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Utilizing Molecular Phylogenetics to Assess Genetic Diversity of Western

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Utilizing Molecular Phylogenetics to Assess Genetic Diversity of Western Comparison of Biogeography Patterns of Two Freshwater Snails - Physa acuta and Helisoma cf. trivolvis by KELLY ROSE MARTIN B.S., University of Wisconsin Madison, 2017 A thesis submitted to the Faculty of the Graduate School of the University of Colorado in partial fulfillment of the requirement for the degree of Master of Science Department of Museum and Field Studies 2019 This thesis entitled: Comparison of Biogeography Patterns of Two Freshwater Snails - Physa acuta and Helisoma cf. trivolvis written by Kelly Rose Martin has been approved for the Department of Museum and Field Studies _____________________________________ Dr. Jingchun Li _____________________________________ Dr. Pieter Johnson _____________________________________ Dr. J. Patrick Kociolek Date____________ The final copy of this thesis has been examined by the signatories, and we find that both the content and the form meet acceptable presentation standard of scholarly work in the above mentioned discipline. Martin, Kelly Martin (M.S., Museum and Field Studies) Comparison of Biogeography Patterns of Two Freshwater Snails - Physa acuta and Helisoma cf. trivolvis Thesis directed by Assistant Professor Dr. Jingchun Li Despite the important roles freshwater gastropods play in aquatic ecosystems, much of their basic biology and ecology are understudied. Particularly, information regarding species distribution, dispersal patterns and population structure is incomplete. This study addressed the biogeography of two native North American freshwater snails, Physa acuta (Gastropoda: Physidae) and Helisoma trivolvis (Gastropoda: Planorbidae), in the western United States and globally. We amplified two genetic markers (COI, 16S) from individuals belonging to multiple populations along the West Coast and downloaded existing genetic data from Genbank for the two species. We utilized minimum spanning networks to compare the population genetic patterns between the species and preformed Analysis of Molecular Variance (AMOVA) and linear regression analyses to determine whether watersheds, geographic distance, or other biotic factors contributed to the observed genetic structuring. We found that P. acuta was more genetically diverse and showed less overall population structuring than H. cf. trivolvis in the West Coast. Overall, we did not find a strong geographical partitioning for either species in the West Coast. Geographic distance and watersheds do not appear to be a predominate factor in shaping the snails’ genetic structure. The North-South genetic similarity indicates that a lack of watershed connectedness does not restrict gene flow. Thus, among watershed dispersal vectors are likely maintaining the snails’ population connectivity. The observed genetic patterns reflect the Pacific Flyway, a major migratory route in the western United States. This suggests that waterfowl are possible vectors in promoting ongoing gene flow over large geographic ranges and impacting the snails’ population structure along the West Coast. An analysis of the population genetics across North America revealed a certain level of East-West genetic structuring in both species. In addition, we found a previously identified P. acuta clade from west of the Rocky Mountains to occur in populations along the eastern slope, suggesting that the clade is not limited to west of the Rockies. The genetic distances among East-West populations in H. cf. trivolvis are relatively high, indicating the presence of a cryptic species. This paper provides an initial framework for continued biogeographical analysis of Physa and Helisoma in their native range. iii Acknowledgments First and foremost, I would like to thank my primary thesis advisor, Dr. Jingchun Li. Her dedication to my success was unparalleled. It was a privilege and an honor to work with someone who cares deeply about the work they do and for her students. She provided critical guidance and expertise throughout this thesis when I needed it most, but she also gave me the space to learn and grow on my own. Thank you for continuously pushing me to be the best scientist I can be. I could not have wished for a better advisor, mentor or advocate than you. I would also like to extend my gratitude to my other committee members, Dr. Pieter Johnson and Dr. Patrick Kociolek. Without their guidance, this thesis would not have been possible. Their willingness to share their expertise and provide meaningful input was essential to the success of this thesis. I would also like to acknowledge the other members of the Li Lab. Your dedication to reading multiple iterations of this thesis was instrumental. Know that your comments and suggestions were greatly