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Examining rates and patterns of nucleotide substitution in plants

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Abstract

Driven by rapid improvements in affordable computing power and by the even faster accumulation of genomic data, the statistical analysis of molecular sequence data has become an active area of interdisciplinary research. Maximum likelihood methods have become mainstream because of their desirable properties and, more importantly, their potential for providing statistically sound solutions in complex data analysis settings. In this chapter, a review of recent literature focusing on rates and patterns of nucleotide substitution rates in the nuclear, chloroplast, and mitochondrial genomes of plants demonstrates the power and flexibility of these new methods. The emerging picture of the nucleotide substitution process in plants is a complex one. Evolutionary rates are seen to be quite variable, both among genes and among plant lineages. However, there are hints, particularly in the chloroplast, that individual factors can have important effects on many genes simultaneously.

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References

  1. Adachi J, Hasegawa M: Tempo and mode of synonymous substitutions in mitochondrial DNA of primates. Mol Biol Evol 13: 200–208 (1996).

    Google Scholar 

  2. Adachi J, Cao Y, Hasegawa M: Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: rapid evolution in warm-blooded vertebrates. J Mol Evol 36: 270–281 (1993).

    Google Scholar 

  3. Barraclough TG, Harvey PH, Nee S: Rate of rbcL gene sequence evolution and species diversification in flowering plants. Proc R Soc Lond B 263: 589–591 (1996).

    Google Scholar 

  4. Bousquet J, Strauss SH, Doerksen AH, Price RA: Extensive variation in evolutionary rate of rbcL gene sequences among seed plants. Proc Natl Acad Sci USA 89: 7844–7848 (1992).

    Google Scholar 

  5. Brunsfeld SJ, Soltis PS, Soltis DE, Gadek PA, Quinn CJ et al.: Phylogenetic relationships among the genera Taxoidiacea and Cupressaceae: evidence from rbcL sequences. Syst Bot 19: 253–262 (1994).

    Google Scholar 

  6. Conti E, Fishbach, A, Sytsma KJ: Tribal relationships in Onagraceae: implication from rbcL sequence data. Ann Miss Bot Gard 80: 672–685 (1993).

    Google Scholar 

  7. Cox DR: Tests of separate families of hypotheses. Proc 4th Berkeley Symp. 1: 105–123 (1961).

    Google Scholar 

  8. Easteal S, Collet C, Betty D: The Mammalian Molecular Clock. R.G. Landes Co., Austin TX (1995).

    Google Scholar 

  9. Eyre-Walker A, Gaut BS: Correlated rates of synonymous site evolution among plant genomes. Mol Biol Evol 14: 455–460 (1997).

    Google Scholar 

  10. Felsenstein J: Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368–376 (1981).

    Google Scholar 

  11. Felsenstein J, Churchill GA: A hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol 13: 93–104 (1996).

    Google Scholar 

  12. Gaut BS:Molecular clocks and nucleotide substitution rates in higher plants. Evol Biol 30: 93–120 (1998).

    Google Scholar 

  13. Gaut BS, Weir BS: Detecting substitution-rate heterogeneity among regions of a nucleotide sequence. Mol Biol Evol 11: 620–629 (1994).

    Google Scholar 

  14. Gaut BS, Muse SV, Clark WD, Clegg MT: Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants. J Mol Evol 35: 292–303 (1992).

    Google Scholar 

  15. Gaut BS, Muse SV, Clegg MT: Relative rates of nucleotide substitution in the chloroplast genome. Mol Phyl Evol 2: 89–96 (1993).

    Google Scholar 

  16. Gaut BS, Clark LG, Wendel JF, Muse SV: Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae). Mol Biol Evol 14: 769–777 (1997).

    Google Scholar 

  17. Goldman N: Statistical tests of models of DNA substitution. J Mol Evol 36: 182–198 (1993).

    Google Scholar 

  18. Goldman N, Yang ZH: Codon-based model of nucleotide substitution for protein coding DNA sequences. Mol Biol Evol 11: 725–736 (1994).

    Google Scholar 

  19. Hasegawa M, Kishino H, Yano T: Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160–174 (1985).

    Google Scholar 

  20. Huelsenbeck JP, Crandall KA: Phylogeny estimation and hypothesis testing using maximum likelihood. Annu Rev Ecol Syst 28: 437–466 (1997).

    Google Scholar 

  21. Huelsenbeck JP, Rannala B: Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276: 227–232 (1997).

    Google Scholar 

  22. Jukes TH, Cantor CR: Evolution of protein molecules. In: Munro HN (ed), Mammalian Protein Metabolism, pp. 21–32. Academic Press, New York (1969).

    Google Scholar 

  23. Kimura M: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111–120 (1980).

    Google Scholar 

  24. Laroche J, Li P, Maggia L, Bousquet J:Molecular evolution of angiosperm mitochondrial introns and exons. Proc Natl Acad Sci USA 94: 5722–5727 (1997).

    Google Scholar 

  25. Li P, Bousquet J: Relative-rate test for nucleotide substitutions between two lineages. Mol Biol Evol 9: 1185–1189 (1992).

