. "13 Gene Genealogies and Population Variation in Plants." Variation and Evolution in Plants and Microorganisms: Toward a New Synthesis 50 Years after Stebbins. Washington, DC: The National Academies Press, 2000.
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Variation and Evolution in Plants and Microorganisms: TOWARD A NEW SYNTHESIS 50 YEARS AFTER STEBBINS
tions, gene migration, and extinction. The genetic aspects of such processes largely remain to be explored, and a historical genealogical approach will be particularly instructive.
The major impediment to wide application of gene genealogies for phylogeographic studies in plants is identifying DNA sequences with appropriate levels of ordered variation within chloroplast, mitochondrial, or nuclear genomes (Schaal et al., 1998). In many cases, the chloroplast spacer regions that have been informative for some species (see above) show little to no intraspecific variation in other plant species. Moreover, chloroplast restriction fragment length polymorphism genealogies based on length variation alone can be confounded by homoplasy. The nuclear genome remains problematic because of the difficulty in finding regions that have sufficient levels of neutral variation and that are not involved in intragenic recombination. Moreover, the effective population size of a nuclear gene is four times that of an organelle gene, because it is diploid and biparentally inherited. The larger effective population size results in increased coalescent times, which in turn, increases the likelihood of encountering ancestral polymorphisms. High-resolution nuclear markers such as random amplified polymorphic DNAs and amplified fragment length polymorphisms are historically unordered, and variants cannot be related easily in a genealogical manner. Because of the difficulty in finding genealogically informative markers, many plant studies have been phylogeographic only in the broad sense, meaning that they detect an association between patterns of genetic variation and geography. Such studies do not incorporate a genealogical perspective.
The search for appropriate markers has turned to nuclear genes that are increasingly the focus for genealogical studies. Nuclear genes often contain multiple introns, and many of the introns contain high levels of neutral variation. This approach has been applied successfully in several animal species: e.g., oysters (Hare and Avise, 1998), fish (Bagley and Gall, 1998), and birds (Degnan, 1993). Nuclear sequences of plants have been used to understand the genetic relationships of wild populations of A. thaliana (Bergelson et al., 1998), selection, and evolution of homeotic genes (Purugganan and Suddith, 1999), as well as in the example from cassava above. Numerous studies of nuclear gene genealogies are currently under way and promise to provide new insights into the processes identified by Stebbins a half century ago as central for the evolution of plants.
This work was supported in part by a grant from the Explorer's Club, by National Science Foundation Doctoral Dissertation Improvement Grant DEB 9801213 to K.M.O., and by grants from the Rockefeller and Guggenheim Foundations to B.A.S.