Brigham Young University BYU ScholarsArchive Theses and Dissertations 2019-11-19 Resolving Relationships and Revealing Hybridization in Aliciella Subsection Subnuda (Polemoniaceae) Theresa Conley Saunders Brigham Young University Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Life Sciences Commons BYU ScholarsArchive Citation Saunders, Theresa Conley, "Resolving Relationships and Revealing Hybridization in Aliciella Subsection Subnuda (Polemoniaceae)" (2019). Theses and Dissertations. 9126. https://scholarsarchive.byu.edu/etd/9126 This Thesis is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected]. Resolving Relationships and Revealing Hybridization in Aliciella Subsection Subnuda (Polemoniaceae) Theresa Conley Saunders A thesis submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Master of Science Leigh A. Johnson, Chair Robert L. Johnson Steven D. Leavitt Department of Biology Brigham Young University Copyright © 2019 Theresa Conley Saunders All Rights Reserved ABSTRACT Resolving Relationships and Revealing Hybridization in Aliciella Subsection Subnuda (Polemoniaceae) Theresa Conley Saunders Department of Biology, BYU Master of Science Phylogenetics is crucial in the study of evolutionary processes and the determination of appropriate conservation units, and often these efforts are complicated by hybridization and introgression. Aliciella subsection Subnuda consists of seven species of herbaceous plants occurring in Utah and the Four Corners region of North America. Previous molecular and morphological work left relationships in the subsection unresolved. Here, we use comparative DNA sequencing of ITS and cpDNA regions and RAD-seq data to clarify phylogenetic relationships and examine the role of hybridization in the subsection. We construct haplotype and nucleotype networks from the cpDNA and ITS sequence matrices and compare nuclear and chloroplast phylogenies to identify multiple putative chloroplast capture events. The RAD-seq maximum likelihood phylogeny robustly resolves relationships between six clades, supportive of merging of two species. We employ STRUCTURE and HyDe on the RAD-seq data to evaluate the influence of hybridization within the subsection. The HyDe results provide evidence of hybridization among and between all species in the subsection. Our study robustly resolves relationships in Aliciella subsection Subnuda and provides a framework for discussing its speciation despite a history of hybridization and introgression. Keywords: RAD-seq, Aliciella, phylogenetics, hybridization, introgression, integrative taxonomy, cytonuclear discordance ACKNOWLEDGEMENTS Thank you so much to everyone who helped me throughout this journey. I know that for most people who might read this thesis, it will not be a particularly life-changing experience, but, for me, my life will never be the same because of this work. Thank you, Dr. Johnson, for the countless hours of guidance and advice and patient repetition. Thank you to the many botanists who helped me in the field. Thank you to all the faculty and students at BYU who taught me how to ask questions and try to find answers (no guarantee they are out there… in fact, odds are they aren’t). Thank you to the wonderful Biology Department for all your support through my unexpected challenges, and thanks to J. Mark Porter for funding our RAD-seq data and providing incredible foundational research in Aliciella. And, of course, thank you, Ben, for believing in me and my dreams. TABLE OF CONTENTS TITLE PAGE ................................................................................................................................... i ABSTRACT .................................................................................................................................... ii ACKNOWLEDGEMENTS ........................................................................................................... iii TABLE OF CONTENTS ............................................................................................................... iv LIST OF TABLES ......................................................................................................................... vi LIST OF FIGURES ...................................................................................................................... vii 1. Introduction ................................................................................................................................. 1 2. Material and methods .................................................................................................................. 5 2.1 Taxon sampling .................................................................................................................................. 5 2.2 Morphology ........................................................................................................................................ 7 2.3 DNA extraction and sequencing ......................................................................................................... 7 2.4 Comparative DNA sequence matrices ................................................................................................ 8 2.5 RAD-seq data processing ................................................................................................................... 9 2.6 Phylogenetic analyses ....................................................................................................................... 11 2.7 Haplotype and nucleotype network construction.............................................................................. 11 2.8 STRUCTURE analysis of RAD-seq data ......................................................................................... 12 2.9 Assessing hybridization via RAD-seq data ...................................................................................... 12 3. Results ....................................................................................................................................... 14 3.1 Morphology ...................................................................................................................................... 14 iv 3.2 Comparative DNA sequence maximum likelihood phylogenies ...................................................... 14 3.3 Comparative DNA sequence haplotype and nucleotype networks ................................................... 15 3.4 RAD-seq phylogenetic reconstruction .............................................................................................. 16 3.5 RAD-seq STRUCTURE results: Complete dataset .......................................................................... 17 3.6 RAD-seq STRUCTURE results: Hierarchical structure analyses .................................................... 18 3.7 Hybridization .................................................................................................................................... 20 4. Discussion ................................................................................................................................. 21 4.1 Phylogeny ......................................................................................................................................... 21 4.2 Hybridization .................................................................................................................................... 25 4.3 Conclusions ...................................................................................................................................... 29 Appendix: Supplementary material .............................................................................................. 40 Bibliography ................................................................................................................................. 61 v LIST OF TABLES Table 1. Sampling information from both the comparative ITS and cpDNA and the RAD-seq datasets.......................................................................................................................................... 32 Table 2. The likelihood of K and the ΔK values from the STRUCTURE analyses of the complete RAD-seq dataset ........................................................................................................................... 37 Table 3. The likelihood of K and the ΔK values from the hierarchical STRUCTURE analyses of the RAD-seq dataset. .................................................................................................................... 49 Table 4. HyDe results for population run based on chloroplast haplotypes with A. formosa as outgroup. ....................................................................................................................................... 52 Table 5. HyDe results for population run based on chloroplast haplotypes with A. caespitosa as outgroup. ....................................................................................................................................... 56 Table 6. HyDe results for species run with A. formosa as outgroup. ........................................... 60 vi LIST OF FIGURES Figure 1. Geographic locations of populations ............................................................................