phyletic, then paraphyletic, with respect to the populations (Neigel and Avise, 1986). In these cases, genealogical relationships among alleles are not expected to correspond to population identity (Fig. 2). Thus, for recently diverged populations, inferences about the history of population divergence based on the gene tree may be misleading or erroneous. In some cases, ancestral allelic variation may actually persist in populations after population divergence. These shared ancestral polymorphisms can easily be misinterpreted as evidence of interpopulation gene flow.
Below, we present several studies that exemplify the usefulness of gene genealogies for studying population-level processes. We begin with several examples from Arabidopsis thaliana, including the homeotic loci APETALA3 and PISTILLATA and the disease-resistance locus RPS2, all of which are subject to selection. Then, we illustrate the utility of genealogies for tracing the postglacial range expansion in a variety of plant species. Finally, the usefulness of a genealogical approach for documenting crop origin is shown for cassava, a staple crop of the tropics.
The model plant, A. thaliana, is being used increasingly often for evolutionary studies. Arabidopsis offers many advantages as a study system, including its small size, simple genome, and rapid generation time. Molecular biologists have elucidated the function of many genes in Arabidopsis; mechanisms of development have been detailed, and the sequence of its genome is nearly complete. All of this work provides fertile ground for evolutionary biologists. There are an increasing number of excellent studies that use this information. For example, the role of homeotic genes in the development of floral structures has furthered understanding of tissue differentiation in plants; this work has provided the background for studies that investigate the evolutionary diversification of morphogenic pathways. Purugganan and Suddith (1999) have examined the molecular evolution of the homeotic loci APETALA3 and PISTILLATA, which affect petal and stamen development in Arabidopsis flowers. They have compared the gene genealogies of these sequences with variation at five other nuclear loci of Arabidopsis. Based on an excess of low-frequency nucleotide polymorphisms and elevated within-species replacement polymorphisms, the authors conclude that A. thaliana has undergone rapid expansion in population numbers and size. Likewise, patterns of variation in restriction fragment length polymorphisms of several nuclear loci and the construction of a multilocus haplotype network have indicated that A. thaliana populations exhibit little to no geographical structuring (Bergelson et al., 1998), a conclusion that is consistent with rapid population expansion.