Rates of nucleotide substitution in Cornaceae (Cornales)-Pattern of variation and underlying causal factors

Molecular Phylogenetics and Evolution

Volumn 49, Issue 1, 2008, Pages 327-342

  Ricklefs, Robert E ^b  

^a Jenny)   (United States)

^b UNIVERSITY OF MISSOURI ST LOUIS   (United States)

Author keywords

Cornaceae; Cornus; Divergence time; Rate of molecular evolution; Rate of morphological evolution; Speciation

Indexed keywords

CHLOROPLAST DNA; NUCLEOTIDE; PLANT DNA;

ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CHLOROPLAST; CHLOROPLAST GENOME; CLASSIFICATION; CORNUS; DNA SEQUENCE; FOSSIL; GENETICS; HISTOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; PLANT GENE; SPECIES DIFFERENTIATION;

BAYES THEOREM; CHLOROPLASTS; CORNUS; DNA, CHLOROPLAST; DNA, PLANT; EVOLUTION, MOLECULAR; FOSSILS; GENES, PLANT; GENETIC SPECIATION; GENOME, CHLOROPLAST; MODELS, GENETIC; NUCLEOTIDES; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

CORNACEAE; CORNALES; CORNUS;

EID: 52049106346     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.07.010     Document Type: Article

References (98)

