Contrasting patterns of nucleotide polymorphism at the alcohol dehydrogenase locus in the outcrossing Arabidopsis lyrata and the selfing Arabidopsis thaliana

Nucleotide variation at the alcohol dehydrogenase locus (Adh) was studied i n the outcrossing Arabidopsis lyrata, a close relative of the selfing Arabi dopsis thaliana. Overall, estimated nucleotide diversity in the North Ameri can ssp. lyrata and two European ssp. petraea populations was 0.0038, lower than the corresponding specieswide estimate for A. thaliana at the same se t of nucleotide sites. The distribution of segregating sites across the gen e differed between the two species. Estimated sequence diversity within an A. lyrata population with a large sample size (0.0023) was much higher than has previously been observed for A. thaliana. This North American populati on has an excess of sites at intermediate frequencies compared with neutral expectation (Tajima's D = 2.3, P < 0.005), suggestive of linked balancing selection or a recent population bottleneck. In contrast, an excess of rare polymorphisms has been found in A. thaliana. Polymorphism within A. lyrata and divergence from A. thaliana appear to be correlated across the Adh gen e sequence. The geographic distribution of polymorphism was quite different from that of A. thaliana, for which earlier studies of several genes found low within-population nucleotide site polymorphism and no overall continen tal differentiation of variation despite large differences in site frequenc ies between local populations. Differences between the outcrossing A. lyrat a and the selfing A. thaliana reflect the impact of differences in mating s ystem and the influence of bottlenecks in A. thaliana during rapid coloniza tion on DNA sequence polymorphism. The influence of additional variability- reducing mechanisms, such as background selection or hitchhiking, may not b e discernible.