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Population-Level Genetic Structure of Acmispon Argophyllus on the Channel Islands of California

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Mississippi State University Scholars Junction Theses and Dissertations Theses and Dissertations 1-1-2013 Population-Level Genetic Structure of Acmispon Argophyllus on the Channel Islands of California Gregory Lawrence Wheeler Follow this and additional works at: https://scholarsjunction.msstate.edu/td Recommended Citation Wheeler, Gregory Lawrence, "Population-Level Genetic Structure of Acmispon Argophyllus on the Channel Islands of California" (2013). Theses and Dissertations. 3568. https://scholarsjunction.msstate.edu/td/3568 This Graduate Thesis - Open Access is brought to you for free and open access by the Theses and Dissertations at Scholars Junction. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of Scholars Junction. For more information, please contact [email protected]. Automated Template A: Created by James Nail 2011 V2.02 Population-level genetic structure of Acmispon argophyllus on the Channel Islands of California By Gregory Lawrence Wheeler A Thesis Submitted to the Faculty of Mississippi State University in Partial Fulfillment of the Requirements for the Degree of Master of Science in Botany in the Department of Biological Sciences Mississippi State, Mississippi December 2013 Copyright by Gregory Lawrence Wheeler 2013 Population-level genetic structure of Acmispon argophyllus on the Channel Islands of California By Gregory Lawrence Wheeler Approved: ____________________________________ Lisa Wallace (Major Professor) ____________________________________ Mark E. Welch (Minor Professor) ____________________________________ Gary N. Ervin (Committee Member/Graduate Coordinator) ____________________________________ R. Gregory Dunaway Professor and Dean College of Arts & Sciences Name: Gregory Lawrence Wheeler Date of Degree: December 1, 2013 Institution: Mississippi State University Major Field: Botany Major Professor: Lisa Wallace Title of Study: Population-level genetic structure of Acmispon argophyllus on the Channel Islands of California Pages in Study: 79 Candidate for Degree of Master of Science The California Channel Islands present an ideal system in which to study unique biogeographical patterns seen in island systems near a mainland source, where spatial barriers are likely to limit gene flow without disrupting it completely. The islands also harbor a number of endemic taxa, suggesting that isolation from the mainland may be strong for some taxa. For this study, Acmispon argophyllus, a legume species found across five of the eight islands as well as on the mainland was used to test hypotheses at three spatial scales. Northern island populations have diverged into what potentially represents a new species; populations on the younger southern islands descent from populations on the older island of San Clemente; the two taxa on San Clemente show signs of genetic structure, with limited evidence of ongoing gene flow. These results demonstrate isolation over short distances in the Channel Islands leading to evolutionary divergence and speciation. DEDICATION To my loving and beautiful wife, Kate. You were there for me all the long days and nights I spent on projects and research, working hard towards this degree. Your patience and understanding kept me sane and your support and encouragement kept me moving forward. Also, telling you about my research always made me feel smart, and that was nice. After a while, feeling stupid just gets exhausting. ii ACKNOWLEDGEMENTS Special thanks to Dr. Lisa Wallace for constant guidance through years of this research. Without her, this project would not have been possible. Thanks also to Dr. Kaius Helenurm for the collection of Acmispon tissue samples and to Dr. Mitchell McGlaughlin for providing valuable nuclear sequence data. Funding for this project was provided primarily by the National Science Foundation through DEB 0842161 and a related REU. Additional funds were provided by the Mississippi State University Shackoul’s Honors College and through the Northeast Mississippi Daily Journal’s Undergraduate Research Award. Assistance was also provided by Mississippi State University’s graduate school, through a Bridge Fund Graduate Research Assistantship. Collection of Acmispon samples was performed with permission from the United States Navy, the Catalina Island Conservancy, the Nature Conservancy (Santa Cruz Island Preserve), Channel Island National Park, the United States Forest Service, and California State Parks. iii TABLE OF CONTENTS DEDICATION .................................................................................................................... ii ACKNOWLEDGEMENTS ............................................................................................... iii LIST OF TABLES ............................................................................................................. vi LIST OF FIGURES .......................................................................................................... vii CHAPTER I. INTRODUCTION .............................................................................................1 Theories to Explain Biodiversity Patterns on Islands ........................................5 Study System: The Channel Islands of California .............................................8 Study Organism: Acmispon argophyllus .........................................................11 II. OBJECTIVES AND HYPOTHESIS ...............................................................15 Hypothesis 1.....................................................................................................16 Hypothesis 2A ..................................................................................................17 Hypothesis 2B ..................................................................................................18 Hypothesis 3.....................................................................................................19 III. MATERIALS AND METHODS .....................................................................20 Sampling ..........................................................................................................20 Extraction and Amplification of DNA .............................................................20 Processing and Analysis of Genetic Data ........................................................24 IV. ANALYTICAL RESULTS .............................................................................32 Measures of Genetic Diversity .........................................................................32 Taxon diversity ..........................................................................................32 Island diversity of var. argenteus...............................................................34 Genetic distance .........................................................................................36 AMOVA analyses ......................................................................................39 Phylogenetic Analyses .....................................................................................41 Chloroplast and nuclear gene trees ............................................................41 Mixed-marker phylogenetic analysis .........................................................42 iv Discrete phylogeographic analysis of A. argophyllus var. argenteus ........43 Network Analyses ............................................................................................46 Nuclear ADH network ...............................................................................46 Chloroplast cpSEQ and cpMSAT network ................................................46 Migration Analysis...........................................................................................50 V. DISCUSSION ..................................................................................................52 Distinctiveness of A. argophyllus var. niveus ..................................................52 Dispersal and Colonization by A. argophyllus var. argenteus .........................53 Endemic A. argophyllus var. adsurgens on San Clemente ..............................58 Status of endemic Acmispon ......................................................................60 Conservation ....................................................................................................62 Broader Implications ........................................................................................62 Future Studies ..................................................................................................65 REFERENCES ..................................................................................................................67 APPENDIX A. DIVERSITY OF ACMISPON POPULATIONS INCLUDED IN THIS STUDY ................................................................................................75 Population Diversity Indices ............................................................................76 B. INDIVIDUAL MARKER PHYLOGENETIC ANALYSES ..........................77 Chloroplast Sequence Phylogenetic Analysis ..................................................78 Nuclear ADH Sequence Phylogenetic Analysis ..............................................79 v LIST OF TABLES 1 Measurements of age, distance to mainland California, distance to nearest island, area, and percent endemism for each island included in this study ..............................................................................17 2 Names and
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  • Checklist of the Vascular Plants of San Diego County 5Th Edition

