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Phylogenetic Systematics of South American Lizards Of PHYLOGENETIC SYSTEMATICS OF SOUTH AMERICAN LIZARDS OF THE GENUS STENOCERCUS (SQUAMATA: IGUANIA) By Omar Torres-Carvajal M. A., University of Kansas, 2001 Licenciado, Pontificia Universidad Católica del Ecuador, 1998 Submitted to the Department of Ecology and Evolutionary Biology and the Faculty of the Graduate School of The University of Kansas in partial fulfillment of the requirements for the degree of Doctor of Philosophy chairperson Committee members Date defended: 11 November 2005 The Dissertation Committee for Omar Torres-Carvajal certifies that this is the approved version of the following dissertation: PHYLOGENETIC SYSTEMATICS OF SOUTH AMERICAN LIZARDS OF THE GENUS STENOCERCUS (SQUAMATA: IGUANIA) chairperson Committee members Date approved: __________________ ii ABSTRACT The South American iguanian lizard genus Stenocercus includes 58 species occurring mostly in the Andes and adjacent lowland areas from northern Venezuela and Colombia to central Argentina at elevations of 0–4000 m. Limited taxon or character sampling have characterized all previous phylogenetic analyses of Stenocercus, which has repeatedly been proposed as sister taxon to the Tropidurus Group. In this study, I use molecular and morphological data to (1) infer the phylogenetic relationships among most species of Stenocercus, (2) perform explicit statistical tests of previous phylogenetic hypotheses, and (3) infer the ancestral distribution of Stenocercus. Using parsimony and Bayesian analyses, monophyly of this genus is strongly supported with a dataset of 32 species of Stenocercus, 12 outgroup taxa, and 1641 bp of mtDNA. Molecular data also are used to analyze evolutionary relationships within Stenocercus with a Bayesian approach based on mixture models, which accommodate variability in the parameters of the rate matrix across sites. Morphological data were obtained from 55 species of Stenocercus and one outgroup taxon; polymorphic and continuous morphological characters were coded using step matrices with frequency parsimony and gap-weighting methods, respectively. Parsimony and Bayesian analyses were performed with a combined dataset of 55 ingroup taxa, one outgroup taxon, and 1764 characters. All analyses support a basal split of Stenocercus into two clades. When all 55 ingroup taxa are included, these clades are composed of 26 (clade A) and 29 (clade B) species. In iii general, species in clade A have small scales and granular scales on the posterior surface of thighs, whereas species in clade B have large scales and non-granular, imbricate scales on posterior surface of thighs. Clade A is restricted to the central Andes except for a few species occurring in the northern Andes in Ecuador and Colombia. Clade B is more widespread and includes species occurring in the northern, central, and southern Andes, as well as species in the Amazon Basin and lowlands in southeastern South America. A dispersal-vicariance analysis suggests that the most recent common ancestor of species of Stenocercus occurred in the central Andes. Four new species of Stenocercus are described from the northern Andes of Colombia, southern Andes of Ecuador, northern and central Andes of Peru, and Cerrado forest in Brazil. In addition, S. torquatus is resurrected and S. variabilis is redescribed. iv ACKNOWLEDGMENTS I want to express my deepest thanks to Linda Trueb and Bill Duellman for opening the doors of the KU herpetology division in 1999, and for all the encouragement and guidance during the last six years. I also thank Rafe Brown, Kevin de Queiroz, Stephen Hasiotis, and Ed Wiley, all members of my dissertation committee, for their criticism and support during my dissertation research. Special thanks to Kevin de Queiroz for being such a great advisor and friend during my one-year stay at the Smithsonian Institution. With his expertise in phylogenetic systematics and lizard evolution, Kevin has been and will remain a valuable source of information for my research. Some of the phylogenetic and statistical analyses included in my dissertation were improved through fruitful discussions with Rafe Brown, Kevin de Queiroz, Jim Schulte II, and Ed Wiley. For the loan of museum specimens I thank A. Almendáriz (EPN), F. Andreone (MZUT), C. Austin (LSUMZ), T. C. S. Avila-Pires (MPEG), J. Campbell (UTA), S. Carreira (ZVC-R), R. Casallas Lasso (MLS), J. E. Castillo and J. M. Rengijo (IND-R), F. Castro (UV), L. A. Coloma (QCAZ), J. Córdova (MHNSM), K. de Queiroz (USNM), L. Ford and D. Frost (AMNH), U. Fritz and E. Lehr (MTD), N. Gilmore (ANSP), R. Günther (ZMB), J. Hanken and J. Rosado (MCZ), G. Köhler (SMF), S. Kretzschmar (FML), J. D. Lynch (ICN), C. McCarthy (BMNH), J. A. McGuire (MVZ), M. Morales (UDAR), R. Nussbaum (UMMZ), M. P. Ramírez v (UIS), T. Reeder and R. Etheridge (SDSU), J.