Skip to main content
SpringerLink
Log in

Molecular Clocks and Nucleotide Substitution Rates in Higher Plants

  • Chapter
Book cover Evolutionary Biology

Part of the book series: Evolutionary Biology ((EBIO,volume 30))

Abstract

In the early 1960s, researchers noticed that the number of differences between amino acid sequences varied roughly linearly with the time of divergence between the species from which the amino acid sequences were sampled (Margoliash, 1963; Zuckerkandl and Pauling, 1962, 1965). This seminal observation led to the formulation of the “molecular clock” hypothesis (Zuckerkandl and Pauling, 1965), which asserts that change at the molecular level occurs regularly through time. An important corollary prediction of the molecular clock hypothesis is that rates of molecular evolution are equal among diverse evolutionary lineages.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Adachi, J., Cao, Y., and Hasegawa, M., 1993, Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level—rapid evolution in warmblooded vertebrates, J. Mol. Evol. 36:270–281.

    Article  PubMed  CAS  Google Scholar 

  • Ahn, S., and Tanksley, S. D., 1993, Comparative linkage maps of the rice and maize genomes, Proc. Natl. Acad. Sci. USA 90:7980–7984.

    Article  PubMed  CAS  Google Scholar 

  • Baldwin, B. G., Sanderson, M. J., Porter, J. M., Wojciechowski, M. F., Campbell, C. S., and Donoghue, M. J., 1995, The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny, Ann. Miss. Bot. Gard. 82:247–277.

    Article  Google Scholar 

  • Barraclough, T. G., Harvey, P. H., and Nee, S., 1996, Rate of rbcL gene sequence evolution and species diversification in flowering plants, Proc. R. Soc. Lond. B 263:589–591.

    Article  Google Scholar 

  • Benton, M. J., 1990, Phylogeny of major tetrapod groups—morphological data and divergence dates, J. Mol. Evol. 30:409–424.

    Article  PubMed  CAS  Google Scholar 

  • Bousquet, J., Strauss, S. H., Doerksen, A. H., and Primce, R. A., 1992, Extensive variation in evolutionary rate of rbcL gene sequences among seed plants, Proc. Natl. Acad. Sci. USA 89:7844–7848.

    Article  PubMed  CAS  Google Scholar 

  • Bowe, L. M., and dePamphilis, C. W., 1996, Effects of RNA editing and gene processing on phylogenetic reconstruction, Mol. Biol. Evol. 13:1159–1166.

    Article  PubMed  CAS  Google Scholar 

  • Britten, R. J., 1986, Rates of DNA sequence evolution differ between taxonomic groups. Science 231:1393–1398.

    Article  PubMed  CAS  Google Scholar 

  • Brown, W. M., George, M., and Wilson, A. C., 1979, Rapid evolution of animal mitochondrial DNA, Proc. Natl. Acad. Sci. USA 76:1967–1971.

    Article  PubMed  CAS  Google Scholar 

  • Brunsfeld, S. J., Soltis, P. S., Soltis, D. E., Gadek, P. A., Quinn, C. J., Strenge, D. D., and Ranker, T. A., 1994, Phylogenetic relationships among the genera Taxoidiacea and Cupressaceae: Evidence from rbcL sequences, Syst. Bot. 19:253–262.

    Article  Google Scholar 

  • Buckler, E. S., and Holtsford, T. P., 1996a, Zea ribosomal repeat evolution and substitution patterns, Mol. Biol. Evol. 13:623–632.

    Article  PubMed  CAS  Google Scholar 

  • Buckler, E. S., and Holtsford, T.P , 1996b, Zea systematics: Ribosomal ITS evidence, Mol. Biol. Evol. 13:612–622.

    Article  PubMed  CAS  Google Scholar 

  • Clegg, M. T., Rawson, J. R. Y., and Thomas, K., 1984, Chloroplast DNA variation in pearl millet and related species, Genetics 106:449–461.

    PubMed  CAS  Google Scholar 

  • Conti, E., Fishbach, A., and Sytsma, K. J., 1993, Tribal relationship in Onagraceae: Implication from rbcL sequence data, Ann. Miss. Bot. Gard. 80:672–685.

    Article  Google Scholar 

  • Dahlgren, R. M. T., Clifford, H. T., and Yeo, P. F., 1985, The Families of the Monocotyledons, Springer-Verlag, Berlin.

