Biogeography and Comparative Phylogenetics in Three Fish Species of the Eastern Guiana Shield
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Biogeography and Comparative Phylogenetics in Three Fish Species of the Eastern Guiana Shield by Bonnie Syme A thesis submitted in conformity with the requirements for the degree of Master of Science Department of Ecology and Evolutionary Biology University of Toronto © Copyright by Bonnie Syme 2018 Biogeography and Comparative Phylogeography in Three Fish Species of the Eastern Guiana Shield Bonnie Syme Master of Science Department of Ecology and Evolutionary Biology University of Toronto 2018 ABSTRACT Comparative phylogeography allows us to investigate the relative importance of species specific biological characteristics versus shared historical conditions on species diversification in a region by studying sympatric populations of different taxa. To examine species specific versus shared evolutionary trajectories of freshwater fishes in the Guiana Shield region of South America, I analyzed and compared the population structure of three co-distributed species of the weakly- electric fish genus Gymnotus using mitochondrial gene sequences (cytochrome b). Population analyses indicate that, generally, Gymnotus species show a lack of contemporary gene flow between drainages. The phylogenetic relationship of fish populations between drainages, however, is not congruent among species. These results suggest that, while historical geological events such as the formation of drainages are important for the diversification of freshwater fish species, individual biological attributes, such as dispersal ability, likely play an influential role as well. ii Acknowledgments First and foremost, this study would not have been possible without the assistance of colleagues who collected and generously provided the tissue samples used in this thesis. Thank you to my supervisor, Dr. Nathan Lovejoy. Without his continuous support, positivity, and patience, in both the academic and personal aspects of this undertaking, I simply would not have been able to complete this project. His ability to both push me to my limits, as well as understand when I was uncomfortable with an aspect of the thesis, is something I appreciate beyond words. The timely completion of my thesis would also not have been possible without the support of the entire Lovejoy lab, whom I cannot thank enough. I owe a huge thanks to JP Fontenelle, for both helping to keep me sane with his endless wit and stories during long days in the office, and for being a boundless source of knowledge about all things phylogenetic and mapping and for always sharing that knowledge without hesitation; Ahmed Elbassiouny, who patiently, and with a sense of humour, managed to take me from a clueless student with zero lab experience to a genetic mastermind (almost) and without whom I never would have come out of my shell and interacted with anyone at all, thanks for all those coffee breaks Ahmed; and finally to Katherine Balasingham, for being a comrade in learning how things work in the Lovejoy lab as a fellow newcomer at the time and for being a source of femininity in a lab otherwise dominated by men. Thank you to my supervisory committee, Dr. Nicholas Mandrak and Dr. Marc Cadotte. Your feedback was invaluable. Lastly, thanks to my friends and family, who continuously supported and encouraged me throughout this entire process. Erik, who was always there when I got frustrated, listened to my lamentations, and took me for walks when I lost motivation; my mother who would always pick up the phone when I needed her and who kept me on track; my father, who will always my role-model; and my brother who could always remind me that I could do this. Without them I would be nowhere. iii Table of Contents Acknowledgments.......................................................................................................................... iii Table of Contents…………………………………………………………………………………iv List of Tables ................................................................................................................................. vi List of Figures ............................................................................................................................... vii Chapter 1: INTRODUCTION......................................................................................................... 1 1.1 South American biogeography and the Guiana shield ................................................................. 1 1.2 Comparative Phylogeography ..................................................................................................... 3 1.3 Gene flow and population genetic structure ................................................................................ 5 1.4 Range size and Genetic Structure ................................................................................................ 5 1.5 Cryptic species ............................................................................................................................ 6 1.6 Phylogeography and population structure of freshwater fishes of the Guianas ........................... 7 1.7 Study taxon ................................................................................................................................. 8 1.8 Objectives, Hypotheses and Predictions ...................................................................................... 9 1.9 Significance .............................................................................................................................. 11 Chapter 2: MATERIALS AND METHODS ................................................................................ 13 2.1 Mapping and Drainage Divisions .................................................................................................... 13 2.2 Taxon Sampling .............................................................................................................................. 14 2.3 DNA Extraction .............................................................................................................................. 15 2.4 Polymerase Chain Reactions and Sequencing ................................................................................. 16 2.5 Sequence Alignments and Matrices ................................................................................................ 17 2.6 Phylogenetic Analysis ..................................................................................................................... 18 2.7 Haplotype Analysis ......................................................................................................................... 18 2.8 Calculating Genetic and Geographic Distance Between Samples ................................................... 19 2.9 Statistical Correlation Analyses ...................................................................................................... 20 Chapter 3: RESULTS ................................................................................................................... 21 3.1 Phylogeny ....................................................................................................................................... 21 3.2 Population structure and phylogeography ....................................................................................... 21 3.2.1 G. carapo occidentalis ............................................................................................................. 22 3.2.2 G. carapo carapo ..................................................................................................................... 22 3.2.3 G. coropinae ............................................................................................................................ 23 3.2.4 Gymnotus anguillaris ............................................................................................................... 25 iv 3.3 Correlation between genetic distance and geographic distance ....................................................... 25 3.4 Cryptic species ................................................................................................................................ 27 Chapter 4: DISCUSSION ............................................................................................................. 28 4.1 Population structure of eastern Guiana Shield Gymnotus species ................................................... 28 4.2 Historical biogeography and comparative phylogeography of Gymnotus carapo, Gymnotus coropinae and Gymnotus anguillaris .................................................................................................... 34 4.3 Relationship between range size and population structure .............................................................. 38 4.4 Presence of cryptic species.............................................................................................................. 40 4.5 Conclusions, Limitations and Future Directions ............................................................................. 41 References ..................................................................................................................................... 44 Tables ............................................................................................................................................ 56 Figures……………………………………………………………………………………………64 v List of Tables Table 1. Gymnotus specimens included in this study…………………………………………57 Table 2. Primers used in this study……………………………………………………………63 Table 3. Summary statistics for study taxa……………………………………………………63