Brigham Young University BYU ScholarsArchive All Theses and Dissertations 2013-07-05 Biogeography and Evolution of Neotropical Small Mammals, with Emphasis on Hystricognath Spiny Rats of the Genus Proechimys (Family Echimyidae) Rafael do Nascimento Leite Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Biology Commons BYU ScholarsArchive Citation Leite, Rafael do Nascimento, "Biogeography and Evolution of Neotropical Small Mammals, with Emphasis on Hystricognath Spiny Rats of the Genus Proechimys (Family Echimyidae)" (2013). All Theses and Dissertations. 3992. https://scholarsarchive.byu.edu/etd/3992 This Dissertation is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in All Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Biogeography and Evolution of Neotropical Small Mammals, with Emphasis on Hystricognath Spiny Rats of the Genus Proechimys (Family Echimyidae) Rafael do Nascimento Leite A dissertation submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Duke S. Rogers, Chair Byron J. Adams Bryan C. Carstens Leigh A. Johnson Jack W. Sites, Jr. Department of Biology Brigham Young University July 2013 Copyright © 2013 Rafael do Nascimento Leite All Rights Reserved ABSTRACT Biogeography and Evolution of Neotropical Small Mammals, with Emphasis on Hystricognath Spiny Rats of the Genus Proechimys (Family Echimyidae) Rafael do Nascimento Leite Department of Biology, BYU Doctor of Philosophy The Neotropical region is the most biologically diverse region on the planet. The region encompasses a variety of ecosystems and has long been the target of researchers interested in patterns of species diversity and distribution. More recently, molecular data have been incorporated into methods for reconstructing the historical relationships among geographical areas and their biotas. Molecular phylogenetics has provided insights into diversification patterns and the influence of Late Cenozoic events on the evolutionary history of the region. Nevertheless, considering the vast extent and complexity of the region, more studies are needed to fully appreciate the patterns of biogeography and the mechanisms that generate and maintain its biodiversity. Therefore, in Chapter 1 I employed molecular methods to reconstruct the phylogenetic relationships of the subfamily Sigmodontinae, which is the most diverse and widespread radiation of Neotropical rodents. I was able to evaluate controversial hypotheses about the paleogeographic scenarios implicated to explain the biogeography of sigmodontines. Advances in sequencing technology and analytical approaches have revolutionized the role of historical biogeography in elucidating the spatial and temporal context of diversification, and the integrative field of phylogeography was fundamental to the development of biogeography at the intraspecific level. However, the potential of phylogeography to unravel diverse historical scenarios in a tractable statistical framework has been largely unexplored for the Neotropics as a whole. In order to integrate more robust hypothesis testing to elucidate the evolutionary history of Amazonia’s biota, I devoted Chapter 2 to a review of Amazonian phylogeography that I anticipate will improve the basis for interpreting the patterns and processes of diversification in Amazonia. Chapter 3 is a thorough species account of spiny rats of the genus Proechimys, which is poorly known taxonomically despite its diversity and widespread distribution in the Neotropics. This taxonomic revision will benefit researchers interested in using such information with coalescent-based methods of species delimitation aimed at an integrative and stable taxonomy. Lastly, Chapter 4 deals with the phylogeography of P. roberti. This species occurs in southeastern Amazonia and the Cerrado of central Brazil. I employed a dense taxon sampling and used coalescent-based methods to demonstrate that rivers and topography have a causal link to the geographic structure of P. roberti populations. In my dissertation, I used a combination of molecular genetics tools to provide a better understanding of the biogeography and evolution of some of the most diverse groups of Neotropical mammals. My dissertation interacts in many levels with my future research interests. These present and future efforts hold promise for unraveling the evolutionary history of the Neotropical region and its biota, and will assist in conservation decisions aiming at preserving its unparalleled biodiversity. Keywords: diversification, coalescent, hypothesis testing, rodents, statistical phylogeography, Proechimys, taxonomy, South America, Amazon Basin ACKNOWLEDGMENTS