    Book  Google Scholar 

  • Downie, S. R., and Palmer, J. D., 1992, Use of chloroplast DNA rearrangments in reconstructing plant phylogeny, in: Molecular Systematics of Plants (P. S. Soltis, D. E. Soltis, and J. J. Doyle, eds.), pp. 14–35, Chapman and Hall, New York.

    Chapter  Google Scholar 

  • Durbin, M. L., Learn, G. H., Huttley, G. A., and Clegg, M. T., 1995, Evolution of the chalcone synthase gene family in the genus Ipomea, Proc. Natl. Acad. Sci. USA 92:3338–3342.

    Article  CAS  Google Scholar 

  • Easteal, S., 1988, Rate constancy of globin gene evolution in placental mammals, Proc. Natl. Acad. Sci. USA 85:7622–7626.

    Article  PubMed  CAS  Google Scholar 

  • Easteal, S., 1990, The pattern of mammalian evolution and the relative rate of molecular evolution, Genetics 124:165–173.

    PubMed  CAS  Google Scholar 

  • Easteal, S., Collet, C., and Betty, D., 1995, The Mammalian Molecular Clock, R. G. Landes, Austin, TX.

    Google Scholar 

  • Eyre-Walker, A., and Gaut, B. S., 1997, Correlated substitution rates among plant genomes. Mol. Biol. Evol. (1997).

    Google Scholar 

  • Fitch, W. M., 1976, Molecular evolutionary clocks, in: Molecular Evolution (F. J. Ayala, ed.), pp. 160–178, Sinauer Associates, Sunderland, MA.

    Google Scholar 

  • Gaut, B. S., Muse, S. V., Clark, W. D., and Clegg, M. T., 1992, Relative rates of nucleotide substitution at the rbcl locus of monocotyledenous plants. J. Mol. Evol. 35:292–303.

    Article  PubMed  CAS  Google Scholar 

  • Gaut, B. S., and Clegg, M. T., 1993, Nucleotide polymorphsim in the Adh1 locus of pearl millet (Pennisetum glaucum) (Poaceae), Genetics 135:1091–1097.

    PubMed  CAS  Google Scholar 

  • Gaut, B. S., and Doebley, J. F., 1997, DNA sequence evidence for the segmental allotetraploid origin of maize. Proc. Natl. Acad. Sci. USA 94:6809–6814.

    Article  PubMed  CAS  Google Scholar 

  • Gaut, B. S., Muse, S. V., and Clegg, M. T., 1993, Relative rates of nucleotide substitution in the chloroplast genome, Mol. Phyl. Evol. 2:89–96.

    Article  CAS  Google Scholar 

  • Gaut, B. S., Morton, B. R., McCaig, B. M., and Clegg, M. T., 1996, Substitution rate comparisons between grasses and palms: Synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL, Proc. Natl. Acad. Sci. USA 93:10274–10279.

    Article  PubMed  CAS  Google Scholar 

  • Gaut, B. S., Clark, L. G., Wendel, J. F., and Muse, S. V., 1997, Comparisons of the molecular evolutionary/process at rbcL and ndhF in the grass family (poaceae). Mol. Biol. Evol. 14:769–777.

    Article  PubMed  CAS  Google Scholar 

  • Gillespie, J. H., 1986, Natural selection and the molecular clock, Mol. Biol. Evol. 3:138–155.

    PubMed  CAS  Google Scholar 

  • Gillespie, J. H., 1995, On Ohta’s hypothesis: Most amino acid substitutions are deleterious, J. Mol. Evol. 40:64–69.

    Article  CAS  Google Scholar 

  • Herbert, G., and Easteal, S., 1996, Relative rates of nuclear DNA evolution in human and Old World monkey lineages, Mol. Biol. Evol. 13:1054–1057.

    Article  PubMed  CAS  Google Scholar 

  • Janzen, D. H., 1976, Why bamboos wait so long to flower, Annu. Rev. Ecol. Syst. 1976:347–391.

    Article  Google Scholar 

  • Jukes, T. H., and Cantor, C. R., 1969, Evolution of protein molecules, in: Mammalian Protein Metabolism (H. N. Munro, ed.), pp. 21–32, Academic Press, New York.

