Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes

Journal of Molecular Evolution

Volumn 58, Issue 4, 2004, Pages 424-441

  Chaw, Shu Miaw ^a   Chang, Chien Chang ^a   Chen, Hsin Liang ^a   Li, Wen Hsiung ^b  

^a INSTITUTE OF PLANT AND MICROBIAL BIOLOGY   (Taiwan)

^b UNIVERSITY OF CHICAGO   (United States)

Author keywords

Age of core eudicots; Angiosperm phylogeny; Chloroplast genome; Divergence of monocot and dicot; Molecular clock; Unequal rate

Indexed keywords

LITHIUM;

ARTICLE; CALIBRATION; CHLOROPLAST; CONTROLLED STUDY; CRETACEOUS; FOSSIL; GENETIC VARIABILITY; GENOME; JURASSIC; MEDICAL RECORD; MOLECULAR BIOLOGY; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PLANT;

CHLOROPLASTS; GENOME, PLANT; PHYLOGENY;

ALBIA; CORE EUDICOTS; DICOTYLEDONEAE; EMBRYOPHYTA; LILIOPSIDA; MAGNOLIOPHYTA; SPERMATOPHYTA; TRACHEOPHYTA;

EID: 2442517979     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-003-2564-9     Document Type: Article

References (103)

1. APG (Angiosperm Phylogeny Group) (1998) An ordinal classification for the families of flowering plants. Annal Mo Bot Gard 85:531-533
2. Basinger JF, Dilcher DL (1984) Ancient bisexual flowers. Science 224:511-513
3. Bousquet J, Strauss SH, Doerksen AH, Price RA (1992) Extensive variation in evolutionary rate of rbcL gene sequences among seed plants. Proc Natl Acad Sci USA 89:7844-7848
4. Bowe LM, Coat G, dePamphilis CW (2000) Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers. Proc Natl Acad Sci USA 97:4092-4097
5. Brandi R, Mann W, Sprintzl M (1992) Estimation of the monocot-dicot age through t-RNA sequences from the chloroplast. Proc R Soc Lond B 249:13-17
6. Bremer K (2000) Early Cretaceous lineages of monocots flowering plants. Proc Natl Acad Sci USA 97:4707-4711
7. Chase MW, et al. (1993) Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcL. Annal Ma Bot Gard 80:528-580
8. Chase MW, et al. (2000) Higher-level systematics of the monocotyledons: An assessment of current knowledge and a new classification. In: Wilson KL, Morrison DA (eds) Monocots: Systematics and evolution. Commonwealth Scientific and Industrial Research Organization, Collingwood, Australia, pp 3-16
9. Chaw SM, Zharkikh HA, Sung HM, Lau TC, Li WH (1997) Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences. Mol Biol Evol 14:56-68
10. Chaw SM, Parkinson CL, Cheng Y, Vincent TM, Palmer JD (2000) Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers. Proc Natl Acad Sci USA 97:4086-4091
11. Clegg MT, Gaut BS, Learn GH Jr, Morton BR (1994) Rates and patterns of chloroplast DNA evolution. Proc Natl Acad Sci USA 91:6795-6801
12. Crane PR (1988) Major clades and relationships in "higher" gymnosperms. In: Beck CB (ed) Origin and evolution of gymnosperms. Columbia University Press, New York, pp 218-272
13. Crepet WL, Feldman GD (1991) The earliest remains of grasses in the fossil record. Am J Bot 78:1010-1014
14. Cronquist A (1988) The evolution and classification of fowering plants, 2nd ed. New York Botanical Garden, Bronx, NY
15. Darwin C, Darwin F, Seward AC (eds) (1903) More letters from Charles Darwin. D. Appleton, New York
16. Delevoryas T, Hope RC (1973) Fertile coniferophyte remains from the Late Triassic Deep River Basin, North Carolina. Am J Bot 60:810-818
17. Doyle JA (1992) Revised palynological correlations of the lower Potomac Group (USA) and the Cocobeach sequence of Gabon (Barremian-Aptian). Cretaceous Res 13:337-349
18. Doyle JA (1998) Molecules, morphology, fossils, and the relationship of angiosperms and Gnetales. Mol Phylogenet Evol 9:448-462
19. Doyle JA, Donoghue MJ (1987) The origin of angiosperms: a cladistic approach. In: Friis EM, Chaloner WG, Crane PR (eds) The origins of angiosperms and their biological consequences. Cambridge University Press, Cambridge, pp 17-49
20. Gallois JL, Achard P, Green G, Mache R (2001) The Arabidopsis chloroplast ribosomal protein L21 is encoded by a nuclear gene of mitochondrial origin. Gene 274:179-185
21. Gantt JS, Baldauf SL, Caline PJ, Weeden NF, Palmer JD (1991) Transfer of rpl22 to the nucleus greatly preceded its loss from the chloroplast and involved the gain of an intron. EMBO J 10:3073-4078
