University of New Mexico UNM Digital Repository Biology ETDs Electronic Theses and Dissertations 7-1-2012 Historical and topographic drivers of tropical insular diversity: comparative phylogeography of Eleutherodactylus antillensis and E. portoricensis, two ecologically distinctive frogs of the Puerto Rican Bank Brittany Barker Follow this and additional works at: https://digitalrepository.unm.edu/biol_etds Recommended Citation Barker, Brittany. "Historical and topographic drivers of tropical insular diversity: comparative phylogeography of Eleutherodactylus antillensis and E. portoricensis, two ecologically distinctive frogs of the Puerto Rican Bank." (2012). https://digitalrepository.unm.edu/biol_etds/3 This Dissertation is brought to you for free and open access by the Electronic Theses and Dissertations at UNM Digital Repository. It has been accepted for inclusion in Biology ETDs by an authorized administrator of UNM Digital Repository. For more information, please contact [email protected]. Brittany S. Barker Candidate Biology Department This dissertation is approved, and it is acceptable in quality and form for publication: Approved by the Dissertation Committee: Robert B. Waide , Chairperson Joseph A. Cook Thomas F. Turner Javier A. Rodríguez-Robles i HISTORICAL AND TOPOGRAPHIC DRIVERS OF TROPICAL INSULAR DIVERSITY: COMPARATIVE PHYLOGEOGRAPHY OF ELEUTHERODACTYLUS ANTILLENSIS AND E. PORTORICENSIS, TWO ECOLOGICALLY DISTINCTIVE FROGS OF THE PUERTO RICAN BANK by BRITTANY SUZANNE BARKER B.S., Zoology, Oregon State University, 2003 DISSERTATION Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Biology The University of New Mexico Albuquerque, New Mexico July, 2012 ii ACKNOWLEDGEMENTS First and foremost, I would like to thank Jed Stoken for his unconditional love and support throughout the entire process of completing this dissertation. I am extremely grateful to my co-advisors, Bob Waide and Joe Cook, for their guidance and financial support through research assistantships, field and laboratory support, to Tom Turner for letting me occasionally use his lab space, and to Javier Rodríguez-Robles for his thoughtful and thorough comments on my manuscripts. I would like to extend my thanks to the many people who helped me conduct field work in Puerto Rico and the Virgin Islands: Fernando Bird-Picó, Tomas Figueroa, Bill Gould, Wilfredo Falcón-Linero, Jose Fumero, Carolyn Krupp, Skip Lazell, Gad Perry, Clive Petrovic, Renata Platenberg, Alberto Puente-Rolón, Alejandro Ríos-Franceschí, Jessica Snider, Richard Thomas, and Larry Woolbright. I thank Steve Poe, Daniel Medina, and Mason Ryan for helping me collect samples from an introduced population of E. antillensis in Panamá City, a side-project which was originally part of this dissertation. Vani Aran, Ashley Montoya, and Mary Farrah helped complete molecular laboratory work for my dissertation. Several friends and colleagues provided feedback and comments on earlier drafts of my dissertation manuscripts, including Cuervo Lab members and affiliates Kayce Bell, Melissa Fleming, Chris Himes, Andrew Hope, Brooks Kohli, Jason Malaney, Bryan McLean, Jolene Rearick, Yadéeh Sawyer, Fernando Torres-Perez, and Jessica Weber, my OGS dissertation writing group members Carson Metzger and Jen Richter, and my other iii colleagues and friends Andrew Crawford, Jennifer Hollis, Jeff Streicher, Matthew Heinicke, Maureen Hickman, Mason Ryan, Daniel Warnock, and Megan Workman. For advice and help with technical analyses I extend my gratitude to Peter Beerli, Kurt Galbreath, Andrew Hope, Tereza Jezkova, Anson Koehler, Jason Malaney, Fernando Torres-Perez, Peter Smouse, and Elizabeth Walkup. iv HISTORICAL AND TOPOGRAPHIC DRIVERS OF TROPICAL INSULAR DIVERSITY: COMPARATIVE PHYLOGEOGRAPHY OF ELEUTHERODACTYLUS ANTILLENSIS AND E. PORTORICENSIS, TWO ECOLOGICALLY DISTINCTIVE FROGS OF THE PUERTO RICAN BANK by Brittany Suzanne Barker B.S., ZOOLOGY, OREGON STATE UNIVERSITY, 2003 PH.D., BIOLOGY, UNIVERSITY OF NEW MEXICO, 2012 Abstract Topographically complex islands present opportunities for in situ (within-island) allopatric speciation because of increased chances for isolation in separate mountain ranges, as well as greater opportunity for fragmentation by high sea levels and climate- driven changes in habitat distribution. Climatic oscillations of the Quaternary (Pleistocene – Holocene; ~2.5 million years ago to the present) may have influenced the severity of vicariant barriers among and within islands, yet how these events influenced evolution of tropical insular biota is not well understood. This dissertation explores the role of topographic complexity and climate-driven range shifts resulting from sea-level changes and habitat suitability in shaping genetic diversity of two Eleutherodactylus frogs (Anura: Eleutherodactylidae) in