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Population Differentiation, Historical Demography and Evolutionary Relationships Among Widespread Common Chaffinch Populations ( Fringilla Coelebs Ssp

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Population Differentiation, Historical Demography and Evolutionary Relationships Among Widespread Common Chaffinch Populations ( Fringilla Coelebs Ssp Population Differentiation, Historical Demography and Evolutionary Relationships Among Widespread Common Chaffinch Populations ( Fringilla coelebs ssp. ) by Pasan Samarasin-Dissanayake A thesis submitted in conformity with the requirements for the degree of Master of Science Ecology and Evolutionary Biology University of Toronto © Copyright by Pasan Samarasin-Dissanayake 2010 Population Differentiation, Historical Demography and Evolutionary Relationships Among Widespread Common Chaffinch Populations ( Fringilla coelebs ssp. ) Pasan Samarasin-Dissanayake Master of Science Department of Ecology and Evolutionary Biology University of Toronto 2010 Abstract Widespread species that occupy continents and oceanic islands provide an excellent opportunity to study evolutionary forces responsible for population divergence. Here, I use multilocus coalescent based population genetic and phylogenetic methods to infer the evolutionary history of the common chaffinch ( Fringilla coelebs ), a widespread Palearctic passerine species. My results showed strong population structure between Atlantic islands. However, the two European subspecies can be considered one panmictic population based on gene flow estimates. My investigation of effects of sampling on concatenated and Bayesian estimation of species tree (BEST) methods demonstrated that concatenation is more sensitive to sampling than BEST. Furthermore, concatenation can provide incorrect evolutionary relationships with high confidence when sample size is small. In conclusion, my results suggest European ancestry for the common chaffinch and Atlantic islands appear to have been colonized sequentially from north to south via Azores. ii Acknowledgements First, I would like to thank Dr. Allan Baker for giving me an opportunity to work in his lab, giving me the independence to explore and learn, and providing guidance when I needed it. Thanks to Dr. Asher Cutter for helpful advice and allowing me to use his cluster for analysis. I am in debt of Oliver Haddrath for training me in molecular laboratory techniques, designing an informative molecular marker (ANON OH) and tremendous support in and out of the lab. Thank you for everyone in the lab including Dr. Erika Tavares, the most helpful postdoc one can imagine; Rosemary Gibson for supporting me in many ways, Alison Cloutier for fun and very educational times in the lab, and Yvonne Verkuil for assistance with analysis and some interesting discussions. Thank you to past and present postdocs Dr. Sergio Pereira and Dr. Debbie Buehler for their assistance, Kristen Choffe for DNA sequencing help, Cathy Dutton and Sue Chopra for administrative support. Thank you to Alivia Dey for friendship. I am very grateful to my parents for their constant support in whatever I chose to do and my sister for running some of my analysis on her computer and annoying me to write this thesis. iii Table of Contents Abstract ………………………………………………………………………………….. ii Acknowledgements …………………………………………………………………….. iii Table of contents ……………………………………………………………………….. iv List of Figures ………………………………………………………………………….. vi List of Tables ………………………………………………………………………….. viii List of Appendices ……………………………………………………………………… ix Chapter 1: General Introduction ………………………………………………………… 1 1.1 Molecular population genetics and molecular phylogenetics ………………. 1 1.2 The common chaffinch ( Fringilla coelebs ) ………………………………… 4 1.3 Thesis objectives ……………………………………………………………. 7 1.4 References …………………………………………………………………… 9 Chapter 2: Population genetic structure and historical demography of the common chaffinch ( Fringilla coelebs ) .………………………...…… 12 2.1 Abstract …………………………………………………………………….. 12 2.2 Introduction ………………………………………………………………… 12 2.3 Methods …………………………………………………………...……….. 17 2.3.1 Sampling ………………………………………………...….……. 17 2.3.2 DNA extraction, amplification and sequencing ………………….. 18 2.3.3 Data analysis ……………………………………………………... 21 2.4 Results ……………………………………………………………………… 24 2.4.1 Summary statistics and neutrality tests …………………………... 24 2.4.2 Haplotype networks …………………………………………….... 28 2.4.3 Genetic clusters and migration rates ……………………………... 32 2.4.4 Effective population sizes and population expansion ……………. 36 2.5 Discussion ………………………………………………………………….. 38 2.5.1 Population structure & subspecies status ……………………….... 41 2.5.2 Effective population size and population expansion …………….. 43 2.5.3 Conclusions ………………………………………………………. 46 2.6 References ………………………………………………………………….. 47 iv Chapter 3: Comparison of multilocus phylogenetic methods for inferring evolutionary relationships among recently diverged common chaffinch subspecies ( Fringilla coelebs ssp. ) ……………………………… 54 3.1 Abstract …………………………………………………………………….. 