UC Santa Cruz

Small populations and rare species offer unique opportunities to study fundamental evolutionary questions, but many rare species are threatened by disturbance and climate change. Molecular population genetics enable biologists to examine evolutionary processes while simultaneously assessing levels of genetic diversity, population structure, and gene flow that can help shape management plans for rare species. However, developing molecular markers can be an expensive, time-consuming process, especially if little is known about the genomes of the species of interest. A new technique, Genotyping by Sequencing (GBS), requires little to no prior information to develop SNP markers. Here I employ this technology to develop hundreds of markers in two rare, serpentine soil-endemic Monardella (Lamiaceae) plant species and a common congener. Using the SNP markers, I investigate population structure, genetic diversity, and hybridization between species. I also use a soil dataset to determine whether species and hybrid zones occur on divergent soils. I find low levels of genetic diversity and little population structure in the two rare species, as expected by rapid genetic drift in small populations. I find evidence of hybridization and introgression among species at sites where multiple species co-occur. Further, Bayesian assignment finds mixed ancestry in one of the rare species. The soil data show that the soils inhabited by the two species are divergent, but not significantly different. Some hybrids occur on soils that seem to be intermediate between the two parental species, but others do not. I synthesize these data with ecological surveys to provide species management recommendations to the USDA Forest Service.