To understand the maintenance of variation within species, and the importance of local selection and demography in natural populations, both within- and amongpopulation sampling are needed. Despite the importance of local population processes to plant evolution, surprisingly little attention has been given to the distribution of DNA sequence diversity among plant populations. Although many studies have used genetic markers to study genetic differentiation among plant populations, so far only a handful have examined DNA sequence diversity within and among natural plant populations. Unlike other molecular marker systems, DNA sequence data provide information about recombination and linkage disequilibrium, which can be highly sensitive to demographic history. Work done to date has demonstrated the need for local sampling to accurately describe Oxysophocarpine patterns of LD, diversity, and the frequency spectrum of polymorphisms in local populations, and shown that even simple demographic processes can better explain observed data than can the assumption of neutral equilibrium. Nonetheless, many of these studies have relied on small samples of loci or groups of candidate genes, neither of which is likely sufficient to capture patterns of genome-wide variation or provide insight into the relative roles of demographic history and selection. Here we present a large-scale population-genetic analysis of sequence diversity in natural populations of Arabidopsis lyrata. A. lyrata is a predominantly self-incompatible, perennial species with a circumpolar distribution across northern and central Europe, Asia, and North America. A. lyrata appears to maintain large, stable populations, particularly in Central Europe, where populations are hypothesized to have served as refugia during the most recent Ice Age. A. lyrata has become a model system for plant molecular population genetics and for investigating local adaptation. For example, divergent selection on trichome production has been found among phenotypically Butenafine hydrochloride differentiated Swedish A. lyrata populations. Flowering time and floral display also appear to 
be under strong selection, with large differences in day-length requirements between Northern and Southern populations. A. lyrata is also of great interest because it is a close relative of A. thaliana, providing opportunities for comparative studies of the consequences of differences in breeding system, demographic history, and selection. To what extent are patterns of genetic diversity at individual loci associated with local adaptation? To begin to address this question, we performed simulations utilizing our inferred demographic model to generate expectations for individual loci under neutrality. For these initial tests, we selected FST as a measure because of its long history as an informative metric of local adaptation. We first used the five demographic models inferred from the pairwise interpopulation comparisons to generate neutral distributions of expected FST for silent sites and for all sites. For each locus and model, we calculated FST from 10,000 single locus coalescent simulations drawn from our estimated posterior distributions. All simulations used the relevant length and observed hw for each locus. We present here two significant advances towards understanding sequence diversity in natural plant populations. The first is simply a much larger data set than in most studies of sequence diversity of natural plant populations, including explicit and extensive sampling both within and among populations.