22. Gaut BS, Muse SV, Clark WD, Clegg MT (1992) Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants. J Mol Evol 35:292-303
23. Gaut BS, Muse SV, Clegg MT (1993) Relative rates of nucleotide substitution in the chloroplast genome. Mol Phylogenet Evol 2:89-96
24. Gaut BS, Clark LG, Wendel JF, Clegg MT, Muse SV (1997) Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae). Mol Biol Evol 14:769-777
25. Goremykin VV, Hansmann S, Martin WF (1997) Evolutionary analysis of 58 proteins encoded in six completely sequenced chloroplast genomes: Revised molecular estimates of two seed plant divergence times. Pl Syst Evol 206:337-351
26. Goremykin VV, Hirsch-Ernst KI, Wolfl S, Hellwig FH (2003) Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm. Mol Biol Evol 20:1499-1505
27. GPWG (Grass Phylogeny Working Group) (2001) Phylogeny and subfamilial classification of the grasses (Poaceae). Ann Mo Bot Gard 88:373-373
28. Gu Z, Cavalcanti ARO, Chen FC, Bouman P, Li WH (2002) Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol Biol Evol 19:256-262
29. Hallick RB, Bairoch A (1994) Proposals for the naming of chloroplast genes. III. Nomenclature for open reading frames encoded in chloroplast genomes. Plant Mol Biol Rep 12:S29-S30
30. Hart JA (1987) A cladistic analysis of conifers: Preliminary results. J Arnold Arbor 68:296-307
31. Herendeen PS, Crane, PR (1995) The fossil history of the monocotyledons. In: Rudall PJ, Cribb PJ, Cutler DF, Humphries CJ (eds) Monocotyledons: Systematics and evolution. Royal Botanic Gardens, Kew, pp 1-21
32. Hiratsuka J, et al. (1989) The complete sequence of the rice (Oryza sativa) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol Gen Genet 217:185-194
33. Hughes NF (1994) The enigma of angiosperm origins. Cambridge University Press, Cambridge
34. Hupfer H, Swiatek M, Hornung S, Hermann RG, Maier RM, Chiu WL, Sears B (2000) Complete nucleotide sequence of the Oenothera elata plastid chromosome, representing plastome I of the five distinguishable euoenothera plastomes. Mol Gen Genet 263:581-585
35. Ikeo K, Ogihara Y (2000) Triticum aestivum chloroplast, complete genome (unpublished)
36. Katayama H, Ogihara Y (1996) Phylogenetic affinities of the grasses to other monocots as revealed by molecular analysis of chloroplast DNA. Curr Genet 29:572-581
37. Kato T, Kaneko T, Sato S, Nakamura Y, Tabata S (2000) Complete structure of the chloroplast genome of a legume, Lotus japonicus. DNA Res 7:323-330
38. Kenrick P, Crane PR (1997) The origin and early evolution of land plants. Nature 389:33-39
39. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA 2: Molecular evolutionary genetics analysis software. Arizona State University, Tempe
40. Laroche J, Li P, Bousquet J (1995) Mitochondrial DNA and monocot-dicot divergence time. Mol Biol Evol 12:1151-1156
41. Li WH, Graur D (1991) Fundamentals of molecular evolution. Sinauer Associates, Sunderland, MA
42. Li WH, Tanimura M (1987) The molecular clock runs more slowly in man than in apes and monkeys. Nature 326:93-96
43. Lin S, Wu H, Jia H, Zhang P, Dixon R, May G, Gonzales R, Roe BA (2000) Medicago truncatula variety Jema Long A-17 chloroplast, complete sequence (unpublished)
44. Lockhart PJ, Howe CJ, Barbrook AC, Larkum AWD, Penny D (1999) Spectral analysis, systematic bias, and the evolution of chloroplasts. Mol Biol Evol 16:573-576
45. Magallón S, Sanderson MJ (2001) Absolute diversification rates in angiosperm clades. Int J Org Evol 55:1762-1780
46. Magallón S, Crane PR, Herendeen PS (1999) Phylogenetic pattern, diversity, and diversification of eudicots. Ann Mo Bot Gard 86:297-372
47. Maier RM, Neckermann K, Igloi GL, Kossel H (1995) Complete sequence of the maize chloroplast genome: Gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J Mol Biol 251:614-628
48. Martin W, Gierl A, Saedler H (1989) Molecular evidence for pre-Cretaceous angiosperm origin. Nature 339:46-48
49. Martin W, Lagrange T, Li YF, Bisanz-Seyer C, Mache R (1990) Hypothesis for the evolutionary origin of the chloroplast ribosomal protein L21 of spinach. Curr Genet 18:553-556
