In the above examples from Arabidopsis, population history has strongly affected patterns of genealogy and molecular evolution. Other loci within the Arabidopsis genome may reflect different evolutionary processes, in particular selection. Arabidopsis has served as a model system for unraveling disease-resistance response, a trait presumed under strong selection. In Arabidopsis, the RPS2 gene is involved in the recognition of the plant pathogen Pseudomonas syringae pv. tomato. RPS2 interacts with an avirulence gene, avrRpt2, of the pathogen to initiate the cascade of events that led to disease resistance. Both the avirulence gene in the pathogen and the resistance gene in the host must be functional to elicit resistance. These genes interact in a specific “gene-for-gene” manner. The close relationship between avirulence genes and resistance genes as well as the obvious fitness consequences of resistance for a plant have led to speculation on the evolutionary dynamics of resistance genes.

RPS2 encodes a 909-amino acid gene product. The gene contains several motifs that suggest it is part of a signaling pathway, including a leucine zipper, leucine-rich repeats, a hydrophobic region, and a nucleotide-binding site. A gene genealogy for the RPS2 locus has been constructed to investigate the molecular evolution of the gene (Caicedo et al., 1999); 17 accessions of A. thaliana, representing a diversity of ecotypes, were sequenced for RPS2, and their resistance to Pseudomonas was determined. The resulting genealogy reveals an intriguing pattern (Fig. 3). Disease-resistance haplotypes (alleles) are clustered on the gene tree, in-

FIGURE 3. Gene tree for the RPS2 locus of A. thaliana. Open circles represent susceptible haplotypes; open squares are resistant haplotypes; and open diamonds are haplotypes intermediate in resistance. Closed circles are haplotypes not present in the sample but inferred from single-step mutations. The figure is modified from Caicedo et al. (1999).