity: an update of classification and diversity in 2013. Zootaxa. 2013; 3703: 5-11.
62. Nielsen C. Six major steps in animal evolution: are we derived sponge larvae? Evol Dev. 2008; 10: 241-257. doi: 10.1111/j.1525-142X.2008.00231.x PMID: 18315817
63. Sperling EA, Peterson KJ, Pisani D. Phylogenetic-signal dissection of nuclear-housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa. Mol Biol Evol. 2009; 26: 2261-2274. doi: 10.1093/molbev/msp148 PMID: 19597161
64. Philippe H, Derelle R, Lopez P, Pick K, Borchiellini C, Boury-Esnault N, et al. Phylogenomics revives traditional views on deep animal relationships. Curr Biol. 2009; doi: 10.1016/j.cub.2009.02.052
65. Hooper JNA, van Soest RWM, editors. Systema Porifera: a guide to the classification of sponges. New York: Kluwer Academic/Plenum Publishers; 2002.
66. Hooper JNA, van Soest RWM, Pisera A. Phylum Porifera Grant, 1826. In: Zhang Z-Q, editor. Animal biodiversity: an outline of higher-level classification and survey of taxonomic richness Zootaxa. 2011; 3148: 13-18.
67. Gazave E, Lapébie P, Ereskovsky AV, Vacelet J, Renard E, Cárdenas P, et al. No longer Demospongiae: Homoscleromorpha formal nomination as a fourth class of Porifera. Hydrobiologia. 2012; 687: 3-10.
68. Jiménez-Guri E, Philippe H, Okamura B, Holland PWH. Buddenbrockia is a cnidarian worm. Science. 2007; 317: 116-118. PMID: 17615357
69. Gruhl A, Okamura B. Development and myogenesis of the vermiform Buddenbrockia (Myxozoa) and implications for cnidarian body plan evolution. Evodevo. 2012; 310: 1-15.
70. Nielsen C. Animal evolution: interrelationships of the living phyla. Oxford, UK: Oxford University Press; 1995.
71. Egger B, Steinke D, Tarui H, De Mulder K, Arendt D, Borgonie G, et al. To be or not to be a flatworm: the acoel controversy. PLoS One. 2009; 45e5502: 1-10.
72. Philippe H, Brinkmann H, Copley RR, Moroz LL, Nakano H, Poustka AJ, et al. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature. 2011; 470: 255-258. doi: 10.1038/nature09676 PMID: 21307940
73. Tyler S, Schilling S. Phylum Xenacoelomorpha Philippe et al, 2011. In: Zhang Z-Q, editor. Animal biodiversity: an outline of higher-level classification and survey of taxonomic richness. Zootaxa. 2011; 3148: 24-25.
74. Riutort M, Álvarez-Presas M, Lázaro E, Solà E, Paps J. Evolutionary history of the Tricladida and the Platyhelminthes: an up-to-date phylogenetic and systematic account. Int J Dev Biol. 2012; 56: 5-17. doi: 10.1387/ijdb.113441mr PMID: 22450992
75. Tyler S. Turbellarian taxonomic database; 2014. Available: http://turbellaria.umaine.edu/. Accessed 3 February 2014.
76. Ruppert EE, Barnes RD. Invertebrate zoology, sixth edition. Orlando: Saunders College Publishing, Harcourt Brace and Company; 1994.
77. Brusca RC, Brusca GJ. Invertebrates, second edition. Sunderland, MA: Sinauer Associates Inc.; 2003.
78. Monks S. Phylogeny of the Acanthocephala based on morphological characters. Syst Parasitol. 2001; 48: 81-116. PMID: 11252279
79. Monks S, Richardson DJ. Phylum Acanthocephala Kohlreuter, 1771. In: Zhang Z-Q, editor. Animal biodiversity: an outline of higher-level classification and survey of taxonomic richness. Zootaxa. 2011; 3148: 234-237.
80. Segers H. Phylum Rotifera Cuvier, 1817. In: Zhang Z-Q, editor. Animal biodiversity: an outline of higher-level classification and survey of taxonomic richness. Zootaxa. 2011; 3148: 231-233.
