Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups"

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 10, 2009, Pages 3859-3864

  Hampl, Vladimir ^a,b,c   Hug, Laura ^a   Leigh, Jessica W ^a   Dacks, Joel B ^d,e   Lang, B Franz ^f   Simpson, Alastair G B ^b   Roger, Andrew J ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

^b DALHOUSIE UNIVERSITY   (Canada)

^c CHARLES UNIVERSITY   (Czech Republic)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^e UNIVERSITY OF ALBERTA   (Canada)

^f UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

Chromalveolata; Discoba; Long branch attraction

Indexed keywords

AMOEBOZOA; ARCHAEPLASTIDA; ARTICLE; CHROMALVEOLATA; DISCOBA; EUKARYOTE; EVOLUTION; EXCAVATA; FLAGELLATE; LONG BRANCH ATTRACTION; MAXIMUM LIKELIHOOD METHOD; MICROBIAL DIVERSITY; MOLECULAR PHYLOGENY; MONOPHYLY; NONHUMAN; OPISTHOKONTA; PHYLOGENETIC TREE; PRIORITY JOURNAL; RHIZARIA;

BASE SEQUENCE; DATABASES, NUCLEIC ACID; EUKARYOTIC CELLS; GENOMICS; MODELS, GENETIC; PHYLOGENY;

AMOEBOZOA; ANDALUCIA; ARCHAEPLASTIDA; CHROMALVEOLATA; DIPLOMONADIDA; EUGLENOZOA; EUKARYOTA; EXCAVATA; FUNGI/METAZOA GROUP; HETEROLOBOSEA; JAKOBIDAE; MALAWIMONAS; MASTIGOPHORA (FLAGELLATES); PARABASALIDEA; PREAXOSTYLA; RHIZARIA; UNIKONTA;

EID: 62649113993     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0807880106     Document Type: Article

References (62)