    Google Scholar 

  • Kimura, M., 1969, The rate of molecular evolution considered from the standpoint of population genetics, Proc. Natl. Acad. Sci.USA 63:1181–1188.

    Article  PubMed  CAS  Google Scholar 

  • Kumura, M., 1980, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, J. Mol. Evol. 16:111–120.

    Article  Google Scholar 

  • Kimura, M., 1983, The neutral theory of molecular evolution, in: Evolution of Genes and Proteins (M. Nei and R. K. Koehn, eds.), pp. 208–233, Sinauer Associates, Sunderland, MA.

    Google Scholar 

  • Kimura, M., and Ohta, T., 1971, Protein polymorphism as a phase of molecular evolution, Nature 229:467–469.

    Article  PubMed  CAS  Google Scholar 

  • Kimura, M., and Ohta, T., 1974, On some principles governing molecular evolution, Proc. Natl. Acad. Sci. USA 71:2848–2852.

    Article  PubMed  CAS  Google Scholar 

  • Laroche, J., Li, P., and Bousquet, J., 1995, Mitochondrial DNA and monocot-dicot divergence time, Mol. Biol. Evol. 12:1151–1156.

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  • Li, W.-H., and Tanimura, M., 1987, The molecular clock runs more slowly in man than in apes and monkeys, Nature 326:93–96.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Li, W.-H., Ellsworth, D. L., Krushkal, J., Chang, B. H.-J., and Emmet, D. H., 1996, Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis, Mol. Phyl. Evol. 5:182–187.

    Article  CAS  Google Scholar 

  • Margoliash, E., 1963, Primary structure and evolution of cytochrome c, Proc. Natl. Acad. Sci. USA 50:672–679.

    Article  PubMed  CAS  Google Scholar 

  • Martin, A. P., and Palumbi, S. R., 1993, Body size, metabolic rate, generation time, and the molecular clock, Proc. Natl. Acad. Sci. USA 90:4087–4091.

    Article  PubMed  CAS  Google Scholar 

  • Martin, A. P., Naylor, G. J. P., and Palumbi, S. R., 1992, Rate of mitochondrial DNA evolution is slow in sharks compared to mammals. Nature 357:153–155.

    Article  PubMed  CAS  Google Scholar 

  • Mathews, S., Sharrock, R. A., 1996, The phytochrome gene family in grasses (Poaceae): A phylogeny and evidence that grasses have a subset of loci found in dicot angiosperms, Mol. Biol. Evol. 13:1141–1150.

    Article  PubMed  CAS  Google Scholar 

  • Mayr, E., 1954, Change of genetic environment and evolution, in: Evolution as a Process (J. Huxley, A. C. Hardy, and E. B. Ford, eds.), pp. 157–180, George, Allen and Unwin. London.

    Google Scholar 

  • Mooers, A. O., and Harvey, P. H., 1994, Metabolic rates, generation time and the rate of molecular evolution in birds, Mol. Phyl. Evol. 3:344–350.

    Article  CAS  Google Scholar 

  • Morton, B. R., 1995, Neighboring base composition and transversion/transition bias in a comparison of rice and maize chloroplast noncoding regions, Proc. Natl. Acad. Sci. USA 92:9717–9721.

    Article  PubMed  CAS  Google Scholar 

  • Morton, B. R., Gaut, B. S., and Clegg, M. T., 1996, Evolution of alcohol dehydrogenase genes in the palm and grass families, Proc. Natl. Acad. Sci. USA 93:11735–11739.

    Article  PubMed  CAS  Google Scholar 

  • Muse, S. V., and Gaut, B. S., 1994, A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11:715–724.

    PubMed  CAS  Google Scholar 

  • Muse, S. V., and Gaut, B. S., 1997, Comparing patterns of nucleotide substitution patterns among chloroplast loci using the relative ratio test, Genetics 146:393–399.

    PubMed  CAS  Google Scholar 

  • Muse, S. V., and Weir, B. S., 1992, Testing for equality of evolutionary rates. Genetics 132: 269–276.

    PubMed  CAS  Google Scholar 

  • Nei, M., and Gojobori, T., 1986, Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418–426.

    PubMed  CAS  Google Scholar 

  • Nickrent, D. L., and Franchina, C. R., 1990, Phylgoenetic relationships of the Santalales and relatives, J. Mol. Evol. 31:294–301.