81. Garey JR, Near TJ, Nonnemacher MR, Nadler SA. Molecular evidence for Acanthocephala as a subtaxon of Rotifera. J Mol Evol. 1996; 43: 287-292. PMID: 8703095
82. Philippe H, Telford MJ. Large-scale sequencing and the new animal phylogeny. Trends Ecol Evol. 2006; 21(11): 614-620. PMID: 16919363
83. Garcia-Varela M, Nadler SA. Phylogenetic relationships among Syndermata inferred from nuclear and mitochondrial gene sequences. Mol Phylogenet Evol. 2006; 40: 61-72. PMID: 16574435
84. Hausdorf B, Helmkampf M, Meyer A, Witek A, Herlyn H, Bruchhaus I, et al. Spiralian phylogenomics supports the resurrection of Bryozoa comprising Ectoprocta and Entoprocta. Mol Biol Evol. 2007; 24(12): 2723-2729. PMID: 17921486
85. Witek A, Herlyn H, Meyer A, Boell L, Bucher G, Hankeln T. EST based phylogenomics of Syndermata questions monophyly of Eurotatoria. BMC Evol Biol. 2008; 8: 345. doi: 10.1186/1471-2148-8-345 PMID: 19113997
86. Gazi M, Sultana T, Min G, Park YC, García-Varela M, Nadler SA, et al. The complete mitochondrial genome sequence of Oncicola luehei (Acanthocephala: Archiacanthocephala) and its phylogenetic position within Syndermata. Parasitol Int. 2012; 61: 307-316. doi: 10.1016/j.parint.2011.12.001 PMID: 22198415
87. Alrichs WH. Ultrastruktur und Phylogenie von Seison nebaliae (Gube 1859) und Seison annulatus (Claus 1876) - Hypothesen zu phylogenetischen Verwandtsschaftsverhaltsnissen innerhalb der Bilateria. Dissertation, Georg-August University, Gottingen Cuvillier-Verlag, Gottingen; 1995.
88. Alrichs WH. Epidermal ultrastructure of Seison nebaliae and Seison annulatus and a comparison of epidermal structures within the Gnathifera. Zoomorphology. 1977; 117: 41-48.
89. Rieger RM, Tyler S. Sister-group relationship of Gnathostomulida and Rotifera-Acanthocephala. Invertebr Biol. 1995; 114: 186-188.
90. Sørensen MV. Further structures in the jaw apparatus of Limnognathia maerski (Micrognathozoa), with notes on the phylogeny of the Gnathifera. J Morphol. 2002; 255: 131-145.
91. Segers H, Melone G. A comparative study of trophi morphology in Seisonidea (Rotifera). J Zool. 2002; 244: 201-207.
92. Kristensen RM, Funch P. Micrognathozoa: a new class with complicated jaws like those of Rotifera and Gnathostomulida. J Morphol. 2000; 246: 1-49. PMID: 11015715
93. De Smet H. A new record of Limnognathia maerski Kristensen & Funch, 2000 (Micrognathozoa) from the subantarctic Crozet Islands, with redescription of the trophi. J Zool. 2002; 258: 381-93.
94. Giribet G, Sørensen MV, Funch P, Kristensen RM, Sterrer W. Investigations into the phylogenetic position of Micrognathozoa using four molecular loci. Cladistics. 2004; 20: 1-13.
95. Nielsen C. Animal evolution: interrelationships of the living phyla, third edition. Oxford: Oxford University Press; 2012.
96. Adrianov AV, Malakhov VV. The phylogeny and classification of the phylum Cephalorhyncha. Zoosyst Ross. 1995; 3: 181-201.
97. Lemburg C. Ultrastructure of sense organs and receptor cells of the neck and lorica of the Halicryptus spinulosus larva (Priapulida). Microfauna Marina. 1995; 10: 7-30.
98. Neuhaus B, Higgins RP. Ultrastructure, biology, and phylogenetic relationships of Kinorhyncha. Integr Comp Biol. 2002; 42: 619-632. doi: 10.1093/icb/42.3.619 PMID: 21708758
99. Mallatt J, Winchell CJ. Ribosomal RNA genes and deuterostome phylogeny revisited: more cyclostomes, elasmobranchs, reptiles, and a brittle star. Mol Phylogenet Evol. 2007; 43: 1005-1022. PMID: 17276090
100. Mallatt J, Craig CW, Yoder MJ. Nearly complete rRNA genes assembled from across the metazoan animals: effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogenetic reconstruction. Mol Phylogenet Evol. 2010; 55: 1-17. doi: 10.1016/j.ympev.2009.09.028 PMID: 19786108