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Lampsilis Cardium) and Improved Prospects for Recovery: How Nuclear and Mitochondrial DNA Analyses Inform Natural History and Conservation

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Lampsilis Cardium) and Improved Prospects for Recovery: How Nuclear and Mitochondrial DNA Analyses Inform Natural History and Conservation Wright State University CORE Scholar Browse all Theses and Dissertations Theses and Dissertations 2009 Conservation genetics of a near threatened freshwater mussel species (Lampsilis cardium) and improved prospects for recovery: how nuclear and mitochondrial DNA analyses inform natural history and conservation Chad D. Ferguson Wright State University Follow this and additional works at: https://corescholar.libraries.wright.edu/etd_all Part of the Environmental Sciences Commons Repository Citation Ferguson, Chad D., "Conservation genetics of a near threatened freshwater mussel species (Lampsilis cardium) and improved prospects for recovery: how nuclear and mitochondrial DNA analyses inform natural history and conservation" (2009). Browse all Theses and Dissertations. 931. https://corescholar.libraries.wright.edu/etd_all/931 This Dissertation is brought to you for free and open access by the Theses and Dissertations at CORE Scholar. It has been accepted for inclusion in Browse all Theses and Dissertations by an authorized administrator of CORE Scholar. For more information, please contact [email protected]. CONSERVATION GENETICS OF A NEAR THREATENED FRESHWATER MUSSEL SPECIES (LAMPSILIS CARDIUM) AND IMPROVED PROSPECTS FOR RECOVERY: HOW NUCLEAR AND MITOCHONDRIAL DNA ANALYSES INFORM NATURAL HISTORY AND CONSERVATION PLANNING A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy By CHAD DAVID FERGUSON B.A., Ohio University, 1993 M.A., Wright State University, 1995 M.S., California University of Pennsylvania, 2002 (Signature of Student) _________________________________ 2009 Wright State University COPYRIGHT BY CHAD DAVID FERGUSON 2009 WRIGHT STATE UNIVERSITY SCHOOL OF GRADUATE STUDIES April 17, 2009 I HEREBY RECOMMEND THAT THE DISSERTATION PREPARED UNDER MY SUPERVISION BY Chad David Ferguson ENTITLED Conservation Genetics of a Near Threatened Freshwater Mussel Species (Lampsilis cardium) and Improved Prospects for Recovery: How Nuclear and Mitochondrial DNA Analyses Inform Natural History and Conservation Planning BE ACCEPTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF Doctor of Philosophy. ______________________ Dan E. Krane, Ph.D. Dissertation Director ______________________ Don Cipollini, Ph.D. Interim Director, Environmental Sciences Ph.D. Program ______________________ Joseph F. Thomas, Jr., Ph.D. Dean, School of Graduate Studies Committee on Final Examination ______________________ G. Allen Burton, Ph.D. ______________________ Michael L. Raymer, Ph.D. ______________________ Michael J. Blum, Ph.D. ______________________ Robert A. Krebs, Ph.D. ABSTRACT Ferguson, Chad David. Ph.D, Environmental Sciences Ph.D. Program, Wright State University, 2009. Conservation Genetics of a Near Threatened Freshwater Mussel Species (Lampsilis cardium) and Improved Prospects for Recovery: How Nuclear and Mitochondrial DNA Analyses Inform Natural History and Conservation Planning Freshwater mussels (Bivalvia: Unionidae) are among the most imperiled organisms in North America. While there is an urgent need for effective conservation planning and management of these organisms, important basic biological information is lacking. This research characterizes levels of genetic diversity and population structure in the Near Threatened (IUCN) freshwater mussel Lampsilis cardium in populations from Twin Creek (southwest Ohio), Little Darby and Big Darby Creeks (central Ohio), and Little Muskingum River (eastern Ohio) and assesses the extent to which regional geological events explain population structuring. Data from the congener Lampsilis ovata from Clinch River (Tennessee) are included for comparison. To characterize these patterns, sequencing of the mtDNA gene cytochrome oxidase c subunit 1 (COI) and nuclear microsatellite genotyping over 12 loci was performed. Additionally, genotype data from both adults and individual glochidia were analyzed to examine parentage and within-population levels of relatedness across common pedigree relationships. Microsatellite data reveal weak population v structuring across glaciated and unglaciated drainages and 900 total river miles. However, haplotype analysis and sequence alignment recovered deeply divergent, cryptic lineages within Lampsilis cardium consistent with ancestral introgressive hybridization with Lampsilis ovata or incomplete lineage sorting. Mito-nuclear discordance argues against ongoing hybridization, although polymorphic species are also consistent with the data, and this affirms the importance of multiple molecular markers. In addition to finding multiple paternity in single broods, a