    Google Scholar 

  26. Li Q, Guy C: Prolonged final extension time increases cloning efficiency of PCR products. Biotechniques 21: 192–196 (1996).

    Google Scholar 

  27. Li W-H, Wu C-I, Luo C-C: A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 2: 150–174 (1985).

    Google Scholar 

  28. Li W-H, Tanimura M, Sharp P: An evaluation of the molecular clock hypothesis using mammalian DNA sequences. J Mol Evol 25: 330–342 (1987).

    Google Scholar 

  29. Muse SV: Evolutionary analyses of DNA sequences subject to constraints on secondary structure. Genetics 139: 1429–1439 (1995).

    Google Scholar 

  30. Muse SV: Estimating synonymous and nonsynonymous substitution rates. Mol Biol Evol 13: 105–114 (1996).

    Google Scholar 

  31. Muse SV, Gaut BS: A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol 11: 715–724 (1994).

    Google Scholar 

  32. Muse SV, Gaut BS: Comparing patterns of nucleotide patterns among chloroplast loci using the relative ratio test. Genetics 146: 393–399 (1997).

    Google Scholar 

  33. Muse SV, Weir BS: Testing for equality of evolutionary rates. Genetics 132: 269–276 (1992).

    Google Scholar 

  34. Nickrent DL, Starr EM: High rates of nucleotide substitution rate in nuclear small-subunit (18S) rDNA from holoparasitic flowering plants. J Mol Evol 39: 62–70 (1994).

    Google Scholar 

  35. Nickrent DL, dePamphilis CW, Wolfe AD, Colwell AE, Young ND et al.: Molecular phylogenetic and evolutionary studies of parasitic plants. In: Soltis PS, Doyle JJ, Soltis DE (eds), Molecular Systematics of Plants 2: DNA sequencing, pp. 211–241. Kluwer Academic Publishers, Boston (1998).

    Google Scholar 

  36. Pederson A-M: A codon-based model designed to describe lentiviral evolution. Mol Biol Evol 15: 1069–1081 (1998).

    Google Scholar 

  37. Rodriguez F, Oliver JF, Marin A, Medina JR: The general stochastic model of nucleotide substitution. J Theor Biol 142: 485–501 (1990).

    Google Scholar 

  38. Sarich VM, Wilson AC: Immunological time scale for hominid evolution. Science 158: 1200–1203 (1967).

    Google Scholar 

  39. Smith JF, Doyle JJ: Chloroplast DNA variation and evolution in the Juglandaceae. Am J Bot 78: 730 (1986).

    Google Scholar 

  40. Stebbins GL: Coevolution of grasses and herbivores. Ann Miss Bot Gard 68: 75–86 (1981).

    Google Scholar 

  41. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM: Phylogenetic inference. In: Hillis DM, Mortiz C, Mable BK (eds), Molecular Systematics, pp. 407–514. Sinauer Associates, Inc., Sunderland, MA (1996).

    Google Scholar 

  42. Tamura K, Nei M: Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10: 512–526 (1993).

    Google Scholar 

  43. Tavare S: Some probabilistic and statistical problems in the analysis of DNA sequences. In: Miura RM (ed.), Lecture on Mathematics in the Life Sciences, pp. 57–86. American Mathematic Society, Providence, RI (1986).

    Google Scholar 

  44. Thorne JL, Goldman N, Jones DT: Combining protein evolution and secondary structure. Mol Biol Evol 13: 666–673 (1996).

    Google Scholar 

  45. Tillier ERM, Collins RA: Neighbor joining and maximum likelihood with RNA sequences: addressing the interdependence of sites. Mol Biol Evol 12: 7–15 (1995).

    Google Scholar 

  46. Wolfe KH, Li W-H, Sharp PM: Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast and nuclear DNAs. Proc Natl Acad Sci USA 84: 9054–9058 (1987).

    Google Scholar 

  47. Wolfe KH, Gouy M, Yang Y-W, Sharp PM, Li W-H: Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci USA 86: 6201–6205 (1989).

    Google Scholar 

  48. Wolfe KH, Sharp PM, Li W-H: Rates of synonymous substitution in plant nuclear genes. J Mol Evol 29: 208–211 (1989).

    Google Scholar 

  49. Wu C-I, Li W-H: Evidence for higher rates of nucleotide substitution in rodents than in man. Proc Natl Acad Sci USA 82: 1741–1745 (1985).

    Google Scholar 

  50. Yang Z: Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol 10: 1396–1401 (1993).

    Google Scholar 

  51. Yang Z: Estimating the pattern of nucleotide substitution. J Mol Evol 39: 105–111 (1994).

    Google Scholar 

  52. Yang Z: A space-time process model for the evolution of DNA sequences. Genetics 139: 993–1005 (1995).

    Google Scholar 

Download references

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Authors and Affiliations

  1. Program in Statistical Genetics, Department of Statistics, North Carolina State University, Raleigh

    Spencer V. Muse

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Muse, S.V. Examining rates and patterns of nucleotide substitution in plants. Plant Mol Biol 42, 25–43 (2000). https://doi.org/10.1023/A:1006319803002

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