Brigham Young University BYU ScholarsArchive Theses and Dissertations 2006-12-01 Phylogenetics of North American Psoraleeae (Leguminosae): Rates and Dates in a Recent, Rapid Radiation Ashley N. Egan Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Microbiology Commons BYU ScholarsArchive Citation Egan, Ashley N., "Phylogenetics of North American Psoraleeae (Leguminosae): Rates and Dates in a Recent, Rapid Radiation" (2006). Theses and Dissertations. 1294. https://scholarsarchive.byu.edu/etd/1294 This Dissertation 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], [email protected]. by Brigham Young University in partial fulfillment of the requirements for the degree of Brigham Young University All Rights Reserved BRIGHAM YOUNG UNIVERSITY GRADUATE COMMITTEE APPROVAL and by majority vote has been found to be satisfactory. ________________________ ______________________________________ Date ________________________ ______________________________________ Date ________________________ ______________________________________ Date ________________________ ______________________________________ Date ________________________ ______________________________________ Date BRIGHAM YOUNG UNIVERSITY As chair of the candidate’s graduate committee, I have read the format, citations and bibliographical style are consistent and acceptable and fulfill university and department style requirements; (2) its illustrative materials including figures, tables, and charts are in place; and (3) the final manuscript is satisfactory to the graduate committee and is ready for submission to the university library. ________________________ _______________________________________ Date Accepted for the Department ________________________ _______________________________________ Date Accepted for the College ________________________ _______________________________________ Date ABSTRACT ACKNOWLEDGMENTS TABLE OF CONTENTS Abstract v Acknowledgements vii Table of Contents ix List of Tables x List of Figures xi Introduction 1 Chapter 1. Theory of Phylogeny Estimation 4 Gene Trees versus Species Trees 5 Sequence Alignment 6 Models of Evolution 8 Distance Methods 10 Optimality Criteria 11 Searching the Tree Space 14 Confidence Assessment 16 Hypothesis Testing in a Phylogenetic Framework 18 Combining Data 19 Case Study: The Origin of Freshwater Crayfish 19 Glossary 23 References 25 Chapter 2. Phylogenetics, Biogeography, and Endemism of Tribe Psoraleeae (Leguminosae) with an Emphasis on North American Taxa 28 Materials and Methods 30 Results 37 Discussion 47 Conclusions 50 References 51 Chapter 3. Divergence and Diversification in North American Psoraleeae (Leguminosae) 56 Materials and Methods 58 Results 62 Discussion 65 Conclusions 67 References 68 Conclusions 70 Appendix: A New Species of Pediomelum (Fabaceae) from the Lower Piedmont Plateau of Georgia and South Carolina 72 Historical Sketch 73 Comparisons with Congeners 80 Habitat and Ecology 82 Conservation Status 84 References 85 LIST OF TABLES Chapter 2 Table 1. Sample collection information 31 Table 2. Primers 34 Table 3. Geographic variables and areas of distribution 37 Table 4. Maximum Parsimony results 39 Table 5. Bayesian Inference and Maximum Likelihood results 40 Table 6. Regression analysis results 47 Chapter 3 Table 1. Model parameters used for branch length estimation 59 Table 2. Divergence dates 62 Table 3. Nucleotide substitution rates 63 Table 4. Whole-tree statistics for Diversification rates 64 Table 5. Beath-Death Likelihood results 64 LIST OF FIGURES Chapter 1 Figure 28.1. Example phylogeny and Terminology 5 Figure 28.2. Gene Trees/Species Trees 6 Figure 28.3. Jukes Cantor and Kimura-2 parameter models 9 Figure 28.4. Nested hierarchy of nucleotide substitution models 10 Box 28.1. Philosophical and methodological differences 12 Figure 28.5. Freshwater Crayfish maximum likelihood tree 20 Chapter 2 Figure 1. A priori hypotheses of Psoraleeae relationships 30 Figure 2. Map of North American Psoraleeae distributions 38 Figure 3. Bayesian inference nrDNA phylogeny 42 Figure 4. Bayesian inference cpDNA phylogeny 43 Figure 5. Bayesian inference total evidence phylogeny 44 Figure 6. Bayesian inference 99 taxon total evidence phylogeny 45 Chapter 3 Figure 1. Most likely Bayesian inference tree 60 Figure 2. MatK chronogram with range bars 63 Figure 3. Lineage through time plot 65 Appendix Figure 1. Pediomelum piedmontanum 75 Figure 2. Holotype of Pediomelum piedmontanum 76 Figure 3. Fall Line and Pediomelum piedmontanum locales 77 Figure 4. Detailed pictures of Pediomelum piedmontanum 79 INTRODUCTION The discipline of phylogenetics centers on understanding