DISSERTATION A STUDY OF PLANT DOMESTICATION AND EVOLUTION THROUGH THE TAXONOMIC REVISION OF WILD NORTH AMERICAN HUMULUS, A PHYTOCHEMICAL ASSAY FOR STIMULANT ALKALOIDS IN CELASTRACEAE, AND A PHYLOGEOGRAPHIC ANALYSIS OF CATHA EDULIS IN AREAS OF HISTORIC CULTIVATION Submitted by Luke Raymond Tembrock Department of Biology In partial fulfillment of the requirements For the Degree of Doctor of Philosophy Colorado State University Fort Collins, Colorado Fall 2015 Doctoral Committee: Advisor: Mark P. Simmons Amy L. Angert Christopher M. Richards Sarah M. Ward Copyright by Luke Raymond Tembrock 2015 All Rights Reserved ABSTRACT A STUDY OF PLANT DOMESTICATION AND EVOLUTION THROUGH THE TAXONOMIC REVISION OF WILD NORTH AMERICAN HUMULUS, A PHYTOCHEMICAL ASSAY FOR STIMULANT ALKALOIDS IN CELASTRACEAE, AND A PHYLOGEOGRAPHIC ANALYSIS OF CATHA EDULIS IN AREAS OF HISTORIC CULTIVATION The cultivation of plant species is essential to the survival of humans. The process of artificial selection that is used to modify wild individuals into improved cultivars results in genetic and morphological changes from wild progenitors. In order to understand the evolutionary patterns and processes involved with artificial selection both wild and cultivated populations must be thoroughly studied. Numerous methods are used to study the process of evolution under cultivation such as biology, chemistry, geography, history, linguistics and archeology. The understanding of evolution in a crop species is essential in current improvement programs to increase yield for a given crop. I employed methods from the fields of taxonomy, analytical chemistry and phylogeography to study the process of evolution in cultivated plant species and/or their wild relatives. From a review of taxonomic, genetic, and phytochemical literature, as well as examination of morphological features I revised the wild North American Humulus (Cannabacae) in a manner that properly delimits the diversity found among the North American species. Using GC–MS and a forensics based derivatization method I assayed for the stimulant alkaloids cathinone, cathine, and similar compounds across the Celastraceae plant family. It was ii found that that qat (Catha edulis) was the only species of those tested that biosynthesized cathinone and cathine. Using phylogeographic and population genetic techniques I inferred three wild regional origins, hybridization and numerous translocations out of the centers of origin for cultivated qat. From farmer interviews I examined what properties, genotype, phenotype, and/or geography explained the naming convention for qat cultivars among qat farmers. The character of stem color was found to highly plastic and thus genotype was not significantly correlated with the naming convention. Geographic patterns were confirmed for several cultivar names suggesting that anthropogenic factors are important in the naming conventions used among qat farmers. These four separate studies provide findings that not only clarify our understanding of evolutionary patterns among wild and cultivated species but provide a framework for breeding, conservation and forensic applications in the future. iii ACKNOWLEDGEMENTS I thank my major advisor Mark P. Simmons for his guidance and many insights during this project. Mark’s continual encouragement and emphasis on quality ultimately made me a better researcher and scientist. I like thank my committee members Amy L. Angert, Christopher M. Richards, and Sarah M. Ward for all of their guidance and technical assistance. I especially thank Chris Richards for holding the necessary DEA permits, and allowing access to the NCGRP facility and equipment. I thank the collections managers at BHSC, BUT, CSCN, ILLS, ISC, MONT, NEB, NY, RM, and US for loaning Humulus specimens for examination. In particular, I thank Jennifer Ackerfield at CS for her assistance in attaining and storing the loans as well as giving botanical advice whenever needed. I thank Corey Broeckling, Adam Heuberger, Sarah Lyons, Jessica Prenni, Frank Stermitz, and the many helpful staff members at the Proteomics and Metabolomics facility at Colorado State University for helping with my phytochemistry work. Assistance from Remi Bonnart, Adam Henk, Pat Reeves, and Ann Reilly at NCGRP was absolutely indispensable to the success of my Catha work and I thank them for this. I thank Terrence and Deena Walters of USDA for their access to imaging equipment and helping me with research assistantships during my graduate work. Funding from the American Institute of Yemeni Studies and Tom and Vernette Jirsa, donors to the H. D. Harrington Fellowship Fund was essential to the success of my project. I thank our many collaborators in Africa and Yemen, and in particular Manuel Curto from the University