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Phylogeny and Morphological Evolution of the Chenopodiaceae-Amaranthaceae Alliance Donald B

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Phylogeny and Morphological Evolution of the Chenopodiaceae-Amaranthaceae Alliance Donald B Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 2003 Phylogeny and morphological evolution of the Chenopodiaceae-Amaranthaceae alliance Donald B. Pratt Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Botany Commons, and the Genetics Commons Recommended Citation Pratt, Donald B., "Phylogeny and morphological evolution of the Chenopodiaceae-Amaranthaceae alliance " (2003). Retrospective Theses and Dissertations. 613. https://lib.dr.iastate.edu/rtd/613 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. UMI films 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 reproduction 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, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. ProQuest Information and Learning 300 North Zeeb Road. Ann Arbor, Ml 48106-1346 USA 800-521-0600 Phytogeny and morphological evolution of the Chcnopodiaccae-Amaranthaccae alliance by Donald B. Pratt 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 (Co-major Professor) Robert S. Wallace (Co-major Professor) Jonathan F. Wendel John Nason Micheal D.K. Owen Iowa State University Ames, Iowa 2003 Copyright Donald B. Pratt, 2003. All rights reserved. UMI Number 3085939 UMI' UMI Microform 3085939 Copyright 2003 by ProQuest Information and Learning Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. ProQuest Information and Learning Company 300 North Zeeb Road P.O. Box 1346 Ann Arbor. Ml 48106-1346 Graduate College Iowa State University This is to certify that the doctoral dissertation of Donald B. Pratt has met the dissertation requirements of Iowa State University Signature was redacted for privacy. Co-major Professor Signature was redacted for privacy. Co-major Professor Signature was redacted for privacy. F he Major Program m TABLE OF CONTENTS LIST OF TABLES vi LIST OF FIGURES vii CHAPTER I. GENERAL INTRODUCTION 1 Dissertation organization 1 General Introduction and Statement of Research l Previous Work in the Chenopodiaceae-Amaranthaceae Alliance 3 Taxonomic history and subfamilial classifications of the Chenopodiaceae-Amaranthaceae Alliance 3 Sarcobatus 6 Molecular Systematics of the Chenopodiaceae-Amaranthaceae Alliance 6 Morphology of the Chenopodiaceae-Amaranthaceae Alliance 7 Literature Cited 10 Tables 12 CHAPTER H. ndhF PHYLOGENY OF THE CHENOPODIACEAE- AMARANTHACEAE ALLIANCE Abstract 14 Introduction 14 Materials and Methods 16 Materials 16 Sequencing Methods 17 Sequence Alignment 17 Parsimony Analysis 18 Bayesian Analysis 19 Maximum Likelihood Analysis 19 Distance Analysis 20 Results 20 Parsimony Analyses 20 Bayesian Analysis 21 Maximum Likelihood Analysis 22 Distance Analysis 22 Discussion 23 Sarcobatus and Monophyly of the Chenopodiaceae-Amaranthaceae Alliance 23 Chenopodiaceae-Amaranthaceae Alliance 23 Amaranthaceae-Polycnemoideae 23 Chenopodieae-Atripliceae 24 Beteae 26 iv Salsoloideac-Salicomioideae 26 Taxonomic Significance 27 Literature Cited 29 Tables 32 Figures 40 CHAPTER ID. MORPHOLOGICAL TRENDS IN THE CHENOPODIACEAE- AMARANTHACEAE ALLIANCE AND THEIR TAXONOMIC SIGNIFICANCE Abstract 48 Introduction 48 General Introduction 48 Materials and Methods 53 Taxon Sampling 53 Character Sampling 53 Parsimony Analysis 54 Character-State Mapping 54 Character-State Correlation 55 Results and Discussion 56 Parsimony Analysis 56 Character-State Optimizations 56 Leaf Characters 57 Breeding System Characters 59 Bract Characters 59 Sepal Characters 63 Stamen Characters 65 Ovule Characters 66 Embryo Characters 66 Dipsersal Units 66 Petal Characters 67 Anatomical Characters 67 Chloroplast Genome Structure 67 Character-Stale Correlation 68 Ovule Number by Dispersal Unit 68 Atriplicoid Floral Syndrome 68 Future Work 70 Literature Cited 72 Tables 75 Figures 80 Appendix 1 98 Appendix 2 100 Appendix 3 102 V CHAPTER IV: A NEW SPECIES OF AMARANTHUS (AMARANTHACEAE) FROM CENTRAL MEXICO Abstract 104 Introduction 104 Note on Staminate Floral Morphology 105 Taxonomic Treatment 106 Distribution 107 Additional