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 Chloroquine Phosphate sequence diversity in natural plant populations. The first is simply a much larger data set than in most LOUREIRIN-B studies of sequence diversity of natural plant populations, including explicit and extensive sampling both within and among populations. Second, we used demographic modeling, which, to date, has mostly focused on humans and Drosophila. Explicit modeling of natural population history remains rare in studies of flowering plants, though it has been applied to studies of cultivated plants and to a lesser extent, conifers. Our efforts permit parameter estimation for biologically meaningful demographic models and provide a direct measure of our confidence in the model and its relevance to our data. Our results build on previous work that documents high differentiation among A. lyrata populations, and points to central European populations as a center of diversity for A. lyrata ssp. petraea. Other studies have further argued that central European populations may have served as refugia from which Northern Europe was re-colonized after glacial cycles during the Pleistocene, and even specifically hypothesized that the Icelandic population of A. lyrata ssp. petraea and North American populations of A. lyrata ssp. lyrata were colonized from Europe. Our results broadly concur with these ideas. Relative to the Central European population surveyed here, other populations reveal the hallmarks of population bottlenecks: lower diversity, loss of singleton and low frequency variants, higher LD and lower estimated.