PHYLOGENETIC AND BIOGEOGRAPHIC ANALYSES OF GREATER ANTILLEAN AND MIDDLE AMERICAN CICHLIDAE by Prosanta Chakrabarty A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Ecology and Evolutionary Biology) in The University of Michigan 2006 Doctoral Committee: Professor William L. Fink, Chair Professor Daniel C. Fisher Professor Gerald R. Smith Associate Professor Diarmaid Ó Foighil © Prosanta Chakrabarty All rights reserved 2006 I dedicate this dissertation to my wife, Annemarie Noël, and to my parents, Chitta and Anurupa Chakrabarty. ii ACKNOWLEDGEMENTS Many people have helped me complete this work. Foremost, I would like to thank my advisor, William L. Fink, for all his hard work teaching me to be a proper scientist. I walked into his office in September 2001 an ambitious student, but also naïve and hasty. In my first year particularly I sometimes bit off more than I could chew, which could have led to a few major setbacks. Instead, Bill was there to save me at times when I was lost; many times he has pointed me in the right direction when I was struggling. I hope I can always be as determined, rigorous and hardworking as he has taught me to be. My other committee members, Jerry Smith, Diarmaid Ó Foighil, and Dan Fisher have been excellent. Jerry and his wife Catherine are not only advisors but friends. It is wonderful to talk to them about everything from fossils to vegetarianism. Diarmaid has always given me straight forward advice about publishing and academia that has always been very useful. My early success as a graduate student has a lot to do with the mentoring I received from then senior graduate students John Sparks, Dan Graf, and Jennifer Ast. Without their encouragement and teaching I would not have been brave enough to try many of things that helped me be successful. Arnold Kluge has been my cladistics guru, and he has taught me a tremendous amount about the philosophy of science for which I iii will always be thankful. I would like to thank the staff at the UMMZ (Norah Daugherty, Beverley Dole, Vlad Miskevich), EEB Graduate Office (Julia Eussen, Barb Klumpp, Connie Rockman, Susan Stark, Kaye Hill) and also Sheila Dunn, Jill Beeson, Chris Psujek, LaDonna Walker and David Bay. All these people made the classes I’ve taught and various EEB events I helped organize go smoothly. They also made my graduate life easier and more enjoyable. I must thank those responsible for the Carl L. and Laura C. Hubbs endowment particularly Clark and Cathy Hubbs. I must thank the anonymous donors behind the Fish Division Graduate Student Fund, the donors behind Rackham grants, and the Hinsdale and Okkelberg EEB grants. Without these funding sources my research would not have been possible. Fish Division graduate students Heok Hee Ng and Ron Oldfield have become great friends and I hope to work with them for the rest of my career. Doug Nelson enriched my days during my time as his research assistant and throughout my graduate studies with his knowledge of fishes and his wonderful stories. I would probably not be in science without the mentoring I received from Melanie Stiassny at the American Museum of Natural History and Robert Carroll at McGill University. Their encouragement and the advice I received from Scott Schaefer, Leo Smith and Bob Schelly led me to Michigan, and I will forever be indebted to them for that. I must thank my fellow EEB graduate students, past and present, who I count among my closest friends: Wendy Grus, Elen Oneal, Cori Richards, Rick Lehtinen, Tim iv Connallon, Glenn Fox, Tanya Dewey, Josh Rest, Ashley Dowling, Matt Wund, Mara Zimmerman, Heather Lerner, Laura Howard, Adam Ehmer, Xiaoxia Wang, Lucia Luna Wong, Tamara Convertino-Waage, Ondrej Podlaha, Heather Adams, Zach Miller, Andrea Walther and Joseph Brown. Also the many faculty members and postdocs I have come to know and have learned so much from Taehwan Lee, Paul Dunlap, Deborah Goldberg, Lacey Knowles, Jo Kurdziel, Bryan Carsten, Jeff Wilson, David Mindell, Miriam Zelditch, Marc Ammerlaan, Tom Duda, Doug Futuyma, Phil Myers, Bob Payne, Jianzhi Zhang, Beverly Rathcke, Y-Qiu, Priscilla Tucker, John Vandermeer and Earl Werner. My dissertation would not have been possible without the collections I made in the Dominican Republic with Carlos Rodríguez, in Mexico with Juan Jacobo Schmitter- Soto and in Belize with Peter Esselman. Although I never met Bob Miller his work and collections of cichlids are an inspiration. His work has also been extremely useful to the work I present here. Without Bob Miller’s work, my work would not be meaningful. I have dedicated this work to my wife and my parents, but I must also thank them. Their love and encouragement have allowed my dreams to come true. I’ve never wanted to be anything else besides a zoologist and they did nothing but support me getting to that goal. v Earlier versions of some chapters were published as: Chakrabarty, P. (2004) Cichlid biogeography: comment and review. Fish and Fisheries 5(2): 97-119. Chakrabarty, P. (2006) Taxonomic status of the Hispaniolan Cichlidae. Occasional Papers of the Museum of Zoology, University of Michigan 737, 1-16. Chakrabarty, P. (2006) Systematics and Historical Biogeography of Greater Antillean Cichlidae. Molecular Phylogenetics and Evolution 39, 619-627. vi TABLE OF CONTENTS Dedication…………………………………………………………………………………ii Acknowledgments………………………………………………………………………..iii List of Figures………………………………………………………………………...