University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School January 2012 Systematics of Harrisia (Cactaceae) Alan R. Franck University of South Florida, [email protected] Follow this and additional works at: http://scholarcommons.usf.edu/etd Part of the American Studies Commons, Molecular Biology Commons, Plant Sciences Commons, and the Systems Biology Commons Scholar Commons Citation Franck, Alan R., "Systematics of Harrisia (Cactaceae)" (2012). Graduate Theses and Dissertations. http://scholarcommons.usf.edu/etd/4044 This Dissertation is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Systematics of Harrisia (Cactaceae) by Alan R. Franck A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Cell Biology, Microbiology, and Molecular Biology College of Arts and Sciences University of South Florida Major Professor: James R. Garey, Ph.D. Bruce J. Cochrane, Ph.D. Diane Te Strake, M.A. Richard P. Wunderlin, Ph.D. Date of Approval: 8 June 2012 Keywords: biogeography, monograph, nomenclature, phylogeny, taxonomy Copyright © 2012, Alan R. Franck DEDICATION This work is dedicated to several supportive persons: Peggy L. Brandewie; Maurice Franck; Douglas D. Springer; Annette Franck; Thomas Brandewie; Andrew L. Franck and family; Melanie L. Chamberlain; Andrew Clark; Jeff Hobensack; Christopher Monday; Franck, Brown, Springer, Combs, Brandewie, and Chamberlain families; Kris Sutter and Shawn Moorman; Matt Weigel; J. J. Oakleaf; Gene Russell Rann and Dave Catalfino; and friends. ACKNOWLEDGMENTS I would like to thank Bruce J. Cochrane and James R. Garey for welcoming me into graduate school and allowing me to freely explore my research interests, Diane Te Strake for supporting my mycological ambitions, Richard P. Wunderlin and Bruce F. Hansen for ingratiating me into the herbarium to facilitate my botanical curiosity. I would like to thank Monica Arakaki, Gérard Ardisson, Elvia Mélendez- Ackerman, Jon Trager of Huntington Botanical Gardens, Virginia Hayes of Lotusland, Mesa Garden, Joël Lodé, Devon Powell of Fairchild Tropical Garden, and Rob Nicholson of Smith College Botanic Garden for providing samples; Lynn Hackett for providing funding for The New Cactus Lexicon; Patrick A. Lewis (UWI), Keron Campbell (IJ), Lori-Ann Harris (IJ), Courtney Lyn (IJ), Teodoro Clase (JBSD), Howard Max Tritt, Mat Cottam, and Paul Watler (CAYM) for field assistance; Gérard Ardisson, Keith A. Bradley, Edyi Yanina Guerrero, Phillip Hughes, Lucas Majure, Jon Moore, Michael Nee, Zoltán Rigerski, Nigel P. Taylor, and Steve Woodmansee for photos of plants in the field; Keith A. Bradley and Steve Woodmansee for information on Florida populations; Haydn Rubelmann, Damian Menning, and Tiehang Wu for lab assistance; Bob Wigden, Kate Hebert, Mackenzie McDonald, and David Owens for carpool support; ASU for processing sequences; staff and curators of many herbaria utilized; specimen collectors and authors of literature utilized; Cactus & Succulent Society, Florida Native Plant Society, Fern Club of Odessa, Riverview Garden Club, and Tampa Garden Club for funding. i TABLE OF CONTENTS List of Tables .......................................................................................................................v List of Figures.................................................................................................................... vi Abstract............................................................................................................................ viii Preface ..................................................................................................................................1 Main Objectives.......................................................................................................3 Literature Cited........................................................................................................6 Chapter One: Low-copy nuclear primers and ycf1 primers in Cactaceae .........................10 Introduction............................................................................................................10 Note to Reader...........................................................................................10 Methods & Results.................................................................................................11 Conclusions............................................................................................................14 Literature Cited......................................................................................................14 Chapter Two: Phylogeny, biogeography, and infrageneric classification of Harrisia (Cactaceae)..................................................................................................19 Introduction............................................................................................................19 Materials & Methods.............................................................................................23 Taxon Sampling & DNA Extraction..........................................................23 Markers & Primers.....................................................................................24 PCR & Sequencing....................................................................................25 Phylogeny ..................................................................................................25 Estimates of Divergence Times .................................................................26 Results ....................................................................................................................27 Sequence Characteristics...........................................................................27 Phylogeny ..................................................................................................28 Divergence Estimates.................................................................................30 Discussion..............................................................................................................30 Monophyly of Harrisia & Generic Relationships .....................................30 Infrageneric Relationships within Harrisia ...............................................32 Biogeography of Harrisia..........................................................................33 Taxonomy of Harrisia ...............................................................................37 Conclusions................................................................................................38 Taxonomy ..............................................................................................................39 Infrageneric Key for Harrisia....................................................................40 ii Literature Cited ......................................................................................................41 Chapter Three: Relationships among the Caribbean species of Harrisia (sect. Harrisia) using AFLP and seven DNA regions .......................................60 Introduction............................................................................................................60 Materials & Methods.............................................................................................62 Morphology................................................................................................62 Datasets......................................................................................................62 DNA Extraction.........................................................................................63 PCR............................................................................................................63 Markers & Primers.....................................................................................63 Sequencing & Alignment...........................................................................64 Bayesian Inference.....................................................................................64 Parsimony Analysis...................................................................................65 Neighbor-net Networks..............................................................................65 Haplotype Network....................................................................................65 AFLP – Gel Extraction ..............................................................................66 AFLP – Digestion & Ligation....................................................................66 AFLP – Preselective PCR Amplification ..................................................67 AFLP – Selective PCR Amplification .......................................................67 AFLP Analysis...........................................................................................68 Results ....................................................................................................................68 Alignment ..................................................................................................68 Sequence Characteristics...........................................................................69 Bayesian & Parsimony Analyses...............................................................70