    Article  PubMed  CAS  Google Scholar 

  • Nickrent, D. L., and Starr, E. M., 1994, High rates of nucleotide substitution rate in nuclear small-subunit (18 S) rDNA from holoparasitic flowering plants, J. Mol. Evol. 39:62–70.

    Article  PubMed  CAS  Google Scholar 

  • Nickrent, D. L., dePamphilis, C. W., Wolfe, A. D., Colwell, A. E., Young, N. D., and Duff, R. J., 1997, Molecular phylogenetic and evolutionary studies of parasitic plants, in: Molecular Sysiematics of Plants (P. S. Soltis, J. J. Doyle, and D. E. Soltis, eds.), Chapman and Hall, New York (in press).

    Google Scholar 

  • Ohta, T., 1992, The nearly neutral theory of molecular evolution, Annu. Rev. Syst. Ecol. 23:263–286.

    Article  Google Scholar 

  • Ohta, T., and Kimura, M., 1971, On the constancy of the evolutionary rate of cistrons, J. Mol. Evol. 1:18–25.

    Article  CAS  Google Scholar 

  • Palmer, J. D., 1992, Mitochondrial DNA in plant systematics: Applications and limitations, in: Molecular Systematics of Plants (P. S. Soltis, D. E. Soltis, and J. J. Doyle, eds.), pp. 36–49, Chapman and Hall, New York.

    Chapter  Google Scholar 

  • Palmer, J. D., and Thompson, W. F., 1982, Chloroplast DNA rearrangements are more frequent when a large inverted repeated sequence is lost, Cell 29:537–550.

    Article  PubMed  CAS  Google Scholar 

  • Palmer, J. D., Nugent, J. M., and Hebron, L. A., 1987, Unusual structure of geranium chloroplast DNA: A triple-sized inverted repeat, extensive gene duplication, multiple inversions, and two repeat families, Proc. Natl. Acad. Sci. USA 84:769–773.

    Article  PubMed  CAS  Google Scholar 

  • Palmer, J. D., Makarooff, C. A., Apel, I. J., and Shirzdegan, M., 1990, Fluid structure of plant mitochondrial genomes: Evolutionary and functional implications, in: Molecular Evolution (M. T. Clegg and S. J. O’Brien, eds.), pp. 85–96, Wiley-Liss, New York.

    Google Scholar 

  • Purugganan, M. D., and Wessler, S. R., 1994, Molecular evolution of the plant R regulatory gene family, Genetics 138:849–854.

    PubMed  CAS  Google Scholar 

  • Purugganan, M. D., Rounsley, S. D., Schmidt, R. J., and Yanofsky, M. F., 1995, Molecular evolution of flower development: Diversification of the plant MADS-box regulatory gene family, Genetics 139:345–356.

    Google Scholar 

  • Rieseberg, L. H., Sinervo, B., Linder, C. R., Ungerer, M. C., and Arias, D. M., 1996, Role of gene interactions in hybrid speciation: Evidence from ancient and experimental hybrids, Science 272:741–745.

    Article  PubMed  CAS  Google Scholar 

  • Rodermel, S. R., and Bogorad, L., 1987, Molecular evolution and nucleotide sequences of the maize plasmid gnes for the subunity of CF1 (atpA) and the poteolipid subunit of CF0 (atpH), Genetics 116:127–139.

    CAS  Google Scholar 

  • Saitou, N., and Nei, M., 1987, The neighbor-joining method: A new method for reconstructing phylogenetic trees, Mol. Biol. Evol. 4:406–425.

    PubMed  CAS  Google Scholar 

  • Sarich, V. M., and Wilson, A. C. 1967, Immunological time scale for hominid evolution, Science 150:1200–1203.

    Article  Google Scholar 

  • Smith, J. F., and Doyle, J. J., 1986, Chloroplast DNA variation and evolution in the Juglandaceae, Am. J. Bot. 78:730.

    Google Scholar 

  • Soltis, P.S., Doyle, J. J., and Soltis, D. E., 1992, Molecular data and polyploid evolution of plants, in: Molecular Systematics of Plants (P. S. Soltis, J. J. Doyle, and D. E. Soltis, eds.), pp. 177–201, Chapman and Hall, New York.