Specimens Examined 107 Discussion 107 Literature Cited 109 Tables 110 Figure 112 CHAPTER V: GENERAL CONCLUSION General Discussion 113 Recommendations for Further Research 114 Literature Cited 116 vi UST OF TABLES CHAPTER L Table 1. Diagnosis of the Amaranthaceae and Chenopodiaceae based on Morphological Characters 12 Table 2 Historical circumscriptions of the Amaranthaceae and Chenopodiaceae 13 CHAPTER H. Table 1. Taxon sampling and voucher information 32 Table 2. Amplification and sequencing primers 34 Table 3. Sequencing primers by taxon 35 Table 4. Parsimony tree descriptions by outgroup substitution 38 Table 5. Indel events 39 CHAPTER HI. Table 1. Traditional diagnosis of the Amaranthaceae and Chenopodiaceae 75 based on morphological characters Table 2. Morphological characteristics of the Chenopodiaceae-Amaranthaceae alliance 76 Table 3. Atriplicoid floral syndrome 77 Table 4. Morphological characters 78 Table 5. Diagnostic characters for the Amaranthoideae-Polycnemoideae clade 79 Table 6. Caracter-state correlations of the atriplicoid floral syndrome 79 CHAPTER IV: Table 1. Diagnostic characteristics of the subgenera of Amaranthus 110 Table 2. Distinguishing characters of Amaranthus hybridus and A. neeamts 110 Table 3. Character-states of Amaranthus neeanus and infrageneric taxa bearing similar character-states 110 vii LIST OF FIGURES CHAPTER II. Figure 1. Maximum parsimony tree, analysis viii—Caryophyllaceae as outgroup 41 Figure 2. Bayesian analysis 43 Figure 3. Maximum likelihood analysis 45 Figure 4. Kimura 2-paramater with gamma rate neighbor-joining tree 47 CHAPTER HI. Figure 1 A. Morphological character optimization, core Chenopodiaceae Expanded 81 Figure IB. Morphological character optimization, Amaranthaceae and Polycnemoideae expanded 83 Figure 2. ACCTRAN and DELTRAN optimizations of pistillate bract disarticulation (character 6) 85 Figure 3. ACCTRAN and DELTRAN optimizations of pistillate sepal connation (character 10) 87 Figure 4. ACCTRAN and DELTRAN optimizations of embryo type (character 16) 89 Figure 5. ACCRAN optimization of dispersal unit (character 17) 91 Figure 6. Guilleminoid phyllotaxy 93 Figure 7. Amaranthaceous bract apparatus 95 Figure 8. Dispersal units 97 CHAPTER IV: Figure 1. Amaranthus neeanus. 112 1 Chapter I: General Introduction Dissertation Organization This dissertation consists of five chapters. Chapter I is a general introduction to the Chenopodiaceae-Amaranthaceae alliance, their taxonomic history, and morphology within the alliance. Chapter n consists of a paper prepared for publication entitled "ndhF Phytogeny of the Chenopodiaceae-Amaranthaceae Alliance." Chapter in is a paper prepared for publication entitled "Morphological Trends in the Chenopodiaceae-Amaranthaceae Alliance and their Taxonomic Significance." Chapter IV contains the description of a new species of Amaranthus prepared for publication entitled "A New Species of Amaranthus (Amaranthaceae) from Central Mexico, co-authored by Ivonne Sânchez-del Pino and Hilda Flores Olvera. Chapter Visa general conclusion. General Introduction and Statement of Research The Chenopodiaceae and Amaranthaceae (here collectively referred to as the Chenopodiaceae-Amaranthaceae alliance or Chen-Am alliance) are closely related families of the Caryophyllales, an order of Angiosperms traditionally consisting of 18 families and 8,600 species circumscribed by free-central or basal placentation; curved embryos; presence of perisperm; beaked integuments; distinctive phloem plastid morphology; and betalain pigmentation (Judd et al. 2002). The Chen-Am alliance is of worldwide distribution, comprising approximately 169 genera and 2,400 species. The Amaranthaceae (ca. 69 genera and 1,000 species) are most diverse in the tropics while the Chenopodiaceae (ca. 100 genera 1,400 species) are most diverse in temperate regions. The Chen-Am alliance is noted for the evolution of C* photosynthesis, halophytism, xerophytism, and a variety of breeding systems (Borsch et al. 2001). The Amaranthaceae and Chenopodiaceae morphologically are very similar and have long been considered a single evolutionary lineage. The Chen-Am alliance shares a core floral 2 formula of
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