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City University of New York (CUNY) CUNY Academic Works All Dissertations, Theses, and Capstone Projects Dissertations, Theses, and Capstone Projects 9-2015 SYSTEMATICS AND EVOLUTION OF THE Ronnbergia ALLIANCE (BROMELIACEAE): HISTORY OF DISJUNCT DIVERSIFICATION IN THREE BIODIVERSITY HOTSPOTS OF THE NEOTROPICS Julian Andres Aguirre Santoro Graduate Center, City University of New York How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/gc_etds/828 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] SYSTEMATICS AND EVOLUTION OF THE Ronnbergia ALLIANCE (BROMELIACEAE): HISTORY OF DISJUNCT DIVERSIFICATION IN THREE BIODIVERSITY HOTSPOTS OF THE NEOTROPICS by JULIÁN ANDRÉS AGUIRRE SANTORO A dissertation submitted to the Graduate Faculty in Biology in partial fulfillment of the requirements for the degree of Doctor of Philosophy, The City University of New York 2015 © 2015 JULIAN ANDRES AGUIRRE SANTORO All Rights Reserved ii This manuscript has been read and accepted for the Graduate Faculty in Biology to satisfy the dissertation requirement for the degree of Doctor of Philosophy. Dr. Fabián Michelangeli Date Chair of Examining Committee Dr. Laurel Eckhardt Date Executive Officer Dr. Ana Carolina Carnaval Dr. Wendy Clement Dr. Dwight Kincaid Dr. Dennis W. Stevenson Dr. William Wayt Thomas THE CITY UNIVERSITY OF NEW YORK iii Abstract SYSTEMATICS AND EVOLUTION OF THE Ronnbergia ALLIANCE (BROMELIACEAE): HISTORY OF DISJUNCT DIVERSIFICATION IN THREE BIODIVERSITY HOTSPOTS OF THE NEOTROPICS by Julián Andrés Aguirre Santoro Adviser: Dr. Fabián Michelnageli The systematics, biogeography and evolution of the “Ronnbergia Alliance,” a nested lineage within the Core Bromelioideae, were investigated. In the first chapter, the phylogenetic relationships of the Ronnbergia Alliance were reconstructed using three chloroplast and three nuclear DNA sequence markers in combination with a wide species sampling across the Core Bromelioideae and a nearly complete species-level sampling of the five species complexes that likely comprise the Ronnbergia Alliance. The analysis indicates that the Ronnbergia Alliance is a robust monophyletic group sister to the remaining Core Bromelioideae, and it is composed by species of the polyphyletic genera Aechmea, Hohenbergia and Ronnbergia. The first of main lineage within the Ronnbergia Alliance, here called the Pacific Clade, contains species of that occur exclusively in the forests of southern Central America to northwestern South America. The second clade, called the Atlantic Clade, contains species mostly limited to the central corridor of the Atlantic Forest and the Greater Antilles. The combination of apically spreading tubular corollas and unappendaged ovules are diagnostic for the Ronnbergia Alliance, whereas flower size, corolla tube length, and petal pigmentation are important characters to differentiate the Pacific and Atlantic Clades. A new taxonomic reorganization and synopsis for this clade was iv proposed in the second chapter. Here, all the species of the Pacific Clade were placed in Ronnbergia, whereas the species of the Atlantic Clade were relocated in the resurrected genus Wittmackia. In the third chapter, a complete taxonomic revision of the Caribbean clade of Wittmackia was conducted. In the fourth chapter, the biogeographic history and evolutionary rate dynamics of the Ronnbergia Alliance were analyzed. These analyses showed that one vicariant event that separated Ronnbergia from Wittmackia in South America, and a later long-distance dispersal event allowed the separation of Wittmackia between the Atlantic Forest and Jamaica. Although the evolutionary rate dynamics remained constant during the diversification of Ronnbergia, these rates were heterogeneous during the radiation of Wittmackia. This is the first species-level approach that combines phylogenetic, ecological, geographic and morphological information to reveal fine-scale processes that shaped the evolution of highly diverse lineages of Bromeliaceae. v Acknowledgements I want to express my most sincere gratitude to my advisor and friend, Dr. Fabián Michelangeli, who gave me his unconditional support and guidance during the development of this dissertation and throughout my doctoral studies. I am thankful to Dr. Dennis W. Stevenson, Dr. Lawerence M. Kelly and Dr. Dwight Kincaid for their commitment to make my doctoral studies successful and provide me with their knowledge and support when I needed it. I also want to thank my other committee members, Dr. Ana Carolina Carnaval, Dr. Wendy Clement, and Dr. Wayt Thomas, for helping me achieve a successful dissertation as the main product of five years of doctoral studies. The completion of my doctoral studies