Phylogenetic analyses of nuclear, mitochondrial, and plastid multigene data sets support the placement of Mesostigma in the Streptophyta

Molecular Biology and Evolution

Volumn 24, Issue 3, 2007, Pages 723-731

  Rodríguez Ezpeleta, Naiara ^a   Philippe, Hervé ^a   Brinkmann, Henner ^a   Becker, Burkhard ^b   Melkonian, Michael ^b  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b UNIVERSITY OF COLOGNE   (Germany)

Author keywords

Chlorokybus; Heterotachy; Mesostigma; Phylogenomics; Systematic error; Taxon sampling

Indexed keywords

ARTICLE; CELL NUCLEUS MEMBRANE; GENETIC DATABASE; GENETIC VARIABILITY; GENOME ANALYSIS; GREEN ALGA; MITOCHONDRIAL GENE; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PLANT TAXONOMY; PLASTID; REFERENCE DATABASE;

BASE SEQUENCE; CELL NUCLEUS; DNA, MITOCHONDRIAL; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANTS; PLASTIDS; SEQUENCE ANALYSIS, DNA;

ALGAE; CHLOROKYBUS; CHLOROPHYTA; EMBRYOPHYTA; MASTIGOPHORA (FLAGELLATES); MESOSTIGMA; MESOSTIGMA VIRIDE; PRASINOPHYCEAE; STREPTOPHYTA; VIRIDIPLANTAE;

EID: 33847637949     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msl200     Document Type: Article

References (70)

