We hope to understand the origin and distribution of complex phenotypic variation within an ecological and evolutionary context. To do so, we have been using comparative and population genomics as a framework for inferring the genetics of complex natural traits. For example, the wild species Solanum pimpinellifoilum¬—a close relative of domesticated tomato—varies in ecologically-critical leaf, root, and floral traits throughout its natural South American range. Using landscape genomics, we have been assessing genome-wide associations between genetic variants (Single Nucleotide Polymorphisms, or SNPs) and features of the abiotic climate across ~140 accessions of this species. SNPs with the strongest environmental associations can then be used to predict and test relevant (adaptive) phenotypic variation, using genome selection or marker assisted selection approaches. Loci containing SNPs with extreme environmental associations are also putative candidate genes for climate adaptation phenotypes.