1. Allmon W.D. A causal analysis of stages in allopatric speciation. In: Futuyama D., and Antonovics J. (Eds). Oxford Surveys in Evolutionary Biology (1992), Oxford University Press, Oxford, UK 219-257
2. Anderberg A.A., Rydin C., and Kallersjo M. Phylogenetic relationships in the order Ericales s.l.: analyses of molecular data from five genes from the plastid and mitochondrial genomes. Am. J. Bot. 89 (2002) 677-687
3. APG (Angiosperm Phylogeny Group), 2003. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot. J. Linn. Soc. 141, 399-436.
4. Barraclough T.G., and Savolainen V. Evolutionary rates and species diversity in flowering plants. Evolution 55 (2001) 677-683
5. Britten R.J. Rates of DNA sequence evolution differ between taxonomic groups. Science 231 (1986) 1393-1398
6. Britton T., Oxelman B., Vinnersten A., and Bremer K. Phylogenetic dating with confidence intervals using mean path lengths. Mol. Phylogenet. Evol. 24 (2002) 58-65
7. Bromham L., Woolfit M., Lee M.S.Y., and Rambraut A. Testing the relationship between morphological and molecular rates of change along phylogenies. Evolution 56 (2002) 1921-1930
8. Brown R.W. Paleocene Flora of the Rocky Mountains and Great Plains (1962), United States Government Printing Office, Washington p. 84, pl. 59, fig. 1
9. Castro L.R., Austin A.D., and Dowton M. Contrasting rates of mitochondrial molecular evolution in parasitic diptera and hymenoptera. Mol. Biol. Evol. 19 (2002) 1100-1113
10. Chandler M.E.J. The upper Eocene flora of Hordle, Hants. Part II. Monogr. Palaeontogr. Soc. London (1926) 52 18 pls
11. Chandler M.E.J. Flora of the lower headon beds of Hampshire and the Isle of Wight. Bull. Brit. Mus. (Nat. Hist.), Geol. 5 (1961) 91-158 30 pls
12. Chandler M.E.J. The lower Tertiary floras of southern England II. Flora of the pipe-clay series of Dorset (Lower Bagshot) (1962), British Museum (Natural History), London
13. Coyne J.A. Ernst Mayr and the origin of species. Evolution 48 (1994) 19-30
14. Coyne J.A., and Orr H.A. The evolutionary genetics of speciation. Philos. Trans. R. Soc. Lond. B 353 (1999) 287-305
15. Coyne J.A., and Orr H.A. Speciation (2004), Sinauer Associates, Inc., Sunderland, MA, USA
16. Crane P.R., Manchester S.R., and Dilcher D.L. A preliminary survey of fossil leaves and well-preserved reproductive structures from the Sentinel Butte Formation (Paleocene) near Almont, North Dakota. Fieldiana Geol. 1418 (1990) 1-63
17. Davies T.J., and Savolainen V. Neutral theory, phylogenies, and the relationships between phenotypic change and evolutionary rates. Evolution 60 (2006) 476-483
18. Dorus S., Vallender E.J., Evans P.D., Anderson J.R., Gilbert S.L., Mahowald M., Wyckoff G.J., Malcom C.M., and Lahn B.T. Accelerated evolution of nervous system genes in the origin of Homo sapiens. Cell 119 (2004) 1027-1040
19. Edwards J., Whitaker D., Klionsky S., and Laskowski M.J. A record-breaking pollen catapult. Nature 435 (2005) 164
20. Eyde R.H. Comprehending Cornus: puzzles and progress in the systematics of the dogwoods. Bot. Rev. 54 (1988) 233-351
21. Fan C.-Z., and Xiang Q.-Y. Phylogenetic relationships within Cornus L. (Cornaceae) based on 26S rDNA sequences. Am. J. Bot. 88 (2001) 1131-1138
22. Fan C.-Z., and Xiang Q.-Y. Phylogenetic analyses of Cornales based on 26S rDNA and combined 26S rDNA-matK-rbcL sequence data. Am. J. Bot. 90 (2003) 1357-1372
23. Fan C., Xiang Q.-Y., Remington D.L., Purugganan M.D., and Wiegmann B.M. Evolutionary patterns in the antR-Cor gene in the dwarf dogwood complex (Cornus, Cornaceae). Genetica 130 (2007) 19-34
24. Gardner, J.S., 1883. Monogr. Brit. Eocene Fl., II (Monogr. Palaeontogr. Soc. London for 1883-1886), p. 22, pl. 9, fig. 1-6.
25. Gaut B.S., Clark L.G., Wendel J.F., and Muse S.V. Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae). Mol. Biol. Evol. 14 (1997) 769-777
26. Gavrilets S., and Hastings A. Founder effect speciation: a theoretical reassessment. Am. Nat. 147 (1996) 466-491
27. Gillespie J.H. The causes of molecular evolution (1991), Oxford University Press, Oxford, UK
28. Gillooly J.F., Brown J.H., West G.B., Savage V.M., and Charnov E.L. Effects of size and temperature on metabolic rate. Science 293 (2001) 2248-2251
29. Gillooly J.F., Allen A.P., West G.B., and Brown J.H. The rate of DNA evolution: effects of body size and temperature on the molecular clock. Proc. Natl. Acad. Sci. USA 102 (2005) 140-145
30. Goldman N., and Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11 (1994) 725-736
31. Hans E. Characteristics, causes and evolutionary consequences of male-biased mutation. Proc. R. Soc. Lond. B 274 (2007) 1-10
32. Harvey P.H., and Pagel M.S. The Comparative Method in Evolutionary Ecology (1991), Oxford University Press, Oxford
33. Hickey, L.J., 1977. Stratigraphy and paleobotany of the Golden Valley Formation (early Tertiary) of western North Dakota. Mem. Geol. Soc. Amer. No. 150.
