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Conservation Genetics of the Sheepnose Mussel (Plethobasus Cyphyus) Sara Margaret Schwarz Iowa State University

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Conservation Genetics of the Sheepnose Mussel (Plethobasus Cyphyus) Sara Margaret Schwarz Iowa State University Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2018 Conservation genetics of the Sheepnose mussel (Plethobasus cyphyus) Sara Margaret Schwarz Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Natural Resources and Conservation Commons Recommended Citation Schwarz, Sara Margaret, "Conservation genetics of the Sheepnose mussel (Plethobasus cyphyus)" (2018). Graduate Theses and Dissertations. 16667. https://lib.dr.iastate.edu/etd/16667 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Conservation genetics of the Sheepnose mussel (Plethobasus cyphyus) by Sara Margaret Schwarz A thesis submitted to the graduate faculty in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Major: Ecology and Evolutionary Biology Program of Study Committee: Kevin Roe, Major Professor John Nason Julie Blanchong The student author, whose presentation of the scholarship herein was approved by the program of study committee, is solely responsible for the content of this thesis. The Graduate College will ensure this thesis is globally accessible and will not permit alterations after a degree is conferred. Iowa State University Ames, Iowa 2018 Copyright © Sara Schwarz, 2018. All rights reserved. ii TABLE OF CONTENTS Page LIST OF FIGURES ........................................................................................................... iv LIST OF TABLES .............................................................................................................. v ACKNOWLEDGMENTS ................................................................................................ vii ABSTRACT ..................................................................................................................... viii CHAPTER 1. INTRODUCTION ....................................................................................... 1 CHAPTER 2. CONSERVATION IMPLICATIONS OF HISTORICAL AND CONTEMPORARY GENE FLOW IN THE SHEEPNOSE MUSSEL (PLETHOBASUS CYPHYUS) ............................................................................................. 7 Abstract .......................................................................................................................... 7 Introduction ................................................................................................................... 8 Methods ....................................................................................................................... 14 Data Collection ....................................................................................................... 14 Study Area and Sampling ................................................................................. 14 Microsatellites ................................................................................................... 16 Mitochondrial Sequences .................................................................................. 16 Data Analysis ......................................................................................................... 17 Microsatellites ................................................................................................... 17 Genetic Diversity ......................................................................................... 17 Population Structure .................................................................................... 18 Estimation of Migration ............................................................................... 18 Changes in Population Size ......................................................................... 20 Mitochondrial Sequences .................................................................................. 21 Sequence Diversity ...................................................................................... 21 Population Expansion .................................................................................. 22 Results ......................................................................................................................... 22 Microsatellites ........................................................................................................ 22 Genetic Diversity .............................................................................................. 22 Population Structure .......................................................................................... 25 Estimation of Migration .................................................................................... 27 Contemporary Migration Estimation ........................................................... 27 Historical Migration Estimation .................................................................. 28 Changes in Population Size ............................................................................... 32 Mitochondrial Sequences ....................................................................................... 32 Sequence Diversity ........................................................................................... 32 Population Expansion ....................................................................................... 34 Discussion .................................................................................................................... 35 Genetic Diversity .................................................................................................... 35 Population Structure ............................................................................................... 36 iii Migration ................................................................................................................ 37 Population Size Changes ........................................................................................ 38 Management Implications ...................................................................................... 38 CHAPTER 3. GENERAL CONCLUSIONS .................................................................... 41 REFERENCES ................................................................................................................. 43 iv LIST OF FIGURES Page Figure 1. Counties where Sheepnose historically occurred (left). Counties where Sheepnose are known to occur since 1990 (right). (United States Fish and Wildlife Service 2002) ........................................................................... 13 Figure 2. Sampling locations of the seven sites from which Sheepnose mussels were sampled for genetic analysis. ........................................................................ 15 Figure 3. Number of genetic populations (K) as determined by the second order rate of change in the distribution of likelihoods of K using the Evanno method. ......................................................................................................... 25 Figure 4. STRUCTURE clustering of the seven sampled Sheepnose populations into K = 2 groups corresponding to Upper Mississippi (CHIP, MER, MISS, and WIS) and Ohio River (ALL, TIPP, and TN) basins. ............................. 26 Figure 5. Neighbor joining tree of all Sheepnose sampling sites based on Nei’s genetic distance. ........................................................................................... 27 Figure 6. Pattern of contemporary gene flow estimated by BAYESASS (Wilson and Rannala 2003) between sampling sites. The arrow colors and arrow heads indicate the direction of migration from the sources. ......................... 28 Figure 7. Pattern of historical gene flow pattern estimated by MIGRATE (Beerli 2008) between sampling sites. The arrow colors and arrow heads indicate the direction of movement of migrants from sources. The dotted lines represent bidirectional migration between sampling sites. ....... 29 Figure 8. Minimum spanning network of 39 haplotypes detected. Colors indicate sites and size of circle represents number of haplotypes. Tick marks indicate number of mutational differences between haplotypes. ................. 34 v LIST OF TABLES Page Table 1. Numbers of Sheepnose mussels sampled from seven study sites for microsatellite and mitochondrial genotyping. .............................................. 15 Table 2. List of loci with the associated repeat motif, annealing temperature, and number of alleles for each locus. * indicates values that were not reported because the locus was dropped from analysis. ............................... 24 Table 3. Observed (Ho) and expected (HE) heterozygosity, allelic richness, private alleles, and fixation index (inbreeding) of each site across all loci. ............. 24 Table 4. Pairwise adjusted FST values among all sites. ................................................... 24 Table 5. Analysis of molecular variance (AMOVA) results for the K = 2 Upper Mississippi and Ohio River based genetic clusters identified using STRUCTURE. .............................................................................................. 26 Table 6. Asymmetrical pairwise contemporary migration rates and associated 95% confidence intervals generated by BAYESASS. The left column represents the source site and
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