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Phylogeography and Conservation of the Arroyo Toad (Bufo Californicus)

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Phylogeography and Conservation of the Arroyo Toad (Bufo Californicus) Loma Linda University TheScholarsRepository@LLU: Digital Archive of Research, Scholarship & Creative Works Loma Linda University Electronic Theses, Dissertations & Projects 3-2009 Phylogeography and Conservation of the Arroyo Toad (Bufo californicus) Robert Edward Lovich Follow this and additional works at: https://scholarsrepository.llu.edu/etd Part of the Biology Commons Recommended Citation Lovich, Robert Edward, "Phylogeography and Conservation of the Arroyo Toad (Bufo californicus)" (2009). Loma Linda University Electronic Theses, Dissertations & Projects. 724. https://scholarsrepository.llu.edu/etd/724 This Dissertation is brought to you for free and open access by TheScholarsRepository@LLU: Digital Archive of Research, Scholarship & Creative Works. It has been accepted for inclusion in Loma Linda University Electronic Theses, Dissertations & Projects by an authorized administrator of TheScholarsRepository@LLU: Digital Archive of Research, Scholarship & Creative Works. For more information, please contact [email protected]. LOMA LINDA UNIVERSITY School of Science and Technology in conjunction with the Faculty of Graduate Studies Phylogeography and Conservation of the ArroyoToad (Rufo californicus) by Robert Edward Lovich A Dissertationsubmitted in partialsatisfaction of therequirements for the degree of Doctor of Philosophy in Biology March 2009 0 2009 Robert Edward Lovich All Rights Reserved Each person whose signature appears below certifies that this dissertation in his/her opinion is adequate, in scope and quality, as a dissertation for the degree of Doctor of Philosophy. Chairperson Ronald Carter, Professor of Biology Co-chairperson L. Lee Grismer, Professor of Biology, LaSierra University P *tL D4 — Penelope Duerksen-Hughes, Professor of Biochemistry and Microbiology Robert Ford, Research Professor/Advisor, Centre for GIS Training and Remote Sensing, National University of Rwanda William Hayes, Professor of Biology Ill ACKNOWLEDGEMENTS I wish to thank my committee and all of the Natural Science Department at Loma Linda University for academic, financial, and laboratory support for the duration of this project. Their unceasing dedication to mentoring me and fostering the best in scientific pursuits has helped me become a successful biologist. Dr. Ron Carter was incredibly helpful to me in every facet of my journey through the PhD. Program at Loma Linda University. I would also like to thank L. Lee Grismer, for his support through my program and inspiration in the field of herpetology, as well as for his friendship. Thanks to Bob Ford for his help in facilitating my research interests well beyond the scope of the PhD. Program, and all the adventures in Honduras. Thanks to Bill Hayes, a tremendous advisor and a good friend for life. Thanks to Penelope Duerksen-Hughes who was invaluable in supporting through my program as well. Beyond the roles that my committee played for me as a student, they also fostered what will be lasting friendships and collaborations that I look forward to. Steve Dunbar performed well beyond his duties as the graduate student coordinator, and I appreciate his friendship and attention to my needs as a student. Valerie Dekle, and Sarah Gordon deserve special mention, for their administrative duties and for withstanding multiple salvos and barrages of information needs and assistance to keep me registered and in good graces with the rest of the department, school, and university. I would also like to thanks the lineage of "Carter lab" and "Grismer Lab" members who shared with me in the highs and lows of student life, and who motivated and assisted one another to make lab life into the success that it was, namely: Nyoka Collie, Michael Cryder, Scott Delay, Ricardo Escobar, Brad iv Hollingsworth, Jessie Grismer, Jack Scarbrough, Jim Smith, Jeff Sonnentag, Roland Sosa, Humberto Wong, and Sam Yamamoto, and Tim Yeomans. Sequencing of samples was conducted by Pavel Lieb, at the DNA Sequencing Facility, California State University, Northridge. Field collection of tissues and specimens from Baja California, Mexico was made possible collaboratively by my friend and colleague Clark Mahrdt, and facilitated by Gustavo Danemann, and Jorge Valdez Villavicencio. Gerald "Luke" Hasty, Taran Grant, Brad Hollingsworth, and Greg Pauly provided critical assistance, information, and support with the laboratory and analysis portions of this project. I could not have done completed my research without them. Words fall short to show my appreciation for my loving wife Kim Gray-Lovich for long hours of help in the laboratory and endless support domestically. Thanks to Hope Lovich