CONSERVATION GENETICS of the FLORIDA GRASSHOPPER SPARROW (Ammodramus Savannarum Floridanus)
Total Page:16
File Type:pdf, Size:1020Kb
CONSERVATION GENETICS OF THE FLORIDA GRASSHOPPER SPARROW (Ammodramus savannarum floridanus) By NATALIE LYNNETTE BULGIN, B.Sc. A Thesis Submitted to the School ofGraduate Studies In Partial Fulfillment ofthe Requirements for the Degree Master of Science McMaster University © Copyright by Natalie Lynnette Bulgin, September 2000 MASTER OF SCIENCE (2000) McMaster University (Biology) Hamilton, Ontario TITLE: Conservation Genetics ofthe Florida Grasshopper Sparrow (Ammodramus savannarum floridmms) AUTHOR:NatalieBlliWn SUPERVISOR: Dr. H.L. Gibbs NUMBER OF PAGES: x, 138 11 ACKNOWLEDGEMENTS I would first like to thank my supervisor, Dr. H. Lisle Gibbs for his time, patience, and commitment to my transition from a naive undergraduate geneticist to a less, but still slightly naive, molecular ecologist. I also thank my committee members, Drs. Bradley N. White and Susan A. Dudley, for stimulating discussion and suggestions regarding my thesis and science in general. I am grateful to our collaborator, Dr. Peter D. Vickery, for organizing the project, for insight into the biology ofthe species, and for making me realize I am not as much ofa naturalist as I once tended to believe. Also, I thank Dr. Allan J. Baker, Centre for Biodiversity and Conservation Biology at the University of Toronto for the use ofhis automated sequencer, and technical and analytical support. Also, I thank Dr. John C. Avise for donating purified mtDNA from various Ammodramus species. I am grateful to Dr. Brian Golding and Liisa Koski for assistance with the phylogenetic analyses. My utmost appreciation goes to Tylan Dean and Dusty Perkins for collection of Grasshopper Sparrow blood samples throughout the United States - God and Bonnie know I couldn't have done it. Special thanks is given to Oliver Haddrath, Centre for Biodiversity and Conservation Biology at the University ofToronto, for help designing the mitochondrial DNA primers, and for technical and analytical support. My sincerest thanks to Liliana De Sousa also for technical and analytical support. Je remercie Marylene Boulet pour avoir commente les versions preliminaires du manuscrit. Finally, I would like to acknowledge my appreciation ofall members ofDr. H. Lisle Gibbs' lab (Liliana De Sousa, Marylene Boulet, Bonnie Woolfenden, Lisa Tabak, Becky Pearce, and m Kevin Shonk) and Dr. Allan J. Baker's lab (Tara Paton, Maryann Burbidge, Nicola Wade, Oliver Haddrath, Andrew Given, Annette Greenslade, and Carol Croke). In upholding my unsentimental-type reputation, I will not address my utmost appreciation for the emotional support from my friends Chantalle, Tim, and Carla, my best-friends Jennifer and Jeff: and my parents, Joyce Rhoda Ethel and Edwin Claude (thank goodness my family isn't one for inheriting names). However, I do hope that they realize this appreciation, and that I have, can, and will return the same. IV TABLE OF CONTENTS Page DESCRIPTIVE NOTE ...........................................................................ii ACKNOWLEDGEMENTS .....................................................................iii TABLE OF CONTENTS.........................................................................v LIST OF TABLES ...............................................................................vii LIST OF FIGURES..............................................................................ix CIIJ\J?TEFl 1-- GENEFlAL INTFlODlJCTION...............................................1 Literature Cited ....................................................................................5 CIIJ\J?TEFl2-- OlJT OF FLOFliDA: PHYLOGEOGFlAPHY AND GENETIC STFllJCTlJFlE OF NOFlTH AMEFliCAN GFlASSHOPPEFl SPARROWS (AMMODRAMUS SAVANNARUM)........................9 Abstract.............................................................................................9 Introduction.......................................................................................12 Methods............................................................................................19 Flesults.............................................................................................30 Discussion.........................................................................................37 Literature Cited ...................................................................................53 Tables..............................................................................................66 Figures.............................................................................................75 Appendix..........................................................................................81 CIIJ\J?TEFl3 - GENETIC ESTIMATES OF DISPEFlSAL AMONG SlJB POPlJLATIONS OF THE FLOFliDA