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Testing the Hypothesis of Allopolyploidy in the Origin Of TESTING THE HYPOTHESIS OF ALLOPOLYPLOIDY IN THE ORIGIN OF PENSTEMON AZUREUS (PLANTAGINACEAE) A Thesis Presented to the faculty of the Department of Biological Sciences California State University, Sacramento Submitted in partial satisfaction of the requirements for the degree of MASTER OF SCIENCE in BIOLOGICAL SCIENCES (Ecology, Evolution, and Conservation) by Travis Joseph Lawrence SUMMER 2013 TESTING THE HYPOTHESIS OF ALLOPOLYPLOIDY IN THE ORIGIN OF PENSTEMON AZUREUS (PLANTAGINACEAE) A Thesis by Travis Joseph Lawrence Approved by: __________________________________, Committee Chair Dr. Shannon Datwyler __________________________________, Second Reader Dr. Nicholas Ewing __________________________________, Third Reader Dr. Jamie Kneitel ________________________ Date ii Student: Travis Joseph Lawrence I certify that this student has met the requirements for format contained in the University format manual, and that this thesis is suitable for shelving in the Library and credit is to be awarded for the thesis. _________________________, Graduate Coordinator _________________ Dr. Jamie Kneitel Date Department of Biological Sciences iii Abstract of TESTING THE HYPOTHESIS OF ALLOPOLYPLOIDY IN THE ORIGIN OF PENSTEMON AZUREUS (PLANTAGINACEAE) by Travis Joseph Lawrence Polyploidy, whole genome duplication, plays a major role in the evolution of angiosperms with multiple paleopolyploid events having been suggested making it plausible that all angiosperms have a polyploid event in their history. There are two types of polyploidy, autopolyploidy genome duplication within a species and allopolyploidy, whole genome duplication coupled with hybridization. Penstemon subsection Saccanthera is a species complex of closely related diploids and polyploids. The species in this complex are P. heterophyllus (2x, 4x), P. parvulus (4x), P. neotericus (8x), P. laetus (2x) and P. azureus (6x). Previous studies have hypothesized that P. azureus is an allopolyploid of P. parvulus (4x) X P. laetus (2x). To test the hypothesis of allopolyploidy in the origin of P. azureus and to determine possible progenitors two nuclear loci (Adh & NIA) and three chloroplast spacer regions (trnD-trnT, rpoB-trnC, rpl32-trnL) were sequenced from P. azureus, P. heterophyllus, P. laetus, P. parvulus, and P. neotericus. These data were analyzed in phylogenetic framework and network analysis was used on the nuclear data. iv The Adh and NIA datasets supported the allopolyploid origin of P. azureus with divergent Adh orthologs recovered in all five accessions P. azureus and divergent NIA orthologs recovered in three of the P. azureus accessions. Furthermore, the Adh and NIA datasets support three hypotheses for the possible progenitors of P. azureus: (1) P. heterophyllus (2x) X P. parvulus (2) P. heterophyllus X P. laetus and (3) P. heterophyllus (2x) X P. heterophyllus (4x). Markedly, all support P. heterophyllus (2x) as a progenitor. In addition, the Adh and NIA trees also suggest that P. neotericus is an allopolyploid, P. parvulus is an autopolyploid with two distinct origins and P. heterophyllus (4x) as an autopolyploid or allopolyploid. The cpDNA analysis resolved geographically structured clades. This pattern is best explained by local adaptation of the chloroplast genome and chloroplast capture. However, multiple origins of the polyploid species and gene flow could explain this pattern. In addition, the cpDNA tree and short branches in the Adh and NIA trees suggests that this species complex rapidly diversified in the Sierra Nevada Mountains. My study provides the first molecular phylogenetic evidence of the allopolyploid origin of P. azureus and has given insight into the origin of the other polyploids in this species complex. Furthermore, it has provided a foundation for further investigations of the diversification, speciation, and reticulation of subsection Saccanthera. ___________________________, Committee Chair Dr. Shannon Datwyler ___________________________ Date v ACKNOWLEDGEMENTS I would like to express my gratitude to Dr. Shannon Datwyler for her guidance, encouragement and critiques of this research work. I would like to acknowledge Dr. Nicolas Ewing for his comments on earlier drafts of this work, advice on laboratory protocols, and laboratory supplies. I would like to thank Dr. Jamie Kneitel for his support and comments on earlier drafts of this work. Finally, I would also like to acknowledge my biggest supporter, my wife Dana Carper, for always encouraging me and never complaining about my long days in the lab. vi TABLE OF CONTENTS Page Acknowledgements ............................................................................................................ vi List of Tables ...................................................................................................................... ix List of Figures ...................................................................................................................... x INTRODUCTION ............................................................................................................... 1 METHODS .......................................................................................................................... 7 Species Distribution and Habitat ............................................................................. 7 Species Selection ..................................................................................................... 9 Taxon Sampling ....................................................................................................... 9 Data Collection ...................................................................................................... 12 Data Analysis ......................................................................................................... 14 RESULTS .......................................................................................................................... 17 Chloroplast DNA ................................................................................................... 17 Adh Data Analysis ................................................................................................. 19 NIA Data Analysis ................................................................................................ 23 Network Analysis .................................................................................................. 24 DISCUSSION .................................................................................................................... 30 Origin of Penstemon azureus ................................................................................ 30 Phylogeography ..................................................................................................... 33 Gene Flow and Local Adaptation or Multiple Origins .......................................... 36 vii Comments on P. neotericus, P. parvulus, and P. heterophyllus (4x) .................... 37 Utility of Low Copy Nuclear Genes in Penstemon Phylogeny ............................. 38 CONCLUSION ................................................................................................................. 40 Appendix A. Supplemental Data ...................................................................................... 41 Literature Cited ................................................................................................................. 49 viii LIST OF TABLES Tables Page 1. Sampling locations and GenBank accession numbers of generated sequences ..................................................................................................................... 10 2. Primers used to amplify chloroplast and nuclear regions ............................................ 13 ix LIST OF FIGURES Figures Page 1. Strict consensus of seven equally parsimonious cpDNA trees with sampling location of colored clades indicated on map .......................................... 18 2. Single most parsimonious Adh tree ....................................................................... 21 3. Single most parsimonious Adh tree, part two ....................................................... 22 4. Strict consensus of 4174 equally parsimonious NIA trees .................................... 25 5. Strict consensus of 4174 equally parsimonious NIA trees, part two ..................... 26 6. Network analysis of the multiple-labeled single most parsimonious Adh tree. ................................................................................................................ 27 7. Network analysis of the multiple-labeled strict consensus of 4174 equally parsimonious NIA trees. ........................................................................... 29 8. Phylogram of the single most parsimonious Adh tree on the right and phylogram of one of the 4174 equally parsimonious NIA trees that was randomly selected .................................................................................... 35 A1. Phylogram recovered from maximum likelihood analysis of the cpDNA dataset ....................................................................................................... 41 A2. Bayesian majority-rule phylogram recovered from Bayesian analysis of the cpDNA dataset .............................................................................. 42 A3. Bayesian majority-rule phylogram recovered from Bayesian analysis of the Adh dataset .................................................................................... 43 x A4. Phylogram
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