34. Hoot S.B., Culham A., and Crane P.R. The utility of atpB gene sequences in resolving phylogenetic relationships: comparison within rbcL and 18S ribosomal DNA sequences in the Lardizabalaceae. Ann. Mo. Bot. Gard. 82 (1995) 194-207
35. Hugall A.F., and Lee M.S.Y. The likelihood node density effect and consequences for evolutionary studies of molecular rates. Evolution 61 (2007) 2293-2307
36. Isaac N.J.B., Agapow P.-M., Harvey P.H., and Purvis A. Phylogenetically nested comparisons for testing correlates of species richness: a simulation study of continuous variables. Evolution 57 (2003) 18-26
37. Jobson R.W., and Albert V.A. Molecular rates parallel diversification contrasts between carnivorous plant sister lineages. Cladistics 18 (2002) 127-136
38. Keiji S., and Hisao N. Late Pleistocene flora from the Pacific coast of Fukushima Prefecture, Japan. Sci. Rep. Tokoku Imp. Univ., Ser. 2, Geol. 42 (1971) 187-198 pls. 27-32
39. Kirchheimer F. Die Laubgewachse der Braunkohlenzeit (1957), W. Knapp, Halle
40. Kishino H., Thorne J.L., and Bruno W.J. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18 (2001) 352-361
41. Kohne D.E. Evolution of higher organism DNA. Q. Rev. Biophys. 33 (1970) 327-375
42. Kokawa, S., 1964. Plant remains of the vicinity of Hamamatsu City. In: Hamamatsu-shi chishitsu chosa hokokusho. (Geology of Hamamatsu City, research report.) Hamamatsu-shiyakusho. Hamamatsu. pp. 203-247.
43. Laroche J., Li P., Maggia L., and Bousquet J. Molecular evolution of angiosperm mitochondrial introns. Proc. Natl. Acad. Sci. USA 94 (1997) 5722-5727
44. Li W.-H. Molecular evolution (1997), Sinauer Associates, Inc., Sunderland, MA
45. Mai D.H., and Walther H. Die Floren der Haselbacher Serie im Weisselster-Becken (Bezirk Leipzig, DDR). Abh. Staatl. Mus. Mineral. Geol., Band 28 (1978)
46. Mai D.H., and Walther H. Dendrobenthamia tegeliensis nov. sp.-Ein neues ostasiatisches Florenelement im Altquartar Europas. Abh. Staatl. Mus. Miner. Geol. 25 (1976) 113-123
47. Manchester S.R. Biogeographical relationships of North American Tertiary floras. Ann. MO. Bot. Gard. 86 (1999) 472-522
48. Martin A.P., and Palumbi S.R. Body size, metabolic rate, generation time, and the molecular clock. Proc. Natl. Acad. Sci. USA 90 (1993) 4087-4091
49. Mayr E. Animal species and evolution (1963), Harvard University Press, Cambridge, MA
50. Miki S. Endocarp of remains of Alangiaceae, Cornaceae, and Nyssaceae in Japan. J. Inst. Polytech Osaka City Univ. Ser. D., Biol. 7 (1956) 275-295
51. Modrich P., and Lahue R. Mismatch repair in replication fidelity, genetic recombination, and cancer biology. Ann. Rev. Biochem. 65 (1996) 101-133
52. Mooers A.O., and Harvey P.H. Metabolic rate, generation time, and the rate of molecular evolution in birds. Mol. Phylogenet. Evol. 3 (1994) 344-350
53. Murrell Z.E. Phylogenetic Relationships in Cornus (Cornaceae). Syst. Bot. 18 (1993) 469-495
54. Murrell Z.E. Dwarf dogwoods: intermediacy and the morphological landscape. Syst. Bot. 19 (1994) 539-556
55. Muse S., and Gaut B. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11 (1994) 715-724
56. Nei M., and Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3 (1986) 418-426
57. Niklas K.J., and Enquist B.J. Invariant scaling relationships for interspecific plant biomass production rates and body size. Proc. Natl. Acad. Sci. USA 98 (2001) 2922-2927
58. Ohta T. Population size and rate of evolution. J. Mol. Evol. 1 (1972) 305-314
59. Ohta T. Amino acid substitution at the Adh locus of Drosophila is facilitated by small population size. Proc. Natl. Acad. Sci. USA 90 (1993) 4548-4551
60. Ohta T. Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J. Mol. Evol. 40 (1995) 56-63
61. Olmstead R.G., Kim K.-J., Jansen R.K., and Wagstaff S.J. The phylogeny of the Asteridae sensu lato based on chloroplast ndhF gene sequences. Mol. Phylogenet. Evol. 16 (2000) 96-112
62. Omland K.E. Correlated rates of molecular and morphological evolution. Evolution 51 (1997) 1381-1393
63. Pagel M., Venditti C., and Meade A. Large punctuational contribution of speciation to evolutionary divergence at the molecular level. Science 314 (2006) 119-121
64. Pagel M., Venditti C., and Meade A. Letter of corrections and clarifications. Science 314 (2006) 925
65. Reid E.M., and Chandler M.E.J. The London Clay flora (1933), British Museum (Natural History), London
66. Ronquist F., and Huelsenbeck J.P. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
67. Sanderson M.J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19 (2002) 101-109
68. Savolainen V., Chase M.W., Hoot S.B., Morton C.M., Soltis D.E., Bayer C., Fay M.F., de Bruijn A.Y., Sullivan S., and Qiu Y. Phylogenetic relationships of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences. Syst. Biol. 49 (2000) 306-362
