Phylogenomics reshuffles the eukaryotic supergroups

PLoS ONE

Volumn 2, Issue 8, 2007, Pages

  Burki, Fabien ^a   Shalchian Tabrizi, Kamran ^a   Minge, Marianne ^b   Skjæveland, Åsmund ^b   Nikolaev, Sergey I ^a   Jakobsen, Kjetill S ^b   Pawlowski, Jan ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

^b UNIVERSITY OF OSLO   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CHLOROPHYLL;

ALGA; ARTICLE; BIODIVERSITY; CLADISTICS; EUKARYOTE; EVOLUTION; EXPRESSED SEQUENCE TAG; GENOMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASTID; RHIZARIA; TAXON; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION;

ALGAE; ALVEOLATA; CHROMALVEOLATA; EUKARYOTA; PROTISTA; RHIZARIA; STRAMENOPILES;

EUKARYOTA; EVOLUTION, MOLECULAR; EXPRESSED SEQUENCE TAGS; GENOMICS; PHYLOGENY; RHIZARIA;

EID: 40749116835     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000790     Document Type: Article

References (50)

1. Keeling PJ, Burger G, Dornford DG, Lang BF, Lee RW, et al. (2005) The tree of eukaryotes. Trends Ecol Evol 20: 670-676.
2. Adl SM, Simpson AGB, Farmer MA, Andersen RA, Anderson OR, et al. (2005) The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists. J Eukaryot Microbiol 52: 399-451.
3. Parfrey LW, Barbero E, Lasser E, Dunthorn M, Bhattacharya D, et al. (2006) Evaluating Support for the Current Classification of Eukaryotic Diversity. PLoS Genet 2: e220.
4. Patterson DJ (1999) The diversity of eukaryotes. Am Nat 154, S96-S124.
5. Cavalier-Smith T (2002) The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Syst Evol Microbiol 52: 297-354.
6. Bhattacharya D, Helmchen T, Melkonian M (1995) Molecular evolutionary analyses of nuclear-encoded small subunit ribosomal RNA identify an independent Rhizopod lineage containing the Euglyphida and the Chlorarachniophyta. J Eukaryot Microbiol 42: 65-69
7. Burki F, Berney C, Pawlowski J (2002) Phylogenetic Position of Gromia oviformis Dujardin inferred from Nuclear-Encoded Small Subunit Ribosomal DNA. Protist 153: 251-260.
8. Cavalier-Smith T (1998) A revised six-kingdom system of life. Biol Rev Camb Philos Soc 73: 203-266.
9. Keeling PJ (2001) Foraminifera and Cercozoa Are Related in Actin Phylogeny: Two Orphans Find a Home? Mol Biol Evol 18: 1551-1557.
10. Longet D, Archibald JM, Keeling PJ, Pawlowski J (2003) Foraminifera and Cercozoa share a common origin according to RNA polyrnerase II phylogenies. Int J Syst Evol Microbiol 53: 1735-1739.
11. Nikolaev SI, Berney C, Fahrni JF, Bolivar I, Polet S, 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.
12. Bodyl A (2005) Do plastid-related characters support the chromalveolate hypothesis? J Phycol 41: 712-719.
13. Harper JT, Waanders E, Keeling PJ (2005) On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes. Int J Syst Evol Microbiol 55: 487-496.
14. Patron NJ, Inagaki Y, Keeling PJ (2007) Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages. Curr Biol 17: 887-891.
15. Li S, Nosenko T, Hackett JD, Bhattacharya D (2006) Phylogenomic Analysis Identifies Red Algal Genes of Endosymbiotic Origin in the Chromalveolates. Mol Biol Evol 23: 663-674.
16. Cavalier-Smith T (1999) Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. J Eukaryot Microbiol 46: 347-366.
17. Cavalier-Smith T, Chao E (2003) Phylogeny and classification of phylum Cercozoa (Protozoa). Protist 154: 341-358.
18. Keeling PJ (2004) Diversity and evolutionary history of plastids and their hosts. Am J Bot 91: 1481-1493.
19. Burki F, Pawlowśki (2006) Monophyly of Rhizaria and Multigene Phylogeny of Unicellular Bikonts. Mol Biol Evol 23: 1922-1930.
20. Nikolaev SI, Berney C, Fahrni J, MyInikov AP, Aleshin VV, et al. (2003) Gymnophrys cometa and Lecythium sp. are core Cercozoa: evolution implications. Acta Protozool 42: 183-190.
21. Burki F, Nikolaev S, Bolivar I, Guiard S, Pawlowski J (2006) Analysis of expressed sequence tags (ESTs) from a naked foraminiferan Reticulomyxa filosa. Genome 49: 882-887.
22. Keeling P, Palmer J (2001) Lateral tranfer at the gene and subgenic levels in the evolution of eukaryotic enolase. Proc Natl Acad Sci USA 98: 10745-10750.
23. Delsuc F, Brinkmann H, Philippe H (2005) Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6: 361-375.