the diversity of life in the context of history. Advances in genetics and molecular biology have increased the number and type of genetic markers available for inferring evolutionary history of the earth’s organisms. Enhancement of DNA sequencing technology and growth of computing power have enabled phylogenetic studies on scales previously unattainable. Today, many studies focus around creating the tree of life, a hypothesis of the evolutionary relationships of all life forms. Plant systematics is leading this foray, with the seminal work of the angiosperm phylogeny group (APG 2003), who have revolutionized plant classification at family and ordinal levels (Soltis, Soltis et al. 2006). Much focus has centered on understanding the origin of land plants (Karol, McCourt et al. 2001) and seed plants (Donoghue and Doyle 2000; Soltis, Soltis et al. 2002; Zanis, Soltis et al. 2002). Many researchers continue to contribute to the plant tree of life through higher level phylogenetic studies among orders and families, with works too numerous to list here. The legume family, Fabaceae or Leguminosae, is one of the most vital plant families in terms of economic importance, with species used for food, fibers, medicine, oils, and industrial materials, to name a few. Leguminosae has benefited from recent phylogenetic work (Doyle, Doyle et al. 1997; Kajita, Ohashi et al. 2001; Wojciechowski, Lavin et al. 2004). As mentioned, much focus has been on higher level studies, providing good support and knowledge concerning the ‘trunk’ of the plant family tree. Less focus has been given to the ‘tips’ of the plant tree of life, meaning lower level phylogenetic studies centered on the generic and species levels (Crandall and Buhay 2004). This dissertation research contributes to the tips of the tree of life and to Legume systematics by estimating molecular phylogenetic relationships within Psoraleeae, a tribe consisting of nine genera worldwide, with five genera endemic to North America. Several attributes make Psoraleeae an interesting group to study in terms of evolutionary history. Lavin, Herendeen et al. (2005) estimated divergence dates across the Legume family and found Psoraleeae to be the second youngest crown clade in the family with a putative divergence date of 6.3 million years ago. Lavin, Herendeen et al. (2005) also found elevated rates of molecular evolution within this group relative to other legume lineages. A large percentage of the North American members of Psoraleeae are narrowly endemic to specific regions of the United States. These attributes 1 combined make Psoraleeae an excellent system in which to study speciation processes within a recent time frame. This dissertation research focuses on phylogenetic methodology and using phylogenies to answer questions concerning evolutionary history, processes, and outcomes. Chapter 1 presents an overview of phylogenetic theory, comparing and contrasting different methods and issues pertaining to estimation of evolutionary relationships. The methods are then applied to tribe Psoraleeae with an emphasis on North American taxa to estimate molecular phylogenies (Chapter 2). This work provides support for taxonomic revisions within Psoraleeae and presents a new species of Pediomelum in the United States (Appendix). A hypothesis of phylogenetic relationships is just the beginning of a model for the evolutionary history of a group. Phylogenies are important not only for illuminating relationships among taxa, but for acting as a framework for comparative studies and testing of evolutionary hypotheses (Soltis and Soltis 2003). The realm of hypothesis testing within a phylogenetic framework includes delving into questions such as testing alternative classification schemes or biogeographic hypotheses, modeling the molecular evolution of a gene and how natural selection has impacted evolution, estimating population level parameters and interactions, testing models of speciation or estimating divergence dates, to name just a few. This dissertation research utilizes the phylogenetic hypotheses of North American Psoraleeae to test alternative classification schemes (Chapter 2), test correlates of endemism within the group (Chapter 2), estimate divergence dates (Chapter 3), investigate nucleotide substitution rates (Chapter 3), test speciation models and diversification shifts (Chapter 3), and test the impact of past and present climate change (Chapter 3). This research thus contributes to the elucidation of the plant tree of life by contributing to the tips of the Leguminosae branch. In addition, this work contributes insight into the processes of evolution by