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With Focus on the Genus Handleyomys and Related Taxa Brigham Young University BYU ScholarsArchive Theses and Dissertations 2015-04-01 Evolution and Biogeography of Mesoamerican Small Mammals: With Focus on the Genus Handleyomys and Related Taxa Ana Villalba Almendra Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Biology Commons BYU ScholarsArchive Citation Villalba Almendra, Ana, "Evolution and Biogeography of Mesoamerican Small Mammals: With Focus on the Genus Handleyomys and Related Taxa" (2015). Theses and Dissertations. 5812. https://scholarsarchive.byu.edu/etd/5812 This Dissertation is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Evolution and Biogeography of Mesoamerican Small Mammals: Focus on the Genus Handleyomys and Related Taxa Ana Laura Villalba Almendra 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 Jerald B. Johnson Leigh A. Johnson Eric A. Rickart Department of Biology Brigham Young University March 2015 Copyright © 2015 Ana Laura Villalba Almendra All Rights Reserved ABSTRACT Evolution and Biogeography of Mesoamerican Small Mammals: Focus on the Genus Handleyomys and Related Taxa Ana Laura Villalba Almendra Department of Biology, BYU Doctor of Philosophy Mesoamerica is considered a biodiversity hot spot with levels of endemism and species diversity likely underestimated. For mammals, the patterns of diversification of Mesoamerican taxa still are controversial. Reasons for this include the region’s complex geologic history, and the relatively recent timing of such geological events. Previous studies, however, support the view that substantial migration between North (NA) and South America (SA) occurred prior or/and during the Great American Biotic Interchange (GABI) ~3.5 Ma. This was followed by repeated periods of isolation during Pleistocene climatic oscillations, which produced most of the diversification in the region. From a North American origin, the subfamily Sigmodontinae migrated to SA, where most of its present day diversity exists. The taxonomic history of this subfamily, and of Oryzomynii, its largest tribe, has been exceptionally complex. Recently, extensive studies have helped to clarify genealogical relationships among major clades, but have left the evolutionary histories of several groups unresolved. Such is the case for the genus Handleyomys that includes nine species; seven of which are endemic to Mesoamerica; and of its phylogenetic position among closely related genera Euryoryzomys, Hylaeamys, Oecomys, Nephelomys and Transandinomys. The results supported the monophyly of Handleyomys, and four clades with inter-generic levels of divergence within the genus, three of these clades restricted to Mesoamerica (the alfaroi, chapmani and melanotis species groups). Furthermore, the estimated time for the split of the Mesoamerican Handleyomys is on average, 2.0 Myr older than the proposed migrations to NA during the GABI. In addition, the position of Handleyomys as the sister clade to Euryoryzomys, Hylaeamys, Oecomys, Nephelomys and Transandinomys was well supported, as it was a biogeographic hypotheses that depicted a polyphyletic origin for these genera and Handleyomys 5.5-6.0 Ma. The integrative approach implemented in this dissertation allowed the development of more biologically realistic hypothesis than has previously been conducted in Mesoamerica, where half of the endemic mammals are listed under the IUCN Red list; and where mammals with small ranges, which are the most vulnerable to extinction, are found largely outside reserves. The continued decline of the ecosystems health in this region calls for a more precise account of its biodiversity for its proper conservation; and for rigorous biogeographic studies for its management, since the region also serves as a biological corridor for intercontinental connectivity. Keywords: Mesoamerica, rodents, biogeography, molecular phylogenetics, ecological niche models, Pliocene-Pleistocene ACKNOWLEDGEMENTS I want to acknowledge my advisor, Duke S. Rogers, for his teachings, continuous support and thorough guidance. I am fortunate to have had this opportunity to learn from him. I am very grateful for the expert advice and encouragement that I have received from my advisory committee members, Byron J. Adams, Jerald B. Johnson, Leigh A. Johnson and Eric Rickart; and for the remarkable contribution of major collaborators; Mark D. Engstrom and Francisco X. González-Cózatl. I acknowledge Bruce L. Patterson (The Field Museum), Consuelo Lorenzo-Monterrubio (El Colegio de la Frontera Sur), Elizabeth Arellano-Arenas (Centro de Investigación en Biodiversidad y Conservación, UAEM), Livia León-Paniagua (Museo de Zoología, UNAM), Mark. D. Engstrom (Royal Ontario Museum), Robb T. Brumfield (Louisiana State University Museum of Natural Science), Robert J. Baker (Texas Tech University) and Suzanne Peurach (National Museum of Natural History) for providing indispensable tissue samples. I am indebt to the Mexican National Council of Science and Technology, the principal sponsor for pursuing a Ph.D. abroad. And I want to acknowledge the BYU’s College of Life Sciences, Department of Biology and Monte L. Bean Museum, for additional funding and for research and teaching assistantships. Also, the Dissertation Improvement Grant from the National Science Foundation, the American Society of Mammalogists Grants-in-Aid of Research and the Theodore Roosevelt grant from the American Museum of Natural History, were valuable financial sources for my Ph.D. research. I thank the BYU’s College of Life Sciences, Department of Biology and Monte L. Bean Museum administrative team, for the continuous assistance and sincere care. I also thank my BYU colleagues, for their helpful advice and genuine manners, which made of my time at BYU a pleasant growing experience. Finally, I would like to extend my appreciation to Parker Frech and family, for their generosity, constant encouragement, and for welcoming me into their family. And to express my deepest gratitude to all of my kin and to my friends, for their absolute love and care, which provides me with an unparalleled emotional comfort that certainly eased the hardest times. TABLE OF CONTENTS TITLE PAGE ................................................................................................................................... i ABSTRACT .................................................................................................................................... ii ACKNOWLEDGEMENTS ........................................................................................................... iii TABLE OF CONTENTS ................................................................................................................ v LIST OF TABLES ........................................................................................................................ vii LIST OF FIGURES ..................................................................................................................... viii INTRODUCTION .......................................................................................................................... 1 Literature Cited ........................................................................................................................... 5 CHAPTER 1: Biogeography of Central American Mammals: Patterns And Processes ............ 10 Abstract ..................................................................................................................................... 11 Geologic Processes and the Great American Biotic Interchange ............................................. 13 Mexico and Central America .................................................................................................... 18 Northwestern South America and Central America ................................................................. 20 Amazon and Central America ................................................................................................... 22 Divergence within Central America ......................................................................................... 24 Summary and Prospectus .......................................................................................................... 28 Acknowledgements ................................................................................................................... 32 Literature Cited ......................................................................................................................... 32 CHAPTER 2: Molecular Phylogenetics of the Handleyomys chapmani complex in Mesoamerica ................................................................................................................................ 53 Abstract ..................................................................................................................................... 54 Introduction ............................................................................................................................... 55 Materials and Methods .............................................................................................................. 57 Results
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