Most of the fundamental questions in evolutionary biology remain unanswered. For example, we still do not know how many genetic changes are required for adaptation, nor do we understand how populations acquire sufficient reproductive isolation to attain the status of biological species. The greatest progress on these issues was made 50 years ago, when Grant, Stebbins, and the Carnegie group began their classic biosystematic studies. These pioneers of plant evolutionary biology established the first links between ecology and genetics, conducting comprehensive studies of the ecology, crossing relationships, and cytogenetics of closely related species. New molecular tools provide the opportunity for a second major advance in the field. Using genetic mapping techniques, we can examine the genetic architecture of traits that contribute to adaptation and speciation in natural populations. The objective is to estimate the number of Quantitative Trait Loci (QTL) that contribute to adaptive traits, as well as the mode of action, location and magnitude of effect of each QTL. Subsequent studies use the genetic mapping information to perform marker-assisted selection, moving particular QTLs into the genomes of sister taxa. In this way we can simulate single mutations, and investigate the fitness consequences of alternative evolutionary trajectories. These methods are now being used to study the evolution of pollination systems in temperate monkeyflowers and neotropical gingers, and the evolution of serpentine adaptation in a California wildflower. Our results provide clear evidence for the role of major genes in adaptive evolution. This finding is at odds with Fisher’s infinitesimal model of evolution, but is consistent with recent theory suggesting that genes of large effect are advantageous during the early stages of adaptation. This work is motivated by our desire to rebuild the links between ecology and genetics that were first established a half-century ago.

Key words: adaptation, evolution, speciation