Variation in rates of molecular evolution in plants and implications for estimating divergence times

Plant Genome Diversity Volume 1: Plant Genomes, their Residents, and their Evolutionary Dynamics

Volumn , Issue , 2012, Pages 103-111

  Burleigh, J Gordon ^a  

^a UNIVERSITY OF FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84948075433     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-7091-1130-7_7     Document Type: Chapter

References (116)

1. Aïnouche AK, Bayer RJ (1999) Phylogenetic relationships in Lupinus (Fabaceae: Papilionoideae) based on internal transcribed spacer sequences (ITS) of nuclear ribosomal DNA. Am J Bot 86:590-607
2. Álvarez I, Wendel JF (2003) Ribosomal ITS sequences and plant phylogenetic inference. Mol Phylogenet Evol 29:417-434
3. Andreasen K, Baldwin BG (2001) Unequal evolutionary rates between annual and perennial lineages of checker mallows (Sidalcea, Malvaceae): evidence from 18S-26S rDNA internal and external transcribed spacers. Mol Biol Evol 18:936-944
4. Aris-Brosou S, Yang Z (2002) Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Mol Biol Evol 20:1947-1954
5. Barraclough TG, Harvey PH, Nee S (1996) Rate of rbcL gene sequence evolution and species diversification in flowering plants. Proc Roy Soc Lond B Bio 263:589-591
6. Bell CD, Soltis DE, Soltis PS (2005) The age of angiosperms: a molecular timescale without a clock. Evolution 59:1245-1258
7. Bell CD, Soltis DE, Soltis PS (2010) The age and diversification of the angiosperms re-revisited. Am J Bot 97:1296-1303
8. Blanc G, Wolfe KH (2004) Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16:1679-1691
9. Boulter D, Ramshaw JAM, Thompson EW, Richardson M, Brown RH (1972) A phylogeny of higher plants based on the amino acid sequences of cytochrome c and its biological implications. Proc Roy Soc Lond B Bio 181:441-455
10. Bousquet J, Strauss SH, Doerksen AH, Price RA (1992) Extensive variation in evolutionary rate of rbcL gene sequence among seed plants. Proc Natl Acad Sci USA 89:7844-7848
11. Brandl R, Mann W, Sprinzl M (1992) Estimation of the monocot-dicot age through tRNA sequences from the chloroplast. Proc Roy Soc Lond B Bio 249:13-17
12. Britton T, Anderson CL, Jaquet D, Lundqvist S, Bremer K (2007) Estimating divergence times in large phylogenetic trees. Syst Biol 56:741-752
13. Brown WM, George M Jr, Wilson AC (1979) Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci USA 76: 1967-1971
14. Charlesworth B (1992) Evolutionary rates in partially self-fertilizing species. Am Nat 140:126-148
15. Charlesworth D, Wright SI (2001) Breeding systems and genome evolution. Curr Opin Genet Evol 11:685-690
16. Cho Y, Mower JP, Qiu Y-L, Palmer JD (2004) Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants. Proc Natl Acad Sci USA 51:17741-17746
17. Clegg MT, Gaut BS, Learn GH, Morton BR (1994) Rates and patterns of chloroplast DNA evolution. Proc Natl Acad Sci USA 91: 6795-6801
18. Davies TJ, Savolainen V, Chase MW, Moat J, Barraclough TJ (2004) Environmental energy and evolutionary rates in flowering plants. Proc Roy Soc Lond B Bio 271:2195-2200
19. dePamphilis CW, Young ND, Wolfe AD (1997) Evolution of plastid gene rps2 in a lineage of hemiparasitic and holoparasitic plants: many losses of photosynthesis and complex patterns of rate variation. Proc Natl Acad Sci USA 94:7367-7372
20. DeRose-Wilson LJ, Gaut BS (2007) Transcription-regulated mutations and GC content drive variation in nucleotide substitution rates across the genomes of Arabidopsis thaliana and Arabidopsis lyrata. BMC Evol Biol 7:66
21. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214
22. Drummond AJ, Ho SYM, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol 4:e88
23. Duff RJ, Nickrent DL (1997) Characterization of mitochondrial small subunit ribosomal RNAs from holoparasitic plants. J Mol Evol 45:631
24. 4 grasses. Proc Natl Acad Sci USA 107:2532-2537
25. Eyre-Walker A, Gaut BS (1997) Correlated rates of synonymous site evolution across plant genomes. Mol Biol Evol 14:455-460
26. Friis EM, Pederson KR, Crane PR (2006) Cretaceous angiosperm flowers: innovation and evolution in plant reproduction. Palaeogeogr Palaeocl 232:251-293