69. Seo T.-K., Kishino H., and Thorne J.L. Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences. Mol. Biol. Evol. 21 (2004) 1201-1213
70. Soltis D.E., Soltis P.S., Endress P.K., and Chase M.W. Phylogeny and Evolution of Angiosperms (2005), Sinauer Associates, Inc., Sunderland, MA, USA
71. Swofford, D.L., 2002. PAUP*. Phylogenetic Analysis Using Parsimony (* and other methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
72. Szafer, W., 1954. Pliocenska flora okolic Czorsztyna l jej stosunek do plejstocenu. Inst. Geol. Prace, Tom 11, 238pp.
73. Templeton A.R. The meaning of species and speciation: a genetic perspective. In: Otte D., and Endler J.A. (Eds). Speciation and Its Consequences (1989), Sinauer, Sunderland, MA
74. Templeton A.R. Experimental evidence for the genetic transilience model. Evolution 50 (1996) 909-915
75. Thorne J.L., Kishino H., and Painter S. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15 (1998) 1647-1657
76. Thorne J.L., and Kishino H. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51 (2002) 689-702
77. Turelli M., Barton N.H., and Coyne J.A. Theory and speciation. Trends Ecol. Evol. 16 (2001) 330-343
78. Webster A.J., Payne R.J.H., and Pagel M. Molecular phylogenies link rates of evolution and speciation. Science 301 (2003) 478
79. Xiang, Q.-Y., Boufford, D.E., 2005. Cornaceae, Mastixiaceae, Toricelliaceae, Helwingiacaee, Aucubaceae. In: Wu, Z.Y., Raven, P.H., (Eds.), Flora of China (Apiaceae through Ericaceae) vol. 14. Science Press, Beijing, and Missouri Botanical Garden Press, St. Louis, pp. 206-234.
80. Xiang Q.-Y., Brunsfeld S.J., Soltis D.E., and Soltis P.S. Phylogenetic relationships in Cornus based on chloroplast DNA restriction sites: implications for biogeography and character evolution. Syst. Bot. 21 (1996) 515-534
81. Xiang Q.-Y.(J.), Manchester S.R., Thomas D., Zhang W.H., and Fan C.-Z. Phylogeny, biogeography, and molecular dating of Cornelian Cherries (Cornus, Cornaceae)-tracking Tertiary plant migration. Evolution 59 (2005) 1685-1700
82. Xiang Q.-Y.(J.), Moody M.L., Soltis D.E., Fan C.-Z., and Soltis P.S. Relationships within Cornales and circumscription of Cornaceae- matK and rbcL sequence data and effects of outgroups and long branches. Mol. Phylogenet. Evol. 24 (2002) 35-57
83. Xiang Q.-Y., Soltis D.E., Morgan D.R., and Soltis P.S. Phylogenetic relationships of Cornus L. sensu lato and putative relatives inferred from rbcL sequence data. Ann. MO. Bot. Gard. 80 (1993) 723-734
84. Xiang Q.-Y., Soltis D.E., and Soltis P.S. Phylogenetic relationships of Cornaceae and close relatives inferred from matK and rbcL sequences. Am. J. Bot. 85 (1998) 285-297
85. Xiang Q.-Y.(J.), and Thomas D.T. Tracking character evolution and biogeographic history through time in Cornaceae-does choice of methods matter?. J. Syst. Evol. 46 (2008) 349-374
86. Xiang Q.-Y.(J.), Thomas D.T., Zhang W., Manchester S.R., and Murrell Z. Species level phylogeny of the Dogwood genus Cornus (Cornaceae) based on molecular and morphological evidence-implication in taxonomy and Tertiary intercontinental migration. Taxon 55 (2006) 9-30
87. Xiang Q.-Y.(J.), Zhang W.H., Ricklefs R.E., Qian H., Cheng Z.D., Wen J., and Li J.H. Regional differences in speciation and ITS evolution: a comparison between eastern Asia and eastern North America. Evolution 58 (2004) 2175-2184
88. Xu W., Jameson D., Tang B., and Higgs P.G. The relationship between the rate of molecular evolution and the rate of genome rearrangement in animal mitochondrial genomes. J. Mol. Evol. 63 (2006) 375-392
89. Yang Z. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15 (1998) 568-573
90. Yang Z., and Bielawski P. Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 15 (2000) 496-503
91. Yang Z., and Nielsen R. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J. Mol. Evol. 46 (1998) 409-418
92. Yang Z., and Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17 (2000) 32-43
93. Yang Z., and Nielsen R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19 (2002) 908-917
94. Yang Z., and Swanson W.J. Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol. Biol. Evol. 19 (2002) 49-57
95. Young N.D., and dePamphilis C.W. Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function. BMC Evol. Biol. 5 (2005) 16
96. Zhang Z., Rosenberg H.F., and Nei M. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc. Natl. Acad. Sci. USA 95 (1998) 3708-3713
97. Zhang W.H., Xiang Q.-Y.(J.), Thomas D.T., Wiegman B.M., Frohlich M.W., and Soltis D.E. Molecular evolution of PISTILLATA-like genes in the dogwood genus Cornus. Mol. Phylogenet. Evol. 47 (2008) 175-195
98. Zhang, W.H., 2006. Molecular evolution of floral homeotic B-class genes in the dogwood genus Cornus (Cornaceae)-gene duplication, selection, and coevolution. Ph.D. dissertation, North Carolina State University. Available from: .