A central question in biology is the molecular basis of biodiversity. Rapid advances in next-generation sequencing are providing novel tools for addressing key ecological and evolutionary questions in integrated biological sciences. However, the study of adaptive molecular variation has been largely limited to model species. Therefore, general patterns in molecular adaptation and speciation remain unclear, but their discovery is essential to enable understanding and prediction of biological responses to naturally and artificially changing environments. Studying adaptive evolution that occurred many times in parallel is an appropriate approach to investigating recurring patterns. We focus on the evolution of self-compatibility, which has been considered to be one of the most frequent evolutionary shifts in flowering plants and has been a major focus in evolutionary biology since Darwin’s research. It is noteworthy that plant sexual reproduction may be particularly vulnerable to the effects of natural and artificial environmental changes, through evolutionary and plastic responses. A broad impact of this proposal to the society would be to reinforce our previous key research finding that climate change, including glacial cycles, may induce rapid—and possibly irreversible—evolution.