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Status and Population Genetics of the Alabama Spike (Elliptio Arca) in the Mobile River Basin

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Status and Population Genetics of the Alabama Spike (Elliptio Arca) in the Mobile River Basin STATUS AND POPULATION GENETICS OF THE ALABAMA SPIKE (ELLIPTIO ARCA) IN THE MOBILE RIVER BASIN A Thesis by DANIEL HUNT MASON Submitted to the Graduate School at Appalachian State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE August, 2017 Department of Biology STATUS AND POPULATION GENTICS OF THE ALABAMA SPIKE (ELLIPTIO ARCA) IN THE MOBILE RIVER BASIN A Thesis by DANIEL HUNT MASON August, 2017 APPROVED BY: Michael M. Gangloff, Ph.D. Chairperson, Thesis Committee Matthew C. Estep, Ph.D. Member, Thesis Committee Lynn M. Siefermann, Ph.D. Member, Thesis Committee Zack E. Murrell, Ph.D. Chairperson, Department of Biology Max C. Poole, Ph.D. Dean, Cratis D. Williams School of Graduate Studies Copyright by Daniel Hunt Mason 2017 All Rights Reserved Abstract STATUS AND POPULATION GENETICS OF THE ALABAMA SPIKE (ELLIPTIO ARCA) IN THE MOBILE RIVER BASIN Daniel H. Mason B.A., Appalachian State University M.A., Appalachian State University Chairperson: Dr. Michael M. Gangloff Declines in freshwater mussels (Bivalvia: Unionioda) are widely reported but rarely rigorously tested. Additionally, the population genetics of most species are virtually unknown, despite the importance of these data when assessing the conservation status of and recovery strategies for imperiled mussels. Freshwater mussel endemism is high in the Mobile River Basin (MRB) and many range- restricted taxa have been heavily impacted by riverine alterations, and many species are suspected to be declining in abundance, including the Alabama Spike (Elliptio arca). I compiled historical and current distributional data from all major MRB drainages to quantify the extent of declines in E. arca range based on naïve occupancy. I calculated change in area of occurrence (AOO) between 1987-2002 and 2003-2016 using 12 digit USGS HUCs as occurrence units. Concurrently, I used microsatellite markers to describe the population-level genetic characteristics of E. arca and identify differentiated lineages within the species. I did not detect a statistically significant change in the occupancy rates over the past 30 y. Calculations iv indicate that AOO increased by 5.6% from 1987-2002 to 2003-2016. My data provide no evidence to indicate that E. arca warrants elevated conservation status. However, genetic data show conflicting measures of diversity, and low rates of gene flow between drainages. Intraspecific genetic structure in E. arca is most significantly related to the geographic separation of the Tombigbee and Tallapoosa River Drainages, at both microsatellite and mitochondrial loci. Secondary structure is present among sites. My research shows that despite a lack of evidence for population declines or decrease in occupied area, detection is low for E. arca even with a species-specific study design, and that there are at least two divergent meta- populations within the species. These findings represent the first population genetic data for a Gulf Slope freshwater mussel and will help inform management decisions for this native and imperiled taxon. v Acknowledgments I’d like to acknowledge and thank Drs. Matt Estep, Sarah Marshburn, Mike Gangloff and Lynn Siefferman, who have contributed a great deal to this thesis through their assistance and critiques. I also owe great thanks to Carla Atkinson, Stuart McGregor, the Franklin family, Monica Winebarger, Worth Pugh, Ashley Yuan, Tara Early, Gary Pandolfi, Michael Thompson, Susie Geda, Dave Werneke, Alex Lamle and the biological staff of the Westervelt Co. for their assistance and support during my field work. The data graciously contributed by Stuart McGregor, Jason Wisnewski, Jeff Powell, Jim Williams and Paul Johnson made much of this study possible, and I wish to express my gratitude for their professional generosity and encouragement. This project was also made possible by internal funding from the Office of Student Research and the Graduate Student Association Senate, and external financial support from Sigma Xi and the North Carolina Wildlife Resource Commission. To Nik Hay, Morgan Harris, Raquel Fagundo, Justin Fischer, Jason Selong and the Gangloff-Siefferman lab members, thank you all for your guidance, encouragement, jokes and lively debates. Carra, I want to thank you for not shunning me despite nearly losing a tooth to my right elbow, and for encouraging my development as a disseminator of science. Gerrit, I’m glad that you’ve gotten your own taste of what it’s like to become a Master, thanks for your wit, humor and for keeping me connected to the world. To Thomas Franklin, I struggle to imagine where I would be without your help and most of all friendship, thank vi you for both. Certainly none of what I’ve achieved would have ever been possible without the loving support of my family and Alexandria Albers, to whom I will never truly be able to explain their significance in my life, nor fully repay them; thank you. vii Table of Contents Abstract .............................................................................................................................. iv Acknowledgments.............................................................................................................. vi List of Tables ..................................................................................................................... ix List of Figures ......................................................................................................................x Foreword ............................................................................................................................ xi Introduction ..........................................................................................................................1 Methods................................................................................................................................5 Results ................................................................................................................................12 Discussion ..........................................................................................................................17 References ..........................................................................................................................26 Appendix A ........................................................................................................................49 Appendix B ........................................................................................................................58 Appendix C ........................................................................................................................98 Vita ...................................................................................................................................106 viii List of Tables Table 1. Summary table of genetic diversity statistics ......................................................43 Table 2. Summary data of 2016 mussel surveys................................................................44 Table 3. Pairwise Fst between sites ....................................................................................47 ix List of Figures Figure 1. Map of past E. arca occurrence records .............................................................38 Figure 2. Map of current E. arca occurrence records ........................................................39 Figure 3. Map of 2016 survey sites and E. arca detections ...............................................40 Figure 4. STRUCTURE bar plots ......................................................................................41 Figure 5. PoPS map of Q-matrices ....................................................................................42 Figure 6. COI haplotype network ......................................................................................43 x Foreword The research resulting in this thesis will be submitted to Conservation Genetics, an international peer-reviewed journal; the body of this thesis has been formatted according to the style guide for that journal. xi Introduction Southeastern North America’s freshwater ecosystems support a huge fraction of the continent’s invertebrate and vertebrate biodiversity. However, many of its freshwater habitats have been subjected to extensive anthropogenic modification. The Mobile River Basin (MRB) is an ancient drainage system, dating from at least the Cretaceous period (Adams 1929; Conant 1964), but today it is one of the most fragmented drainages in the world (Pringle et al. 2000). The MRB and its fauna have been extensively altered by 30 large dams, thousands of low head dams (≤ 10 m high), extensive regions of canals and locks, and the Tennessee-Tombigbee Waterway, a 377 km barge canal linking the Tombigbee River and the Tennessee River drainages in northeastern Mississippi. These extreme habitat modifications fragment stream habitat and have been associated with dramatic changes to MRB freshwater mussel populations (Gangloff et al. 2015; Gangloff and Feminella 2007; Hamstead 2013; Hartfield and Jones 1990; Jones 1991; Mirarchi et al. 2004; Williams et al. 1992). Numerous freshwater mussel taxa have been reported to be experiencing alarming rates of extinction and population declines in the southeastern US (Groombridge and Jenkins 1998; Lydeard and Mayden 1995) yet there are few widely applicable hypotheses about why these declines are occurring (Haag and Williams 2014). It is possible that mussel populations have
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