-M. Touzet (FHGO), L. Trueb (KU), and H. Voris and M. Kearney (FMNH). I am indebted to many individuals for their assistance in completing my dissertation research. I thank Richard Etheridge, one of the most distinguished lizard systematists of all times, for his constant motivation and encouragement, and for sharing with me his broad knowledge by providing great, useful comments, as well as personal notes and photographs that have improved the quality of my research. I was introduced to the marvelous world of "molecular work" by Jim Schulte II; all I know about DNA lab work is thanks to him and my dissertation would probably not include a molecular component if it was not for Jim's expertise, patience, and constant motivation. Mark Pagel is one of the proponents of mixture models in phylogenetic analysis; I thank him for all his suggestions and comments regarding this complex subject. Yoshinori Nakazawa was kind enough to let me use his computer to run some of my time-consuming analyses. For assistance in the field I thank Martha Carvajal-Aguirre, Amaranta Carvajal-Campos, Lena Echelle, Sofía Carvajal-Endara, Eugenia Paredes, Jenny Pramuk, the guards of Puyango Protected Forest, and residents from María Teresa (Departamento Pasco, Peru) and Purunuma (Provincia Loja, Ecuador). The following people from the KU herpetology division played different roles in helping me complete my degree: Hugo Alamillo, Barb Banbury, Raul Díaz, William E. Duellman, Eli Greenbaum, Juan Guayasamin, Edgar Lehr, David McLeod, Jenny Pramuk, Analía Púgener, Chris Sheil, and John Simmons. Finally, I am grateful to Fernando Ayala for help with egg incubation, Elisa vi Bonaccorso for assistance with GIS software, John Cadle for providing valuable information and tissue samples, Andrew Campbell and María Castañeda for taking x- ray radiographs, Juan Carlos Chaparro and Pablo Venegas for useful information on Stenocercus from Peru, Steve Gotte for assistance with clearing-and-double-staining, Blaise Mulhauser for examination of type material of S. crassicaudatus at MHNN, Jose Rosado for data on various MCZ specimens, and the following individuals for providing color photographs: L. A. Coloma (LAC), W. E. Duellman (WED), K. I. Miyata (KIM), R. W. McDiarmid (RWM), and P. Venegas (PAV). Specimens of S. puyango were collected under permit 006-IC-FAU-DBAP/MA issued to the QCAZ by the Ministerio de Ambiente of Ecuador; collecting and export permits for specimens of S. torquatus were issued by the Ministerio de Agricultura (INRENA), Lima, Peru. This research was partially funded by a predoctoral fellowship from the Smithsonian Institution, AMNH and FMNH Collection Study Grants, MCZ Ernst Mayr Travel Grant, and KU Natural History Museum Panorama Society Small Grants. I am extremely grateful for the love, friendship, and endless moral support of Stephanie, whose patience during the last few months of my dissertation are admirable, and my parents and brother, who have managed to remain next to me despite the long distance that separates Kansas from Ecuador. vii TABLE OF CONTENTS Abstract..................................................................................................................... iii Acknowledgments.......................................................................................................v Table of contents..................................................................................................... viii List of tables.............................................................................................................. xi List of figures........................................................................................................... xii List of appendices .................................................................................................. xvii Introduction.................................................................................................................1 Chapter I. Phylogenetic relationships among species of Stenocercus as inferred from mtDNA sequence data.....................................................................................4 Materials and methods ..........................................................................................4 Taxon sampling..................................................................................................4 Laboratory protocols..........................................................................................5 Sequence alignment and phylogenetic analysis.................................................6 Hypothesis testing............................................................................................10 Results.................................................................................................................11
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