27. Ganko EW, Meyers BC, Vision TJ (2007) Divergence in expression between duplicated genes in Arabidopsis. Mol Biol Evol 24:2298-2309
28. Gaut BS, Muse SV, Clark D, Clegg MT (1992) Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants. J Mol Evol 35:292-303
29. Gaut BS, Muse SV, Clegg MT (1993) Relative rates of nucleotide substitution in the chloroplast genome. Mol Phylogenet Evol 2:89-96
30. Gaut BS, Morton BR, McCaig BC, Clegg MT (1996) Substitution rate comparisons between grasses and palms: synonymous differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci USA 93:10274-10279
31. Gaut BS, Clark LG, Wendel JF, Muse SV (1997) Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae). Mol Biol Evol 14:769-777
32. Gossmann TI, Song B-H, Windsor AJ, Mitchell-Olds T, Dixon CJ, Kapralov MV, Filatov DA, Eyre-Walker A (2010) Genome wide analyses reveal little evidence for adaptive evolution in plant species. Mol Biol Evol 27:1822-1832
33. Graur D, Martin W (2004) Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet 20:80-86
34. Gray RD, Atkinson QD (2003) Language-tree divergence times support the Anatolian theory of Indo-European origin. Nature 426:435-439
35. Guindon S (2010) Bayesian estimation of divergence times from large sequence alignments. Mol Biol Evol 27:1768-1781
36. Hahn MW, Conant GC, Wagner A (2004) Molecular evolution in large genetic networks: does connectivity equal constraint? J Mol Evol 58:203-211
37. Heckman DS, Geiser DM, Eidell BR, Stauffer RL, Kardos NL, Hedges SB (2001) Molecular evidence for the early colonization of land by fungi and plants. Science 293:1129-1133
38. Ho SYW (2009) An examination of phylogenetic models of substitution rate variation among lineages. Biol Lett 5:421-424
39. Hollister JD, Ross-Ibarra J, Gaut BS (2009) Indel-associated mutation rate varies with mating system in flowering plants. Mol Biol Evol 27:409-416
40. Huelsenbeck JP, Rannala B (2000) Using stratigraphic information in phylogenetics. In: Wiens JJ (ed) Phylogenetic analysis of morphological data. Smithsonian Institution Press, Washington, DC, pp 165-191
41. Huelsenbeck JP, Larget B, Swofford D (2000) A compound poisson process for relaxing the molecular clock. Genetics 154:1879-1892
42. Jobson RW, Albert VA (2002) Molecular rates parallel diversification contrasts between carnivorous plant sister lineages. Cladistics 18:127-136
43. Kay KM, Whittall JB, Hodges SA (2006) A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects. BMC Evol Biol 6:36
44. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
45. Kishino H, Thorne JL, Bruno WJ (2001) Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol Biol Evol 18:352-361
46. Korall P, Schuettpelz E, Pryer KM (2010) Abrupt deceleration of molecular evolution linked to the origin of arborescence in ferns. Evolution 64:2786-2792
47. Kubatko LS, Carstens BC, Knowles LL (2009) STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 25:971-973
48. Laird CD, McConaughy BL, McCarthy BJ (1969) Rate of fixation of nucleotide substitutions in evolution. Nature 224:149-154
49. Lancaster LT (2010) Molecular evolutionary rates predict both extinction and speciation in temperate angiosperm lineages. BMC Evol Biol 10:162
50. Laroche J, Bousquet J (1999) Evolution of mitochondrial rps3 intron in perennial and annual angiosperms and homology to nad5 intron 1. Mol Biol Evol 16:441-452
51. Laroche J, Li P, Bousquet J (1995) Mitochondrial DNA and the monocot-dicot divergence time. Mol Biol Evol 12:1151-1156
52. Laroche J, Li P, Maggia L, Bousquet J (1997) Molecular evolution of angiosperm mitochondrial introns and exons. Proc Natl Acad Sci USA 94:5722-5727
53. Lartillot N, Poujol R (2011) A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters. Mol Biol Evol 28:729-744
54. Lepage T, Tupper P, Bryant D, Lawi S (2006) Continuous and tractable models of the variation of evolutionary rates. Math Biosci 199:216-233
55. Lewis PO (2001) A likelihood approach to estimating phylogeny from discrete morphological data. Syst Biol 50:913-925
56. Li WL, Rodrigo AG (2009) Covariation of branch lengths in phylogenies of functionally related genes. PLoS One 4:e8487