appreciated. Your friendship and encouragement mean a lot to me. Additionally, I would like to thank all of the individuals in the Johnson Lab and Jay Bowerman, who facilitated the collection of the specimens used in this study. The scale of this research was only possible with your help. Most importantly, I would like to thank my parents for their constant love and support. You both have taught me to never set a limit on what is possible and to embrace opportunity with an open heart and unwavering mind. You supported me through the highs and lows of this journey and for that I am profoundly grateful. This is for you. I love you. Finally, I am incredibly grateful to all the individuals in the Museum & Field Studies Graduate Program that have contributed to my growth and continued passion for museum collections. I would like to thank the University of Colorado Museum of Natural History for providing financial support of this thesis. iv Table of Contents 1. Introduction………………………………………………………………………………1 2. Methods 2.1 Sampling……………………………………………………………………….……...5 2.2 DNA amplification……………………………………………………………………5 2.3 Population Structure…………………………………………………………………..7 3. Results 3.1 West Coast…………………………………………………………………………….8 3.2 Global………………………………………………………………………………..10 4. Discussion 4.1 West Coast…………………………………………………………………...……....12 4.2 Global………………………………………………………………………………...15 4.3 Broader Implications & Ecological Interactions……………………………………..18 4.3.1 Host-Parasite Interactions………………………………………………….19 4.3.2 Conservation……………………………………………………………….20 4.3.3 Invasive Species……………………………………………………………21 5. Conclusions……………………………………………………………………………...21 Literature Cited………………………………………………………………………………23 Appendix……………………………………………………………………………………..39 v Tables 1. Analysis of molecular variance……………………………………………………………….30 2. Population statistics and molecular diversity indexes, by watershed…………………………30 3. Overall molecular diversity indexes, West Coast……………………………………………..31 4. Population ΦST values between watersheds…………………………………………………...31 vi Figures 1. Museum examples of Physa acuta and Helisoma cf. trivolvis……………………………...32 2. Map of sampling locations………………………………………………………………….32 3. COI haplotype network in the West Coast, Physa acuta…………………………………...33 4. 16S haplotype network in the West Coast, Physa acuta…………………………………....33 5. COI haplotype network in the West Coast, Helisoma cf. trivolvis………………………….34 6. 16S haplotype network in the West Coast, Helisoma cf. trivolvis…………………………..34 7. Global COI haplotype network, Physa acuta………………………………………….……35 8. Global 16S haplotype network, Physa acuta……………………………………….……….35 9. Global COI haplotype network, Helisoma cf. trivolvis…………………………….….……36 10. Effect of geographic distance on pairwise genetic distance, 16S………………….….…...36 11. Effect of geographic distance on pairwise genetic distance, COI………………….….…..37 12. Effect of longitudinal distance on pairwise genetic distance, 16S………………………...37 13. Effect of longitudinal distance on pairwise genetic distance, COI………………………..38 vii 1. Introduction Freshwater snails play important roles in complex ecological interactions. For example, many freshwater snails are intermediate hosts of diverse parasites that ultimately infect vertebrate hosts, including humans (Adema et al. 2012). Some freshwater snails are invasive species, which disrupt ecosystem function, negatively impact agriculture, and threaten native species through predation and competition (Carlsson et al. 2004; Robert 2002; Burlakova et al. 2009). Additionally, freshwater snails can be excellent bioindicators of water quality because of their sensitivity to small-scale disturbances. Unfortunately, freshwater mollusks also represent one of the most threatened animal groups on Earth (Lydeard et al. 2004). Compared to other gastropods, freshwater snails face a disproportionately large risk of extinction (Strong et al. 2007; Lydeard et al. 2004). Their biodiversity losses are a result of anthropogenic impacts, such as habitat loss, degradation and manipulation (Strong et al. 2007). Despite the important roles freshwater gastropods play in aquatic ecology, climatology, conservation, and epidemiology, their basic biology and ecology are still understudied (Adema et al. 2012). Particularly, the understanding of their systematics is largely incomplete (Strong et al. 2007). The taxonomical status of many taxa is uncertain, which is further impaired by a lack of information on species distribution, dispersal patterns and population structure (Strong et al. 2007). If fundamental questions regarding freshwater gastropod ecosystem functions are to be answered, a thorough understanding of their biogeography is essential (Ebbs et al. 2018; Morgan et al. 2002). One of the major factors that determines biogeographical distribution of freshwater snails is their dispersal mode and ability (Brown & Lydeard 2010). Aquatic
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