50. Martin W, Lydiate D, Brinkmann H, Forkmann G, Saedler H, Cerff R (1993) Molecular phylogenies in angiosperm evolution. Mol Biol Evol 10:140-162
51. Martin W, Stoebe B, Goremykin V, Hansmann S, Hasegawa M, Kowallik KV (1998) Gene transfer to the nucleus and the evolution of chloroplasts. Nature 393:162-165
52. Martin W, et al. (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
53. Mathews S, Donoghue MJ (1999) The root of angiosperm phylogeny inferred from duplicate phytochrome genes. Science 286:947-950
54. Matsuoka Y, Yamazaki Y, Ogihara Y, Tsunewaki K (2002) Whole chloroplast genome comparison of rice, maize, and wheat: implications for chloroplast gene diversification and phylogeny of cereals. Mol Biol Evol 19:2084-2091
55. Millen RS, Olmstead RG, Adams KL, Palmer JD, Lao NT, Heggie L, Kavanagh TA, Hibberd JM, Gray JC, Morden CW, Calie PJ, Jermiin LS, Wolfe KH (2001) Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell 13:645-658
56. Miller Jr CN (1977) Mesozoic conifers. Bot Rev 43:217-280
57. Miller Jr CN (1988) The origin of modern conifer families. In: Beck CB (ed) Origin and evolution of gymnosperms. Columbia University Press, New York, pp 448-486
58. Muse SV, Gaut BS (1997) Interlocus comparisons of the nucleotide substitution process in the chloroplast genome. Genetics 146:393-399
59. Nicholas KB, Nicholas HB Jr (1997) GeneDoc: Analysis and visualization of genetic variation. http://www.cris.com/~Ketchup/genedoc.shtml
60. Nicholas KJ, Tiffney BH, Knoll AH (1983) Patterns in vascular land plant diversification. Nature 303:614-616
61. Nickrent DL, Parkinson CL, Palmer JD, Duff RJ (2000) Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants. Mol Biol Evol 17:1885-1895
62. Ogihara Y, Isono K, Kojima T, Endo A, Hanaoka M, Shiina T, Terachi T, Utsugi S, Murata M, Mori N, Takumi S, Ikeo K, Gojobori T, Murai R, Murai K, Matsuoka Y, Ohnishi Y, Tajiri H, Tsunewaki K (2002) Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA. Mol Gen Genomics 266:740-746
63. Ohyama K, Fukuzawa H, Kohchi T, Shirai H, Sano T, Sano S, Umesono K, Shiki Y, Takeuchi M, Chang Z, Aota S, Inokuchi H, Ozeki H (1986) Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322:572-574
64. Palmer JD (1985a) Comparative organization of chloroplast genomes. Annu Rev Genet 19:325-354
65. Palmer JD (1985b) Evolution of chloroplast and mitochondrial DNA in plants and algae. In: MacIntyre RJ (ed) Molecular evolutionary genetics. Plenum Press, New York, pp 131-240
66. Parkinson CL, Adams KL, Palmer JD (1999) Multigene analyses identify the three earliest lineages of extant flowering plants. Curr Biol 9:1485-1488
67. Price RA, Thomas J, Strauss SH, Gadek PA, Quinn CJ, Palmer JD (1993) Familial relationships of the conifers from rbcL sequence data. Am J Bot 80:172
68. Pryer KM, Schneider H, Smith AR, Cranfill R, Wolf PG, Hunt JS, Sipes SD (2001) Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants. Nature 409:618-622
69. Qiu YL, Lee J, Bernasconi-Quadroni F, Soltis DE, Soltis PS, Zanis M, Chen Z, Savolainen V, Chase MW (1999) The earliest angiosperms: Evidence from mitochondrial, plastid and nuclear genomes. Nature 402:404-407
70. Rai HS, O'Brien HE, Reeves PA, Olmstead RG, Graham SW (2003) Inference of higher-order relationships in the cycads from a large chloroplast data set. Mol Phylogenet Evol 29:350-359
71. Ramshaw JAM, Richardson DL, Meatyard BT, Brown RH, Richardson M, Thompson EW, Boulter D (1972) The time of origin of the flowing plants determined by using amino acid sequence data of cytochrome C. New Phytol 71:773-779
72. Renzaglia KS, Johnson TH, Gates HD, Whittier DP (2001) Architecture of the sperm cell of Psilotum. Am J Bot 88:1151-1163
73. Rost B (1999) Twilight zone of protein sequence alignments. Protein Eng 12:85-94
74. Saito N, Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
75. Sanderson MJ (1997) A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol Biol Evol 14:1218-1231
