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Population Structure and Gene Flow in Two Rare, Isolated Quercus Species: Q. Hinckleyi and Q. Pacifica by JANET RIZNER BACKS B

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Population Structure and Gene Flow in Two Rare, Isolated Quercus Species: Q. Hinckleyi and Q. Pacifica by JANET RIZNER BACKS B Population structure and gene flow in two rare, isolated Quercus species: Q. hinckleyi and Q. pacifica BY JANET RIZNER BACKS B.A., Loretto Heights College M.A., University of Wisconsin, Madison M.S., Northeastern Illinois University M.S., University of Illinois at Urbana-Champaign THESIS Submitted as partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Sciences in the Graduate College of the University of Illinois at Chicago, 2014 Chicago, Illinois Defense Committee: Mary V. Ashley, Chair and Advisor Roberta Mason-Gamer Emily Minor Andrew Hipp, Morton Arboretum Andrea Kramer, Chicago Botanic Garden ACKNOWLEDGMENTS Special thanks to my advisor, Dr. Mary Ashley, for affording me the opportunity to pursue graduate research in oaks, and especially Quercus hinckleyi, and giving me the space and freedom to learn new disciplines and skills. The Ashley Lab has been a source of friendship, support, encouragement, and sharing of the ups and downs of research. Without all of the people in the Lab, especially Saji Abraham, David Zaya, and Eun Sun Kim, this work would not have been possible. Thank you to my Committee for reading and listening to my proposals and finally my results. I appreciate your time and help. Funding for this research was through the University of Illinois at Chicago Hadley Grant. My research of Quercus hinckleyi was aided by the help of many people in Texas. Special thanks to Martin Terry and Molly Klein of Sul Ross University in Alpine, TX, volunteers from Texas Master Naturalists, and Troy Rinehart, Rio Grande Mining Co., for their assistance in locating and collecting specimens for this study. Collection permits were granted by Texas Parks and Wildlife Department and the U.S. Fish and Wildlife Service. The National Park Service at Guadalupe Mountains National Park permitted taking samples of the putative hybridizers, Q. pungens and Q. vaseyana; collecting was done by Jeremy Markuson with the NPS. Likewise, my research of Quercus pacifica could not have been completed without the help of many people in ii ACKNOWLEDGMENTS (continued) California. Collection of samples from the three islands was made possible through Scott Sillett, Smithsonian Migratory Bird Center. Collectors were: Sarah Ratay, Catalina Island Conservancy; Jongmin Yoon & Michelle Desrosiers, Colorado State University; and Mario Pesendorfer, University of Nebraska. Mainland samples of Q. berberidifolia and Q. dumosa were collected with the help of Martha Witter, Tarja Sagar, Tony Valois, Crystal Anderson, and Keith Lombardo, all of the National Park Service. Photographs were taken by William Backs of Evanston, Illinois. Finally, thank you to my friends and family members, some of whom are no longer with me in life, but always will be with me in spirit. These people have made me who I am. For your support and encouragement, special thanks to my husband Bill Backs and to E.D.D. for her words of wisdom without which I would not have ‘done what I knew I wanted to do.’ JRB iii Table of Contents Chapter Page 1. A STORY OF SURVIVAL OF A RARE, ISOLATED SPECIES: A TOUGH, LITTLE WEST TEXAS OAK, QUERCUS HINCKLEYI C.H. MULLER ......................................... 1 1.1 Introduction ........................................................................................................ 1 1.2 Materials and Methods ....................................................................................... 4 1.2.1 Study species ............................................................................................ 4 1.2.2 Study sites and sample collection ............................................................. 6 1.2.3 DNA extraction and microsatellite analysis ............................................... 7 1.2.4 Data analysis ............................................................................................. 8 1.3 Results ............................................................................................................. 10 1.4 Discussion ........................................................................................................ 16 1.4.1 Quercus hinckleyi as a rare isolated species .......................................... 16 1.4.2 Conservation management ..................................................................... 19 1.5 References ....................................................................................................... 22 2. HYBRIDIZATION AS A CONSERVATION CONCERN FOR THE THREATENED SPECIES, QUERCUS HINCKLEYI C.H. MULLER (FAGACEAE) ................................ 