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Chloroplast DNA Variation and Plant Phylogeny

Jeffrey D. Palmer, Robert K. Jansen, Helen J. Michaels, Mark W. Chase and James R. Manhart
Annals of the Missouri Botanical Garden
Vol. 75, No. 4 (1988), pp. 1180-1206
DOI: 10.2307/2399279
Stable URL: http://www.jstor.org/stable/2399279
Page Count: 27
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Chloroplast DNA Variation and Plant Phylogeny
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Abstract

Several features, foremost its conservative mode of evolution, make chloroplast DNA an extremely valuable molecule for phylogenetic studies. Its conservatism is also its only serious drawback, as this can limit the amount of useful DNA variation at the intraspecific level. Comparative restriction site mapping is currently the preferred molecular method for examining interspecific relationships. At this level, one typically encounters less than 5% homoplasy. Furthermore, the predominantly uniparental inheritance of chloroplast DNA provides unique insights into the origin of hybrid and polyploid complexes, as illustrated by examples from the genus Brassica. In many families of angiosperms, such as the Asteraceae and Orchidaceae, restriction site mapping can also be used to determine intergeneric relationships. The greater expense of DNA sequencing makes it most appropriate only at those higher taxonomic levels-above the family level-where restriction site mapping fails. Within angiosperms, the rbcL gene appears to be the chloroplast gene of choice for phylogenetic studies. Twenty-five rbcL sequences have already been accumulated, and several laboratories are making a coordinated effort to sequence this gene widely among angiosperms and gymnosperms. The more conservatively evolving ribosomal RNA genes hold the greatest promise for resolving the deepest branchings of plant evolution and, indeed, have already settled the ultimate question of chloroplast evolution, namely, its endosymbiotic origin. A third approach to extracting phylogenetic information from chloroplast DNA is by analyzing the distribution of major structural rearrangements, such as inversions and the loss or gain of genes and introns. Although such rearrangements are rare relative to point mutations, their great rarity and freedom from homoplasy also make them extremely powerful characters. Examples to be discussed include an inversion defining the most ancient branching in the Asteraceae, rearrangements that mark several major divisions within the Fabaceae, and events that identify the green algal ancestors of land plants.

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