University of Nevada, Reno Habitat preferences, intraspecific variation, and restoration of a rare soil specialist in northern Nevada A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Natural Resources and Environmental Science by Jamey D. McClinton Dr. Elizabeth A. Leger/Thesis Advisor December, 2019 Copyright by Jamey D. McClinton 2019 All Rights Reserved We recommend that the thesis prepared under our supervision by Jamey D. McClinton Entitled Habitat preferences, intraspecific variation, and restoration of a rare soil specialist in northern Nevada be accepted in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Elizabeth Leger, Ph.D., Advisor Paul Verburg, Ph.D., Committee member Thomas Parchman, Ph.D., Graduate School Representative David W. Zeh, Ph.D., Dean, Graduate School December-2019 i Abstract Edaphic specialization in plants is associated with the development of novel adaptations that frequently lead to speciation, causing unique edaphic environments to be associated with rare and endemic plant species worldwide. These species contribute significantly to global biodiversity, but are especially vulnerable to disturbance and climate change because of their inherently patchy distributions and locally adapted populations. Successful conservation of these species depends upon understanding their habitat requirements and the amounts and distributions of genetic and phenotypic diversity among populations. Little is known about the habitat requirements or levels of genetic and phenotypic diversity of edaphic specialists in the Great Basin of the western United states. Therefore, to improve understanding of edaphic specialization in this region, and to create a foundation of knowledge for species conservation, we used phenotypic measurements in the field, greenhouse common garden studies, and next-generation genetic sequencing techniques to investigate the associations between soil variation and plant phenotypes, and between genetic and phenotypic diversity in Eriogonum crosbyae, a rare edaphic specialist on soils developed from hydrothermally altered volcanic ash in the north-western Great Basin. We found that soil properties were poor predictors of site occupation among outcrops of known or potential habitat in our study area, and that site occupation could change over time. E. crosbyae showed phenotypically plastic responses to soil variation in the greenhouse, and there were associations between soil properties and plant form in the field. Growth was generally better in relatively milder and more fertile field soils when grown without competition, and differences in seedlings’ ability to establish in different soil types may partially explain the species’ patchy distribution in potential habitat. Our genetic analyses revealed high levels of nucleotide diversity and the presence of three highly differentiated genetic groups that often co-occurred within individual sites. The distribution of these groups across the landscape may be consistent with periods of allopatric diversification and subsequent secondary contact. Phenotypic diversity ii varied more clearly among groups than among sites dominated by a single group, and this variation was more apparent in seedlings grown in the greenhouse than in mature plants measured in the wild. Further studies exploring growth responses to variation in individual soil properties and plant performance in the presence of competition would improve understanding of the mechanisms underlying edaphic specialization in this species. Additionally, more information on the evolutionary history and taxonomy of the genetic groups and how they relate to other edaphically specialized Eriogonum in this region would improve understanding of diversity in these unique edaphic habitats in the Great Basin. Our results highlight the potential for simple- seeming systems to contain significant levels of cryptic diversity, and suggest that caution is warranted when considering potential impacts to these unique habitats. iii Acknowledgements I would like to thank my advisors, Beth Leger and Tom Parchman, for the enormous amounts of time and effort they both invested in helping me complete this project, and for all of the constructive feedback and collaboration that has helped me grow so much over the last few years. As my primary advisor, Beth’s passion for science and mentorship, infectious positivity, and constant encouragement and understanding in the face of many challenges have inspired me since we met, and I could not have done this work without her. I would also like to thank my third committee member, Paul Verburg for his valuable guidance on soil sampling and analysis and for feedback on my writing. Thank you also to my co-author, Kathy