27 2.1. Introduction ......................................................................................................... 27 2.2 Materials and Methods ......................................................................................... 30 iv Table of Contents (continued) 2.2.1 Study Species ......................................................................................... 30 2.2.2 Study Sites and Sample Collection ......................................................... 32 2.2.3 Microsatellite Genotyping ........................................................................ 32 2.2.4 Genetic data analysis .............................................................................. 33 2.3 Results ................................................................................................................. 34 2.4 Discussion ............................................................................................................ 39 2.5 References ........................................................................................................... 43 3. GENETIC CLUSTERING AND GENE FLOW IN AN ENDEMIC CHANNEL ISLAND OAK: QUERCUS PACIFICA K. NIXON & C.H. MULLER (FAGACEAE) ....................... 47 3.1 Introduction .......................................................................................................... 47 3.2 Materials and Methods ......................................................................................... 51 3.2.1 Study Species ......................................................................................... 51 3.2.2 Genetic Analysis ..................................................................................... 52 3.2.3 Data analysis ........................................................................................... 56 3.3 Results ................................................................................................................. 58 3.4 Discussion ............................................................................................................ 66 3.5 References ........................................................................................................... 71 v Table of Contents (continued) 4. UNRAVELLING THE TAXONOMIC PUZZLE OF THREE CALIFORNIA SHRUB OAK SPECIES: QUERCUS DUMOSA NUTT., Q. BERBERIDIFOLIA LIEBM. AND Q. PACIFICA NIXON & C.H. MULLER .............................................................................. 80 4.1 Introduction .......................................................................................................... 80 4.2 Materials and Methods ......................................................................................... 83 4.2.1 Genetic Analysis ..................................................................................... 83 4.2.2. Data analysis .......................................................................................... 85 4.3. Results ................................................................................................................ 86 4.4 Discussion ............................................................................................................ 92 4.5 References ....................................................................................................... 94 5. VITA ........................................................................................................................ 99 vi LIST OF TABLES TABLE I: Q. HINCKLEYI RAMETS AND MULTILOCUS GENOTYPES. .................................................. 10 TABLE II: Q. HINCKLEYI DESCRIPTIVE STATISTICS. .......................................................................... 11 TABLE III: DESCRIPTIVE STATISTICS FOR Q. HINCKLEYI, Q. PUNGENS, AND Q. VASEYANA. ..... 35 TABLE IV: Q. PUNGENS AND Q. VASEYANA: PROPORTION OF MEMBERSHIP OF EACH PRE- DEFINED POPULATION IN EACH OF THE 2 INFERRED CLUSTERS. .......................................... 36 TABLE V: INDIVIDUALS IDENTIFIED MORPHOLOGICALLY AS Q. HINCKLEYI OR Q. PUNGENS WITH INFERRED LEVELS OF INTROGRESSION............................................................................ 37 TABLE VI: QUERCUS PACIFICA SAMPLE (ID) LOCATIONS. ............................................................... 54 TABLE VII: DESCRIPTIVE STATISTICS FOR QUERCUS PACIFICA BY ISLAND ON WHICH IT IS FOUND. ............................................................................................................................................... 59 TABLE VIII: PAIRWISE DIFFERENTIATION INDEX USING GST AND DJOST FOR Q. PACIFICA ON SANTA ROSA, SANTA CRUZ AND SANTA CATALINA. .................................................................. 60 TABLE IX: Q. PACIFICA INFERRED CLUSTER MEMBERSHIP BASED ON SPATIAL CLUSTERING ANALYSIS. .......................................................................................................................................... 65 TABLE X: Q. BERBERIDIFOLIA,
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