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Population Genetics and Phylogenetic Context of Weed Evolution in the Genus Amaranthus: Amaranthaceae) Katherine Waselkov Washington University in St

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Population Genetics and Phylogenetic Context of Weed Evolution in the Genus Amaranthus: Amaranthaceae) Katherine Waselkov Washington University in St Washington University in St. Louis Washington University Open Scholarship All Theses and Dissertations (ETDs) Summer 8-12-2013 Population Genetics and Phylogenetic Context of Weed Evolution in the Genus Amaranthus: Amaranthaceae) Katherine Waselkov Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/etd Recommended Citation Waselkov, Katherine, "Population Genetics and Phylogenetic Context of Weed Evolution in the Genus Amaranthus: Amaranthaceae)" (2013). All Theses and Dissertations (ETDs). 1162. https://openscholarship.wustl.edu/etd/1162 This Dissertation is brought to you for free and open access by Washington University Open Scholarship. It has been accepted for inclusion in All Theses and Dissertations (ETDs) by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. WASHINGTON UNIVERSITY IN ST. LOUIS Division of Biology and Biomedical Sciences Evolution, Ecology and Population Biology Dissertation Examination Committee: Kenneth M. Olsen, Chair James M. Cheverud Allan Larson Peter H. Raven Barbara A. Schaal Alan R. Templeton Population Genetics and Phylogenetic Context of Weed Evolution in the Genus Amaranthus (Amaranthaceae) by Katherine Elinor Waselkov A dissertation presented to the Graduate School of Arts and Sciences of Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy August 2013 St. Louis, Missouri © Copyright 2013 by Katherine Elinor Waselkov. All rights reserved. TABLE OF CONTENTS List of Tables .................................................................................................................... vi List of Figures .................................................................................................................. vii Acknowledgments .............................................................................................................. x Abstract of the Dissertation .......................................................................................... xvi Introduction of the Dissertation .......................................................................................1 Study System: The Genus Amaranthus ...................................................................6 Study System: Amaranthus tuberculatus .................................................................8 Dissertation Overview ...........................................................................................10 Literature Cited ......................................................................................................10 Chapter 1: Molecular Phylogeny of Amaranthus (Amaranthaceae) and Trait Associations with Weediness in the Genus ..........................................................17 Introduction ............................................................................................................18 Materials and Methods ...........................................................................................22 Taxon Sampling ....................................................................................................... 22 DNA Extraction and Sequencing ............................................................................. 23 Phylogenetic Analyses ............................................................................................. 25 Topology Testing ..................................................................................................... 28 Trait Associations with Weediness .......................................................................... 29 Results ....................................................................................................................31 DNA Sequencing ...................................................................................................... 31 Phylogenetic Trees ................................................................................................... 32 Topology Tests ......................................................................................................... 41 ii Trait Associations with Weediness .......................................................................... 43 Discussion ..............................................................................................................44 Phylogenetic Relationship and Topology Tests ....................................................... 44 Trait Associations with Weediness .......................................................................... 52 Literature Cited ......................................................................................................56 Tables and Figures .................................................................................................64 Chapter 2: Population Genetics and Origin of the Native Midwestern Agricultural Weed, Waterhemp (Amaranthus tuberculatus) .......................................................................109 Introduction ..........................................................................................................110 Materials and Methods .........................................................................................112 Study System .......................................................................................................... 112 Sample Collection .................................................................................................. 114 DNA Extraction and Genotyping ........................................................................... 115 Microsatellite Data Analysis .................................................................................. 116 Results ..................................................................................................................120 Genetic Diversity and Isolation by Distance .......................................................... 120 Population Structure ............................................................................................... 121 Discussion ............................................................................................................124 Literature Cited ....................................................................................................133 Tables and Figures ...............................................................................................139 Chapter 3: Agricultural and Local Adaptation Shape Invasiveness in Waterhemp, Amaranthus tuberculatus (Amaranthaceae) ................................................................163 Introduction ..........................................................................................................164 Materials and Methods .........................................................................................168 iii Common Garden Design ........................................................................................ 168 Plant Measurements, 2010 ..................................................................................... 172 Plant Measurements, 2011 ..................................................................................... 173 Data Analysis ......................................................................................................... 174 Results ..................................................................................................................175 Plant Height ............................................................................................................ 175 Days to Flowering .................................................................................................. 176 Mature Plant Data ................................................................................................... 177 Dry Above-Ground Biomass .................................................................................. 178 Analyses by Plant Sex ............................................................................................ 178 Discussion ............................................................................................................179 Literature Cited ....................................................................................................188 Tables and Figures ...............................................................................................195 Chapter 4: Presence of Agriculturally-Adaptive Herbicide Resistance Alleles in Natural Populations of Ohio Waterhemp (Amaranthus tuberculatus) ....................................212 Introduction ..........................................................................................................213 Materials and Methods .........................................................................................217 Sample Collection .................................................................................................. 217 Greenhouse Herbicide Screening ........................................................................... 217 PCR-Restriction Enzyme Assay ............................................................................. 219 ALS Sequencing ...................................................................................................... 221 Results ..................................................................................................................221 Greenhouse Herbicide Screening ..........................................................................
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