Skip to main content

Chloroplast DNA and the Study of Plant Phylogeny: Present Status and Future Prospects

  • Chapter
Molecular Systematics of Plants

Abstract

More than a quarter of a century has passed since the publication of Zuckerkandl and Pauling’s (1965) seminal article on the evolutionary implications of macromolecular sequence data. Two fundamental suggestions were made in that article: first, Zuckerkandl and Pauling pointed out that molecular change (nucleotide or amino acid substitutions) might occur at a rate that is proportional to clock time (the molecular clock hypothesis); and second, they noted that the topology of evolutionary branchings (phylogenies) could be deduced from the pattern of molecular change. These two related suggestions form the theoretical underpinnings of the science of molecular evolution.

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

Access this chapter

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight 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.

Similar content being viewed by others

References

  • Clegg, M.T., Learn, G.H., and Golenberg, E.M. (1990) Molecular evolution of chloroplast DNA. In: Evolution at the Molecular Level (eds. R.K. Selander, A.G. Clark, and T.S. Whittam), Sinauer Associates, Sunderland, MA.

    Google Scholar 

  • Church, G.M., and Gilbert, W. (1984) Genomic sequencing. Proc. Natl. Acad. Sci. USA 81, 1991–1995.

    Article  PubMed  CAS  Google Scholar 

  • Cronquist, A. (1981) An Integrated System of Classification of Flowering Plants. Columbia University Press, New York.

    Google Scholar 

  • Doebley, J., Durbin, M.L., Golenberg, E.M., Clegg, M.T., and Ma, D.P. (1990) Evolutionary analysis of the large subunit of carboxylase (rbcL) nucleotide sequence among the grasses (Gramineae). Evolution 44, 1097–1108.

    Article  CAS  Google Scholar 

  • Downie, S.R., Olmstead, R.G., Zurawski, G., Soltis, D.E., Soltis, P.S., Watson, J.C., and Palmer, J.D. (1991) Six independent losses of the chloroplast DNA rpl2 intron in dicotyledons: molecular and phylogenetic implications. Evolution, in press.

    Google Scholar 

  • Felsenstein, J. (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27, 401–410.

    Article  Google Scholar 

  • Felsenstein, J. (1988) Phylogenies from molecular sequences: inference and reliability. Ann. Rev. Genet. 22, 521-565.

    Article  PubMed  CAS  Google Scholar 

  • Fitch, W.M., and Margoliash, E. (1967) Construction of phylogenetic trees. Science 155, 279–284.

    Article  PubMed  CAS  Google Scholar 

  • Giannasi, D.E., and Niklas, K.J. (1977) Flavonoid and other chemical constituents of fossil Miocene Celtis and Ulmus (Succor Creek Flora). Science 191, 765–767.

    Google Scholar 

  • Giannasi, D.E., Zurawski, G., Learn, G.H., and Clegg, M.T.. (1992) Evolutionary relationships of the Caryophyllidae based on comparative rbcL sequences. Syst. Bot., in press.

    Google Scholar 

  • Golenberg, E.M., Giannasi, D.E., Clegg, M.T., Smiley, C.J., Durbin, M., Henderson, D., and Zurawski, G. (1990) Chloroplast DNA sequence from a Miocene Magnolia species. Nature 344, 656–658.

    Article  PubMed  CAS  Google Scholar 

  • Hiratsuka, J., Shimada, H., Whittier, R., Ishibashi, T., Sakamoto, M., Mori, M., Kondo, C., Honji, Y., Sun, C.-R., Meng, B.-Y., Li, Y.-Q., Kano, A., Nishizawa, Y., Hirai, A., Shinozaki, K., and Sugiura, M. (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.

    Article  PubMed  CAS  Google Scholar 

  • Kimura, M. (1968) Evolutionary rate at the molecular level. Nature 217, 624–626.