the Puerto Rican Bank, an archipelago in the eastern Caribbean Sea. Sea level changes significantly altered the size, area, and degree of isolation of terrestrial habitats in the Puerto Rican Bank, and habitat shifts may have occurred in the main island of Puerto Rico. Whereas the Mountain Coquí, E. v portoricensis, is restricted to cool and moist understory montane forest habitat in Puerto Rico, the Red-eyed Coquí, E. antillensis, is a habitat generalist with a broad elevational distribution on most of the larger islands of the Puerto Rican Bank. Hypotheses of population history were formulated using data from paleoenvironmental records and ecological niche models, and tested using a suite of population genetic, phylogenetic, and coalescent analyses of DNA sequence data. I show how basin barriers and Quaternary climatic fluctuations shaped the distribution of genetic diversity in E. portoricensis in the Luquillo and Cayey Mountains in eastern Puerto Rico, and how varying degrees of terrestrial connectivity and isolation influenced the persistence and colonization dynamics of E. antillensis across the Puerto Rican Bank. To infer whether climate-driven, historical shifts in distributions occurred in E. portoricensis and E. antillensis, this dissertation also compares patterns of genetic isolation and demography of these species in Puerto Rico, where elevational gradients may have accommodated range shifts during climatic extremes of the Quaternary. The collective findings of this dissertation improve our understanding of topographic and historic factors that promote population divergence and that ultimately produce regional patterns of biodiversity in tropical archipelagos. vi TABLE OF CONENTS CHAPTER 1 – Introduction.............................................................................................1 References....................................................................................................7 CHAPTER 2 – Deep intra-island divergence of a montane endemic: phylogeography of the Puerto Rican frog Eleutherodactylus portoricensis (Anura: Eleutherodactylidae)............................................................................................11 Abstract..................................................................................................................11 Introduction............................................................................................................13 Materials and Methods...........................................................................................16 Results....................................................................................................................26 Discussion..............................................................................................................29 References..............................................................................................................37 Figures and Tables.................................................................................................50 Supporting Information..........................................................................................58 CHAPTER 3 – Sea level, topography, and island diversity: phylogeography of the Puerto Rican Red-eyed Coquí, Eleutherodactylus antillensis...........................69 Abstract..................................................................................................................69 Introduction............................................................................................................71 Materials and Methods...........................................................................................74 Results....................................................................................................................85 vii Discussion..............................................................................................................89 References..............................................................................................................97 Figures and Tables...............................................................................................110 Supporting Information........................................................................................126 CHAPTER 4 – Habitat stability as a driver of tropical insular diversity: comparative phylogeography of Eleutherodactylus antillensis and E. portoricensis, two ecologically distinctive Puerto Rican frogs...........................................................149 Abstract................................................................................................................149 Introduction..........................................................................................................151