Lateral transfer of the gene for a widely used marker, α-tubulin, indicated by a multi-protein study of the phylogenetic position of Andalucia (Excavata)

Molecular Phylogenetics and Evolution

Volumn 47, Issue 1, 2008, Pages 366-377

  Simpson, Alastair G B ^a,b   Perley, Thomas A ^a   Lara, Enrique ^c  

^a DALHOUSIE UNIVERSITY   (Canada)

^b CANADIAN INSTITUTE FOR ADVANCED RESEARCH   (Canada)

^c UNIVERSITÉ PARIS SUD   (France)

Author keywords

Eukaryote evolution; Excavate; Horizontal gene transfer; Jakobid; Lateral gene transfer; Opisthokont; Protist; Protozoa; Reclinomonas; Tubulin

Indexed keywords

ANDALUCIA; ANIMALIA; DIPLOMONADIDA; EUGLENOZOA; EUKARYOTA; EXCAVATA; FUNGI; FUNGI/METAZOA GROUP; HETEROLOBOSEA; JAKOBIDAE; PARABASALIDEA; PREAXOSTYLA; PROTISTA; PROTOZOA; RECLINOMONAS;

EID: 41049109535     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2007.11.035     Document Type: Article

References (58)

1. 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 O., Mozley-Standridge S.E., Nerad T.A., Shearer C.A., Smirnov A.V., Spiegel F.W., and Taylor M.F.J.R. The new higher-level classification of eukaryotes with emphasis on the taxonomy of protists. J. Eukaryot. Microbiol. 52 (2005) 399-451
2. Andersson J.O. Lateral gene transfer in eukaryotes. Cell. Mol. Life Sci. 11 (2005) 1182-1197
3. Andersson J.O., Roger A.J., and Sarchfield S.W. Gene transfers from Nanoarchaeota to an ancestor of diplomonads and parabasalids. Mol. Biol. Evol. 22 (2005) 85-90
4. Arisue N., Hasegawa M., and Hashimoto T. Root of the Eukaryota tree as inferred from combined maximum likelihood analyses of multiple molecular sequence data. Mol. Biol. Evol. 22 (2005) 409-420
5. Baldauf S.L. The deep roots of eukaryotes. Science 300 (2003) 1703-1706
6. Baldauf S.L., and Palmer J.D. Animals and Fungi are each others closest relatives-congruent evidence from multiple proteins. Proc. Natl. Acad. Sci. USA 90 (1993) 11158-11562
7. Baldauf S.L., Roger A.J., Wenk-Siefert I., and Doolittle W.F. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290 (2000) 972-977
8. Bapteste E., Brinkmann H., Lee J.A., Moore D.V., Sensen C.W., Gordon P., Durufle L., Gaasterland T., Lopez P., Müller M., and Philippe H. The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc. Natl. Acad. Sci. USA 99 (2002) 1414-1419
9. 2S gradient in a supersulfidic anoxic fjord (Framvaren, Norway). Appl. Environ. Microbiol. 72 (2006) 3626-3636
10. Bernard C., Simpson A.G.B., and Patterson D.J. Some free-living flagellates (Protista) from anoxic habitats. Ophelia 52 (2000) 113-142
11. Berney C., Fahrni J., and Pawlowski J. How many novel eukaryotic "kingdoms"? Pitfalls and limitations of environmental DNA surveys. BMC Biol. 2 (2004) 13
12. Burki F., and Pawlowski J. Monophyly of Rhizaria and multigene phylogeny of unicellular bikonts. Mol. Biol. Evol. 23 (2006) 1922-1930
13. Burki F., Shalchian-Tabrizi K., Minge M., Skjaeveland A., Nikolaev S.I., Jakobsen K.S., and Pawlowski J. Phylogenomics reshuffles the eukaryotic supergroups. PLoS ONE 2 (2007) 790
14. Cavalier-Smith T. 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 (2003) 1741-1758
15. Cavalier-Smith T. Only six kingdoms of life. Proc. Royal Soc. Lond. B 271 (2004) 1251-1262
16. Ciccarelli F.D., Doerks T., von Mering C., Creevey C.J., Snel B., and Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science 311 (2006) 1283-1287
17. Clark C.G., and Diamond L.S. Ribosomal RNA genes of pathogenic and non-pathogenic Entamoeba histolytica are distinct. Mol. Biochem. Parasitol. 49 (1991) 297-302