1. Hashimoto T, et al. (1994) Protein phylogeny gives a robust estimation for early divergences of eukaryotes - phylogenetic place of a mitochondria-lacking protozoan Giardia lamblia. Mol Biol Evol 11:65-71.
2. Hashimoto T, et al. (1995) Phylogenetic place of mitochondrion-lacking protozoan, Giardia lamblia inferred from amino acid sequences of elongation factor 2 Mol Biol Evol 12:782-793.
3. Kumar S, Rzhetsky A (1996) Evolutionary relationships of eukaryotic kingdoms. J Mol Evol 42:183-193.
4. Sogin ML, Silberman JD (1998) Evolution of the protists and protistan parasites from the perspective of molecular systematics. Int J Parasitol 28:11-20.
5. Edgcomb VP, Roger AJ, Simpson AGB, Kysela DT, Sogin ML (2001) Evolutionary relationships among "jakobid" flagellates as indicated by alpha- and beta-tubulin phylogenies. Mol Biol Evol 18:514-522.
6. Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401-410.
7. Hirt RP, et al. (1999) Microsporidia are related to fungi: Evidence from the largest subunit of RNA polymerase II and other proteins. Proc Natl Acad Sci USA 96:580-585.
8. Stiller JW, Hall BD (1999) Long-branch attraction and the rDNA model of early eukaryotic evolution. Mol Biol Evol 16:1270-1279.
9. Philippe H (2000) Opinion: Long branch attraction and protist phylogeny. Protist 151:307-316.
10. Dacks JB, Marinets A, Doolittle WF, Cavalier-Smith T, Logsdon JM (2002) Analyses of RNA polymerase II genes from free-living protists: Phylogeny, long branch attraction, and the eukaryotic big bang. Mol Biol Evol 19:830-840.
11. Gribaldo S, Philippe H (2004) in Organelles, Genomes and Eukaryote phylogeny, eds Horner DS, Hirt RP (CRC, London), pp 27-53.
12. Andersson JO (2005) Lateral gene transfer in eukaryotes. Cell Mol Life Sci 62:1182-1197.
13. Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972-977.
14. Hampl V, et al. (2005) Inference of the phylogenetic position of oxymonads based on nine genes: Support for Metamonada and Excavata. Mol Biol Evol 22:2508-2518.
15. Simpson AGB, Inagaki Y, Roger AJ (2006) Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes. Mol Biol Evol 23:615-625.
16. Bapteste E, et al. (2002) The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc Natl Acad Sci USA 99:1414-1419.
17. Arisue N, Hasegawa M, Hashimoto T (2005) Root of the eukaryota tree as inferred from combined maximum likelihood analyses of multiple molecular sequence data. Mol Biol Evol 22:409-420.
18. Burki F, Pawlowski J (2006) Monophyly of Rhizaria and multigene phylogeny of unicellular bikonts. Mol Biol Evol 23:1922-1930.
19. Rodriguez-Ezpeleta N, et al. (2007) Detecting and overcoming systematic errors in genome-scale phylogenies. Syst Biol 56:389-399.
20. Rodriguez-Ezpeleta N, et al. (2007) Toward resolving the eukaryotic tree: The phylogenetic positions of jakobids and cercozoans. Curr Biol 17:1420-1425.
21. Patron NJ, Inagaki Y, Keeling PJ (2007) Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages. Curr Biol 17:887-891.
22. Burki F, et al. (2007) Phylogenomics reshuffles the eukaryotic supergroups. PLoS ONE 2:e790.
23. Burki F, Shalchian-Tabrizi K, Pawlowski J (2008) Phylogenomics reveals a new "megagroup" including most photosynthetic eukaryotes. Biol Lett 4:366-369.
24. Brinkmann H, van der Giezen M, Zhou Y, Poncelin de RG, Philippe H (2005) An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. Syst Biol 54:743-757.
25. Baldauf SL (2003) The deep roots of eukaryotes. Science 300:1703-1706.
26. Simpson AGB, Roger AJ (2004) The real "kingdoms" of eukaryotes. Curr Biol 14:R693-R696.
27. Keeling PJ, et al. (2005) The tree of eukaryotes. Trends Ecol Evol 20:670-676.
28. Adl SM, et al. (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukc Microbiol 52:399-451.
29. Archibald JM, Longet D, Pawlowski J, Keeling PJ (2003) A novel polyubiquitin structure in Cercozoa and Foraminifera: Evidence for aneweukaryotic supergroup. Mol Biol Evol 20:62-66.
30. Nikolaev SI, et al. (2004) The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proc Natl Acad Sci USA 101:8066-8071.
31. Bass D, et al. (2005) Polyubiquitin insertions and the phylogeny of Cercozoa and Rhizaria. Protist 156:149-161.
32. Richards TA, Cavalier-Smith T (2005) Myosin domain evolution and the primary divergence of eukaryotes. Nature 436:1113-1118.
33. Rodriguez-Ezpeleta N, et al. (2005) Monophyly of primary photosynthetic eukaryotes: Green plants, red algae, and glaucophytes. Curr Biol 15:1325-1330.