GFlASSHOPPEFl SPAFlFlOW v (AMMODRAMUS SAVANNARUM FLORIDANUS) ......................90 Abstract............................................................................................90 Introduction.......................................................................................92 Methods...........................................................................................101 Results.............................................................................................104 Discussion........................................................................................I 07 Literature Cited ..................................................................................117 Tables.............................................................................................125 Figures............................................................................................131 Appendix.........................................................................................134 CHAPTER 4- GENERAL CONCLUSIONS ..............................................136 VI LIST OF TABLES Chapter2 Table Description Page I. Grasshopper Sparrow microsatellite primer sequences, repeat motif, size ofcloned fragment, and annealing temperatures .............................. 66 2. Summary ofthe mtDNA variation per population ..................................67 3. Summary ofthe microsatellite DNA variation per locus and per population ...68 4. Observed (Ho) and expected (He) heterozygosity for each ofthe six microsatellite loci per population as determined using GENEPOP ...............70 5. FsT values between population pairs based on distance-weighted mtDNA sequence data ............................................................................71 6. Theta and rho values for pair-wise comparisons among the five populations ..72 7. Results ofthe recent bottleneck test ..................................................73 8. Genetic imbalance index values for individual Grasshopper Sparrow populations..............................................................................74 Appendix 1. Sequence for Grasshopper Sparrow haplotype (GRSP) 1 .........................81 2. Distribution ofmtDNA haplotypes among the five populations ..................82 3. Variance in allele size per locus per population for original rho calculations, removing alleles at a frequency ofless than 5%, and using a floridanus sample size of25 ..........................................................85 VII 4. Psuedo-jackknife neighbor-joining trees inferred from microsatellite data using Nei's genetic distance and the Cavalli-Sforza and Edwards chord distance...................................................................................88 Chapter3 Table Description Page 1. Variation in mtDNA among Florida sub-populations ............................125 2. Microsatellite DNA variation in Florida Grasshopper Sparrow sub-populations........................................................................ 126 3. Frequency ofobserved (Ho) and expected (He) heterozygotes per locus per sub-population...........................................................................127 4. Fs-r-based values for pair-wise comparisons ofmtDNA haplotype frequencies and weighted for amount ofdivergence between haplotypes among the four floridanus sub-populations........................................128 5. Theta and rho values for pair-wise comparisons among the four jloridanus sub-populations...........................................................129 6. Assignments ofindividuals to sub-populations within Florida .................. 130 Appendix I. Distribution ofjloridanus haplotypes among the four sub-populations ....... 134 V1ll LIST OF FIGURES Chapter Two Figure Description Page I. Locations of sampled populations and subspecies boundaries in the United States .............................................................................75 2. Relative location ofprimers used to amplify and sequence the Grasshopper Sparrow mtDNA control region and their amplification product sizes ..........76 3. Variable sites among the 58 Grasshopper Sparrow haplotypes ...................77 4. Minimum-spanning tree ofthe 58 Grasshopper Sparrow haplotypes, the Jamaican Grasshopper Sparrow, and two outgroup species (the Yellow-Browed Sparrow and the Grassland Sparrow .............................. 78 5. Consensus neighbor-:ioining tree ofthe 58 Grasshopper Sparrow haplotypes, a Jamaican sample (A. s. savannarum), and two outgroup taxa (A. humeralis and A. aurifrons) ................................................79 6. Unrooted neighbor-:ioining trees depicting evolutionary relationships of the five populations using Nei's genetic distance and Cavalli-Sforza and Edwards chord distance ...............................................................80