Applied Species Delimitation in Microbial Taxa and Plants

Species are a fundamental concept in biology, and many subdisciplines in biology utilize species in aspects of theory and in the communication of results. Given the centrality of species in biological science, it can seem surprising that there is no universal definition amongst biologists of what, strictly speaking, a species is. In fact, there are, by some estimates, over 20 different "species concepts", and this lack of a consensus is termed "the species problem". This problem has theoretical underpinnings, but has become more relevant as advances in sequencing technologies over the past two decades have allowed researchers to probe the genetics of populations, and in doing so, uncover instances of genetically distinct populations within a species. This thesis explores issues in species delimitation in two broadly different scenarios. The first, in Chapter 2, involves grouping individuals in microbial communities, and using phylogenetics to inform the effects of different species boundary thresholds. The second, in Chapter 3, explores the genetic differences between varieties of a species complex of plant endemic to the Great Basin region of the western United States, including a variety endemic to Logan Canyon (Primula cusickiana variety maguirei, or Maguire's primrose). While the contexts of these chapters are largely different, they nevertheless share a distinguishing trait, common throughout much of biology: ambiguous species boundaries.