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Phylogeography of the Neotropical Fish Genus Rhoadsia (Teleostei: Characidae) in Ecuador

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Phylogeography of the Neotropical Fish Genus Rhoadsia (Teleostei: Characidae) in Ecuador DePaul University Via Sapientiae College of Science and Health Theses and Dissertations College of Science and Health Winter 3-22-2019 Phylogeography of the Neotropical Fish Genus Rhoadsia (Teleostei: Characidae) in Ecuador Roberto Valentino Cucalón Tamayo DePaul University, [email protected] Follow this and additional works at: https://via.library.depaul.edu/csh_etd Part of the Biology Commons Recommended Citation Cucalón Tamayo, Roberto Valentino, "Phylogeography of the Neotropical Fish Genus Rhoadsia (Teleostei: Characidae) in Ecuador" (2019). College of Science and Health Theses and Dissertations. 310. https://via.library.depaul.edu/csh_etd/310 This Thesis is brought to you for free and open access by the College of Science and Health at Via Sapientiae. It has been accepted for inclusion in College of Science and Health Theses and Dissertations by an authorized administrator of Via Sapientiae. For more information, please contact [email protected]. Phylogeography of the Neotropical Fish Genus Rhoadsia (Teleostei: Characidae) in Ecuador A thesis presented in partial fulfillment of the requirement for the degree of Master of Science By Roberto Valentino Cucalón Tamayo March 2019 Advisor: Dr. Windsor E. Aguirre Department of Biological Sciences College of Science and Health DePaul University Chicago, Illinois Table of Contents Acknowledgments ........................................................................................................................................ iii Abstract ......................................................................................................................................................... 1 CHAPTER I...................................................................................................................................................... 3 Review of the Literature ............................................................................................................................... 3 The Biodiversity Crisis ............................................................................................................................... 3 Endemism in Western Ecuador ................................................................................................................. 5 The Genus Rhoadsia ................................................................................................................................. 5 Major Rivers of Western Ecuador ............................................................................................................. 7 Phylogeography ........................................................................................................................................ 9 Use of Molecular Markers in Evolutionary Studies................................................................................. 10 CHAPTER II .................................................................................................................................................. 13 Introduction ................................................................................................................................................ 13 Methods ...................................................................................................................................................... 18 Data Collection ........................................................................................................................................ 18 DNA Extraction ........................................................................................................................................ 19 Mitochondrial Genes Amplification (Cyt-b and COI)............................................................................... 20 Microsatellite Amplification .................................................................................................................... 21 Sequence Editing and Genotyping .......................................................................................................... 22 DNA Sequence Editing ........................................................................................................................ 22 Microsatellite Genotyping .................................................................................................................. 22 Phylogeographic and Population Genetics Analyses .............................................................................. 23 Linkage Disequilibrium and Hardy Weinberg Equilibrium .................................................................. 23 Neutrality Test..................................................................................................................................... 23 Mantel Test ......................................................................................................................................... 23 Genetic Diversity ................................................................................................................................. 24 Genetic Differentiation ....................................................................................................................... 25 Phylogenetic Analysis .......................................................................................................................... 25 Haplotype Networks ........................................................................................................................... 26 Population Structure Analysis ............................................................................................................. 27 Results ......................................................................................................................................................... 29 Genetic Divergence Between Rhoadsia and the Outgroups .................................................................. 29 Analysis of Mitochondrial Genes (Rhoadsia populations) ...................................................................... 30 i Neutrality Test ........................................................................................................................................ 31 Analysis of Microsatellite Loci ................................................................................................................. 31 Genetic Diversity Indices ......................................................................................................................... 31 Genetic Differentiation ........................................................................................................................... 35 Phylogenetic Analysis .............................................................................................................................. 38 Haplotype Network ................................................................................................................................. 40 Population Structure Analysis with Microsatellites ................................................................................ 41 Discussion.................................................................................................................................................... 44 Species Delimitation and Evolutionary Relationship of Rhoadsia in Ecuador ............................................ 45 Diversification of Rhoadsia in Western Ecuador ........................................................................................ 48 Evolutionary Significant Units of Rhoadsia minor ....................................................................................... 51 Esmeraldas, mostly comprised of panmictic populations of Rhoadsia minor with some genetically distinctive populations ............................................................................................................................ 52 Evolutionary Significant Units of Rhoadsia altipinna .................................................................................. 53 Northern Guayas populations form a transition zone between R. minor and R. altipinna .................... 53 Southern Guayas, genetically distinct from northern Guayas ................................................................ 54 Taura, genetically similar to neighboring sites ....................................................................................... 55 San Pablo and high-elevation Jubones are closely related ..................................................................... 56 Low-elevation and high-elevation Jubones, ancient divergence or independent origins? .................... 57 Santa Rosa, closely related to low-elevation populations of Jubones but independent enough to be considered an evolutionary significant unit ............................................................................................ 58 Possible Geographic Origin of the Genus Rhoadsia .................................................................................... 59 Guayas the most diverse and the most likely place of origin of Rhoadsia ............................................. 60 Evolutionary relationship of Rhoadsia to the neighboring genera Carlana and Parastremma in the subfamily Rhoadsiinae. ........................................................................................................................... 61 Zoogeographic Regions and Potential Evolutionary Breaches of Freshwater Fishes in Western Ecuador 63 Conclusions ................................................................................................................................................
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