and Kaitlin Lovich for helping their father find toads, and for enduring their father's academic endeavors in lieu of absorbing the whole of their childhood. Thanks to the rest of my family who supported my ambitions throughout my program, and I wish to extend special thanks to my brother, and fellow herpetologist Jeffrey Lovich, along with mom, Janet Lovich, father, George Lovich, and sister, Cindy Pandolfe. Special acknowledgements are due my grandmother, Helen Imhoff, who always supported me in so many ways, but who passed away before seeing me achieve this degree. Necessary permits for collection of material were obtained from the United States Fish and Wildlife Service, Secretada de Medio Ambiente y Recursos Naturales, California Department of Fish and Game, United States Forest Service, Bureau of Land Management, Anza Borrego Deseit State Park, Marine Corps Base Camp Pendleton, Fort Hunter-Liggett, and the International Animal Care and Use Committee at Loma Linda University. An earlier version of Chapter 4 was reviewed by Jeffrey E. Lovich, and partial funding was provided by the Chicago Herpetological Society and Conservation International. Working in Mexico would not have been accomplishedwithout the field and technical assistance of T. Akre, H. Batche, J. Blackburn, B. Downer, M. Mendelson, T. Robison, J. Saurwein, E. MeRink, B. Hollingsworth, D. Casas, H. Ceballos, and B. Freiermuth. We thank the following institutions for providing Mexican locality records: Kent Beaman (LACM), George Bradley (UAZ), S. Gotte (USNM), Brad Hollingsworth (SDSNH), C. Lieb (UTEP), A. Resetar (FMNH), S. Rogers (CMNH), J. V. Villavicencio and A. Peralta (UABC), G. Schneider (UMMZ), and J. Campbell (UTA), Permits were provided by SEMARNAT. Additional thanks for laboratory and/or field assistance to the following persons: Ryan Bourque, Chris Brown, Steve Carroll, Ed Ervin, Eric Dugan, Alan Hebbert, Richard Hermann, Dan Holland, Valerie Hubbard, Mark Mendelson, Julie Nicewanger, Ruben Ramirez, Curtis Rehling, Chris Rodriguez, Jeff Saurwein, Norm Scott, Drew Stokes, T'shaka Toure, Manna Warburton, Dustin Wood, and Sal Zimmitti. For technical assistance in facilitating access to lands, tissues, permits, software, or otherwise, the following persons deserve special mention: Bill Brown, Liz Clark, Kevin Cooper, Robert Fisher, Eric Mellink, Tom Murphey, Terry Schwaner, and Jamie Uyehara. Thanks to Naval Facilities Engineering Command, Southwest for enduring my multitude of leave requests and absences from work in order to grow professionally by achieving this degree. vi In the course of my dissertation there were numerous individuals who supported my research in a multitude of ways. They tolerated my incessant manner and facilitated my goals at each step of the way. To everyone who helped me along the way, I offer my collective thanks. vii C ONTENTS Approval Page iii Acknowledgements iv Table of Contents viii List of Figures xi List of Tables xii Abstract xii Chapter 1. Introduction Arroyo Toad 1 Biology and Ecology 1 Distribution Historic Versus Present Status ............... 6 Listing and Protections 8 United States 8 Mexico 8 Prior Genetic Analyses . Allozyme Variation 9 Microsattelite Variation MtDNA SequenceVariation 10 Rangewide Variation 10 Approach of Studies 11 Significance of Studies 11 References 13 2. Phylogeography of the Arroyo Toad (Bufo californicus) 16 Abstract 16 Introduction.. 17 Materials and Methods 18 viii Sampling ••••••••• 18 Laboratory Protocols ••••••••• • • 21 Tree Reconstructio • •••••••••• ••••• 23 Outgroup Selection ... ••••••••••• • ••• •••••• ••••••• 26 Confidence and Signal ••• ••••••• 27 Results..... ••••• ••••••••• •••• 28 Phylogenetic signal ........ ••• . 29 DNA Sequences Data ••••••••••••••• ... ..29 Maximum Parsimony Analysis 32 ND! . ••••• . 32 Dloop ••• ••••• 34 Combined ND1 and Dloop ...... ••••• . 36 Maximum Likelihood Analysis ••• 38 ND1 •• * •••••••••.••••• .38 Dloop ••• •••.•••••• ••••••••••••• •••••••••• . .40 Combined ND1 and Dloop ..... •••• ***** ••••••• . 40 Bayesian Analysis •••• ....43 ND! ••• . •••••••••••••• 43 Mop._ ......... ••••••• ••••• ••••••••• •• . 43 Combined ND1 and Dloop..... ...46 Discussion ••••••••••••• ••••••••••••••• 46 Phylogeographic Patterns . 48 Phylogeographic Comparison ••••••••••••••••••••••••••••• 50 Regional Biogeography . 51 MtDNA Variation ••••••• ••••• 52 Conclusions •••• •• ••• 54 References ••••••••• .....55 3. Conservation Genetics of the Arroyo Toad (Bufo califomicus) 61 Abstract ••••• • •••••• •• ••••••• ••••••••••••••••••••• ••••• OOOOO • 61 Introduction........ • 61. Materials and Methods ••••••••••••••••• ••••• 63 Prior Genetic Studies ••••••• •••••••••• ..64 Conservation Units ••••••••• 64 ix Results 66 Discussion 67 References 70 4. The distribution, threats, and conservation status of the Arroyo Toad
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