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Phylogenetic Relationships Among the Temperate Bamboos (Poaceae: Bambusoideae) with an Emphasis on Arundinaria and Allies Jimmy K

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Phylogenetic Relationships Among the Temperate Bamboos (Poaceae: Bambusoideae) with an Emphasis on Arundinaria and Allies Jimmy K Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 2008 Phylogenetic relationships among the temperate bamboos (Poaceae: Bambusoideae) with an emphasis on Arundinaria and allies Jimmy K. Triplett Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Botany Commons Recommended Citation Triplett, Jimmy K., "Phylogenetic relationships among the temperate bamboos (Poaceae: Bambusoideae) with an emphasis on Arundinaria and allies" (2008). Retrospective Theses and Dissertations. 15723. https://lib.dr.iastate.edu/rtd/15723 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Phylogenetic relationships among the temperate bamboos (Poaceae: Bambusoideae) with an emphasis on Arundinaria and allies by Jimmy K. Triplett A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Botany (Systematics and Evolution) Program of Study Committee: Lynn G. Clark, Major Professor Gregory W. Courtney John D. Nason Robert S. Wallace Jonathan F. Wendel Iowa State University Ames, Iowa 2008 Copyright © Jimmy K. Triplett 2008. All rights reserved 3316248 3316248 2008 ii TABLE OF CONTENTS LIST OF FIGURES iv LIST OF TABLES viii ABSTRACT x CHAPTER 1. OVERVIEW 1 Organization of the Thesis 1 Literature Review 2 Literature Cited 10 CHAPTER 2. PHYLOGENY OF THE TEMPERATE WOODY BAMBOOS (POACEAE: BAMBUSOIDEAE) WITH AN EMPHASIS ON ARUNDINARIA AND ALLIES. A manuscript to be submitted to Systematic Botany. Jimmy K. Triplett and Lynn G. Clark 15 Abstract 15 Introduction 16 Materials and Methods 20 Results 26 Discussion 32 Acknowledgements 49 Literature Cited 49 Appendix 1 56 CHAPTER 3. PHYLOGENETIC RELATIONSHIPS WITHIN ARUNDINARIA (POACEAE: BAMBUSOIDEAE) IN NORTH AMERICA. A manuscript to be submitted to Evolution or American Journal of Botany. Jimmy Triplett, Kimberly A. Oltrogge, and Lynn G. Clark 59 Abstract 59 Introduction 60 Materials and Methods 66 Results 74 Discussion 86 iii Acknowledgements 94 Literature Cited 95 CHAPTER 4. HILL CANE (ARUNDINARIA APPALACHIANA), A NEW SPECIES OF BAMBOO (POACEAE: BAMBUSOIDEAE) FROM THE SOUTHERN APPALACHIAN MOUNTAINS. A version of a manuscript published in SIDA. Jimmy Triplett, Alan S. Weakley and Lynn G. Clark 104 Abstract 104 Introduction 104 Materials and Methods 108 Results and Discussion 109 Taxonomic Treatment 115 Acknowledgements 122 Literature Cited 123 CHAPTER 5. RETICULATE EVOLUTION IN THE ARUNDINARIA CLADE (POACEAE: BAMBUSOIDEAE). A manuscript to be submitted to New Phytologist. Jimmy Triplett and Lynn G. Clark 127 Abstract 127 Introduction 128 Materials and Methods 133 Results 139 Discussion 158 Acknowledgements 178 Literature Cited 179 Appendix 1 187 CHAPTER 6. GENERAL CONCLUSIONS 190 General Conclusions 190 Future Directions 192 Literature Cited 194 ACKNOWLEDGEMENTS 195 iv LIST OF FIGURES CHAPTER 2. Figure 1. Strict consensus of 768 equally most parsimonious trees based on the 4-region dataset (rps16-trnQ, trnC-rpoB, trnD-trnT, trnT-trnL). Numbers above lines indicate bootstrap values (MP/ML). Numbers below the line indicate posterior probabilities from the Bayesian analysis. 28 Figure 2. Strict consensus of 6 equally most parsimonious trees based on the 12-region dataset. Numbers above lines indicate bootstrap values (MP/ML), and numbers below lines indicate posterior probabilities from the Bayesian analysis. 31 CHAPTER 3. Figure 1. Map of southeastern North America showing geographical distribution of Arundinaria species. Black triangles = A. gigantea; open circles = A. appalachiana; black circles = A. tecta; x = putative hybrids. 67 Figure 2. cp DNA haplotype phylogeny. Single most parsimonious tree (Length = 9, CI = 1.0, RI = 1.0) resulting from the analysis of trnTL and including indels recoded as binary present/absent characters. Bootstrap values greater than 50% are given above the branches. Haplotype accessions are summarized in Table 2. 77 Figure 3. A. Genetic relationships among 83 populations of Arundinaria inferred from AFLP data using a neighbor-joining analysis of Nei-Li distances. Tree rooted with Sasa. Parenthetical codes designate trnTL haplotypes. Numbers above branches indicate bootstrap support values (>70%). B. Neighbor-joining phylogram, excluding hybrid accessions. (Sasa removed for clarity). Bootstrap values are indicated for major clusters only. 79 Figure 4. Neighbor-net of AFLP data based on Nei-Li distances, highlighting the positions of putative hybrid accessions relative to species of Arundinaria. cp DNA haplotypes of the putative hybrids are indicated in parentheses. 81 Figure 5. Two-dimensional ordination of accessions representing Arundinaria gigantea (G), A. appalachiana (A), A. tecta (T), and putative hybrids (indicated by v voucher numbers). Ordination was conducted using nonmetric multidimensional scaling on a pairwise distance matrix calculated using the Nei-Li dissimilarity coefficient. Final stress was reached after 50 iterations. Final stress = 1.169095. 82 Figure 6. Contribution of amplified fragment length polymorphism (AFLP) fragments to Arundinaria species and hybrids. LETTER CODES – G: present only in A. gigantea; T: present only in A. tecta; A: present only in A. appalachiana; a/t: present in both A. appalachiana and A. tecta COLOR CODES – Black: present in all three species; White: present only in A. gigantea; Grey: present in A. appalachiana and/or A. tecta. 83 Figure 7. Strict consensus of 7385 most parsimonious trees obtained from the AFLP dataset, excluding putative hybrid accessions. Tree length (L) 655, CI = 0.5061, RI = 0.9364. Parenthetical codes designate trnTL haplotypes. Bootstrap values greater than 70% are given above the branches. 85 CHAPTER 4. Figure 1. Distribution of Arundinaria appalachiana in the southeastern United States. Filled circles based on documented specimens; open circles based on unvouchered sight records. 111 Figure 2. Arundinaria appalachiana. A. Top knot of new shoot. B. Foliage leaf complement from midculm node. C. Foliage leaf, showing apex of sheath, fimbriae, pseudopetiole, and base of blade. D. Detail of abaxial surface of blade showing tessellation and pilose vestiture. E. Culm leaf at midculm node. F. Branch complement showing compressed basal internodes and reiterative secondary branch (arrow). Scale bar = 1 cm unless otherwise noted. All drawings based on Triplett and Ozaki 99. (Illustrations by J. Triplett) 116 Figure 3. Arundinaria appalachiana. A. Partially dissected spikelet showing two florets. B. Synflorescence with five spikelets. Scale bar = 1 cm. Drawings based on Ahles and Leisner 15147. (Illustrations by J. Triplett) 117 vi Figures 4 and 5. Arundinaria appalachiana. 4. Habit, in Rhea Co., Tennessee. 5. Close- up of primary branch with compressed basal internodes, Dekalb Co., Alabama. (Photos by J. Triplett) 118 CHAPTER 5. Figure 1. Strict consensus of 6 equally most parsimonious trees based on the 4-region dataset (rps16-trnQ, trnC-rpoB, trnD-trnT, trnT-trnL). Numbers above lines indicate bootstrap values (MP/ML). Numbers below the line indicate posterior probabilities from the Bayesian analysis. 141 Figure 2. A. Genetic relationships among 52 accessions of the Arundinaria Clade inferred from AFLP data using a neighbor-joining analysis of Nei-Li distances. Tree rooted with Phyllostachys. Numbers above branches indicate bootstrap support values (>65%). B. Summary of the UPGMA dendrogram for the same dataset. Clusters that received bootstrap support over >70% are indicated by asterisks. 143 Figure 3. Two-dimensional ordination of accessions representing the Arundinaria Clade. Putative hybrid associations are indicated between parent genera (circled) and nothogenera (indicated by arrows). See Fig. 1 for species names (by voucher number). Ordination was conducted using nonmetric multidimensional scaling on a pairwise distance matrix calculated using the Nei-Li dissimilarity coefficient. Final stress was reached after 5 iterations. Final stress = 16.059440. 145 Figure 4. A. Summary phylogram of genetic relationships among 248 accessions of the Arundinaria Clade inferred from AFLP data using a neighbor-joining analysis of Nei-Li distances. Tree rooted with Phyllostachys. B. Summary UPGMA dendrogram for the same dataset. Major clusters that received bootstrap support over >70% are indicated by asterisks. 147 Figure 5. A and B. Mid-point rooted phylogram of genetic relationships among 248 accessions of the Arundinaria Clade inferred from AFLP data using a neighbor- vii joining analysis of Nei-Li distances. Numbers above branches indicate bootstrap support values (>70%). 148-149 Figure 6. Contribution of amplified fragment length polymorphism (AFLP) fragments to putative hybrid taxa. Putative parents are indicated under the name of the hybrid. LETTER CODES – A, B: proportion of bands diagnostic of parent A or B, respectively. SHADING – White: parent A; Black: parent B; Light Grey (upper left): bands present in both parents and the hybrid; Dark Grey: bands unique to the hybrid. 152 Figure 7. A. Neighbor-net of AFLP data based on Nei-Li distances, highlighting the positions of Pseudosasa japonica accessions relative to species
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