number of parent-offspring, full-sibling, and half-sibling relationships for adults and glochidia are described. Numerous instances are noted in which likely full-siblings or half-siblings were located several kilometers apart, demonstrating that DNA-based evidence can describe the spatial nature of dispersal in unionid mussels. In a first report, the likely father of three glochidia from one female's brood was identified 16.2 kilometers upstream, which suggests the possibility of long-distance transport of spermatozoa in Lampsilis cardium. Given the similarity with which Lampsilines reproduce, it is predicted that other members of this genus are also capable long-distance fertilization. If fertilization in populations of freshwater mussels is indeed not limited by the density of breeding adults, the prospects for recovery in this fauna may be better than recently imagined. vi TABLE OF CONTENTS Page I. GENETIC DIVERSITY, POPULATION STRUCTURE, NATURAL HISTORY, AND RESEARCH OBJECTIVES..........................................1 Introduction, Literature Review, and Significance ........................ 1 Specific Research and Conservation Objectives ......................... 15 Methods ............................................................................. 17 Study sites and searches .................................................. 17 Mussel handling and obtaining tissue samples ..................... 18 DNA processing ............................................................... 19 II. GENETIC DIVERSITY, POPULATION STRUCTURE, AND MITOCHONDRIAL-NUCLEAR DISCORDANCE...................................20 Introduction ........................................................................ 20 Materials and Methods .......................................................... 24 Sample collection ............................................................ 24 Mitochondrial DNA, haplotype diversity, and phylogenetics .... 25 Nuclear microsatellite markers, species delineation, population structure, genetic diversity, and bottlenecks ....................... 27 vii Results ............................................................................... 30 mtDNA haplotype diversity and distribution ......................... 30 Nuclear microsatellite markers, species delineation, population structure, genetic diversity, and bottlenecks ....................... 34 Discussion ........................................................................... 38 Cryptic lineages, introgression, and mito-nuclear discordance 38 Phylogenetics, haplotype distribution, and absence of Pleistocene signatures ...................................................... 42 Population structure, genetic diversity, and bottlenecks ........ 44 III. PATERNITY, FAMILY-LEVEL RELATIONSHIPS, AND LONG- DISTANCE TRANSPORT OF SPERMATOZOA ................................... 50 Introduction ........................................................................ 50 Materials and Methods .......................................................... 53 Field collection of tissue samples ....................................... 53 Molecular processing ........................................................ 55 Multiple paternity ............................................................ 56 Estimates of the most likely number of paternal contributors . 56 Family structure .............................................................. 58 Results ............................................................................... 62 viii Multiple paternity ............................................................ 62 Estimates of the most likely number of paternal contributors . 63 Family structure .............................................................. 64 Discussion ........................................................................... 65 Multiple paternity ............................................................ 67 Estimates of the most likely number of paternal contributors . 69 Family structure .............................................................. 70 Spatial distribution and long-distance transport of spermatozoa ................................................................... 75 IV. WORKS CITED .................................................................. 106 V. APPENDIX A ...................................................................... 124 VI. APPENDIX B ..................................................................... 125 VII. APPENDIX C .................................................................... 148 VIII. APPENDIX D .................................................................. 150 IX. APPENDIX E ..................................................................... 151 XI. APPENDIX F ..................................................................... 217 XII. APPENDIX G ...................................................................
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