    Article  PubMed  CAS  Google Scholar 

  • Li, W.-H., Luo, C.-C., and Wu, C.-I. (1985) Evolution of DNA sequences. In: Molecular Evolutionary Genetics (ed. R.J. MacIntyre), Plenum Press, New York, pp. 1–94.

    Chapter  Google Scholar 

  • Ohyama, K., Fukuzawa, H., Kohchi, T., Shirai, H., Sano, T., Sano, S., Umesono, K., Shiki, Y., Takeuchi, M., Chang, Z., Aota, S., Inokuchi, H., and Ozeki, H. (1986) Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322, 572–574.

    Article  CAS  Google Scholar 

  • Ritland, K., and Clegg, M.T. (1987) Evolutionary analysis of plant DNA sequences. Am. Nat. 130, S74–S100.

    Article  CAS  Google Scholar 

  • Rodman, J.E., Oliver, M.K., Nakamura, R.R., McClammer, J.U., Jr., and Bledsoe, A.H. (1984) A taxonomic analysis and revised classification of Centrospermae. Syst. Bot. 9, 297–323.

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Shinozaki, K., Ohme, M., Tanaka, M., Wakasugi, T., Haysida, N., Matsubayashi, T., Zaita, N., Chungwongse, J., Obokata, J., Yamaguchi-Shinozaki, K., Ohto, C., Torazawa, K., Meng, B.Y., Sugita, M., Deno, H., Kamogashira, T., Yamada, K., Kusuda, J., Takaiwa, F., Kata, A., Tohdoh, N., Shimada, H., and Sugiura, M. (1986) The complete nucleotide sequence of the tobacco chloroplast genome. Plant Mol. Biol. Rep. 4, 110–147.

    Article  Google Scholar 

  • Soltis, D.E., Soltis, P.S., Clegg, M.T., and Durbin, M.L. (1990) rbcL sequence divergence in the Saxifragaceae sensu lato. Proc. Natl. Acad. Sci. USA 87, 4640–4644.

    Article  PubMed  CAS  Google Scholar 

  • Wilson, M.A., Gaut, B., and Clegg, M.T. (1990) Chloroplast DNA evolves slowly in the palm family (Arecaceae). Mol. Biol. Evol. 7, 303–314.

    PubMed  CAS  Google Scholar 

  • Wolfe, K.H., and Sharp, P.M. (1988) Identification of functional open reading frames in chloroplast genomes. Gene 66, 215–222.

    Article  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., 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 

  • Zuckerkandl, E., and Pauling, L. (1965) Evolutionary divergence and convergence in proteins. In: Evolving Genes and Proteins, (eds. V. Bryson and H.J. Vogel), Academic Press, New York.

    Google Scholar 

  • Zurawski, G., and Clegg, M.T. (1984) The barley chloroplast DNA atpBE, trnM2, and trnv1 loci. Nucl. Acids Res. 12, 2549–2559.

    Article  PubMed  CAS  Google Scholar 

  • Zurawski, G., and Clegg, M.T. (1987) Evolution of higher-plant chloroplast DNA-encoded genes: implications for structure-function and phylogenetic studies. Ann. Rev. Plant Physiol. 38, 391–418.

    Article  CAS  Google Scholar 

  • Zurawski, G., Clegg, M.T., and Brown, A.H.D. (1984) The nature of nucleotide sequence divergence between barley and maize chloroplast DNA. Genetics 106, 735–749.

    PubMed  CAS  Google Scholar 

Download references

Authors

Editor information

Pamela S. Soltis Douglas E. Soltis Jeff J. Doyle

Rights and permissions

Reprints and permissions

Copyright information

© 1992 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Clegg, M.T., Zurawski, G. (1992). Chloroplast DNA and the Study of Plant Phylogeny: Present Status and Future Prospects. In: Soltis, P.S., Soltis, D.E., Doyle, J.J. (eds) Molecular Systematics of Plants. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-3276-7_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-4615-3276-7_1

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-0-412-02241-8

  • Online ISBN: 978-1-4615-3276-7

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics