Phylogeny and Classification of the Bamboos (Poaceae: Bambusoideae) Based on Molecular and Morphological Data Wei-Ping Zhang Iowa State University

Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 1996 Phylogeny and classification of the bamboos (Poaceae: Bambusoideae) based on molecular and morphological data Wei-Ping Zhang Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Botany Commons Recommended Citation Zhang, Wei-Ping, "Phylogeny and classification of the bamboos (Poaceae: Bambusoideae) based on molecular and morphological data " (1996). Retrospective Theses and Dissertations. 11430. https://lib.dr.iastate.edu/rtd/11430 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]. INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UME fihns the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reprodactioii is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, begiiming at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. Each original is also photographed in one exposure and is included in reduced form at the back of the book. Photographs included in the original manuscript have been reproduced xerographically in this copy. BSgher quality 6" x 9" black and white photographic prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UME directly to order. UMI A Bell & Howell Information Company 300 North Zed) Road, Ann Aibor MI 48106-1346 USA 313/761-4700 800/521-0600 Phylogeny and classification of the bamboos (Poaceae: Bambusoideae) based on molecular and morphological data by Wei-Ping Zhang 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) Major Professors: Lynn G. Clark and Jonathan F. Wendel Iowa State University Ames, Iowa 1996 Copyright © Weiping Zhang, 1996. All right reserved. UMI Nxunber: 9712621 Copyright 1996 by Zhang, Welping All rights reserved. UMI Microform 9712621 Copyright 1997, by UMI Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. UMI 300 North Zeeb Road Ann Arbor, MI 48103 11 Graduate College Iowa State University This is to certify that the doctoral dissertation of Weiping Zhang . has met the dissertation requirements of Iowa State University Signature was redacted for privacy. o-major Professor Signature was redacted for privacy. o-major Professor Signature was redacted for privacy. or Program Signature was redacted for privacy. For the iii TABLE OF CONTENTS LISTOFHGURES v LIST OF TABLES vi ABSTRACT vii CHAPTER L GENERAL INTRODUCTION 1 Introduction 1 Dissertation Organization 2 Statement of Researcti and Literature Review 3 Literature Cited 9 CHAPTER 2. PHYLOGENY AND CLASSMCATION OF THE BAMBUSOIDEAE (POACEAE) BASED ON ndhF SEQUENCE AND MORPHOLOGICAL DATA 14 Abstract 14 Introduction 15 Materials and Methods 17 Results 41 Discussion 62 Taxonomic Treatment 75 Acknowledgments 80 Literature Cited 80 CHAPTERS. BAMBOOZLED AGAIN!: INADVERTENT ISOLATION OF FUNGAL rDNA SEQUENCES FROM BAMBOOS (POACEAE: BAMBUSOIDEAE) 88 Abstract 88 Introduction 89 Materials and Methods 91 Results 97 Discussion 105 Acknowledgments 112 i V Literature Cited 112 CHAPTER 4. GENERAL CONCLUSIONS 119 General Discussion 119 Recommendations for Future Research 121 Literature Cited 123 APPENDIX. COMPLETE ndhF GENE SEQUENCE DATA MATRIX 125 ACKNOWLEDGMENTS 161 V LIST OF HGURES CHAPTER 2. Figure 1. Silica body diagram 38 Figure 2. One most parsimonious tree of the complete ndtiF sequence data set 44 Figure 3. Strict consensus tree of the complete ndhF sequence data set 46 Figure 4. Neighbor-Joining tree of the complete ndhF sequence data using Kimura 2- parameter distance measure 49 Figure 5. One most parsimonious tree of the morphological and anatomical data set 52 Figure 6. Strict consensus tree of the morphological and anatomical data set 54 Figure 7. One most parsimonious tree of the reduced ndhF sequence data set 57 Figure 8. One most parsimonious tree of the combined data sets 60 CHAPTER 3. Figure 1. Aligned data matrix of 5.8S sequences for representative ascomycetes (A), basidiomycetes (B) and angiospermous plants (P) 99 Figure 2. Strict consensus of the 15 shortest trees found in parsimony analysis of plant, fungal, and "contaminating fungal" 5.8S sequences, rooted with angiosperms 102 Figure 3. Strict consensus of 414 equally most parsimonious trees found in parsimony analysis of 5.8S sequences from basic^omycetes and putative basidiomycetous fungi associated with bamboos, rooted wi^ three representative ascomycetes 104 Figure 4. Scannmg electron micrographs of the leaf surfaces of four species of bamboos 110 V i LIST OF TABLES CHAPTER 2. Table 1. Taxa, voucher specimens, and GenBank accession numbers 18 Table 2. Morphological and leaf anatomical characters and character states used in the analysis 24 Table 3. Data matrix of morphological and anatomical characters and character states used for cladistic analysis in the bambusoid clade 31 Table 4. Indels (insertions and deletions) in the Bambusoideae ndhP gene sequences 41 Table 5. Sequence variation within the complete ndhF sequence data set and the subsets of bambusoid taxa 61 Table 6. Proportion of nucleotide difference and standard errors of ndhF gene among different groups of bambusoids and other grasses 63 CHAPTER 3. Table 1. Taxa, vouchers, and GenBank accession numbers for species studied 91 Table 2. Primers (5' to 3') used for PCR ampUfication of the ITS region 95 vii ABSTRACT Chloroplast ndhF gene sequences, morphological and leaf anatomical characters were analyzed separately and as combined data sets to reconstruct the phylogeny of subfamily Bambusoideae. The analyses further confirmed that the monophyletic bambusoid clade consists of only two monophyletic lineages: the woody bamboos, and the herbaceous olyroid bamboos. Buergersiochloa was resolved as the basal lineage in the herbaceous olyroids, whereas Pariana/Eremitis was sister to the rest of the olyroids. The woody bamboos were divided into two main groups: temperate woody bamboos and tropical woody bamboos; and the tropical clade was further subdivided along geographic lines into the Old World Bambuseae and the New World Bambuseae. Puelia was resolved as the most basal Uneage of the 'higher grasses' and thus was excluded from the bambusoid clade. Streptogyneae joined the oryzoids including the Oryzeae and Ehrharteae to form another separate monophyletic clade. The results of this study clearly indicate that the current Bambusoideae is not acceptable phylogenetically. Therefore a new circumscription of the Bambusoideae with two tribes is proposed in which only members of the bambusoid clade are included; the woody bamboos are classifed as one tribe, the Bambuseae, and the herbaceous olyroid bamboos are classified in another tribe, the Olyreae. In order to provide additional resolution of phylogenetic relationships within the bambusoid clade, an attempt to generate nuclear ribosomal ITS sequence data of bamboos was made. However, polymerase chain reaction amplification (PGR) led to the recovery of fungal instead of bamboo sequences. Phylogenetic analyses based on the 5.8S sequences indicated that all the sequences belonged to basidiomycetes and that none was an ascomycete. A diverse assemblege of basidiomycetes was isolated from different bamboo hosts and various fungi coexisted in the same host plant. No evidence showed that closely related fungi associated viii witJi closely related bamboo hosts. True bamboo ITS sequences were obtained only after leaf surface sterilization before DNA isolation. This study highlights the possibility of inadvertent PGR amplification of "contaminating DNA" in molecular phylogenetic studies. The results also indicate that a close ecological association between epiphytic basidiomycetes and bamboo leaves may exist, but fiuther study is needed. I CHAPTER 1. GENERAL INTRODUCTION Introduction The bamboos are known for their uses in fishing, papermaking, landscape gardening, handicrafts, medicine, art, and food, and more recendy have become publicized as the main source of food for the endangered giant panda. Bamboos have played a very important role in the cultural heritage of Far Eastern countries such as China, Korea, and Japan. Bamboos were used to record historical events and cultural treasures before the invention of paper. In tropical regions, the bamboos were regarded as the "timber of the poor" because people used bamboos for house construction,

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