1. Akaike H. 1973. Information theory and an extension of the maximum likelihood principle. In: Csaki, editor. Proceedings 2nd International Symposium on Information Theory. Budapest (Hungary): Akademia Kiado. p. 267-281.
2. Bapteste E, Brinkmann H, Lee JA, et al. (11 co-authors). 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.
3. Bhattacharya D, Weber K, An SS, Berning-Koch W. 1998. Actin phylogeny identifies Mesostigma viride as a flagellate ancestor of the land plants. J Mol Evol. 47:544-550.
4. Bremer K, Humphries CJ, Mishler BD, Churchill SP. 1987. On cladistic relationships in green plants. Taxon. 36:339-349.
5. Brinkmann H, van der Giezen M, Zhou Y, Poncelin de Raucourt G, Philippe H. 2005. An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. Syst Biol. 54:743-757.
6. Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17:540-552.
7. Christensen, T. 1962. Alger. In: Böcher TW, Lange M, and Sørensen T, editors. Botanik, Systematisk Botanik vol. 2, Copenhagen: Munksgaard p. 1-178.
8. Delwiche CF, Karol KG, Cimino MT, Sytsma KJ. 2002. Phylogeny of the genus Coleochaete (Coleochaetales, Charophyta) and related taxa inferred by analysis of the chloroplast gene rbcL. J Phycol. 38:394-403.
9. Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool. 27:401-410.
10. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.
11. Hendy MD, Penny D. 1989. A framework for the quantitative study of evolutionary trees. Syst Zool. 38:297-309.
12. Hrdy I, Hirt RP, Dolezal P, Bardonova L, Foster PG, Tachezy J, Embley TM. 2004. Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I. Nature. 432:618-622.
13. Hurvich CM, Tsai C-L. 1989. Regression and time series model selection in small samples. Biometrika. 76:297-307.
14. Jeffroy O, Brinkmann H, Delsuc F, Philippe H. 2006. Phylogenomics: the beginning of incongruence? Trends Genet. 22:225-231.
15. Jobb G, von Haeseler A, Strimmer K. 2004. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol. 4:18.
16. Karol KG, McCourt RM, Cimino MT, Delwiche CF. 2001. The closest living relatives of land plants. Science. 294:2351-2353.
17. Kishino H, Miyata T, Hasegawa M. 1990. Maximum likelihood inference of protein phylogeny, and the origin of chloroplasts. J Mol Evol. 31:151-160.
18. Kolaczkowski B, Thornton JW. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature. 431:980-984.
19. Lauterborn R. 1894. Über die Winterfauna einiger Gewässer der Oberrheinebene. Biol Zbl. 14:390-398.
20. Lemieux C, Otis C, Turmel M. 2000. Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution. Nature. 403:649-652.
21. Lewis LA, McCourt RM. 2004. Green algae and the origin of land plants. Am J Bot. 91:1535-1556.
22. Lockhart P, Novis P, Milligan BG, Riden M, Rambaut A, Larkum T. 2006. Heterotachy and tree building: a case study with plastids and eubacteria. Mol Biol Evol. 23:40-45.
23. Lopez P, Casane D, Philippe H. 2002. Heterotachy, an important process of protein evolution. Mol Biol Evol. 19:1-7.
24. Madsen O, Scally M, Douady CJ, Kao DJ, DeBry RW, Adkins R, Amrine HM, Stanhope MJ, de Jong WW, Springer MS. 2001. Parallel adaptive radiations in two major clades of placental mammals. Nature. 409:610-614.
25. Manton I, Ettl H. 1965. Observations on the fine structure of Mesostigma viride Lauterborn. J Linn Soc Lond Bot. 59:175-184.
26. Marin B, Melkonian M. 1999. Mesostigmatophyceae, a new class of streptophyte green algae revealed by SSU rRNA sequence comparisons. Protist. 150:399-417.
27. Martin W, Deusch O, Stawski N, Grünheit N, Goremykin V. 2005. Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution. Trends Plant Sci. 10:203-209.
28. Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M, Penny D. 2002. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci USA. 99:12246-12251.
29. McCourt RM, Delwiche CF, Karol KG. 2004. Charophyte algae and land plant origins. Trends Ecol Evol. 19:661-666.
30. Melkonian M. 1983. Mesostigma, a key organism in the evolution of two major classes of green algae and related to the ancestry of land plants. Br Phycol J. 18:206.
31. Melkonian M. 1989. Flagellar apparatus ultrastructure in Mesostigma viride (Prasinophyceae). Plant Syst Evol. 164:93-122.
32. Melkonian M. 1990. Phylum Chlorophyta: class Prasinophyceae. In: Margulis L, Corliss JO, Melkonian M, Chapman DJ, editors. Handbook of protoctista. Boston (MA): Jones and Bartlett Publishers. p. 600-607.
33. Melkonian M, Marin B, Surek B. 1995. Phylogeny and evolution of the algae. In: Arai K, Kato M, Doi Y, editors. Biodiversity and evolution. Tokyo (Japan): The National Science Mueseum Foundation. p. 153-176.
34. Moestrup Ø. 1970. The fine structure of mature spermatozoids of Chara corralina, with special reference to microtubules and scales. Planta. 93:295-308.
35. Moestrup Ø. 1991. Further studies of presumably primitive green algae, including the description of Pedinophyceae class. Nov. and Resultor gen. nov. J Phycol. 27:119-133.
36. Moestrup Ø. 2002. Phylum Prasinophyta. In: John DM, Whitton BA, Brook AJ, editors. The freshwater algal flora of the British Isles. Cambridge (UK): Cambridge University Press. p. 281-286.
