What is the molecular basis of adaptive trait variation? How do new species evolve? The threespine stickleback fish is an excellent organism in which to address such questions in vertebrates: diverse naturally occuring populations with rapidly evolving adaptive phenotypes, over 250 sequenced genomes, plus a suite of powerful genetic and transgenic tools. We exploit natural evolutionary replicates to functionally dissect the molecular mechanisms and evolutionary processes underlying adaptive traits and the evolution of new species.Whole genome analysis of parallel divergent stickleback ecotypes has resulted in one of the highest resolution maps of adaptive loci in vertebrates (Jones et al Nature, 2012). The majority of adaptive loci are intergenic (non-coding) and in regions of low recombination, suggesting that mutations in regulatory sequence and the recombination landscape are important in adaptive evolution. These results show that, adaptation to new freshwater environments often involves the use of pre-existing ‘standing’ genetic variation that is present at low frequencies in the marine population. One of the projects available will use bioinformatic analyses of whole genomes sampled from marine and freshwater populations to i) characterize molecular signatures of selection across the genome, ii) model and quantify mechanisms that promote and constrain the availability of adaptive standing genetic variation and iii) build and empirically test population genetic models of selective sweeps from standing genetic variation.