18. Edgcomb V.P., Roger A.J., Simpson A.G.B., Kysela D., and Sogin M.L. Evolutionary relationships among "jakobid" flagellates as indicated by alpha- and beta-tubulin phylogenies. Mol. Biol. Evol. 18 (2001) 514-522
19. Edlind T.D., Li J., Visvesvara G.S., Vodkin M.H., McLaughlin G.L., and Katiyar S.K. Phylogenetic analysis of β-tubulin sequences from amitochondrial protozoa. Mol. Phylogenet. Evol. 5 (1996) 359-367
20. Gile G.H., Patron N.J., and Keeling P.J. EFL GTPase in cryptomonads and the distribution of EFL and EF-1α in chromalveolates. Protist 157 (2006) 435-444
21. Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
22. Hackett J.D., Yoon H.S., Li S., Reyes-Prieto A., Rümmele S.E., and Bhattacharya D. Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of 'Rhizaria' with chromalveolates. Mol. Biol. Evol. 24 (2007) 1702-1713
23. Hampl V., Horner D.S., Dyal P., Kulda J., Flegr J., Foster P., and Embley T.M. Inference of the phylogenetic position of oxymonads based on nine genes: support for Metamonada and Excavata. Mol. Biol. Evol. 22 (2005) 2508-2518
24. Harper J.T., Waanders E., and Keeling P.J. On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes. Int. J. Syst. Evol. Microbiol. 55 (2005) 487-496
25. Henze K., Horner D.S., Suguri S., Moore D.V., Sanchez L.B., Müller M., and Embley T.M. Unique phylogenetic relationships of glucokinase and glucosephosphate isomerase of the amitochondriate eukaryotes Giardia intestinalis, Spironucleus barkhanus and Trichomonas vaginalis. Gene 281 (2001) 123-131
26. Huang J., Xu Y., and Gogarten J.P. The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic. Mol. Biol. Evol. 22 (2005) 2142-2146
27. Jobb G., von Haeseler A., and Strimmer K. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol. Biol. 4 (2004) 18
28. Keeling P.J. Foraminifera and Cercozoa are related in actin phylogeny: two orphans find a home?. Mol. Biol. Evol. 18 (2001) 1551-1557
29. Keeling P.J., Burger G., Durnford D.G., Lang B.F., Lee R.W., Pearlman R.E., Roger A.J., and Gray M.W. The tree of eukaryotes. Trends Ecol. Evol. 20 (2005) 670-676
30. Keeling P.J., and Doolittle W.F. Alpha-tubulin from early-diverging eukaryotic lineages and the evolution of the tubulin family. Mol. Biol. Evol. 13 (1996) 1297-1305
31. Keeling P.J., and Inagaki Y. A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor 1 alpha. Proc. Natl. Acad. Sci. USA 101 (2004) 15380-15385
32. Kim E., Simpson A.G.B., and Graham L.E. Evolutionary relationships of apusomonads inferred from taxon-rich analyses of six nuclear-encoded genes. Mol. Biol. Evol. 23 (2006) 2455-2466
33. Lara E., Berney C., Ekelund F., Harms H., and Chatzinotas 1 A. Molecular comparison of cultivable protozoa from a pristine and a polycyclic aromatic hydrocarbon polluted site. Soil. Biol. Biochem. 39 (2007) 139-148
34. Lara E., Chatzinotas A., and Simpson A.G.B. Andalucia (gen. nov,): a new taxon for the deepest branch within jakobids (Jakobida; Excavata), based on morphological and molecular study of a new flagellate from soil. J. Eukaryot. Microbiol. 53 (2006) 112-120
35. Li J., Katiyar S.K., Hamelin A., Visvesvara G.S., and Edlind T.D. Tubulin genes from AIDS-associated microsporidia and implications for phylogeny and benzimidazole sensitivity. Mol. Biochem. Parasitol. 78 (1996) 289-295
36. Luo Q.W., Krumholz L.R., Najar F.Z., Peacock A.D., Roe B.A., White D.C., and Elshahed M.S. Diversity of the microeukaryotic community in sulfide-rich Zodletone Spring (Oklahoma). Appl. Environ. Microbiol. 71 (2005) 6175-6184
37. Medlin L., Elwood H.J., Stickel S., and Sogin M.L. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71 (1988) 491-499