I want to express my gratitude to several people and institutions that assisted me throughout the course of my doctoral studies. I would like to thank all members of my graduate committee for their valuable scientific feedback and academic follow-up. In particular, I want to thank my advisor, Dr. Duke Rogers, for always being so supportive over the years, for listening to my worries and for being willing to share his ideas and good advice at all times, and for his lifetime friendship. I am indebted to the Brazilian governmental agency Coordination for the Improvement of Higher Education Personnel (CAPES) for making it possible to pursue my doctorate abroad and for sponsoring me with a three-year fellowship (BEX 1861/07-7). I am thankful to the Institute of International Education (IIE) for administering my exchange visitor status and grant in the United States. I want to express my appreciation to my program officers at CAPES and IIE and the staff of the Department of Biology and International Services at BYU for their valued assistance during my Ph.D. studies, in particular to Peter Raucci and Sarah Willardson for their dedication to assist me. I also want to thank the professors who have shared their knowledge in graduate classes. I would like to acknowledge the following funding sources that have provided additional support to my Ph.D. research: a Doctoral Dissertation Improvement Grant (DEB 1115208) from the National Science Foundation; BYU’s Graduate Student Society for research and presentation awards; Julia Greenwell scholarships from BYU’s College of Life Sciences; BYU’s Department of Biology and Monte L. Bean of Life Science Museum for research assistantships; an American Society of Mammalogists Grants-in-Aid of Research; and Idea Wild. I am indebted to several museums and scientific collections, and their respective curators and staff, that granted me invaluable tissue loans: [Brazil] Instituto Nacional de Pesquisas da Amazônia (INPA); Museu de Zoologia da Universidade de São Paulo (MZUSP); Museu Nacional da Universidade Federal do Rio de Janeiro (MN); Museu Paraense Emílio Goeldi (MPEG); Universidade de Brasília (UnB); Universidade de São Paulo (USP); Universidade Estadual do Maranhão (UEMA); Universidade Federal do Espírito Santo (UFES); Universidade Federal do Mato Grosso (UFMT); Universidade Federal do Pará (UFPA); [Canada] Royal Ontario Museum (ROM); [United States] American Museum of Natural History (AMNH); Carnegie Museum of Natural History (CM); Kansas University (KU); Museum of Southwestern Biology (MSB); Museum of Vertebrate Zoology (MVZ); National Museum of Natural History (USNM); Texas Tech University (TTU); and [Venezuela] Museo de Estación Biológica de Rancho Grande (EBRG). I am thankful to numerous people that helped me in the acquisition of tissue samples: Ana Carolina Loss, Ana Carolina Pavan, Ana Paula Carmignotto, Carla Bantel, Cibele Bonvicino, Cleuton Miranda, Ísis Arantes, Juliana Ribeiro, Manoela Borges, Marcela Lima, Maria José Silva, Mariana Viana, Ligia Tchaicka, Pedro De Podestà, Silvia Pavan, Roberta Figueiredo, Roberto Vilela, and Yuri Leite. I also thank the Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio/Sisbio 16375) for issuing of collecting permits that made possible the inclusion of complementary samples obtained during fieldwork. I am grateful to Igor Santos, Juarez, Leonardo Gomes, Luciana Alves and Luiz Felipe Silvestre for their assistance prior to or during field trips, and to the landholders and employees of CIKEL, Juruá Florestal, Fazenda Cabeceira, Fazenda São José da Fortaleza and Reserva Ecológica do IBGE (RECOR) for giving me access and logistic support to do fieldwork at these sites. I thank Dr. ! Guarino Colli for providing the logistics at the University of Brasília during the final stages of my dissertation back in Brazil. I also thank the co-authors of my papers/manuscripts (Duke Rogers, Fernanda Werneck, Francisca Almeida, Jim Patton, Marcelo Weksler, Maria Nazareth da Silva and Sergios Kolokotronis) for their important contributions. I owe a special thanks to Jim Patton for his generosity and for sharing his knowledge of Proechimys with me, and also to Fernanda Werneck and Arley Camargo for invaluable academic discussions and assistance in my research. I appreciate the kindness and friendship of special people I have met in the US: Ana Laura Almendra, Arley Camargo and family, Becky Williams, Duke Rogers and family, Leandro de Souza and family, and Rodrigo Ferreira and family. I am also thankful to my family in Brazil for their constant support and for believing in my career aspirations.