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University of California, San Diego UNIVERSITY OF CALIFORNIA, SAN DIEGO Evolutionary Genetics of Self-incompatibility in Solanaceae and Papaveraceae A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biology by Timothy Paape Committee in charge: Professor Joshua R. Kohn, Chair Professor Ronald S. Burton Professor Lin Chao Professor Stephen G. Weller Professor Christopher Wills 2009 Copyright Timothy Paape, 2009 All rights reserved. ii The dissertation of Timothy Paape is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego iii Table of Contents Signature Page............................................................................................................. iii Table of Contents ........................................................................................................ iv List of Tables .............................................................................................................. vi List of Figures ............................................................................................................. viii Acknowledgements ..................................................................................................... x Vita and Publications................................................................................................... xi Abstract of the Dissertation ......................................................................................... xiii Chapter I ..................................................................................................................... 1 A 15 Million Year Old Genetic Bottleneck..................................................................1 Abstract....................................................................................................................... 2 Introduction................................................................................................................. 3 Materials and Methods ................................................................................................ 6 Genealogy of S-alleles from Solanaceae ............................................................. 7 Species Phylogeny and Divergence Time............................................................ 9 Results ........................................................................................................................ 13 Discussion................................................................................................................... 15 Acknowledgements ..................................................................................................... 22 References................................................................................................................... 25 Reprint Acknowledgement .......................................................................................... 30 iv Chapter II.................................................................................................................... 31 Differential Selection in S-RNases in the genera Physalis and Solanum....................... 31 Abstract....................................................................................................................... 32 Introduction................................................................................................................. 33 Materials and Methods ................................................................................................ 37 Sequences and Phylogeny Construction .............................................................. 37 Selection Estimates............................................................................................. 38 Results ........................................................................................................................ 44 Discussion................................................................................................................... 48 Acknowledgements ..................................................................................................... 55 References................................................................................................................... 62 Chapter III................................................................................................................... 68 Evolutionary Genetics of S-locus in Papaveraceae....................................................... 68 Abstract....................................................................................................................... 69 Introduction................................................................................................................. 70 Materials and Methods ................................................................................................ 73 Results ........................................................................................................................ 80 Discussion................................................................................................................... 89 Acknowledgements ..................................................................................................... 98 References................................................................................................................... 110 v List of Tables Chapter I Table 1. Prior probability and posterior probability distribution estimates of the Solanaceae phylogeny................................................................... ...................22 Chapter II Table 1. Average pairwise nucleotide divergence among S-alleles. ............................ ..55 Table 2. Rate distributions of non-synonymous and synonomous substitutions in each dataset.....................................................................................................56 Table 3. Sites predicted to be under differential positive selection using the Bayesian ratio of omegas test and the fixed effects likelihood (FEL) test... ....................57 Table 4. Estimates of average non-synonymous (dN) and synonymous (dS) substitutions at terminal branches. ............................................................... ..57 Chapter III Table 1. Results of hand pollinations among Argemone munita full sibs with matching genotype....................................................................................... 99 Table 2. Results of hand pollinations of Platystemon californicus full sibs with matching genotypes. .................................................................................... 100 Table 3. Statistics of combined full sib crosses from each species............................. 100 Table 4. Average pairwise nucleotide divergence among sequences within genera.... 101 vi Table 5. Results of PAML analysis of positive selection on 5’ sequences from Papaver, Argemone and Platystemon…………………………………………….....102 Table 6. Results of non-parametric permutation analyses of recombination and coalescent likelihood estimates of ρ = 4Ner…………………………………….....103 Table 7. Simulation results testing the power to detect recombination under variable levels of genetic diversity….......................................................... 103 vii List of Figures Chapter I Figure 1. Maximum likelihood phylogeny of 72 S-alleles from Solanaceae................. 23 Figure 2. Bayesian consensus species phylogeny and divergence time estimates of the Solanaceae based on sequence data from 2 chloroplast genes. ............... 24 Chapter II Figure 1. Phylogeny of Physalis and Solanum S-RNases........................................... 58 Figure 2. Posterior probability scores of sites predicted to be under positive selection in Physalis and Solanum.............................................................. 59 Figure 3. Bayesian estimate of the ratio of omega values ........................................... 60 Figure 4. Contrast of point estimates of dN/dS for Physalis and Solanum for sites that were found to have omega ratios significantly above 1 ........................ 61 Figure 5. Fixed effects likelihood comparisons of non-synonymous (dN) substitutions at sites predicted to be under significantly different selection pressures .................................................................................................... 61 Figure 6. Power test for Fixed Effects Likelihood test of positive selection on Physalis and Solanum datasets ................................................................... 62 viii Chapter III Figure 1. Amino acid alignment of all sequences containing 5’ ends.......................... 104 Figure 2. Maximum likelihood phylogeny of known Papaver S-alleles putative S- alleles from Alaskan and Californian taxa. ................................................. 105 Figure 3. Sliding window analysis of average pairwise nucleotide diversity of putative S alleles with 5’ ends .................................................................... 106 Figure 4. Sliding window analysis of average pairwise nucleotide diversity of putative S-alleles with 3’ ends.................................................................... 107 Figure 5. RT-PCR of putative S-locus genes from stigmatic, stem and leaf tissues using allele-specific forward primers and a universal amplification reverse primer ............................................................................................ 108 Figure 6. Posterior probabilities
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