INFORMATION TO USERS This manuscripthas been reproduced from the microfilm master. UMI films the text directly from the original or copysubmitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from anytype of computerprinter. The quality of this l'eproductioD is dependent upon the quality ef the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adverselyaffect reproduction. In the unlikely.event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to rightin equal sectionswith small overlaps. Each original is also photographed in one exposure and is included in reduced form at the back of the book. Photographs included in the original manuscript have been reproduced xerographically in this copy. Higher quality 6" x 9" black and white photographic prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UMIdirectly to order. UMI A Bell & Howell Information Company 300 North Zeeb Road. Ann Arbor. MI48106-1346 USA 313!761-47oo 800:521-0600 ------- _._.."., ... __ .. -.~-~.~'-~-~='=====~~~ ---------,,--~-~.,---- A MOLECULAR PHYLOGENETIC ANALYSIS OF REEF-BUILDING CORALS A DISSERTATION SUBMIt lED TO THE GRADUATE DIVISION OF THE UNIVERSITY OF HAWAII IN PARTIAL FULFILLMENT OFTHE REQUIREMENTS FOR THE DEGREE OF oocroaOF PHILOSOPHY IN ZOOLOGY MAY 1995 By Sandra L. Romano Dissertation Committee: Stephen R. Palumbi, Chairperson H. Gert deCouet James E. Maragos Robert H. Richmond Rebecca L Cann ------~---_.~. _...~- ._~ .. _- ---------~-- ---~ UMI Number: 9532623 Copyright 1995 by Romano, Sandra L. All rights reserved. OM! Microform 9532623 Copyright 1995, by OM! Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. UMI 300 North Zeeb Road Ann Arbor, MI 48103 © Copyright 1995 by Sandra L. Romano All Rights Reserved iii ------------- ... to my Mom (1940-1993) and my Daddy iv ------------ _._- ACKNOWLEDGMENTS Financial support for this research has come from NSF grants to Dr. Stephen Palumbi, a NIH grant to Dr. Robert Richmond, the Dept. of Zoology, the Edmondson Research Fund, Sigma Xi, the Constance Endicott Hartt Fund through the American Associaton of University Women, and John and Veronica Romano. I gratefully acknowledge the persons who obtained coral samples for me: Dr. Robert Richmond, Dr. James Maragos (who perfected his 'coral chop' in the Solomon Islands), Dr. Bruce Carlson (who risked pens, sunglasses and clean clothes in the pruning of his pet corals) of the Waikiki Aquarium, Dr. Stephen Cairns of the National Museum of Natural History, Dr. David Krupp, Dave Gulko, and Richard Chock. I thank my advisor, friend, and mentor, Steve Palumbi, for giving freely of his time and energy through all phases of this research. He has provided me with endless enthusiasm, inspiration, and support. I thank my committee members who have provided advice, support and encouragment when I've needed it most in seeing this project through. Charlie Veron provided valuable insight into and helpful discussion about coral evolution at a crucial time during analyses. I acknowledge Cindy Hunter for her technical assistance. Robert Hixson and Chris Simon provided advice on secondary structure. George Roderick provided assistance with figures. The members of the Palumbi Lab have been instrumental in this project. They have all provided. camaraderie and technical expertise in the lab as well as helpful comments and discussion as I was trying to understand the twists and turns of my dataset. I thank them for their assistance (especially in overseeing my mini-gels), support, and encouragement. Bailey Kessing and v Andrew Martin were especially valuable, and most of the time patient, as I " made my first forays into the laboratory and the world of molecular biology. Ed Metz and Owen McMillan survived four years in the lab with me and made the ex-perience lively, educational, and fun. I thank Paul Armstrong, Tom Duda, and Frank Cipriano for helping to keep life in the lab in perspective over the last year. The administrative support of Lori Yamamura, Sally Oshiro and Audrey Shintani of the Zoology Dept., as well as of Frances Okimoto and Geri Mintomi at Kewalo Marine Lab is gratefully acknowledged. I'd like to give special thanks to the following people for helping me to maintain some sense of reality as I have been writing and to 'finish up' in as pain-free and pleasant a way as possible: Steve Palumbi, the participants in GWIZ, Cindy Hunter, Kim. del Carmen, Theresa Cabrera, Krista Ingram, Flo Thomas, Rosie Gillespie, Leanne Fernandes, Dr. Erik Meesters, Dave