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Phylogenetic Studies of the Charales: The ABSTRACT Title of dissertation: PHYLOGENETIC STUDIES OF THE CHARALES: THE CLOSEST LIVING RELATIVES OF LAND PLANTS Kenneth Gregory Karol, Doctor of Philosophy, 2004 Dissertation directed by: Associate Professor Charles F. Delwiche Department of Plant Biology The embryophytes (land plants) consist of organisms such as mosses, ferns, conifers and flowering plants. Although land plants have long been thought to be related to the green algal group Charophyceae, the nature of this relationship has been unresolved for over a century. A four-gene phylogenetic analysis supports the hypothesis that land plants arose from within the Charophyta and unambiguously identifies the Charales as the closest living relatives of plants. With a robust phylogeny, it is now possibly to explore phylogeny-dependant questions that were previously difficult to assess. Estimating the divergence time of the land plant lineage is one such question. A recent time estimate for the colonization of land by plants is 1,061 ± 109 mya and 703 ± 45 mya for the divergence of vascular plants and bryophytes, a result much older than the fossil record suggests (roughly 470 mya). Unlike most algae, a rich fossil record exists for the Charales in the form of calcified oospores. Representative fossils that can be attributed to five extant lineages in the Charales have been identified with reasonable accuracy. These multiple calibration points were used in conjunction with the four-gene DNA data set to estimate the divergence time of the land plant and Charales lineages. The Bayesian relaxed-clock approach estimated divergence of the Charales/land plant common ancestor in the Late Proterozoic (674.10 ± 99.96 MYA), modern land plants in the Cambrian (497.78 ± 75.66 MYA), and modern Characeae at the Paleozoic/Mesozoic boundary (247.75 ± 25.98 MYA). The genus Nitella is one of the most diverse genera in the Charales. Wood and Imahori’s worldwide monograph divides Nitella into three subgenera with seventeen sections and radically modified the taxonomy of this group my submerging over 200 Nitella species into 53 loosely defined species. Phylogenetic analyses of rbcL sequence data from 79 Nitella species (plus outgroups) support the monophyly of Nitella and two subgenera (Hyella and Tieffallenia). Subgenus Nitella formed two paraphyletic lineages at the base of the genus. Few sections were monophyletic and species diversity is interpreted as being much higher than proposed by Wood. PHYLOGENETIC STUDIES OF THE CHARALES: THE CLOSEST LIVING RELATIVES OF LAND PLANTS by Kenneth Gregory Karol Dissertation submitted to the Faculty of the Graduate School of the University of Maryland, College Park in partial fulfillment of the requirement for the degree of Doctor of Philosophy 2004 Advisory Committee: Associate Professor Charles F. Delwiche, Chair Professor Todd J. Cooke Dr. Richard M. McCourt Professor Charles Mitter Dr. Elizabeth A. Zimmer ©Copyright by Kenneth G. Karol 2004 To Gregory A. French ii Acknowledgements As an undergraduate student at the University of Madison I distinctly remember asking a group of graduate students “What does a Ph.D mean?” After some discussion, the group converged on the answer that a Ph.D. demonstrates a students’ ability to ‘perform independent research at a high academic level.’ Now that I have been through this process I must disagree. If it weren’t for the assistance and support of numerous friends and colleagues this dissertation would have been impossible. I am particularly indebted to my graduate committee. Chuck Delwiche for offering the opportunity to be his student and supplying the environment for brutally honest scientific discussion and the freedom to think out loud. Todd Cook for recognizing the more unusual side of my personality and allowing it to grow, not to mention stimulating conversations in the halls and on the loading dock. Rick McCourt for his never-ending friendship and for introducing me to the Characeae. Liz Zimmer for her encouragement, friendship and scientific integrity and Charlie Mitter for keeping me on my toes. Tsetso Bachvaroff, Matt Cimino, Chris Drummond, John Hall, Malin Hibbs, Jeff Lewandowski, Tanya Marushak, Virginia Sanchez-Puerta, Steve Snyder and Adam Zacardii, members of the Delwiche lab, deserve special thanks. For sharing conversation and Characeae material I thank Mitch Alix, Rob Bartleson, Mary Bisson, Becky Bixby, Jelena Blazencic, Jon Bollback, Robb Brumfield, Michelle Casanova, John Clayton, Monique Feist, Adriana Garcia, David Hewitt, Henry Mann, John Porter, James Reveal, Robin Scribailo, Ingaborg Soule-Marche, Mary de Winton and the International Group on Charophytes (IRGC). I would like to thank Vern iii Proctor for sharing his culture collection, field experience and hypotheses of charophyte evolution. I am indepted to my partner Greg French for his unconditional support and encouragement. iv TABLE OF CONTENTS Chapter I: General introduction ......................................................................................... 1 Introduction...................................................................................................................... 1 Overview of the Charophyta......................................................................................... 1 Overview of the Charales.............................................................................................. 2 Aims.............................................................................................................................. 7 Chapter II: The closest living relatives of land plants ....................................................... 8 Introduction...................................................................................................................... 8 Materials and Methods................................................................................................... 12 DNA isolation, PCR, and sequencing......................................................................... 12 Phylogenetic analyses ................................................................................................. 17 Results............................................................................................................................ 19 Taxa and data set......................................................................................................... 19 Discussion...................................................................................................................... 33 Chapter III: Estimating divergence times in the Charophyta........................................... 37 Introduction.................................................................................................................... 37 Overview..................................................................................................................... 37 The fossil record ......................................................................................................... 40 Materials and Methods................................................................................................... 42 Taxon sampling........................................................................................................... 42 DNA isolation, PCR, and sequencing......................................................................... 44 Phylogenetic analyses ................................................................................................. 46 Estimating divergence times....................................................................................... 47 Results............................................................................................................................ 51 Phylogenetic analyses ................................................................................................. 51 Estimating divergence times....................................................................................... 55 Discussion...................................................................................................................... 69 Phylogenetic analyses ................................................................................................. 69 'Simple’ and ‘complex’ models .................................................................................. 71 The fossil record of Characeae genera........................................................................ 72 Single versus multiple calibration points.................................................................... 75 Proterozoic origin and diversification of the Charophyta........................................... 76 Diversification of land plants...................................................................................... 78 Chapter IV: Phylogeny of Nitella (Charales: Charophyta).............................................. 81 Introduction.................................................................................................................... 81 Overview..................................................................................................................... 81 Materials and Methods................................................................................................... 87 DNA isolation, PCR, and sequencing......................................................................... 87 Phylogenetic analyses ................................................................................................. 90 Results and Discussion .................................................................................................
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