The Pennsylvania State University The Graduate School Eberly College of Science A MOLECULAR PHYLOGENETIC PERSPECTIVE ON THE EVOLUTIONARY HISTORY OF TERRARANAN FROGS, A VERTEBRATE MEGA-RADIATION A Dissertation in Biology by Matthew Paul Heinicke © 2009 Matthew Paul Heinicke Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy December 2009 The dissertation of Matthew P. Heinicke was reviewed and approved* by the following: S. Blair Hedges Professor of Biology Dissertation Advisor Edward C. Holmes Professor of Biology Chair of Committee Kateryna D. Makova Associate Professor of Biology David M. Geiser Professor of Plant Pathology Douglas R. Cavener Professor of Biology Head of the Department of Biology *Signatures are on file in the Graduate School ii ABSTRACT Terraranans are one of the largest vertebrate radiations, with over 900 species (13% of all amphibians) distributed in the West Indies, Central America, and South America. Unlike most frogs, they lay eggs on land which hatch into froglets rather than tadpoles (direct development). In order to better understand the evolutionary pattern of this group, I have gathered DNA sequence data for over 300 terraranan species. Several main results have emerged. First, most terraranan species fall into four main groups (genera), each predominating in a different geographic region (Central America, the West Indies, northern and western South America, and southeast Brazil). Molecular clock analyses show that these genera are relatively young (between 20 and 50 million years old). Because land connections among Central America, the West Indies, and South America were broken by the beginning of the Cenozoic, these times of divergence suggest parallel origins by overwater dispersal for the West Indian and Central American clades. By using broad taxonomic sampling, and performing analyses with multiple nuclear and mitochondrial genes, a well-supported phylogeny was produced which is the basis of a new classification of terraranan frogs. An enigmatic undescribed frog was placed in a 17-gene molecular phylogeny. This phylogeny demonstrated that it represents the most basal species in Terrarana. Furthermore, this same analysis identified the marsupial frogs as the closest relatives of Terraranans. Together they form an enlarged clade of direct-developing species, suggesting this life-history trait evolved earlier than previously thought. Phylogenies and divergence time analyses of several non-terraranan vertebrate clades (West Indian Leptodactylus, lungfishes, and cartilaginous fishes) are also presented, which provide contrasts in diversification and biogeographic history to the terraranans. iii TABLE OF CONTENTS LIST OF FIGURES .......................................................................................................... vii LIST OF TABLES............................................................................................................. ix ACKNOWLEDGMENTS ...................................................................................................x Chapter 1. General Introduction ..........................................................................................1 1.1 Overview............................................................................................................1 1.2 Molecular clocks and amphibian evolution .......................................................5 1.3 Dispersal, vicariance, and molecular clocks......................................................8 1.4 Systematics in the molecular era........................................................................8 1.5 Mitochondrial data in molecular phylogenetics...............................................10 Chapter 2. Major Caribbean and Central American frog faunas originated by ancient oceanic dispersal ....................................................................................................12 2.1 Abstract............................................................................................................12 2.2 Introduction......................................................................................................12 2.3 Materials and Methods.....................................................................................14 2.4 Results..............................................................................................................20 2.5 Discussion........................................................................................................24 2.6 Acknowledgments............................................................................................29 Chapter 3. New World direct-developing frogs (Anura: Terrarana): molecular phylogeny, classification, biogeography, and conservation .................37 3.1 Abstract............................................................................................................37 3.2 Introduction......................................................................................................38 3.3 Materials and Methods.....................................................................................42 iv 3.4 Results..............................................................................................................48 3.5 Discussion........................................................................................................58 3.6 Acknowledgments............................................................................................68 Chapter 4. A new frog family (Anura: Terrarana) and an expanded direct-developing clade revealed by molecular phylogeny.................................................................78 4.1 Abstract............................................................................................................78 4.2 Introduction......................................................................................................78 4.3 Materials and methods .....................................................................................79 4.4 Results..............................................................................................................85 4.5 Discussion........................................................................................................97 4.6 Acknowledgments............................................................................................98 Chapter 5. Molecular phylogeny and biogeography of West Indian frogs of the genus Leptodactylus (Anura: Leptodactylidae)..............................................................107 5.1 Abstract..........................................................................................................107 5.2 Introduction....................................................................................................108 5.3 Materials and methods ...................................................................................110 5.4 Results and discussion ...................................................................................112 5.5 Acknowledgments..........................................................................................117 5.6 Species, localities, and sequence accession numbers ....................................117 Chapter 6. Lungfish evolutionary relationships and divergence times............................119 6.1 Abstract..........................................................................................................119 6.2 Introduction....................................................................................................119 6.3 Methods..........................................................................................................121 6.4 Results and discussion ...................................................................................122 v 6.5 Acknowledgments..........................................................................................123 Chapter 7. Cartilaginous fish evolutionary relationships and divergence times..............124 7.1 Abstract..........................................................................................................124 7.2 Introduction....................................................................................................124 7.3 Methods..........................................................................................................128 7.4 Results and discussion ...................................................................................129 7.5 Acknowledgments..........................................................................................133 Chapter 8. Concluding remarks .......................................................................................135 References........................................................................................................................138 Appendix. Systematic accounts .......................................................................................171 vi LIST OF FIGURES 2-1 Composite distribution of eleutherodactyline frogs and Brachycephalus...................14 2-2 Major clades of eleutherodactyline frogs. ML phylogeny from two genes and 280 species..........................................................................................................................22 2-3 A time tree of eleutherodactyline frogs, based on ML phylogeny from five genes and 65 species.....................................................................................................................23