Based on calculations of the genome wide proportion of base substitutions fixed by natural selection (alpha), we conclude that a significant proportion of the most divergent SNPs represent selectively advantageous mutations: in all cases the ratio of non-synonymous to synonymous fixed differences was significantly greater than that for non-synonymous to synonymous polymorphisms (alpha, Table 3). By focusing on specific gene categories and examining patterns of polymorphism and divergence, we were able to provide additional evidence of adaptive evolution (Table 4). Gene categories exhibiting high alpha values included a number of biological processes that have previously been reported as undergoing positive selection in sunflowers, including defense response to fungus, flower development, lipid catabolic process, lipid metabolic process, and response to biotic stimulus . Interestingly, we found one category, response to biotic stimulus, showing parallel levels of elevated alpha among species pairs. This is important given that parallel trends add stronger evidence for the role of selection in driving divergence for these particular traits . Thus, natural selection imposed by other organisms appears to play an important role in driving protein evolution in wild sunflowers. However, we also acknowledge the dangers of story telling based on GO analysis and these trends should be confirmed before any strong conclusions can be reached .