24. McMahon MM, Sanderson MJ (2006) Phylogenetic Supermatrix Analysis of GenBank Sequences from 2228 Papilionoid Legumes. Systematic Biol 55: 818-836.
25. Philippe H, Snell EA, Bapteste E, Lopez P, Holland PWH, et al. (2004) Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments. Mol Biol Evol 21: 1740-1752.
26. Wiens JJ (2006) Missing data and the design of phylogenetic analyses. J Biomed Inform 39: 34-42.
27. Wiens JJ (2005) Can Incomplete Taxa, Rescue Phylogenetic Analyses from Long-Branch Attraction? Systematic Biol 54: 73-742.
28. Nozaki H, Iseki M, Hasegawa M, Misawa K, Nakada T, et al. (2007) Phylogeny of Primary Photosynthetic Eukaryotes as Deduced from Slowly Evolving Nuclear Genes. Mol Biol Evol.
29. Hackett JD, Youn HS, Li S, Reyes-Prieto A, Rummele SE, et al. (2007) Phylogenomic Analysis Supports the Monophyly of Cryptophytes and Haptophytes and the Association of 'Rhizaria' with Chromalveolates. Mol Biol Evol. pp msm089.
30. Shimodaira H (2002) An approximately unbiased test of phylogenctic tree selection. Systematic Biol 51: 492-508.
31. Rogers MB, Gilson PR, Su V, McFadden GI, Keeling PJ (2007) The Complete Chloroplast Genome of the Chlorarachniophyte Bigelowiella natans: Evidence for Independent Origins of Chlorarachniophyte and Euglenid Secondary Endosymbionts. Mol Biol Evol 24: 54-62.
32. Polet S, Berney C, Fahrni J, Pawlowski J (2004) Small-subunit ribosomal RNA gene sequences of Phaeodarea challenge the monophyly of Haeckel's Radiolaria. Protist 155: 53-63.
33. Shalchian-Tabrizi K, Eikrem W, Klaveness D, Vaulot D, Minge MA, et al. (2006) Telonemia, a new protist phylum with affinity to chromist lineages. Proc R Soc Lond 273: 1833-1842.
34. Shalchian-Tabrizi K, Kauserud H, Massana R, Klaveness D, Jakobsen KS (2007) Analysis of Environmental 18S Ribosomal RNA Sequences reveals Unknown Diversity of the Cosmopolitan Phylum Telonemia. Protist 158: 173-180.
35. Fast NM, Kissinger JC, Roos DS, Keeling PJ (2001) Nuclear-Encoded, Plastid-Targeted Genes Suggest a Single Common Origin for Apicomplexan and Dinoflagellate Plastids. Mol Biol Evol 18: 418-426.
36. Harper J, Keeling P (2003) Nucleus-Encoded, Plastid-Targeted Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) Indicates a Single Origin for Chromalveolate Plastids. Mol Bio Evol 20: 1730-1735.
37. Patron NJ, Rogers MB, Keeling PJ (2004) Gene Replacement of Fructose-1,6-Bisphosphate Aldolase Supports the Hypothesis of a Single Photosynthetic Ancestor of Chromalveolates. Eukaryotic Cell 3: 1169-1175.
38. Bachvaroff TR, Sanchez Puerta MV, Delwiche CF (2005) Chlorophyll c-Containing Plastid Relationships Based on Analyses of a Multigene Data Set with All Four Chromalveolate Lineages. Mol Biol Evol 22: 1772-1782.
39. Shalchian-Tabrizi K, Skanseng M, Ronquist F, Klaveness D, Bachvaroff TR, et al. (2006) Heterotachy Processes in Rhodophyte-Derived Secondhand Plastid Genes: Implications for Addressing the Origin and Evolution of Dinoflagellate Plastids. Mol Biol Evol 23: 1504-1515.
40. Cavalier-Smith T (2004) Chromalveolate diversity and cell megaevolution: interplay of membranes, genomes and cytoskeleton. In Organelles, Genomes and Eukaryotic Evolution; Hirt R, Horner DS, eds. London: Taylor and Francis, 32.
41. Rodriguez-Ezpeleta N, Brinkmann H, Burey SC, Roure B, Burger G, et al. (2005) Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes. Curr Biol 15: 1325-1330.
42. Jobb G, von Haeseler A, Strimmer K (2004) TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol 4: 18.
43. Roure B, Rodriguez-Ezpeleta N, Philippe H (2007) SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics. BMC Evol Biol 7 Suppl 1: S2.
44. Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
45. Posada D, Buckley T (2004) Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests. Systematic Biol 53: 793-808.
46. Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 2104-2105.
47. Felsenstein J (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 40: 783-791.
48. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
49. Robinson-Rechavi M, Huchon D (2000) RRT ?? Relative-Rate Tests between groups of sequences on a phylogenetic tree. Bioinformatics 16: 296-297.
50. Shimodaira H, Hasegawa M (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17: 1246-1247.