The Revised Classification of Eukaryotes

Overview

Journal J Eukaryot Microbiol

Publisher Wiley

Specialties Microbiology
Parasitology

Date 2012 Oct 2

PMID 23020233

Citations 449

Authors

Sina M Adl

Alastair G B Simpson

Christopher E Lane

Julius Lukes

David Bass

Samuel S Bowser

Matthew W Brown

Fabien Burki

Micah Dunthorn

Vladimir Hampl

Aaron Heiss

Mona Hoppenrath

Enrique Lara

Line Le Gall

Denis H Lynn

Hilary McManus

Edward A D Mitchell

Sharon E Mozley-Stanridge

Laura W Parfrey

Jan Pawlowski

Sonja Rueckert

Laura Shadwick

Lora Shadwick

Conrad L Schoch

Alexey Smirnov

Frederick W Spiegel

Affiliations

Soon will be listed here.

Abstract

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.

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References

Gong Y, Yu Y, Villalobo E, Zhu F, Miao W . Reevaluation of the phylogenetic relationship between mobilid and sessilid peritrichs (Ciliophora, Oligohymenophorea) based on small subunit rRNA genes sequences. J Eukaryot Microbiol. 2006; 53(5):397-403. DOI: 10.1111/j.1550-7408.2006.00121.x. View

Hampl V, Hug L, Leigh J, Dacks J, Lang B, Simpson A . Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups". Proc Natl Acad Sci U S A. 2009; 106(10):3859-64. PMC: 2656170. DOI: 10.1073/pnas.0807880106. View

Heiss A, Walker G, Simpson A . Clarifying the taxonomic identity of a phylogenetically important group of eukaryotes: Planomonas is a junior synonym of Ancyromonas. J Eukaryot Microbiol. 2010; 57(3):285-93. DOI: 10.1111/j.1550-7408.2010.00477.x. View

Burki F, Shalchian-Tabrizi K, Pawlowski J . Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes. Biol Lett. 2008; 4(4):366-9. PMC: 2610160. DOI: 10.1098/rsbl.2008.0224. View

Kim E, Simpson A, Graham L . Evolutionary relationships of apusomonads inferred from taxon-rich analyses of 6 nuclear encoded genes. Mol Biol Evol. 2006; 23(12):2455-66. DOI: 10.1093/molbev/msl120. View

Jeffroy O, Brinkmann H, Delsuc F, Philippe H . Phylogenomics: the beginning of incongruence?. Trends Genet. 2006; 22(4):225-31. DOI: 10.1016/j.tig.2006.02.003. View

Burki F, Shalchian-Tabrizi K, Minge M, Skjaeveland A, Nikolaev S, Jakobsen K . Phylogenomics reshuffles the eukaryotic supergroups. PLoS One. 2007; 2(8):e790. PMC: 1949142. DOI: 10.1371/journal.pone.0000790. View

Adl S, Simpson A, Farmer M, Andersen R, Anderson O, Barta J . The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol. 2005; 52(5):399-451. DOI: 10.1111/j.1550-7408.2005.00053.x. View

Wiens J . Missing data and the design of phylogenetic analyses. J Biomed Inform. 2005; 39(1):34-42. DOI: 10.1016/j.jbi.2005.04.001. View

10.

Zwickl D, Hillis D . Increased taxon sampling greatly reduces phylogenetic error. Syst Biol. 2002; 51(4):588-98. DOI: 10.1080/10635150290102339. View

11.

Richards T, Cavalier-Smith T . Myosin domain evolution and the primary divergence of eukaryotes. Nature. 2005; 436(7054):1113-8. DOI: 10.1038/nature03949. View

12.

Spiegel F . A proposed phylogeny of the flagellated protostelids. Biosystems. 1991; 25(1-2):113-20. DOI: 10.1016/0303-2647(91)90017-f. View

13.

Brown M, Spiegel F, Silberman J . Phylogeny of the "forgotten" cellular slime mold, Fonticula alba, reveals a key evolutionary branch within Opisthokonta. Mol Biol Evol. 2009; 26(12):2699-709. DOI: 10.1093/molbev/msp185. View

14.

Howe A, Bass D, Scoble J, Lewis R, Vickerman K, Arndt H . Novel cultured protists identify deep-branching environmental DNA clades of cercozoa: New Genera Tremula, Micrometopion, Minimassisteria, Nudifila, Peregrinia. Protist. 2011; 162(2):332-72. DOI: 10.1016/j.protis.2010.10.002. View

15.

Burki F, Inagaki Y, Brate J, Archibald J, Keeling P, Cavalier-Smith T . Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, telonemia and centroheliozoa, are related to photosynthetic chromalveolates. Genome Biol Evol. 2010; 1:231-8. PMC: 2817417. DOI: 10.1093/gbe/evp022. View

16.

Burki F, Okamoto N, Pombert J, Keeling P . The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins. Proc Biol Sci. 2012; 279(1736):2246-54. PMC: 3321700. DOI: 10.1098/rspb.2011.2301. View

17.

Burki F, Kudryavtsev A, Matz M, Aglyamova G, Bulman S, Fiers M . Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists. BMC Evol Biol. 2010; 10:377. PMC: 3014934. DOI: 10.1186/1471-2148-10-377. View

18.

Baurain D, Brinkmann H, Petersen J, Rodriguez-Ezpeleta N, Stechmann A, Demoulin V . Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles. Mol Biol Evol. 2010; 27(7):1698-709. DOI: 10.1093/molbev/msq059. View

19.

Minge M, Silberman J, Orr R, Cavalier-Smith T, Shalchian-Tabrizi K, Burki F . Evolutionary position of breviate amoebae and the primary eukaryote divergence. Proc Biol Sci. 2008; 276(1657):597-604. PMC: 2660946. DOI: 10.1098/rspb.2008.1358. View

20.

Hedtke S, Townsend T, Hillis D . Resolution of phylogenetic conflict in large data sets by increased taxon sampling. Syst Biol. 2006; 55(3):522-9. DOI: 10.1080/10635150600697358. View