Torrence and the BLM Black Rock Field Office for conceiving of this project, securing major funding, and for hands-on involvement with feedback, permitting and fieldwork assistance throughout the project. I am grateful to all of our undergraduate technicians and to my friend Mandy Fuller, for help with soil and tissue collection, off-road travel, and planting, monitoring, and harvesting. Thank you also to my family, especially my mom Susan Wilcher, for boundless love and support. Lastly, thank you to my husband, Logan McClinton, for the countless hours he spent helping me in the field and in the greenhouse, for helping me maintain a sense of balance as my climbing and running partner, and for his encouragement, understanding, and many hugs and laughter. iv Table of contents Abstract ………………………………………………………………………………...…….....… i Acknowledgements ……………………………………………………………………....…..…. iii Table of Contents …………………………………………………………………….…..……… iv List of Tables ………………………………………………………………………….…………. v List of Figures …………………………………………………………………………….…...… vi Thesis Introduction …………………………………………………………………...…….….. viii Chapter 1. How specialized is a soil specialist? Responses of a rare Eriogonum to site-level variation in volcanic soils …………………………………………………….…………..……… 1 Chapter 2. Genetic and phenotypic diversity of a rare, soil-specialist Eriogonum in North America. 38 ……………………………………………………………………………………... 37 Chapter 1 Appendix ………………………………………………….………………………..... 73 Chapter 2 Appendix ……………………………………………………………….……………. 95 Summary, Conclusions, and Recommendations …………………………………..……...…… 111 v List of Tables Chapter 1: List of Tables Table 1. Comparisons of total biomass, root mass ratio (RMR), emergence, and survival of seedlings grown in soils from field sites with varying occupation status for E. crosbyae in the wild. Chapter 2: List of Tables Table 1. Differences in E. crosbyae seed and seedling characteristics among genetic groups in greenhouse common gardens. Table 2. Differences in E. crosbyae plant form between genetic groups from field measurements at 16 sites. vi List of Figures Chapter 1 List of Figures Figure 1: E. crosbyae individual in flower, and an example of typical Nevada, USA habitat on hydrothermally altered volcanic outcrops. Figure 2: Map of E. crosbyae habitat sampling locations and site occupation status in Nevada, USA. Figure 3: Ordination based on the first two principal components from PCA of E. crosbyae habitat soil characteristics in all sampling sites. Figure 4: Variation in field plant form of E. crosbyae by sampling location in northwestern Nevada, USA. Figure 5: Significant (p<0.05) associations between native soil characteristics and morphology of E. crosbyae individuals at field sites in northwestern Nevada, USA. Figure 6: Comparison of total biomass, root mass ratio, and emergence of E. crosbyae seedlings grown in field soils and in a more fertile soil from Washoe Valley, NV, USA. Figure 7: Significant (p<0.05) effects of variation in field soils from E. crosbyae habitat on seedling growth in the greenhouse at the University of Nevada, Reno, USA. Chapter 2 List of Figures Figure 1: Map of Eriogonum sampling sites in northern Nevada, USA colored by the genetic group assigned to the most individuals from each location. Figure 2a: Genetic groupings of individuals sampled in the wild from populations previously identified as E. crosbyae in northern Nevada, USA. vii Figure 2b: Phylogenetic analysis of Eriogonum individuals sampled in the wild in northern Nevada, USA. Figure 3: Map of Eriogonum sampling sites in northern Nevada, USA colored by the genetic group assigned to each individual. Fig. 4: Tukey pairwise comparisons of phenotypic differences in greenhouse seed and seedling traits in Eriogonum by dominant genetic group for 16 source sites, with analyses including dominant genetic group as a categorical variable. Fig.5: Tukey pairwise comparisons of phenotypic differences in Eriogonum plant form in the field by dominant genetic group for 16 source sites, with dominant genetic group for each field location considered as a categorical variable. viii Thesis Introduction Edaphic variation is a major driver of global biodiversity, and creates landscape-level patterns of different floras that have adapted to variations in soil properties (Rajakaruna 2004). Edaphic specialists are plant species that are found primarily or exclusively on outcrops of unusual soils, such as serpentine, gypsum, limestone, and dolomite, among many others (Baskin and Baskin 1988, Kelso, Bower et al. 2003, Rajakaruna, Boyd et al. 2014, Vanderplank, Moreira- Muñoz et al. 2014, Escudero, Palacio et al. 2015, Rajakaruna 2018). These outcrops can vary in size from dozens or hundreds of square meters to many