    Chapter  Google Scholar 

  • Stebbins, G. L., 1981, Coevolution of grasses and nerbivores. Ann. Miss. Bot. Gard. 68:75–86.

    Article  Google Scholar 

  • Suguira, M., 1989, The chloroplast chromosomes in land plants, Annu. Rev. Cell Biol. 5:51–70.

    Article  Google Scholar 

  • Suguira, M., 1992, The chloroplast genome, Pl. Mol. Biol. 19:149–468.

    Article  Google Scholar 

  • Tajima, F., 1983, Evolutionary relationship of DNA sequences in finite populations, Genetics 105:437–460.

    PubMed  CAS  Google Scholar 

  • Takezaki, N. A., Rzhetsky, and Nei, M., 1995, Phylogenetic test of the molecular clock and linearized trees, Mol. Biol. Evol. 12:823–833.

    PubMed  CAS  Google Scholar 

  • Wakasugi, T., Tsudzuki, J., Ito, S., Nakashima, K., Tsudzuki, T., and Sugiura, M., 1994, Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergu, Proc. Natl. Acad. Sci. USA 91:9794–9798.

    Article  CAS  Google Scholar 

  • Waters, E. R., 1995, The molecular evolution of the small heat-shock proteins in plants, Genetics 141:785–795.

    PubMed  CAS  Google Scholar 

  • Wolfe, K. H., Li, W.-H., and Sharp, P. M., 1987, Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast and nuclear DNAs, Proc. Natl. Acad. Sci. USA 84:9054–9058.

    Article  PubMed  CAS  Google Scholar 

  • Wolfe, K. H., Gouy, M., Yang, Y.-W., Sharp, P. M., and Li, W.-H., 1989a, Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data, Proc. Natl. Acad. Sci. USA 86:6201–6205.

    Article  PubMed  CAS  Google Scholar 

  • Wolfe, K. H., Sharp, P. M., and Li, W.-H., 1989;, Rates of synonymous substitution in plant nuclear genes, J. Mol. Evol. 29:208–211.

    Article  CAS  Google Scholar 

  • Wolfe, K. H., Katz-Downie, D. S., Morden, C. W., and Palmer, J. D., 1992a, Evolution of the plastid ribosomal RNA Operon in a nongreen parasitic plant: Accelerated sequence evolution, altered promoter structure, and tRNA pseudogenes, Pl. Mol. Biol. 18:1037–1048.

    Article  CAS  Google Scholar 

  • Wolfe, K. H., Morden, C. W., and Palmer, J. D., 1992b, Function and evolution of a minimal plastid genome from a nonphotosynthetic parasite, Proc. Natl. Acad. Sci. USA 89:10648–10652.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Zimmer, E. A., Jupe, E. R., and Walbot, V., 1988, Ribosomal gene structure, variation and inheritance in maize and its ancestors, Genetics 120:1125–1136.

    PubMed  CAS  Google Scholar 

  • Zuckerkandl, E., and Pauling, L., 1962, Molecular disease, evolution, and genetic heterogeneity, in: Horizons in Biochemistry (B. Bryson and H. J. Vogel, eds.), pp. 189–225, Academic Press, New York.

    Google Scholar 

  • Zuckerkandl, E., and Pauling, L., 1965, Evolutionary divergence and convergence in proteins, in: Evolving Genes and Proteins (B. Bryson and H. Vogel, eds.), pp. 97–116, Academic Press, New York.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, 92697-2525, USA

    Brandon S. Gaut

Authors
  1. Brandon S. Gaut
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Queens College, City University of New York, Flushing, New York, USA

    Max K. Hecht

  2. Cornell University, Ithaca, New York, USA

    Ross J. Macintyre

  3. University of California, Riverside, Riverside, California, USA

    Michael T. Clegg

Rights and permissions

Reprints and permissions

Copyright information

© 1998 Springer Science+Business Media New York

About this chapter

Cite this chapter

Gaut, B.S. (1998). Molecular Clocks and Nucleotide Substitution Rates in Higher Plants. In: Hecht, M.K., Macintyre, R.J., Clegg, M.T. (eds) Evolutionary Biology. Evolutionary Biology, vol 30. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-1751-5_4

Download citation

  • DOI: https://doi.org/10.1007/978-1-4899-1751-5_4

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4899-1753-9

  • Online ISBN: 978-1-4899-1751-5

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation