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MIAMI UNIVERSITY the Graduate School MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Kentaro Inoue Candidate for the Degree: Doctor of Philosophy ______________________________________ David J. Berg, Director ______________________________________ Bruce J. Cochrane, Reader ______________________________________ Thomas O. Crist, Reader ______________________________________ Brian Keane, Reader ______________________________________ Richard C. Moore, Graduate School Representative ABSTRACT A COMPREHENSIVE APPROACH TO CONSERVATION BIOLOGY: FROM POPULATION GENETICS TO EXTINCTION RISK ASSESSMENT FOR TWO SPECIES OF FRESHWATER MUSSELS by Kentaro Inoue Species conservation is an enormously complex task, which includes identification of phenomena that affect the loss, maintenance, and restoration of biodiversity and advocate for sustaining evolutionary processes that promote all levels of biological organization. Endangered species conservation requires a comprehensive approach to evaluate the conservation status of a given species, develop optimal recovery plans, and establish quantitative recovery criteria, in order to remove the necessity of protection. In my dissertation, I demonstrate such a comprehensive approach for evaluating the conservation status of two imperiled freshwater mussel species: Cumberlandia monodonta and Popenaias popeii, and providing guidance for development of species recovery plans. I characterized novel microsatellite markers for the species in order to assess population genetic diversity and structure (Chapter 1 and 3). I assessed fine-scale population structure of C. monodonta and used ecological and genetic simulations to investigate the effects of future climate change on distributional shifts in suitable habitats and population genetic connectivity (Chapter 2). I also investigated evolutionary history and genetic structure of P. popeii and used long-term mark-and-recapture monitoring to determine population dynamics (Chapter 4 and 5). I used demographic and population genetic information acquired from the previous chapters to develop recovery strategies for these species (Chapter 6). Using a large number of polymorphic microsatellite markers for both species, I revealed that climate change during the mid-to-late-Pleistocene likely shaped current distribution and genetic structure in both species. Current genetic structure of C. monodonta is likely a consequence of connectivity of suitable habitat; however, future climate change will likely reduce connectivity across populations. Climate change during the mid-to-late Pleistocene caused regional and local population structures of P. popeii. A long-term demographic study revealed that reduced river discharge is associated with significant decreased survival. Current anthropogenic activities threaten the availability of high-quality habitat for P. popeii. Demographic parameters during early life stages interact to influence the extinction probability and population growth rates for both species. The trajectories of population genetic persistence were influenced by initial allele frequency within populations, population size, and population growth rates. I used freshwater mussels to demonstrate the importance of considering evolution and ecology of organisms when developing species recovery strategies and making conservation decisions. I hope that my dissertation encourages others to utilize ecological and genetic studies in developing recovery plans for species from this and other highly imperiled groups. A COMPREHENSIVE APPROACH TO CONSERVATION BIOLOGY: FROM POPULATION GENETICS TO EXTINCTION RISK ASSESSMENT FOR TWO SPECIES OF FRESHWATER MUSSELS A DISSERTATION Presented to the Faculty of Miami University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Biology by Kentaro Inoue The Graduate School Miami University Oxford, Ohio 2015 Dissertation Director: David J. Berg © Kentaro Inoue 2015 TABLE OF CONTENTS General Introduction .................................................................................................................... 1 Chapter 1: Isolation and characterization of 17 polymorphic microsatellite loci in the spectaclecase, Cumberlandia monodonta (Bivalvia: Margaritiferidae) .................................. 10 Abstract ..................................................................................................................................... 10 Introduction ............................................................................................................................... 10 Methods ..................................................................................................................................... 11 Results and Discussion .............................................................................................................. 12 Acknowledgements ................................................................................................................... 12 References ................................................................................................................................. 13 Table .......................................................................................................................................... 15 Chapter 2: Predicting the effects of climate change on population connectivity and genetic diversity in riverine systems ....................................................................................................... 17 Abstract ..................................................................................................................................... 17 Introduction ............................................................................................................................... 18 Methods ..................................................................................................................................... 20 Results ....................................................................................................................................... 25 Discussion ................................................................................................................................. 29 Acknowledgements ................................................................................................................... 33 References ................................................................................................................................. 33 Tables and Figures .................................................................................................................... 39 Supplementary Information ....................................................................................................... 49 Chapter 3: Development and characterization of 20 polymorphic microsatellite markers for the Texas hornshell, Popenaias popeii (Bivalvia: Unionidae), through next-generation sequencing .................................................................................................................................... 55 Abstract ..................................................................................................................................... 55 Introduction ............................................................................................................................... 55 Methods ..................................................................................................................................... 56 Results and Discussion .............................................................................................................. 57 Acknowledgements ................................................................................................................... 57 iii References ................................................................................................................................. 58 Table .......................................................................................................................................... 60 Chapter 4: Past climate change drives current genetic structure of an endangered freshwater mussel species ........................................................................................................... 62 Abstract ..................................................................................................................................... 62 Introduction ............................................................................................................................... 63 Methods ..................................................................................................................................... 66 Results ....................................................................................................................................... 71 Discussion ................................................................................................................................. 75 Acknowledgements ................................................................................................................... 79 References ................................................................................................................................. 80 Tables and Figures .................................................................................................................... 88 Supplementary Information ......................................................................................................
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