34. Parfrey LW, et al. (2006) Evaluating support for the current classification of eukaryotic diversity. PLoS Genet 2:e220.
35. Hackett JD, et al. (2007) Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of "Rhizaria" with chromalveolates. Mol Biol Evol 24:1702-1713.
36. Stechmann A, Cavalier-Smith T (2002) Rooting the eukaryote tree by using a derived gene fusion. Science 297:89-91.
37. Stechmann A, Cavalier-Smith T (2003) The root of the eukaryote tree pinpointed. Curr Biol 13:R665-R666.
38. Simpson AGB, Patterson DJ (1999) The ultrastructure of Carpediemonas membranifera (Eukaryota) with reference to the "Excavate hypothesis." Eur J Protistol 35:353-370.
39. Simpson AGB (2003) Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota). Int J Syst Evol Microbiol 53:1759-1777.
40. Simpson AGB, Roger AJ (2004) in Organelles, Genomes and Eukaryote phylogeny, eds Horner DS, Hirt RP (CRC, London), pp 27-53.
41. Cavalier-Smith T (1998) A revised six-kingdom system of life. Biol Rev Camb Philos Soc 73:203-266.
42. Henze K, et al. (2001) Unique phylogenetic relationships of glucokinase and glucosephosphate isomerase of the amitochondriate eukaryotes Giardia intestinalis, Spironucleus barkhanus and Trichomonas vaginalis. Gene 281:123-131.
43. Dacks JB, et al. (2001) Oxymonads are closely related to the excavate taxon Trimastix. Mol Biol Evol 18:1034-1044.
44. Cavalier-Smith T (2002) The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Syst Evol Microbiol 52:297-354.
45. Andersson JO, Sarchfield SW, Roger AJ (2005) Gene transfers from Nanoarchaeota to an ancestor of diplomonads and parabasalids. Mol Biol Evol 22:85-90.
46. Page FC, Blanton RL (1985) The Heterolobosea (Sarcodina, Rhizopoda), A new class uniting the Schizopyrenida and the Acrasidae (Acrasida). Protistologica 21:121-132.
47. Fenchel T, Patterson DJ (1986) Percolomonas cosmopolitus (Ruinen) n.gen., a new type of filter feeding flagellate from marine plankton. J Mar Biol Ass UK 66:465-482.
48. Flavin M, Nerad TA (1993) Reclinomonas americana n. g., n. sp., a new freshwater heterotrophic flagellate. J Eukaryot Microbiol 40:172-179.
49. O'Kelly CJ (1993) The jakobid flagellates - structural features of Jakoba, Reclinomonas and Histiona and implications for the early diversification of eukaryotes J Euk Microbiol 40:627-636.
50. Simpson AGB (1997) The identity and composition of the Euglenozoa. Arch Protistenk 148:318-328.
51. Simpson AGB, Patterson DJ (2001) On core jakobids and excavate taxa: The ultrastructure of Jakoba incarcerata. J Euk Microbiol 48:480-492.
52. Silberman JD, et al. (2002) Retortamonad flagellates are closely related to diplomonads - Implications for the history of mitochondrial function in eukaryote evolution. Mol Biol Evol 19:777-786.
53. Simpson AGB, et al. (2002) Evolutionary history of "early- diverging" eukaryotes: The excavate taxon Carpediemonas is a close relative of Giardia. Mol Biol Evol 19:1782-1791.
54. Cavalier-Smith T (2003) The excavate protozoan phyla Metamonada Grasse emend. (Anaeromonadea, Parabasalia, Carpediemonas, Eopharyngia) and Loukozoa emend (Jakobea, Malawimonas): Their evolutionary affinities and new higher taxa. Int J Syst Evol Microbiol 53:1741-1758.
55. Lara E, Chatzinotas A, Simpson AGB (2006) Andalucia (n. gen.) - the deepest branch within jakobids (Jakobida; Excavata), based on morphological and molecular study of a new flagellate from soil. J Euk Microbiol 53:112-120.
56. Simpson AGB, Perley TA, Lara E (2007) Lateral transfer of the gene for a widely used marker, alpha-tubulin, indicated by amulti-protein study of the phylogenetic position of Andalucia (Excavata). Mol Phylogenet Evol 47:366-377.
57. Wilkinson MF, McInerney JO, Hirt RP, Foster PG, Embley TM (2007) (2007) Of clades and clans: Terms for phylogenetic relationships in unrooted trees. Trends Ecol Evol 22:114-115.
58. Brinkmann H, Philippe H (2007) The diversity of eukaryotes and the root of the eukaryotic tree. Adv Exp Med Biol 607:20-37.
59. Leigh JW, Susko E, Baumgartner M, Roger AJ (2008) Testing congruence in phylogenomic analysis. Syst Biol 57:104-115.
60. Lartillot N, Philippe H (2004) A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol 21:1095-1109.
61. Bhattacharya D, Yoon HS, Hackett JD (2004) Photosynthetic eukaryotes unite: Endosymbiosis connects the dots. Bioessays 26:50-60.
62. Stamatakis A (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.