The chapters of this dissertation are designed to investigate speciation in the plant genus Stephanomeria. Genetic markers were developed, and population genetic studies performed. In the first study, the goal was to investigate: the putative homoploid hybrid origin of Stephanomeria diegensis; whether this species arose once or on multiple occasions; and which subspecies of the parental taxa were involved in the original speciation event. The data presented support a hybrid origin of S. diegensis. In addition, the results showed the S. diegensis most likely arose once, and that S. exigua ssp. exigua or S. exigua ssp. deanei were involved in the formation. It was not possible to identify the subspecies of S. virgata involved. The second study investigates the allopolyploid origin of S. elata. The number of origins was investigated, as was the level of differentiation between two recognizable morphotypes, termed the Northern and Southern morphotype. This work identified three origins, with two origins found in the Southern morphotype and one in the Northern morphotype. The third study analyzed population genetic diversity in a disjunct population of S. exigua ssp. coronaria termed the Frenchglen population. This population is of particular interest because it is a peripheral isolate that gave rise to the endangered S. malheurensis. The Frenchglen population was found to be genetically robust, and unique from populations from the balance of the range of S. exigua ssp. coronaria.