37. Moestrup Ø, Throndsen J. 1988. Light and electron microscopical studies on Pseudoscourfieldia marina, a primitive scaly green flagellate (Prasinophyceae) with posterior flagella. Can J Bot. 66:1415-1434.
38. Nakayama T, Marin B, Kranz HD, Surek B, Huss VAR, Inouye I, Melkonian M. 1998. The basal position of scaly green flagellates among the green algae (Chlorophyta) is revealed by analyses of nuclear-encoded SSU rRNA sequences. Protist. 149:367-380.
39. Nedelcu AM, Borza T, Lee RW. 2006. A land plant-specific multigene family in the unicellular Mesostigma argues for its close relationship to Streptophyta. Mol Biol Evol. 23:1011-1015.
40. Petersen J, Teich R, Becker B, Cerff R, Brinkmann H. 2006. The GapA/B gene duplication marks the origin of Streptophyta (charophytes and land plants). Mol Biol Evol. 23:1109-1118.
41. Philippe H. 1993. MUST, a computer package of management utilities for sequences and trees. Nucleic Acids Res. 21:5264-5272.
42. Philippe H, Delsuc F, Brinkmann H, Lartillot N. 2005. Phylogenomics. Annu Rev Ecol Evol Syst. 36:541-562.
43. Philippe H, Lartillot N, Brinkmann H. 2005. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol Biol Evol. 22:1246-1253.
44. Philippe H, Snell EA, Bapteste E, Lopez P, Holland PW, Casane D. 2004. Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol Biol Evol. 21:1740-1752.
45. Philippe H, Zhou Y, Brinkmann H, Rodrigue N, Delsuc F. 2005. Heterotachy and long-branch attraction in phylogenetics. BMC Evol Biol. 5:50.
46. Phillips MJ, Delsuc F, Penny D. 2004. Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol. 21:1455-1458.
47. Pickett-Heaps JD, Marchant HJ. 1972. The phylogeny of the green algae: a new proposal. Cytobios. 6:255-264.
48. Pombert J-F, Lemieux C, Turmel M. 2006. The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes. BMC Biol. 4:3.
49. Pombert J-F, Otis C, Lemieux C, Turmel M. 2005. The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages. Mol Biol Evol. 22:1903-1918.
50. Posada D, Buckley TR. 2004. Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. Syst Biol. 53:793-808.
51. Qiu YL, Lee J, Bernasconi-Quadroni F, Soltis DE, Soltis PS, Zanis M, Zimmer EA, Chen Z, Savolainen V, Chase MW. 1999. The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature. 402:404-407.
52. Rodriguez-Ezpeleta N, Brinkmann H, Burey SC, Roure B, Burger G, Loffelhardt W, Bohnert H, Philippe H, Lang BF. 2005. Monophyly of primary photosynthetic eukaryotes: green plans, red algae, and glaucophytes. Curr Biol. 15:1325-1330.
53. Rodriguez-Ezpeleta N, Brinkmann H, Roure B, Lartillot N, Lang BF, Philippe H. 2007. Detecting and overcoming systematic errors in genome-scale phylogenies. Syst Biol. In press.
54. Rogers CE, Domozych DS, Stewart KD, Mattox KR. 1981. The flagellar apparatus of Mesostigma viride (Prasinophyceae): multilayered structures in a scaly green flagellate. Plant Syst Evol. 138:247-258.
55. Rogers CE, Mattox KR, Stewart KD. 1980. The zoospore of Chlorokybus atmophyticus, a charophyte with sarcinoid growth habit. Am J Bot. 67:774-783.
56. Salter LA. 2001. Complexity of the likelihood surface for a large DNA dataset. Syst Biol. 50:970-978.
57. Schmidt HA, Strimmer K, Vingron M, von Haeseler A. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 18:502-504.
58. Simon A, Glöckner G, Felder M, Melkonian M, Becker B. 2006. EST analysis of the scaly green flagellate Mesostigma viride (Streptophyta): implications for the evolution of green plants (Viridiplantae). BMC Plant Biol. 6:2.
59. Stabenau H, Winkler U. 2005. Glycolate metabolism in green algae. Physiol Plant. 123:235-245.
60. Steel M. 2005. Should phylogenetic models be trying to 'fit an elephant'? Trends Genet. 21:307-309.
61. Swofford DL. 2002. PAUP* phylogenetic analysis using parsimony (*and other methods). Version 4. Sunderland: Sinauer Associates.
62. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
63. Turmel M, Ehara M, Otis C, Lemieux C. 2002. Phylogenetic relationships among streptophytes as inferred from chloroplast small and large subunit rRNA gene sequences. J Phycol. 38:364-375.
64. Turmel M, Otis C, Lemieux C. 2002a. The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum: insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants. Proc Natl Acad Sci USA. 99:11275-11280.
65. Turmel M, Otis C, Lemieux C. 2002b. The complete mitochondrial DNA sequence of Mesostigma viride identifies this green alga as the earliest green plant divergence and predicts a highly compact mitochondrial genome in the ancestor of all green plants. Mol Biol Evol. 19:24-38.
66. Turmel M, Otis C, Lemieux C. 2005. The complete chloroplast DNA sequences of the charophycean green algae Staurastrum and Zygnema reveal that the chloroplast genome underwent extensive changes during the evolution of the Zygnematales. BMC Biol. 3:22.
67. Turmel M, Otis C, Lemieux C. 2006. The chloroplast genome sequence of Chara vulgaris sheds new light into the closest green algal relatives of land plants. Mol Biol Evol. 23:1324-1338.
68. Whelan S, Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol. 18:691-699.
69. Yang Z. 1996. Maximum-likelihood models for combined analyses of multiple sequence data. J Mol Evol. 42:587-596.
70. Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556.