University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2013-05-01 The Landscape Genetic Patterns of Culaea inconstans Kremer, Cory S. Kremer, C. S. (2013). The Landscape Genetic Patterns of Culaea inconstans (Unpublished master's thesis). University of Calgary, Calgary, AB. doi:10.11575/PRISM/28227 http://hdl.handle.net/11023/686 master thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY The Landscape Genetic Patterns of Culaea inconstans by Cory Stuart Kremer A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE DEPARTMENT OF BIOLOGICAL SCIENCES CALGARY, ALBERTA APRIL, 2013 © Cory Stuart Kremer 2013 Abstract Landscape genetics is a new field that investigates the consequences of landscape features on population genetic patterns. The small lakes of Alberta, and the brook stickleback (Culaea inconstans) that inhabit them, provide a unique system where populations are highly fragmented and isolated from one another. These lakes are prone to winterkills hypothesized to precipitate frequent bottleneck events in brook stickleback populations. As predicted, brook stickleback populations exhibited a high degree of population structure, and were hierarchically structured by small scale watersheds. AIC analyses of the role of spatial features found support for basin characteristics in driving patterns of genetic diversity, which was also consistent with the detection of recent bottlenecks in at least five of the sampled lakes. These results suggest that brook stickleback population genetic patterns are primarily controlled by processes that accelerate genetic drift, reinforcing the importance of connectivity in the maintenance of genetic diversity in fragmented landscapes. ii Acknowledgements I first wish to thank my Supervisor and Co-Supervisor, Sean Rogers and Steve Vamosi, for resources that they allocated to myself, and my project during my time in their labs. Next, I would like to thank the Alberta Conservation Association for their funding of this project. This project was also funded through Sean Rogers’ NSERC Discovery and Alberta Innovates Technology Futures grants, and so I wish to also thank these funding agencies. A special thank you is owed to Stefan Dennenmoser (a Ph.D. student also supervised by Sean Rogers and Steve Vamosi), for his daily input, guidance, and support into my project. Another special thank you is owed to Stephen Hausch (a Ph.D. student supervised by Steve Vamosi and Jeremy Fox), for his analytical suggestions, input, and support. I also thank all my other lab mates who provided suggestions or technical support, and the two field assistants, Tasha Hansen (2011) and Brandon Allen (2012), who assisted me in the collection and DNA extraction of my samples. I would also like to thank my family, and in particular my Mother (Carolyn Kremer) and Father (Rob Kremer) for their never ending support throughout not only this part of my journey, but through all of it. Lastly, I would like to thank Anke Nijenhuis for her support and friendship on the ‘frontline’ during my work on this project. iii Table of Contents Abstract............................................................................................................................... ii Acknowledgements............................................................................................................iii Table of Contents............................................................................................................... iv List of Tables ..................................................................................................................... vi List of Figures and Illustrations .......................................................................................viii Glossary .............................................................................................................................. x Chapter 1: General Introduction ......................................................................................... 1 1.1 What is Landscape Genetics? ................................................................................... 1 1.2 Applications of Landscape Genetics......................................................................... 5 1.3 Methodological and Conceptual Challenges of Landscape Genetics....................... 6 1.3.1 Molecular Tools................................................................................................. 7 1.3.2 Experimental Design and Analytical Considerations ...................................... 14 1.4 Population and Landscape Genetics in Freshwater Piscine Systems...................... 17 Chapter 2: The Landscape Genetic Patterns of Culaea inconstans .................................. 21 2.1 Introduction............................................................................................................. 21 2.2 Methods................................................................................................................... 26 2.2.1 Study Area Description.................................................................................... 26 2.2.2 Field Methods .................................................................................................. 27 2.2.3 GIS Methods .................................................................................................... 28 2.2.4 Molecular Methods .......................................................................................... 33 2.2.5 Population Genetics Statistics.......................................................................... 35 2.2.6 Landscape Genetics Statistics.......................................................................... 40 iv 2.3 Results..................................................................................................................... 43 2.4 Discussion............................................................................................................... 48 2.4.1 General Conclusions ........................................................................................ 58 2.5 Tables and Figures .................................................................................................. 63 Bibliography ..................................................................................................................... 96 Appendix 1: The brook stickleback capture statistics regarding the 52 lakes sampled.. 113 Appendix 2: The microsatellite primers tested for amplification and polymorphism, the species that they were originally characterized for, the forward and reverse sequences, their amplification success in brook stickleback, the number of alleles identified (NA, if selected for genotyping), the observed heterozygosity (Ho), and the expected heterozygosity of genotyped markers (He). An asterisk associated with allele size range indicates that the size range includes a M13 tag............................................................. 115 Appendix 3: The source code for several R functions that were written and used in the data manipulation and assemblage of input data files for the analysis of genetic data. 120 Appendix 4: The spatial metrics associated with the 52 lakes sampled. ........................ 125 Appendix 5: The genotypes of all individuals genotyped in GENEPOP format, including individuals that were excluded from analysis as a result of missing 3 or more loci. Missing data are denoted by 000000. ............................................................................. 128 v List of Tables Table 2.1: Linear model classification and justification for describing allelic and private allelic richness. All spatial metrics were included as univariate models, and so their justification is also included in this table.......................................................................... 77 Table 2.2: Details of the spatial data used to calculate landscape metrics and pairwise distances............................................................................................................................ 81 Table 2.3: The proportion of loci deviating from Hardy-Weinberg expectations in brook stickleback populations in 25 small lakes in Central Alberta, when adjusted using two different corrections for multiple comparisons (Sequential Bonferroni, SB, and False Discovery Rate, FDR)....................................................................................................... 82 Table 2.4: The percentage of populations deviating from Hardy-Weinberg expectations (HWE) at 11 loci in brook stickleback populations in 25 small lakes in Central Alberta, when adjusted using two different corrections for multiple comparisons (Sequential Bonferroni, SB, and False Discovery Rate, FDR)............................................................ 83 Table 2.5: The percentage of tests demonstrating significant linkage disequilibrium (LD) at 11 loci in brook stickleback populations in 25 small lakes in Central Alberta, when adjusted using two different corrections for multiple comparisons