could not have been possible without the full financial and logistic support of the following institutions: the Administrative Department of Science, Technology and Innovation of Colombia (COLCIENCIAS); The New York Botanical Garden (Oliver Hazard Perry Fellowship); The Graduate Center of the City University of New York; and the Academic and Professional Programs for the Americas (LASPAU). Additionally, I want to thank the following agencies for their partial financial support to execute the fieldwork and training of my dissertation: the American Society of Plant Taxonomists, The Botanical Garden of Rio de Janeiro (Brazil), The Explorers Club of America, The Systematic Association and Linnaean Society of London, The Torrey Botanical Society, and the National Science Foundation. I want to thank my colleagues and friends who shared their knowledge, ideas, and advice with me, especially Nelson Salinas, Marcelo Reginato, Ricardo Kriebel, Fernando Matos, Fernanda Dos Santos Silva, Marcela Thadeo, Vinson Doyle, Jessica Allen, Donald McClelland, Jenna Dorey, and Annie Virnig. vi I thank the following colleagues who provided logistic support in the field and in the laboratory, and others who contributed with photographs, samples and specimens for the successful execution of this dissertation: André Amorim, Michael Baxter, Eldis Becquer, Julio Betancur, Keron Campbell, Lisa Campbell, Laura Clavijo, Tracy Commock, Lukas Daneu, Rafaela C. Forzza, Favio González, Bruce K. Holst, Elton Leme, Raquel Monteiro, Antoine Nicholas, Andreas Oberli, Paola Pedraza, Gregory Plunkett, Ivón Ramírez-Morillo, Lauren Raz, Wes Rouse, Eugenio Santiago, Matthew Sewell, Wayt Thomas, Tania Wendt, and Alejandro Zuluaga. Finally, I am grateful to my family in Colombia and my Timm family in the U.S. for their loving and enthusiastic support to my career as a botanist. This thesis is dedicated to my wife, Jennifer Timm, who gave me all her love and support during these five years and had the patience and genuine interest in helping me with the writing and analytic process of this dissertation. vii Table of Contents 1 Molecular Phylogenetics of the Ronnbergia Alliance (Bromeliaceae, Bromelioideae) and insights about its morphological evolution .............................................................. 1 1.1 Abstract ................................................................................................................ 1 1.2 Introduction.......................................................................................................... 3 1.3 Materials and methods ........................................................................................ 9 1.3.1 Taxon sampling ............................................................................................... 9 1.3.2 Sample collection, DNA extraction, amplification, and sequencing ............ 22 1.3.3 Sequence alignment and phylogenetic analyses ............................................ 24 1.3.4 Congruence .................................................................................................... 27 1.3.5 Phylogenetic hypothesis testing .................................................................... 28 1.3.6 Morphological character data ........................................................................ 29 1.3.7 Ancestral character state reconstructions ...................................................... 34 1.4 Results ................................................................................................................. 36 1.4.1 Phylogenetic analysis of the individual markers, cpDNA and nrDNA datasets, and congruence ....................................................................................................... 36 1.4.2 Phylogenetic analysis of the combined dataset and primary concordance tree 41 1.4.3 Hypothesis testing ......................................................................................... 44 1.4.4 Morphological analysis ................................................................................. 45 viii 1.5 Discussion ........................................................................................................... 55 1.5.1 Monophyly, phylogenetic position, and diagnosis of the Ronnbergia Alliance 55 1.5.2 Phylogenetic relationships within the Ronnbergia Alliance clade and diagnostic characters ............................................................................................................. 58 1.5.2.1 Pacific Clade ............................................................................................ 58 1.5.2.2 Atlantic Clade .........................................................................................
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