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Population Genetics of the Native Rodents of the Galápagos Islands, Ecuador

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Population Genetics of the Native Rodents of the Galápagos Islands, Ecuador Population Genetics of the Native Rodents of the Galápagos Islands, Ecuador A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at George Mason University By Sarah Johnson Master of Science Stephen F. Austin State University, 2005 Bachelor of Science Texas A&M University, 2003 Director: Dr. Cody W. Edwards, Assistant Professor Department of Environmental Science and Public Policy Summer Semester 2009 George Mason University Fairfax, VA Copyright 2009 Sarah Johnson All Rights Reserved ii ACKNOWLEDGMENTS I would like to thank my parents (Michael and Kay Johnson) and my sisters (Kris and Faith) for their unwavering support throughout my academic career. This dissertation is lovingly dedicated to my parents. I would like to thank my Aggie Family (Brad and Kristin Atchison, Reece and Erin Flood, Samir Moussa, Doug Fuentes, and the rest of the IV Horsemen). They have always lovingly provided a shoulder to lean on and kind ear willing to listen. I would like to thank my fellow graduate students at GMU (Jeff Streicher, Mike Jarcho, Kat Bryant, Tammy Henry, Geoff Cook, Ryan Peters, Kristin Wolf, Trishna Dutta, Sandeep Sharma, and Jolanda Luksenburg) for their help in the field, lab, classroom, and all aspects of student life. I am eternally indebted to Dr. Pat Gillevet and Masi Sikaroodi for their invaluable assistance in the lab, and to Dr. Jesús Maldonado for his assistance in writing the dissertation. They are infinite sources of help and support for which I am forever grateful. The project would not have been possible without Dr. Cody W. Edwards and Dr. Robert C. Dowler. Finally, I would like to thank my committee members for their support, critique, counseling, and advice. iii TABLE OF CONTENTS Page LIST OF TABLES .........................................................................................................vi LIST OF FIGURES..................................................................................................... viii ABSTRACT....................................................................................................................x INTRODUCTION...........................................................................................................1 The Galápagos Islands.................................................................................................2 Native Rodents ............................................................................................................4 Systematics of the Native Rodents...........................................................................7 Description of Nesoryzomys.....................................................................................8 Description of Aegialomys. ......................................................................................9 Previous Studies Involving Native Galápagos Rodents. .........................................11 Human Impacts .........................................................................................................17 Human Settlements................................................................................................17 Tourism.................................................................................................................18 Introduced Species.....................................................................................................19 Conservation .............................................................................................................22 Eradication Efforts.................................................................................................23 Status of the Native Rodents..................................................................................24 OBJECTIVES ...............................................................................................................27 HYPOTHESES .............................................................................................................28 Aegialomys bauri...................................................................................................28 Nesoryzomys swarthi .............................................................................................28 Nesoryzomys fernandinae and Nesoryzomys narboroughi ......................................29 Nesoryzomys and Aegialomys ................................................................................29 METHODS ...................................................................................................................30 Justification of Molecular Markers ............................................................................30 Population Genetics...................................................................................................31 Sample Collection..................................................................................................31 iv DNA Isolation .......................................................................................................33 Microsatellite Protocols .........................................................................................33 Microsatellite Analyses..........................................................................................35 D-loop Protocol .....................................................................................................40 D-loop Analyses ....................................................................................................42 RESULTS.....................................................................................................................44 Phylogenetic Results ………………………………………………………………….46 Aegialomys bauri.......................................................................................................47 Microsatellite Results ............................................................................................47 D-loop Results.......................................................................................................53 Nesoryzomys swarthi .................................................................................................56 Microsatellite Results ............................................................................................56 D-loop Results.......................................................................................................61 Nesoryzomys narboroughi .........................................................................................64 Microsatellite Results ............................................................................................64 D-loop Results.......................................................................................................69 Nesoryzomys fernandinae ..........................................................................................72 Microsatellite Results ………………………………………………………………72 D-loop Results.......................................................................................................77 DISCUSSION ...............................................................................................................79 Aegialomys bauri.......................................................................................................80 Nesoryzomys swarthi .................................................................................................83 Nesoryzomys narboroughi .........................................................................................86 Nesoryzomys fernandinae ..........................................................................................88 CONCLUSION.............................................................................................................91 Future Work ..............................................................................................................91 Laboratory Recommendations ...............................................................................91 Additional Studies .................................................................................................93 Applications ..............................................................................................................96 APPENDIX...................................................................................................................99 LITERATURE CITED................................................................................................113 v LIST OF TABLES Table Page 1. History and location of native rodents in the Galápagos Islands. .................................6 2. Tests of linkage equilibrium p-values between loci in A. bauri..................................48 3. Allelic diversity and deviation from Hardy-Weinberg proportion among microsatellite loci in A. bauri...................................................................................50 4. Genetic diversity indices per locus for pooled samples of A. bauri............................52 5. Tests for linkage equilibrium p-values between loci in N. swarthi subpopulations.....56 6. Allelic diversity and deviation from Hardy-Weinberg proportion among microsatellite loci in N. swarthi.. .............................................................................59 7. Genetic diversity indices per locus in pooled samples of N. swarthi..........................60 8. Tests for linkage equilibrium p-values between loci in N. narboroughi.....................64 9. Allelic diversity and deviation from Hardy-Weinberg proportion among microsatellite
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