57. Liu L, Pearl DK (2007) Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst Biol 56:504-514
58. Liu L, Pearl DK, Brumfield RT, Edwards SV (2008) Estimating species trees using multiple-allele DNA sequence data. Evolution 62: 2080-2091
59. Lu Y, Rausher MD (2003) Evolutionary rate variation in anthocyanin pathway genes. Mol Biol Evol 20:1844-1853
60. Maddison WP, Knowles LL (2006) Inferring phylogeny despite incomplete lineage sorting. Syst Biol 55:21-30
61. Magallón S (2010) Using fossils to break long branches in molecular dating: a comparison of relaxed clocks applied to the origin of angiosperms. Syst Biol 59:384-399
62. Magallón S, Sanderson MJ (2005) Angiosperm divergence times: the effect of genes, codon positions, and time constraints. Evolution 59:1653-1670
63. Martin W, Gierl A, Saedler H (1989) Molecular evidence for pre-Cretaceous angiosperm origins. Nature 339:46-48
64. Mayrose I, Otto SP (2011) A likelihood model for detecting traitdependent shifts in rate of molecular evolution. Mol Biol Evol 28:759-770
65. Muse SV (2000) Examining rates and patterns of nucleotide substitution in plants. Plant Mol Biol 42:25-43
66. Muse SV, Gaut BS (1994) A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol 11:715-724
67. Muse SV, Gaut BS (1997) Comparing patterns of nucleotide substitution rates among chloroplast loci using the relative ratio test. Genetics 146:392-399
68. Nichols R (2001) Gene trees and species trees are not the same. Trends Ecol Evol 16:358-364
69. Nickrent DL, Starr EM (1994) High rates of nucleotide substitution in nuclear small-subunit (18S) rDNA from holoparasitic flowering plants. J Mol Evol 39:62-70
70. Ohta T (1992) The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst 23:263-286
71. Ohta T (1993) An examination of the generation-time effect on molecular evolution. Proc Natl Acad Sci USA 90:10676-10680
72. Rabonsky DL (2010) Extinction rates should not be estimated from molecular phylogenies. Evolution 64:1816-1824
73. Ramshaw JAM, Richardson DL, Meatyard BT, Brown RH, Richardson M, Thompson EW, Boulter D (1972) The time of origin of the flowering plants determined by using amino acid sequence data of cytochrome c. New Phytol 71:773-779
74. Rannala B, Yang Z (2007) Inferring speciation times under an episodic molecular clock. Syst Biol 56:453-466
75. Rausher MD, Miller RE, Tiffin P (1999) Patterns of evolutionary rate variation among genes of the anthocyanin biosynthetic pathway. Mol Biol Evol 16:266-274
76. Rausher MD, Lu Y, Meyer K (2008) Variation in constraint versus positive selection as an explanation for evolutionary rate variation among anthocyanin genes. J Mol Evol 67:137-144
77. Renner SS (2005) Relaxed molecular clocks for dating historical plant dispersal events. Trends Plant Sci 10:550-558
78. Ritland K, Clegg MT (1987) Evolutionary analysis of plant DNA sequences. Am Nat 130:S74-S100
79. Rutschmann F (2006) Molecular dating of phylogenetic trees: a brief review of current methods that estimate divergence times. Divers Distrib 12:35-48
80. Sanderson MJ (1997) A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol Biol Evol 14:1218-1231
81. Sanderson MJ (2002) Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol Biol Evol 19:101-109
82. Sanderson MJ (2003a) Molecular data from 27 proteins do not support a Precambrian origin of land plants. Am J Bot 90:954-956
83. Sanderson MJ (2003b) r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19:301-302
84. Sanderson MJ, Doyle JA (2001) Sources of error and confidence intervals in estimating the age of angiosperms from rbcL and 18S rDNA data. Am J Bot 88:1499-1516
85. Sanderson MJ, Thorne JL, Wikström N, Bremer K (2004) Molecular evidence on plant divergence times. Am J Bot 91:1656-1665
86. Sarich VM, Wilson AC (1973) Generation time and genomic evolution in primates. Science 179:1144-1147
87. Savard L, Li P, Strauss SH, Chase MW, Michaud M, Bousquet J (1994) Chloroplast and nuclear gene sequences indicate Late Pennsylvanian time for the last common ancestor of extant seed plants. Proc Natl Acad Sci USA 91:5163-5167
88. Slotte T, Foxe JP, Hazzouri KM, Wright SI (2010) Genome-wide evidence for efficient positive and purifying selection in Capsella grandiflora, a plant species with a large effective population size. Mol Biol Evol 27:1813-1821
