Population Genetics, Natural Selection and Genetic Architecture of the Selfing Syndrome in the Morning Glory Ipomoea lacunosa by Joanna Lucy Rifkin University Program in Genetics and Genomics Duke University Date: June 2 2017 Approved: ___________________________ Mark Rausher, Supervisor ___________________________ Tom Mitchell-Olds ___________________________ John Willis ___________________________ Kathleen Donohue Dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the University Program in Genetics and Genomics in the Graduate School of Duke University 2017 ABSTRACT Population Genetics, Natural Selection and Genetic Architecture of the Selfing Syndrome in the Morning Glory Ipomoea lacunosa by Joanna Lucy Rifkin University Program in Genetics and Genomics Duke University Date: June 2 2017 Approved: ___________________________ Mark Rausher, Supervisor ___________________________ Tom Mitchell-Olds ___________________________ John Willis ___________________________ Kathleen Donohue An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the University Program in Genetics and Genomics in the Graduate School of Duke University 2017 Copyright by Joanna Lucy Rifkin 2017 Abstract The evolutionary transition from outcrossing to self-pollination occurs frequently in flowering plants and has direct and indirect effects on genomics, life history and floral morphology. The life history and floral traits common to selfing plants are collectively called the "selfing syndrome." This dissertation uses the highly selfing morning glory Ipomoea lacunosa to address three major questions in the evolution of highly selfing plants: what are the genomic consequences of selfing, do the morphological changes associated with the transition to self-pollination result from natural selection or genetic drift, and how does the genetic architecture of those morphological traits affect their evolution? In the first chapter, we analyze genetic data from I. lacunosa and its outcrossing sister species I. cordatotriloba to compare the genomic consequences of selfing in I. lacunosa to theoretical predictions. We find that the reduction in genetic diversity is greater than that predicted by theory, suggesting a population bottleneck in I. lacunosa's history. There is also evidence for the relaxation of natural selection. The second chapter combines these genetic data with phenotypic measurements in a Qst-Fst comparison to determine whether natural selection is responsible for life history and floral morphology differences between I. lacunosa and its outcrossing relative I. cordatotriloba. Our analyses reveal that several component traits in the selfing syndrome diverged in response to natural selection. Chapter Three uses a quantitative trait locus (QTL) mapping approach to characterize the genetic architecture of the selfing syndrome and investigate how genetic correlations between traits affected its evolution. We find generally lower levels of genetic correlation between selfing syndrome traits than previous QTL studies of the selfing syndrome. The low level of genetic correlation indicates that independent selection on selfing syndrome traits is responsible for the evolution of the syndrome as a whole. ii Table of Contents Abstract ......................................................................................................................................... vi List of Tables ............................................................................................................................... vii List of Figures ............................................................................................................................ viii Acknowledgements ..................................................................................................................... ix Introduction ................................................................................................................................... 1 Study System ........................................................................................................................... 3 Outline of Chapters ................................................................................................................ 4 1 Evolution of Reduced Genetic Variation and Relaxed Selection in the highly selfing species Ipomoea lacunosa: a Genomic Perspective .................................................................. 6 1.1 Introduction .................................................................................................................. 6 1.2 Methods ........................................................................................................................ 9 1.2.1 Study system ............................................................................................................ 9 1.2.2 Genome Sequencing and Assembly ................................................................... 11 1.2.3 Transcriptome Sequencing................................................................................... 12 1.2.4 SNP Identification ................................................................................................. 13 1.2.5 Data Analysis ......................................................................................................... 13 1.2.6 Demographic Modeling ....................................................................................... 16 1.3 Results ......................................................................................................................... 18 1.3.1 Genetic Diversity ................................................................................................... 18 1.3.2 Linkage Disequilibrium ........................................................................................ 19 1.3.3 Relaxation of Selection .......................................................................................... 20 iii 1.3.4 Demographic Modeling ....................................................................................... 24 1.4 Discussion ................................................................................................................... 26 1.4.1 Patterns of genetic diversity ................................................................................ 26 1.4.2 Relaxed Selection ................................................................................................... 29 2 Selection is Responsible for the Selfing Syndrome of Ipomoea lacunosa .................... 32 2.1 Introduction ................................................................................................................ 32 2.2 Methods ...................................................................................................................... 35 2.2.1 Study system .......................................................................................................... 35 2.2.2 Samples and plant culture ................................................................................... 36 2.2.3 Phenotypic measurements ................................................................................... 36 2.2.4 Phenotypic comparisons ...................................................................................... 38 2.2.5 SNP calling ............................................................................................................. 38 2.2.6 Calculation of Fst and Qst .................................................................................... 39 2.3 Results ......................................................................................................................... 40 2.3.1 Differences between species ................................................................................ 41 2.3.2 Fst-Qst analysis ...................................................................................................... 42 2.4 Discussion ................................................................................................................... 45 3 The Genetic Architecture of the Selfing Syndrome in Ipomoea lacunosa .................... 52 3.1 Introduction ................................................................................................................ 52 3.2 Methods ...................................................................................................................... 58 3.2.1 Study system .......................................................................................................... 58 3.2.2 Plant material ......................................................................................................... 58 iv 3.2.3 Phenotypic measurements ................................................................................... 59 3.2.3.1 Life history traits ........................................................................................... 59 3.2.3.2 Floral traits ..................................................................................................... 60 3.2.4 Marker identification ............................................................................................ 63 3.2.5 Bioinformatics pipeline ........................................................................................ 64 3.2.6 Linkage map construction .................................................................................... 66 3.2.7 QTL mapping ........................................................................................................