54 3.2 Introduction ………………………………………………………………… 54 3.3 Methods ……………………………………………………………………. 63 3.3.1 Sampling, DNA extraction, amplification and sequencing ……… 63 3.3.2 Data analysis ……………………………………………………... 66 3.4 Results ……………………………………………………………………… 69 3.5 Discussion ………………………………………………………………….. 73 3.5.1 Effects of sampling on phylogenetic inference …………………... 76 3.5.2 Species tree estimates with some gene flow ……………………... 81 3.5.3 Conclusion ……………….……………….……………………… 82 3.6 References ………………………………………………………………….. 83 Chapter 4: General conclusions ………………………………………………………... 89 4.1 References ………………………………………………………………….. 91 v List of Figures Chapter 1 Figure 1: Evolutionary relationships among Fringilla sp . ……………………................ 4 Figure 2: Distribution map of the common chaffinch ( Fringilla coelebs ) showing part of its total range …………………………………………….….. 5 Chapter 2 Figure 1: Map of sampled common chaffinch populations ……………………………. 17 Figure 2: Median- joining haplotype network of the control region of mtDNA ………. 29 Figure 3: Median- joining haplotype network of nuclear loci EF1 α and PTPN ………. 30 Figure 4: Median- joining haplotype network of nuclear loci TROP and UBIQ ……… 31 Figure 5: Plot of likelihood of data for assumed number of populations (K) in Structure …………………………………………………………………... 33 Figure 6: Probabilistic assignment of individual genotypes to populations (K=5) in Structure ……………………………………………………………. 33 Chapter 3 Figure 1: Discordance between gene trees and the species tree ……………………….. 57 Figure 2: Geographic locations of sampled common chaffinch subspecies (Fringilla coelebs ssp.) ………………………………………………………. 60 Figure 3: Expected phylogenetic relationships among Atlantic island subspecies under different colonization hypothesis …………………………...…………. 62 Figure 4: Evolutionary relationships among common chaffinch subspecies from concatenated Bayesian inference …………………………………………….. 70 Figure 5: Evolutionary relationships among common chaffinch subspecies from estimation of species tree (BEST) method …………………………………… 71 vi Figure 6: The large data set molecular clock tree from Bayesian estimation of species tree (BEST) method ……...……………………………………….. 73 Figure 7: Effect of sampling when multiple gene lineages persist in recently diverged populations ……………………………………………... 76 Figure 8: Most probable colonization pattern of Atlantic Islands and Africa …………. 79 vii List of Tables Chapter 2: Table 1: Sampled loci for population genetic analysis ………………………… 20 Table 2: Population genetic summary statistics ………………………………... 26 Table 3: Migration rate estimates between common chaffinch populations …... 35 Table 4: Effective population size and population expansion ……………….… 37 Chapter 3: Table 1: Details of 9 nuclear loci sampled for phylogenetic analysis …………. 65 viii List of Appendices Appendix 1: Details of the Chaffinch samples used in the study ……………………… 92 ix Chapter 1 General Introduction The study of evolutionary processes responsible for population divergence and speciation is a very important area of research in evolutionary biology. Investigation of structured populations is a key component in understanding how population divergence eventually leads to speciation. According to a simple allopatric model of speciation, an ancestral population splits into two daughter populations and a barrier restricts gene flow between the two daughter populations. In absence of gene flow, the two daughter populations go on different evolutionary trajectories as each population experience random mutations, drift and/or selection. As genetic differences between the two daughter populations accumulate, reproductive isolation may result due to genetic incompatibilities (Coyne and Orr 2004). Understanding details of this process from initial divergence to complete reproductive isolation is an ongoing research goal in evolutionary biology. But it generally takes a long time to go from initial divergence to reproductive isolation; hence study of earth’s biodiversity is historical in nature. The fields of population genetics and phylogenetics attempt to understand historical evolutionary and demographic process responsible for current species distribution, and infer past population divergence events using current molecular data. 1.1 Molecular population genetics and molecular phylogenetics Historically, the fields of population genetics and phylogenetics have asked different questions and have employed different methods. While population genetics is concerned with evolutionary forces acting within a species, the primary goal of 1 phylogenetics is to infer how species relate to each other. However, these two fields can be thought as being part of a continuum that goes from initial divergence of populations to accumulation of genetic differences between those populations to reach reproductive isolation, hence crossing the “species
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