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Fishes As a Template for Reticulate Evolution University of Arkansas, Fayetteville ScholarWorks@UARK Theses and Dissertations 12-2016 Fishes as a Template for Reticulate Evolution: A Case Study Involving Catostomus in the Colorado River Basin of Western North America Max Russell Bangs University of Arkansas, Fayetteville Follow this and additional works at: http://scholarworks.uark.edu/etd Part of the Evolution Commons, Molecular Biology Commons, and the Terrestrial and Aquatic Ecology Commons Recommended Citation Bangs, Max Russell, "Fishes as a Template for Reticulate Evolution: A Case Study Involving Catostomus in the Colorado River Basin of Western North America" (2016). Theses and Dissertations. 1847. http://scholarworks.uark.edu/etd/1847 This Dissertation is brought to you for free and open access by ScholarWorks@UARK. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of ScholarWorks@UARK. For more information, please contact [email protected], [email protected]. Fishes as a Template for Reticulate Evolution: A Case Study Involving Catostomus in the Colorado River Basin of Western North America A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology by Max Russell Bangs University of South Carolina Bachelor of Science in Biological Sciences, 2009 University of South Carolina Master of Science in Integrative Biology, 2011 December 2016 University of Arkansas This dissertation is approved for recommendation to the Graduate Council. _____________________________________ Dr. Michael E. Douglas Dissertation Director _____________________________________ ____________________________________ Dr. Marlis R. Douglas Dr. Andrew J. Alverson Dissertation Co-Director Committee Member _____________________________________ Dr. Thomas F. Turner Ex-Officio Member Abstract Hybridization is neither simplistic nor phylogenetically constrained, and post hoc introgression can have profound evolutionary effects. Most studies have focused on tractable model systems, rather than organisms with complicated phylogenetic histories. Finescale Sucker (genus Catostomus) in western North America is recognized as a paradigm of fish hybridization. Yet, its extent of historic and contemporary introgression is largely unstudied, an aspect that impedes the resolution of its phylogeny as a baseline for conservation. To explore reticulation in this group, I assayed variation of 20 Catostomus species across temporal and geographic scales by analyzing hundreds of samples and employing a combination of molecular and bioinformatic approaches. Chapter-1 examined hybridization among native suckers in an anthropogenically- fragmented environment using sequence analysis of mitochondrial and nuclear markers. Introgression was not detected, but hybridization with Utah Sucker likely lowers recruitment in the rarer Bluehead Sucker in the Bonneville Basin. Chapter-2 tested discordant mitochondrial and morphological hypotheses by evaluating historical introgression in Catostomus using 14,007 ddRAD loci comprising 179,811 SNPs. A well-supported phylogeny offered insights into the effects of admixture on different phylogenetic methods, but tests for introgression allowed resolving previous taxonomic discords. Chapter-3 dissected phylogenomic patterns and tested species-delimitations for taxa with admixed ancestry. Comparative population genetic and phylogenetic analyses supported taxonomic revisions in two species of conservation concern, and highlight that response to vicariant events is modulated by species-specific life history variation. Chapter-4 assessed historic and contemporary admixture across 10 co-occurring endemic and invasive species using ~90k SNPs with hundreds of unlinked, fixed species-specific markers. This genomic approach allowed to discern complex hybridization patterns across an entire basin and revealed elevated reproductive isolation at greater phylogenetic distance. In combination, these analyses examined evolutionary reticulation among freshwater fishes of conservation concern in a large, geographically diverse, but heavily altered watershed, the Colorado River Basin, and highlighted both the complexity and constraints of introgressive hybridization. Insights from this study will aid in conservation of aquatic ecosystems in the arid Southwest further jeopardized by anthropogenic threats and an uncertain climatic future. Acknowledgements Numerous state, federal, and tribal agencies contributed field expertise, specimens, technical assistance, collecting permits, funding or comments for completion of this projects, Particular thanks goes to Paul Thompson and Krissy Wilson from Utah Division of Wildlife Resources who provided samples and support for Chapter 1. Samples were also provided by Brian Sidlauskas from the Oregon State Museum, Thomas Turner and Lex Snyder from the Museum of Southwestern Biology at University of New Mexico, Mary Peacock at the University of Nevada, and Jonathan Richmond at USGS. I would also like to acknowledge my fellow lab mates especially Steve Mussman and Tyler Chafin for their assistance and comments. I also acknowledge my advisors Michael Douglas and Marlis Douglas as well as my committee members Thomas Turner and Andrew Alverson for providing guidance and support. The Arkansas High Performance Computing Center also provided support and hardware accent. This research would not have been possible without funding provided by various state and federal agencies, and last but not least by the University of Arkansas through scholarships and generous endowments: The Bruker Professorship in Life Sciences (M.R.D.), 21st Century Chair in Global Change Biology (M.E.D.), Professor Delbert Swartz Endowed Graduate Fellowship, and James and Carol Hendren Fellowship. Table of Contents I. Introduction ............................................................................................................... 1 II. Anthropogenic Impacts Facilitate Native Fish Hybridization in the Bonneville Basin of Western North America .............................................................................. 10 A. Abstract ............................................................................................................... 10 B. Introduction ......................................................................................................... 11 C. Methods ............................................................................................................... 12 D. Results ................................................................................................................. 14 E. Discussion ........................................................................................................... 15 F. Conclusion .......................................................................................................... 17 G. Acknowledgements ............................................................................................. 18 H. References ........................................................................................................... 19 I. Tables .................................................................................................................. 22 J. Figure Headings .................................................................................................. 25 III. The Effects of Introgression in Resolving Phylogenetic Discord in Catostomus (Pisces: Catostomidae) .............................................................................................. 28 A. Abstract ............................................................................................................... 28 B. Introduction ......................................................................................................... 29 C. Methods ............................................................................................................... 32 D. Results ................................................................................................................. 37 E. Discussion ........................................................................................................... 41 F. Conclusion .......................................................................................................... 50 G. Acknowledgements ............................................................................................. 53 H. References ........................................................................................................... 54 I. Tables .................................................................................................................. 62 J. Figure Headings .................................................................................................. 69 IV. Comparative Species Delimitations in the Presence of Interspecific Gene Flow: Flannelmouth (Catostomus latipinnis) and Bluehead Sucker (C. Pantosteus discobolus) as Case Studies ....................................................................................... 74 A. Abstract ............................................................................................................... 74 B. Introduction ......................................................................................................... 76 C. Methods ............................................................................................................... 79 D. Results ................................................................................................................
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