…x List of Tables…………………………………………………………………………...xv Abstract………………………………………………...………………………………xvi Chapter I. CICHLID BIOGEOGRAPHY:UPDATED COMMENT AND REVIEW...1 Abstract…………………………………...………………....…….1 Introduction………………………………………………………..1 Cichlid Biogeography: Overview of the Debate…………..2 Selecting Among Biogeographic Hypotheses…………….3 Alternative Plate Tectonic Reconstructions ………………6 Proposed Cichlid Relationships…………………………...8 Phylogenies Congruent With Vicariance Scenarios……....8 Phylogenies That Falsify Vicariance Scenarios.……….....9 Molecular Clocks……………………………………..….21 Indian, Malagasy Phylogenetic Relationships……………….......23 Geological History……………………………………….23 Vicariance………………………………………………..24 The Greater Antilles……………………………………..………25 Greater Antillean Cichlids…………..…………………..25 Phylogenetic Relationships……………………………..26 The Middle East, Europe and Adjacent Areas…………………...29 Current Distribution and Sister Relationships………….29 Fossils From the Area………………………………….30 The Global Cichlid Fossil Record………………………………..32 Minimum Ages……..………………………………….32 The Acanthomorph Record…………………………….33 Discussion……………………………………………………......35 Literature Cited…………………………….………...…………..42 vii II. TAXONOMIC STATUS OF THE HISPANIOLAN CICHLIDAE……...51 Abstract……………………………….……...…………....……..51 Introduction………………………………………………………51 Materials and Methods……………………...……………………53 Institutional Abbreviations……………………………55 Systematic Accounts……………………………………………..57 Nandopsis haitiensis……...…………………………..57 Nandopsis woodringi…………………………………68 Additional Materials Examined………………………………….73 Literature Cited…..………………………………………………74 III. SYSTEMATICS AND HISTORICAL BIOGEOGRAPHY OF GREATER ANTILLEAN CICHLIDAE…………………………………………….…..76 Abstract……………………………….……...…………....……..76 Introduction………………………………………………………77 Materials and Methods…………………………………………...79 Acquisition of DNA Dataset….…………….……………79 Phylogenetic Analyses and Support Indices…..…………81 Date Estimation and Calibration…………………………83 Results……………..……………………………… ………….…86 Model Selection, Likelihood Assumption Set………..….86 Phylogenetic Analyses and Support………….…...……..86 Estimated Dates………………………………………….90 Discussion…………………...……………………….…….….....92 Literature Cited…………………………………………….....….97 IV. A MORPHOLOGICAL PHYLOGENETIC ANALYSIS OF NEOTROPICAL CICHLIDS IN THE SECTION ‘NANDOPSIS’ SENSU REGAN……………………………....………………………………….…103 Abstract……………………………….……...…………....……103 Introduction………………………………………………..……103 Materials and Methods………………………………………….107 Results……………..……………………………… …………...108 1- Internal Morphology Oral Region (A) Upper and Lower Jaw…........110 (B) Oral Teeth….........................117 Skull (C) Neurocranium……..…..….....120 viii Branchiocranium (D) Upper Pharyngeal Jaw……….126 (E) Lower Pharyngeal Toothplate.128 (F) Soft Tissue Elements…….......131 Post Cranial Elements (H) Vertebrae…………………….130 (I) Caudal Skeleton…………..….135 (J) Meristics………….…….........137 2 – External Features (A) Color and Pigmentation…….139 (B) Scales……………………….142 (C) Soft Tissue …………………146 (D) Fins…...…………………….150 (E) Sensory Pores…………….…154 (F) Morphometrics……………....157 Discussion…………………...……………………….…….…...161 Materials Examined………………………………………….…186 Literature Cited……………………………………………....…194 V. NUCLEAR, MITOCHONDRIAL, AND MORPHOLOGICAL, COMBINED PHYLOGENETIC ANALYSES OF MIDDLE AMERICAN CICHLIDAE………………………………………………………………197 Abstract……………………………….……...…………....……197 Introduction…………………………………………………..…198 Materials and Methods………………………………………….200 Results……………..……………………………… …………...201 Discussion…………………...……………………….…….…...211 Biogeography of the Greater Antilles…………………215 Taxonomy……………………………………………..219 Materials Examined…………………………………………….224 Literature Cited……...…………………………………….....…232 ix LIST OF FIGURES Figure I.1. Cichlid worldwide distribution in black, redrawn from Sparks (2001)..……..2 I.2. Congruent cladograms for three hypothetical taxa, divided into six by allopatric speciation………………………………………………...……..4 I.3. A demonstration of how an area cladogram can imply a sequence of geological fragmentation that is incongruent with the actual sequence