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Phylogenetic Systematics, Biogeography, and Evolutionary Louisiana State University LSU Digital Commons LSU Master's Theses Graduate School 2007 Phylogenetic systematics, biogeography, and evolutionary ecology of the true crocodiles (Eusuchia: Crocodylidae: Crocodylus) Jamie Richard Oaks Louisiana State University and Agricultural and Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_theses Recommended Citation Oaks, Jamie Richard, "Phylogenetic systematics, biogeography, and evolutionary ecology of the true crocodiles (Eusuchia: Crocodylidae: Crocodylus)" (2007). LSU Master's Theses. 674. https://digitalcommons.lsu.edu/gradschool_theses/674 This Thesis is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Master's Theses by an authorized graduate school editor of LSU Digital Commons. For more information, please contact [email protected]. PHYLOGENETIC SYSTEMATICS, BIOGEOGRAPHY, AND EVOLUTIONARY ECOLOGY OF THE TRUE CROCODILES (EUSUCHIA: CROCODYLIDAE: CROCODYLUS) A Thesis Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Master of Science in The Department of Biological Sciences by Jamie Richard Oaks B.S., University of Wisconsin Oshkosh, 2004 August 2007 ACKNOWLEDGMENTS I would like to thank the members of my advisory committee, Christopher Austin, Robb Brumfield, Mark Hafner, and Fred Sheldon for their patience and helpful advice. I especially acknowledge Robb for his generosity with computer software and resources, and help with primer design, lab protocols, computer programming, and analyses. For tissue samples, I thank the crew of the LSUMNS Genetic Resources Collection: Donna Dittmann, Robb Brumfield, and Fred Sheldon. Additionally, I am indebted to Kent Vliet of the University of Florida Department of Zoology for providing the remaining tissue samples, without which this thesis would not have been possible. I would like to extend thanks to Jesse Grismer, CJ Hayden, Ali Hamilton, Nathan Jackson, Jesse Prejean, Nanette Crochet, Susan Murray, Ron Eytan, Zac Cheviron, Matt Carling, Josh Meyer, Curt Burney, and James Maley for help with project ideas, lab protocols, analyses, and for being good friends. I am especially grateful to James Maley for his generosity with computational resources. I thank Mike Hellberg for suggesting relevant literature on marine phylogeography. I must credit Prissy Milligan, Peggy Simms, Gwen Mahon, and Tammie Jackson for helping ensure I stayed enrolled and received paychecks. I am indebted to professors Scott Snyder, Colleen McDermott, and Greg Adler for invaluable undergraduate research experience. Scott introduced me to science and academia, and also informed me of the monetary benefits of postgraduate education; if I did not know I would be paid for this stuff, I may never have enrolled in graduate school. I thank Greg for accepting me into the Tropical Rat Lab, and helping formulate my career and research interests. ii For funding, I am grateful to the Sigma Xi Scientific Research Society, LSUMNS, and BioGrads. I also thank Chris Austin for funding a portion of my lab expenses (NSF grant DEB 0445213). I am forever grateful to my parents and siblings, especially my brother Bill, for encouraging my early interest in herpetology. I must extend a heartfelt thanks to Amaya, Bos, Jinx, Chloe, and especially my wife, Liz, for helping preserve my sanity while living in Baton Rouge. Also, an extra thanks is owed to Liz for tolerating my bizarre and mostly nocturnal work schedule during the final year of my thesis research. iii TABLE OF CONTENTS ACKNOWLEDGMENTS.......................................................................................................... ii ABSTRACT.... .........................................................................................................................vii CHAPTER 1 REVIEW OF CROCODYLIAN SYSTEMATIC LITERATURE .........................1 INTRODUCTION TO CROCODYLIAN SYSTEMATICS ..................................................1 THE TAXONOMY OF CROCODYLIA...............................................................................5 REVIEW OF PHYLOGENETIC ESTIMATES OF CROCODYLUS.....................................5 MONOPHYLY OF CROCODYLUS ...................................................................................14 A RECENT RADIATION AND TRANSOCEANIC DISPERSAL EVENTS .....................15 OUT OF AFRICA?.............................................................................................................20 SURVIVING EXTINCTION ..............................................................................................22 THE NILE CROCODILE(S)...............................................................................................23 THE NEW GUINEA CROCODILE(S)...............................................................................24 THE BORNEO CROCODILE ............................................................................................24 THE EVOLUTION OF NESTING HABIT.........................................................................25 THE EVOLUTION OF BODY SIZE AND HABITAT PREFERENCE..............................25 SUMMARY AND RESEARCH OBJECTIVES BY CHAPTER.........................................26 SUMMARY ................................................................................................................26 CHAPTER 2................................................................................................................27 CHAPTER 3................................................................................................................28 CHAPTER 2 MOLECULAR PHYLOGENETICS AND BIOGEOGRAPHY OF CROCODYLIA .................................................................................................29 INTRODUCTION ..............................................................................................................29 MONOPHYLY OF CROCODYLUS ............................................................................31 ISSUES OF DIVERSITY WITHIN CROCODYLUS....................................................31 A RECENT RADIATION AND TRANSOCEANIC DISPERSAL EVENTS ..............33 OUT OF AFRICA?......................................................................................................35 A NOTE ON CROCODYLIAN TAXONOMY ...........................................................36 MIXED-MODELS IN PHYLOGENETICS .................................................................38 OBJECTIVES..............................................................................................................40 METHODS.........................................................................................................................40 SAMPLING AND DATA COLLECTION...................................................................40 SEQUENCE ANALYSIS ............................................................................................44 BAYESIAN PHYLOGENETIC ANALYSES OF THE FULL DATASET ..................48 BAYESIAN PHYLOGENETIC ANALYSES OF THE ROOT DATASET .................50 PARTITIONED MAXIMUM-LIKELIHOOD PHYLOGENETIC ANALYSES..........50 DETERMINING THE OPTIMAL PARTITIONING SCHEME FOR BAYESIAN ANALYSES ................................................................................................................52 DETERMINING THE OPTIMAL PARTITIONING SCHEME FOR MAXIMUM- LIKELIHOOD ANALYSES........................................................................................55 TESTING OF PHYLOGENETIC HYPOTHESES.......................................................57 BIOGEOGRAPHIC ANALYSES OF CROCODYLUS ................................................58 iv DATING DIVERGENCES WITHIN CROCODYLIA.................................................64 RESULTS...........................................................................................................................68 SEQUENCE ALIGNMENTS ......................................................................................68 PHYLOGENETICS.....................................................................................................72 SELECTION OF THE OPTIMAL PARTITIONING STRATEGY............................107 BIOGEOGRAPHIC ANCESTRAL CHARACTER-STATE RECONSTRUCTIONS 110 DIVERGENCE DATING..........................................................................................121 DISCUSSION...................................................................................................................127 MODEL SELECTION CRITERIA AND PARTITION CHOICE ..............................127 HARMONIC MEANS AND THE BAYES FACTOR................................................129 ML AND BAYESIAN ANCESTRAL CHARACTER-STATE RECONSTRUCTIONS ..................................................................................................................................130 PUTATIVE HYBRIDS..............................................................................................132 MONOPHYLY OF CROCODYLUS ..........................................................................132 THE NILE CROCODILES........................................................................................133 THE FRESHWATER CROCODILES OF THE NEW GUINEA AND PHILIPPINE ISLANDS..................................................................................................................133 RECENT RADIATION.............................................................................................134
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