The commonness of a trait within a clade is influenced both by its effects on individual fitness—selection within species—and by its effects on lineage diversification—selection among species. Traits involved in reproduction are particularly good candidates for influencing speciation or extinction rates, but a strong test of species selection on any trait has proven difficult. Focusing first on breeding system in the nightshade plant family, I present phylogenetic analyses indicating that although self-incompatibility (a genetic mechanism that prevents self-fertilization) is frequently lost, it is maintained at high frequency because species with it have a higher net rate of lineage diversification. Focusing next on sexual system in a wide variety of angiosperm genera, I present evidence of very different macroevolutionary dynamics underlying the distribution of dioecy (male and female function on separate individuals). Intermingled, I discuss recent challenges and developments in phylogenetic comparative methods for testing species selection.