89. Smith SA, Donoghue MJ (2008) Rates of molecular evolution are linked to life history in flowering plants. Science 322:86-89
90. Smith SA, Beaulieu JM, Donoghue MJ (2010) An uncorrelated relaxedclock analysis suggests an earlier origin for flowering plants. Proc Natl Acad Sci USA 107:5897-5902
91. Soria-Hernanz DF, Fiz-Palacios O, Braverman JM, Hamilton MB (2008) Reconsidering the generation time hypothesis based on nuclear ribosomal ITS sequence comparisons in annual and perennial angiosperms. BMC Evol Biol 8:344
92. Sun G, Ji Q, Dilcher DL, Zheng S, Nixon KC, Wang X (2002) Archaefructaceae, a new basal angiosperm family. Science 296:899-904
93. Svennblad B (2008) Consistent estimation of divergence times in phylogenetic trees with local molecular clocks. Syst Biol 57:947-954
94. Svennblad B, Britton T (2007) Improving divergence time estimation in phylogenetics: more taxa vs. longer sequences. Stat Appl Genet Mol Biol 6:35
95. Thorne JL, Kishino H, Painter IS (1998) Estimating the rate of evolution of the rate of evolution. Mol Biol Evol 15:1647-1657
96. Wang H-C, Singer GAC, Hickey DA (2004) Mutational bias affects protein evolution in flowering plants. Mol Biol Evol 21:90-96
97. Webster AJ, Payne RJH, Pagel M (2003) Molecular phylogenies link rates of evolution and speciation. Science 301:478
98. Welch JJ, Bromham L (2005) Molecular dating when rates vary. Trends Ecol Evol 20:320-327
99. Whittle C-A (2006) The influence of environmental factors, the pollen: ovule ratio and seed bank persistence on molecular evolutionary rates in plants. J Evol Biol 19:302-308
100. Whittle C-A, Johnston MO (2003) Broad-scale analysis contradicts the theory that generation time affects molecular evolutionary rates in plants. J Mol Evol 56:223-233
101. Wikström N, Savolainen V, Chase MW (2001) Evolution of the angiosperms: calibrating the family tree. Proc Roy Soc Lond B Bio 268:2211-2220
102. Wolfe AD, dePamphilis CW (1998) The effect of relaxed functional constraints on the photosynthetic gene rbcL in photosynthetic and nonphotosynthetic parasitic plants. Mol Biol Evol 15:1243-1258
103. Wolfe KH, Li W-H, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci USA 84:9054-9058
104. Wolfe KH, Sharp PM, Li W-H (1989a) Rates of synonymous substitution in plant nuclear genes. J Mol Evol 29:208-211
105. Wolfe KH, Gouy M, Yang Y-W, Sharp PM, Li W-H (1989b) Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci USA 86:6201-6205
106. Wolfe KH, Morden CW, Ems SC, Palmer JD (1992) Rapid evolution of the plastid translational apparatus in a nonphotosynthetic plant: loss or accelerated sequence evolution of tRNA and ribosomal protein genes. J Mol Evol 35:304-317
107. Woolfit M, Bromham L (2005) Population size and molecular evolution on islands. Proc Roy Soc Lond B Bio 272:2277-2282
108. Wright S, Keeling J, Gillman L (2006) The road from Santa Rosalia: a faster tempo of evolution in tropical climates. Proc Natl Acad Sci USA 103:7718-7722
109. Yang L, Gaut BS (2011) Factors that contribute to variation in evolutionary rate among Arabidopsis genes. Mol Biol Evol 28: 2359-2369
110. Yang Y-H, Zhang F-M, Ge S (2009) Evolutionary rate patterns of the gibberellin pathway genes. BMC Evol Biol 9:206
111. Yoder AD, Yang ZH (2000) Estimation of primate speciation dates using local molecular clocks. Mol Biol Evol 17:1081-1090
112. Young ND, dePamphilis CW (2005) Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function. BMC Evol Biol 5:16
113. Yue J-X, Li J, Wang D, Araki H, Yang S (2010) Genome-wide investigation reveals high evolutionary rates in annual model plants. BMC Plant Biol 10:242
114. Zhang L, Vision TJ, Gaut BS (2002) Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Mol Biol Evol 19:1464-1473
115. Zimmer A, Lang D, Richardt S, Frank W, Reski R, Rensing SA (2007) Dating the early evolution of plants: detection and molecular clock analyses of orthologs. Mol Genet Genomics 278:393-402
116. Zuckerkandl E, Pauling L (1965) Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ (eds) Evolving genes and proteins. Academic, New York, pp 97-166