Genetic Diversity and Phylogeographic Structure of the Parasitic Plant Genus Conopholis (Orobanchaceae): Implications for System

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Genetic Diversity and Phylogeographic Structure of the Parasitic Plant Genus Conopholis (Orobanchaceae): Implications for System Genetic Diversity and Phylogeographic Structure of the Parasitic Plant Genus Conopholis (Orobanchaceae): Implications for Systematics and Post-glacial Colonization of North America by Anuar Gregory Rodrigues A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Ecology and Evolutionary Biology University of Toronto © Copyright by Anuar Gregory Rodrigues 2013 Genetic Diversity and Phylogeographic Structure of the Parasitic Plant Genus Conopholis (Orobanchaceae): Implications for Systematics and Post-glacial Colonization of North America Anuar Gregory Rodrigues Doctor of Philosophy Ecology and Evolutionary Biology University of Toronto 2013 Abstract Parasitism in plants is often accompanied by a suite of morphological and physiological changes resulting in a condition known as the ‘parasitic reduction syndrome’. With changes including extreme vegetative reduction, frequently beyond any resemblance to its photosynthetic relatives, accompanied by significant losses of genes linked to photosynthesis, the study of parasitic plants can be challenging. Conopholis (Orobanchaceae) is a small holoparasitic genus distributed across eastern and southwestern North America and Central America. This genus has never been the subject of a molecular phylogenetic or morphometric analyses. In addition, very little is known of the relationships among populations and of their post-glacial history. To investigate the species limits and phylogenetic relationships in Conopholis, we conducted a comprehensive molecular phylogenetic study of the genus as well as a fine-scale morphometric study. Based on plastid and nuclear sequences, Conopholis was found to contain three distinct and well-supported lineages which have varying degrees of overlap with previously proposed taxa. The clustering and ordination analyses of the morphometric study corroborated the molecular data, demonstrating the morphological differentiation between the three lineages ii detected within Conopholis. A taxonomic re-alignment is proposed for the genus that recognizes three species, C. americana, C. panamensis, and C. alpina. To address genetic diversity and phylogeographic structure of C. americana in eastern North America, microsatellite markers were developed and characterized for the first time in this species. Using these newly generated markers along with sequences from the plastid genome, the persistence of a minimum of two glacial refugia at the last glacial maximum were inferred, one in Florida and southern Alabama and another in the Appalachian Mountains near the southern tip of Blue Ridge Mountains. The diversity seen across the southern Appalachian Mountains supports the hypothesis that populations derived from the southern and northern refugia come together in this area. iii Acknowledgments I would like to express my deepest appreciation to my supervisor, Saša Stefanović. Thank you for all the guidance and support you have given me over these past years and for always challenging me every step of the way. Thank you for everything Saša. I also wish to acknowledge my committee members Dr. John Stinchcombe and Dr. Tim Dickinson for all their support, guidance, and insight. Tim, thank you very much for all the assistance and encouragement during the time spent in your lab obtaining data for morphometric analyses. The support received from my supervisor and committee members was invaluable and greatly appreciated. In addition, I would also like to thank the extended members of my examination committee, Dr. James Eckenwalder, Dr. Peter Kotanen, and external examiner Dr. Daniel Nickrent. I would like to thank all of my colleagues in the Stefanović lab for their support over the years and for making the lab environment an excellent one. Thank you Thomas Braukmann, Dr. Eugenio Lo, Dr. Maria Kuzmina, Michael Wright, Shana Shaya, and Lily Xiao. Thomas, we began our degree together as strangers, but I know we will be friends for life. To all my friends at the UTM campus, both students and staff, thank you for all the coffees, laughs, and great memories over the years. To my mother who has always been my biggest fan, thank you for always believing in me, pushing me to dream big and supporting me in all my decisions. You have given me so much for which I am eternally grateful and I look forward to always making you proud! Finally, to Adam who has been my rock and constant source of support, love, and patience. Thank you for always understanding and for supporting me through the many highs and lows while I was iv completing my degree. I have always told you, words will never be able to describe how thankful and appreciative I am for absolutely everything you have given me and done for us. v Table of Contents Acknowledgments.................................................................................................................................iv Table of Contents..................................................................................................................................vi List of Tables .........................................................................................................................................ix List of Figures......................................................................................................................................... x List of Appendices ................................................................................................................................xi 1 Overview...........................................................................................................................................1 1.1 Parasitism in plants.............................................................................................................................. 1 1.2 Consequences of parasitism in plants .............................................................................................. 2 1.3 The parasitic plant family Orobanchaceae and its holoparasitic genus Conopholis ............. 4 1.4 Project description ............................................................................................................................... 6 2 Molecular systematics of the parasitic genus Conopholis (Orobanchaceae) inferred from plastid and nuclear sequences ..................................................................................................8 2.1 Abstract .................................................................................................................................................. 9 2.2 Introduction.........................................................................................................................................10 2.3 Materials and Methods......................................................................................................................13 2.3.1 Taxon sampling..............................................................................................................................................13 2.3.2 DNA extraction, amplification, and sequencing.................................................................................14 2.3.3 Phylogenetic analyses..................................................................................................................................15 2.3.4 Network analyses ..........................................................................................................................................16 2.3.5 Parsimony analyses.......................................................................................................................................16 2.3.6 Bayesian analyses..........................................................................................................................................17 2.3.7 Evaluation of the rooting ............................................................................................................................18 2.3.8 Testing of alternative topologies..............................................................................................................19 2.4 Results...................................................................................................................................................19 2.4.1 DNA regions and alignments ....................................................................................................................19 2.4.2 Individual data set analyses .......................................................................................................................20 2.4.3 Phylogenetic analyses of combined data...............................................................................................21 2.4.4 Molecular clock and placement of the root ..........................................................................................22 vi 2.4.5 Tests of alternate topologies......................................................................................................................24 2.5 Discussion .............................................................................................................................................24 2.5.1 Phylogenetic and taxonomic implications ............................................................................................25 2.5.2 Historical biogeography..............................................................................................................................28 2.6 Conclusions ..........................................................................................................................................32
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