The University of Southern Mississippi The Aquila Digital Community Dissertations Spring 5-2016 A Comparative Study of Isolation in Headwater Fishes Bjorn Victor Schmidt University of Southern Mississippi Follow this and additional works at: https://aquila.usm.edu/dissertations Part of the Biology Commons, Genetics and Genomics Commons, and the Marine Biology Commons Recommended Citation Schmidt, Bjorn Victor, "A Comparative Study of Isolation in Headwater Fishes" (2016). Dissertations. 356. https://aquila.usm.edu/dissertations/356 This Dissertation is brought to you for free and open access by The Aquila Digital Community. It has been accepted for inclusion in Dissertations by an authorized administrator of The Aquila Digital Community. For more information, please contact [email protected]. A COMPARATIVE STUDY OF ISOLATION IN HEADWATER FISHES by Bjorn Victor Schmidt A Dissertation Submitted to the Graduate School and the Department of Biological Sciences at The University of Southern Mississippi in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Approved: ________________________________________________ Dr. Jake Schaefer, Committee Chair Professor, Biological Sciences ________________________________________________ Dr. Brian Kreiser, Committee Member Professor, Biological Sciences ________________________________________________ Dr. David Duvernell, Committee Member Professor, Biological Sciences, Southern Illinois University Edwardsville ________________________________________________ Dr. Donald Yee, Committee Member Associate Professor, Biological Sciences ________________________________________________ Dr. Micheal Davis, Committee Member Associate Professor, Biological Sciences ________________________________________________ Dr. Karen S. Coats Dean of the Graduate School May 2016 COPYRIGHT BY Bjorn Victor Schmidt 2016 Published by the Graduate School ABSTRACT A COMPARATIVE STUDY OF ISOLATION IN HEADWATER FISHES by Bjorn Victor Schmidt May 2016 Headwater resident fishes may be prone to a high rate of population fragmentation within river networks because large streams have habitat conditions outside of their preferred ecological niche and may limit gene flow in the dendritic ecological network. To investigate patterns of population structure, asymmetrical gene flow, and influences on genetic distance and isolation from connecting habitat pathways, species specific ecological traits, and basin scale characteristics, a multi-species, multi-regional study was performed. Six headwater species of fish from four taxonomic groupings were sampled for genetic material in three regions of paired neighbor drainages and then genotyped for eight microsatellite loci. All species were found to have a nested hierarchical population structure relating to regional and geographical structure of drainages. There were also differences in rates of fragmentation across the species and regions studied, with Fundulus olivaceus and the Lower Mississippi River having the lowest rates. Most of the headwater species were found to have patterns with the majority of drainages supporting asymmetrical upstream gene flow along the main stem of the networks. Five of the species were found to have significant Isolation by Distance, and four of the species were found to have significant Isolation by Resistance due to large streams. The reservoir in the Pearl River was found to not significantly increase genetic distance, while the reservoir in the Little Red River significantly increased genetic distance. Headwater specialization and a combination of ii opportunistic strategy and periodic strategy life history traits were found to increase isolation rates across species. The amount of available habitat within drainages and the shape of the drainage were found to have the most influence on genetic distance patterns at large scales. This study shows that natural fragmentation of populations within networks is common across different species of headwater fishes, and is related to specific ecological characteristics of those species and regional characteristics of the drainage network. This project contributes to the understanding of how habitat preference within dendritic networks influences genetic population structure and provides a background rate of fragmentation in common headwater species that can be used for comparison with threatened or endangered species. iii ACKNOWLEDGMENTS I would like to thank my committee members for their guidance and advice in completing this project. I would especially like to thank my advisor, Jake Schaefer, for the technical advice for methods and statistics and project design and scope, for helping with sampling equipment and logistics, and for helping review this document. I would like to especially thank Brian Kreiser for teaching me genetic techniques used in the study and for generously allowing me to use lab equipment for this study. I would also like to thank Kyle Pillar for his advice and help with earlier stages of the project. I would like to thank Chazz Coleman, Yadong Shi Schmidt, Scott Clark, Charles Champagne, Laura Stewart, Paul Mickle, Jared Harris, Mikaela Howie, and Justin Dyer for help collecting samples in the field. I would also like to thank Justin Dyer for performing DNA extractions for some of the species in the dataset. I would like to thank the following fish research collections for providing presence localities for the study: University of Alabama Ichthyological Collection, Auburn University Museum of Natural History, Florida Museum of Natural History Ichthyology Collection, Illinois Natural History Survey, University of Kansas Biodiversity Institute, Los Angeles County Museum of Natural History, Mississippi Museum of Natural Science, Ohio State University – Fish Division, Sam Noble Oklahoma Museum of Natural History, University of Southern Mississippi Ichthyology Collection, Museum of Southwestern Biology, University of Tennessee – Etnier Ichthyological Research Collection, Texas A&M University Biodiversity Research and Teaching Collection, Tulane University Museum of Natural History – Royal D. Suttkus Fish Collection, and Yale University Peabody Museum. iv DEDICATION Luck affects everything; let your hook always be cast; in the stream where you least expect it, there will be a fish. – Ovid For my son Andrew, may you always have the courage to cast your hook in life. v TABLE OF CONTENTS ABSTRACT ........................................................................................................................ ii ACKNOWLEDGMENTS ................................................................................................. iv DEDICATION .................................................................................................................... v LIST OF TABLES ............................................................................................................. ix LIST OF ILLUSTRATIONS ............................................................................................ xii LIST OF ABBREVIATIONS ........................................................................................... xx CHAPTER I – COMPARATIVE HIERARCHICAL POPULATION STUCTURE OF HEADWATER FISHES ..................................................................................................... 1 Introduction ..................................................................................................................... 1 Methods........................................................................................................................... 6 Results ........................................................................................................................... 10 Discussion ..................................................................................................................... 16 References ..................................................................................................................... 62 CHAPTER II – DIRECTIONAL GENE FLOW BETWEEN HEADWATER SYSTEMS ALONG THE MAIN STEM OF A RIVER NETWORK ................................................ 71 Introduction ................................................................................................................... 71 Methods......................................................................................................................... 75 Results ........................................................................................................................... 79 Discussion ..................................................................................................................... 79 vi References ................................................................................................................... 105 CHAPTER III – ISOLATION BY DISTANCE AND ISOLATION BY CONNECTING PATHWAY RESISTANCE FOR HEADWATER FISHES .......................................... 109 Introduction ................................................................................................................. 109 Methods....................................................................................................................... 114 Results ......................................................................................................................... 117 Discussion ................................................................................................................... 119 References ..................................................................................................................