38. Nikolaev S.I., Berney C., Fahrni J.F., Bolivar I., Polet S., Mylnikov A.P., Aleshin V.V., Petrov N.B., and Pawlowski J. The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proc. Natl. Acad. Sci. USA 101 (2004) 8066-8071
39. Nikolaev S.I., Mylnikov A.P., Berney C., Fahrni J., Pawlowski J., Aleshin V.V., and Petrov N.B. Molecular phylogenetic analysis places Percolomonas cosmopolitus within Heterolobosea: evolutionary implications. J. Eukaryot. Microbiol. 51 (2004) 575-581
40. Noble G.P., Rogers M.B., and Keeling P.J. Complex distribution of EFL and EF-1alpha proteins in the green algal lineage. BMC Evol. Biol. 7 (2007) 82
41. Nozaki H., Iseki M., Hasegawa M., Misawa K., Nakada T., Sasaki N., and Watanabe M. Phylogeny of primary photosynthetic eukaryotes as deduced from slowly evolving nuclear genes. Mol. Biol. Evol. 24 (2007) 1592-1595
42. Parfrey L.W., Barbero E., Lasser E., Dunthorn M., Bhattacharya D., Patterson D.J., and Katz L.A. Evaluating support for the current classification of eukaryotic diversity. PLoS Genet. 2 (2006) 2062-2073
43. Patron N.J., Inagaki Y., and Keeling P.J. Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages. Curr. Biol. 17 (2007) 887-891
44. Philippe H., Snell E.A., Bapteste E., Lopez P., Holland P.W.H., and Casane D. Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol. Biol. Evol. 21 (2004) 1740-1752
45. Richards T.A., and Cavalier-Smith T. Myosin domain evolution and the primary divergence of eukaryotes. Nature 436 (2005) 1113-1118
46. Rodríguez-Ezpeleta N., Brinkmann H., Burey S.C., Roure B., Burger G., Loffelhardt W., Bohnert H.J., Philippe H., and Lang B.F. Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes. Curr. Biol. 15 (2005) 1325-1330
47. Rodríguez-Ezpeleta N., Brinkmann H., Burger G., Roger A.J., Gray M.W., Philippe H., and Lang B.F. Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans. Curr. Biol. 17 (2007) 1420-1425
48. Ronquist F., and Huelsenbeck J.P. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
49. Shalchian-Tabrizi K., Eikrem W., Klaveness D., Vaulot D., Minge M.A., Le Gall G., Romari K., Throndsen J., Botnen A., Massana T., Thomsen H.A., and Jakobsen K.S. Telonemia, a new protist phylum with affinity to chromist lineages. Proc. R. Soc. Lond. B Biol. Sci. 273 (2006) 1833-1842
50. Simpson A.G.B. Cytoskeletal organisation phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota). Int. J. Syst. Evol. Microbiol. 53 (2003) 1759-1777
51. Simpson A.G.B., Inagaki Y., and Roger A.J. Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes. Mol. Biol. Evol. 23 (2006) 615-625
52. Simpson A.G.B., and Patterson D.J. On core jakobids and excavate taxa: the ultrastructure of Jakoba incarcerata. J. Eukaryot. Microbiol. 48 (2001) 480-492
53. Simpson A.G.B., and Roger A.J. The real 'kingdoms' of eukaryotes. Curr. Biol. 14 (2004) R693-R696
54. Simpson A.G.B., Roger A.J., Silberman J.D., Leipe D.D., Edgcomb V.P., Jermiin L.S., Patterson D.J., and Sogin M.L. Evolutionary history of "early diverging" eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia. Mol. Biol. Evol. 19 (2002) 1782-1791
55. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22 (2006) 2688-2690
56. Steenkamp E.T., Wright J., and Baldauf S.L. The protistan origins of animals and fungi. Mol. Biol. Evol. 23 (2006) 93-106
57. Strimmer K., and von Haeseler A. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13 (1996) 964-969
58. Yubuki N., Inagaki Y., Nakayama T., and Inouye I. Ultrastructure and ribosomal RNA phylogeny of the free-living heterotrophic flagellate Dysnectes brevis n. gen., n. sp., a new member of the Fornicata. J. Eukaryot. Microbiol. 54 (2007) 191-200