76. Sanderson MJ, Doyle JA (2001) Sources of error and confidence intervals in estimating the age of angiosperms from rbcL and 18S rDNA data. Amer J Bot 88:1499-1516
77. Sato S, Nakamura Y, Kaneko T, Asamizu E, Tabata S (1999) Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res 6:283-290
78. Schmitz-Linneweber C, Maier RM, Alcaraz JP, Cottet A, Herrmann RG, Mache R (2001) The plastid chromosome of spinach (Spinacia oleracea): Complete nucleotide sequence and gene organization. Plant Mol Biol 45:307-315
79. Shinozaki K, et al. (1986) The complete nucleotide sequence of tobacco chloroplast genome: Its gene organization and expression. EMBO J 5:2043-2049
80. Soltis DE, et al. (2000) Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequendes. Bot J Linn Soc 133:381-461
81. Soltis PS, Soltis DE, Chase MW (1999) Angiosperm phylogeny inferred from multiple genes: A research tool for comparative biology. Nature 402:402-404
82. Soltis PS, Soltis DE, Savolainen V, Crane PR, Barraclough TG (2002) Rate heterogeneity among lineages of tracheophytes: Integration of molecular and fossil data and evidence for molecular living fossils. Proc Natl Acad Sci USA 99:4430-4435
83. Stebbins GL (1981) Coevolution of grasses and herbivores. Ann Mo Bot Gard 68:75-76
84. Stebbins GL (1987) Grass systematics and evolution: Past, present and future. In: Sonderstrom TR, Hilu KH, Campbell CS, Varkworth ME (eds) Grass systematics and evolution. Smithsonian Institution Press, Washington, DC, pp 359-367
85. Stewart WN, Rothwell GW (1993) Paleobotany and the evolution of plants, 2nd ed. Cambridge University Press, Cambridge
86. Stoebe B, Martin W, Kowallik KV (1998) Distribution and nomenclature of protein-coding genes in 12 chloroplast genomes. Plant Mol Biol Rep 16:243-255
87. Sun G, Ji Q, Dilcher DL, Zheng S, Nixon KC, Wang X (2002) Archaefructaceae, a new basal angiosperm family. Science 296:899-904
88. Swiss-Prot Protein Knowledgebase (2003) List of chloroplast and cyanelle encoded proteins. http://bioinformatics.weizmann.ac.il/databases/swiss-prot/ release/plastid.txt, released 28 Feb
89. Swofford DL (1998) PAUP 4.0 b1: Phylogenetic analysis using parsimony (and other methods). Sinauer Associates, Sunderland, MA
90. Tajima F (1993) Unbiased estimate of evolutionary distance between nucleotide sequences. Mol Biol Evol 10:677-688
91. Takezaki N, Rzhetsky A, Nei M (1995) Phylogenetic test of the molecular clock and linearized trees. Mol Biol Evol 12:823-833
92. Taylor TN, Taylor EL (1993) The biology and evolution of fossil plants, 1st ed. Prentice Hall, Englewood Cliffs, NJ
93. Thomas BA, Spicer RA (1987) The evolution and paleobiology of land plants. Croom Helm, London
94. Thomasson JR (1987) Fossil grasses. In: Sonderstrom TR, Hilu KH, Campbell CS, Varkworth ME (eds) Grass systematics and evolution. Smithsonian Institution Press, Washington, DC, pp 1820-1986
95. Wakasugi, T, Tsudzuki J, Ito S, Nakashima K, Tsudzuki T, Sugiura M (1994) Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc Natl Aad Sci USA 91:9794-9798
96. Wakasugi, T, Nishikawa A, Yamada K, Sugiura M (2002) Complete nucleotide sequence of the chloroplast genome from a fern, Psilotum nudum (unpublished; available from NCBI, accession No. AP004638)
97. Whitfeld PR, Bottemley W (1983) Organization and structure of chloroplast genes. Annu Rev Plant Physiol 34:279-310
98. Wikström N, Savolainen V, Chase M (2001) Evolution of the angiosperms: Calibrating the family tree. Proc R Soc Lond B 268:2211-2220
99. Willis KJ, McElwain JC (2002) The evolution of plants. Oxford University Press, New York
100. Wolfe KH, Li WH, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci USA 84:9054-9058
101. Wolfe KH, Gouy MY, Yang W, Sharp PM, Li WH (1989) Date of the monocot-dicot divergence estimated from chloroplast chloroplast DNA sequence data. Proc Natl Acad Sci USA 86:6201-6205
102. Yang YW, Lai KN, Tai PY, Li WH (1999) Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and the other angiosperm lineages. J Mol Evol 48:597-560
103. Zhang W (2000) Phylogeny of the grass family (Poaceae) from rpl16 intron sequence data. Mol Phylogenet Evol 15:135-146