    Checklist of the Vascular Plants of San Diego County 5Th Edition

    cHeckliSt of tHe vaScUlaR PlaNtS of SaN DieGo coUNty 5th edition Pinus torreyana subsp. torreyana Downingia concolor var. brevior Thermopsis californica var. semota Pogogyne abramsii Hulsea californica Cylindropuntia fosbergii Dudleya brevifolia Chorizanthe orcuttiana Astragalus deanei by Jon P. Rebman and Michael G. Simpson San Diego Natural History Museum and San Diego State University examples of checklist taxa: SPecieS SPecieS iNfRaSPecieS iNfRaSPecieS NaMe aUtHoR RaNk & NaMe aUtHoR Eriodictyon trichocalyx A. Heller var. lanatum (Brand) Jepson {SD 135251} [E. t. subsp. l. (Brand) Munz] Hairy yerba Santa SyNoNyM SyMBol foR NoN-NATIVE, NATURaliZeD PlaNt *Erodium cicutarium (L.) Aiton {SD 122398} red-Stem Filaree/StorkSbill HeRBaRiUM SPeciMeN coMMoN DocUMeNTATION NaMe SyMBol foR PlaNt Not liSteD iN THE JEPSON MANUAL †Rhus aromatica Aiton var. simplicifolia (Greene) Conquist {SD 118139} Single-leaF SkunkbruSH SyMBol foR StRict eNDeMic TO SaN DieGo coUNty §§Dudleya brevifolia (Moran) Moran {SD 130030} SHort-leaF dudleya [D. blochmaniae (Eastw.) Moran subsp. brevifolia Moran] 1B.1 S1.1 G2t1 ce SyMBol foR NeaR eNDeMic TO SaN DieGo coUNty §Nolina interrata Gentry {SD 79876} deHeSa nolina 1B.1 S2 G2 ce eNviRoNMeNTAL liStiNG SyMBol foR MiSiDeNtifieD PlaNt, Not occURRiNG iN coUNty (Note: this symbol used in appendix 1 only.) ?Cirsium brevistylum Cronq. indian tHiStle i checklist of the vascular plants of san Diego county 5th edition by Jon p. rebman and Michael g. simpson san Diego natural history Museum and san Diego state university publication of: san Diego natural history Museum san Diego, california ii Copyright © 2014 by Jon P. Rebman and Michael G. Simpson Fifth edition 2014. isBn 0-918969-08-5 Copyright © 2006 by Jon P.