of Porto in developing qat SSR’s. iv I thank my colleagues Jennifer Cappa, Todd Gilligan, and Jenna McAleer for the many hours of assistance and discussion in completing my project. Lastly I thank my family for all of their support and understanding—especially Bill and Kathy Tembrock. v TABLE OF CONTENTS ABSTRACT………………………………………………………………………………………i ACKNOWLEDGEMENTS……………………………………………………………………....iv CHAPTER 1: TAXONOMY, PHYTOCHEMISTRY, AND PHYLOGEOGRAPHY IN THE EMPIRICAL AND APPLIED STUDY OF EVOLUTION IN CROPS AND THEIR WILD RELATIVES………………………………………………………………………1 REFERENCES……………………………………………………………………………………7 CHAPTER 2: A REVISION OF NORTH AMERICAN HUMULUS (CANNABACEAE)……10 REFERENCES…………………………………………………………………………………..42 CHAPTER 3: EMPLOYING GC-MS AND TWO-STAGE DERIVATIZATION TO ASSAY FOR CATHINE AND RELATED STIMULANT ALKALOIDS ACROSS THE CELASTRACEAE………………………………………………………………………48 REFERENCES…………………………………………………………………………………..71 CHAPTER 4: THE ORIGINS, DISPERSAL, AND EVOLUTION OF CATHA EDULIS (QAT, CELASTRACEAE) IN AREAS OF HISTORIC CULTIVATION……………………..79 REFERENCES…………………………………………………………………………………114 CHAPTER 5: CLONAL DIVERSITY AND THE ETHNOTAXONOMY OF CULTIVATED CATHA EDULIS (QAT, CELASTRACEAE): HOW COLOR, GENOTYPE, AND GEOGRAPHY CORRESPOND IN THE FORMATION OF CULTIVAR IDENTITY……………………………………………………………………………...123 REFERENCES…………………………………………………………………………………150 APPENDICES………………………………………………………………………………….155 vi LIST OF TAXA SAMPLED FOR ALKALOID EXTRACTION…………………….155 DNA EXTRACTION FROM CATHA EDULIS……………………………………….157 THE DISTRIBUTION OF ALLELE SIZES BY GEOGRAPHIC ORIGIN INDICATING A POSSIBLE CONVERGENCE AMONG YEMENI CULTIVATED QAT AT LOCUS CE 22…………….……………………………………………………………………..160 PRIVATE ALLELES AMONG CULTIVATED GENOTYPES COLLECTED IN MARSABIT AND THEIR SUBSEQUENT PRESENCE IN MT KULAL AND MT MARSABIT HYBRIDS………………………………………………………………..161 vii CHAPTER 1: TAXONOMY, PHYTOCHEMISTRY, AND PHYLOGEOGRAPHY IN THE EMPIRICAL AND APPLIED STUDY OF EVOLUTION IN CROPS AND THEIR WILD RELATIVES Introduction The study of cultivated plants has been fundamental to our understanding of evolutionary processes. Human selection on plants in order to isolate desired traits has been regarded as one of humanity’s largest biological experiments (Gepts 2004) from which much of the data have yet to be collected. Darwin (1876) introduced the concept of selection in the first chapter of On the Origin of Species by discussing how domesticated animals and plants are selected through human actions and how this process in some respects is analogous to natural selection. Researchers have continued to employ cultivated species to understand mechanisms underlying evolutionary patterns ever since (Ross-Ibarra 2007). Additionally, patterns of evolution in cultivated plants often parallel human historical and evolutionary patterns, thus providing an additional line of evidence in understanding human history (e.g., Verginelli et al. 2009; Hancock et al. 2010; Westengen et al. 2014). Humans rely on plants for survival; with plants providing food, shelter, medicine, and fuel. Early humans consumed plant resources directly from natural environments with no evident conscious effort toward cultivating these plants outside their natural habitats. Beginning around 12,000 BP (before present) human societies began to cultivate plants, shifting from collecting plant resources from wild populations to growing plants in specially prepared environments (e.g. Kuijt & Goodale 2009; Zeder 2011). This shift toward an agrarian lifestyle altered human 1 societies to be more sedentary and dependent on plant cultivation (reviewed in Kuijt & Goodale 2009). The artificial selection process by which wild plants are grown in cultivated settings involve morphologic and genetic changes from wild progenitors (Emshwiller 2006; Pickersgill 2009). These changes are related to the use of a given species. For instance grain size has increased since selection from wild progenitors in grass species such as wheat and barley (Purugannan & Fuller 2011). Morphological changes among cultivated plants often include increase in fruit and/or seed size, decrease in overall plant size, loss of seed dormancy, a shift toward annual life cycle, sterility, loss of defensive structures, increase or decrease of metabolites, changes in photoperiodic control, and changes in breeding system (Harlan 1992; Careau et al. 2010). A general consistency and predictability in the way that genetic and morphologic changes occur as a result of artificial selection is referred to as the “domestication syndrome” (Harlan 1992). Thus the definition of domestication encompasses the degree to which the domestication syndrome has altered a given cultivar, ranging from early cultivated individuals that are nearly identical to wild progenitors