Hopper, Jean-Sylvain Bussac, George Roderick, Sweet William Roderick, and the members of the Delaware Expedition to Hawaii. Leanne Fernandes and Dr. Erik Meesters, while trying to be as unobtrusive as possible in our common living space so as not to disturb me, contributed enormously to maintaining my sanity and peace of mind on a daily basis in the final stages of writing this dissertation. Finally, I thank my family for their support in every way throughout my years as a graduate student. vi --------_._--- --- ABSTRAcr Review of the evolutionary history of scleractinian corals demonstrates the great deal of knowledge gained from their 240 million year fossil record, and from studies of all aspects of their biology and ecology. By contrast, forces driving the evolution of corals are not well understood due to the great variability that exists in characters used in classification and to difficulties in working with fossil specimens. Traditional hypotheses about relationships among families and suborders are tenuous and somewhat contradictory. Molecular techniques were used for the first time to evaluate relationships among corals. A segment of the mitochondrial16S ribosomal gene from 34 species in 14 families was amplified via the Polymerase Chain Reaction and sequenced. These sequences are homologous to each other and to other metazoan 165 ribosomal sequences in terms of nucleotide composition, patterns of transition and transversion substitutions, spatial patterns of substitutions, rates of divergence, and secondary structure. Parsimony analysis of the aligned sequences results in a phylogram whose major groups are supported at bootstrap values of 80% or higher. Comparisons of molecular and morphological hypotheses demonstrate that 1) this molecular topology is robust by itself, 2) it is robust in relation to traditional morphological topologies, and 3) available morphological characters are not a reliable tool for inferring family and suborder relationships. Although this molecular hypothesis supports traditional hypotheses for relationships within genera and families, clades on the molecular phylogram do not correspond to morphologically based family and suborder relationships. This molecular hypothesis suggests vii two major lineages of Scleractinia diverged from a common ancestor at least 300 mya. One of these lineages, the robust corals, tends to be heavily calcified and less architecturally complex forming predominantly massive or plate-like colonies which grow by intratentacular budding. The second lineage, the complex corals, is characterized by less heavily calcified skeletons that are architecturally complex, forming predominantly branching colonies which grow by extratentacular budding. A switch between hermaphroditism and gonochorism appears to have occurred at least 3 times. Some of the recent changes in scleractinian taxonomy are supported by this molecular hypothesis which also suggests new relationships among families to be considered. viii -------- -_. _._- TABLE OF CONTENTS ACKl\TOWLEDGMENTS v ABSTRACT ., vii LIST OF TABLES ..........•...•.............•...••..••......•...•..••..•............•.....•...............................xiii LIST OFFIGURES xiv IN'TRODUCTION 1 CHAPTER 1. The Evolutionary History of Scleractinian Corals: A Review 0 •••••••••••••••••••••••••••••••••••••••••••••••••••••4 Introduction 4 Evolution of Scleractinians through geological time 5 The Triassic 7 The Jurassic 10 The Cretaceous : 11 The Paleogene 14 World climate and geography during the Neogene 15 The Miocene 16 The Pliocene 17 Evolution of biogegograpic provinces 18 Distribution of azooxanthe11ate corals 19 Distribution of reef-building corals 21 The Indo-Pacific. 22 Distribution of reef-building corals in the Atlantic 25 Theories of coral distribution 28 Evolution and taxonomy of scleractinian groups 31 ix Scleractinian evolution as described by Wells (1956) 33 Scleractinian evolution as described by Veron (1995) 38 Scleractinian classification according to Alloiteau (1952) 42 Scleractinian classification according to Chevalier and Beauvais (1987) 43 Scleractinian evolution based entirely on microstructural analysis 45 Summary of classifications 46 Non-morphological methods of scleractinian classification 47 Quantitative analyses of relationships among the Scleractinia 48 Biochemical studies of scleractinian evolution 49 Summary 51 CHAPTER 2. Molecular Evolution of a Portion of the Mitochondrial 16S Ribosomal Gene