UC San Diego

Flowering plants are able to avoid inbreeding by several genetically based mechanisms. Gametophytic self- incompatibility (GSI) occurs when pollen is rejected in the style or on the stigma if it possesses a matching allele with either of the ovule parent's S-alleles. This mechanism typically involves a single genetic locus that is highly polymorphic within populations and species. S- alleles are maintained by strong negative frequency dependent selection that essentially favors alleles when they become rare in a population. This type of balancing selection preserves variation at the S-locus for millions of years enabling us to infer ancient demographic patterns through phylogenetic analyses of genealogies of S-alleles. GSI has been described in several taxa of Solanaceae but only one genus of Papaveraceae, the genus Papaver. Although the molecular mechanisms of self-recognition in these respective families differ remarkably, the underlying theoretical predictions regarding their genetics and evolution are expected to be similar. In Chapter I of this dissertation, I first explore the evolutionary history of a genetic bottleneck in the Solanaceae. Self-incompatible species in the sister genera Physalis and Witheringia share restricted variation at the S-locus indicative of an ancient bottleneck that occurred in a common ancestor. Using phylogenic approaches to look at S-allele variation in species of the subtribe Iochrominae, the clade containing Physalis and Witheringia, we are able to determine when this bottleneck event occurred. We then use two chloroplast markers, fossil calibrations and a Bayesian relaxed molecular clock approach to determine the approximate date of the bottleneck. In Chapter II, I examine the molecular evolution of individual codons from S-alleles from the bottlenecked lineages of Physalis compared to those of the non-bottlenecked lineages of Solanum. Because Physalis S- RNases appear to have diversified more recently than those of Solanum, we find significantly different patterns among amino acids undergoing positive selection using maximum likelihood phylogenetic and Bayesian coalescent methods. (increase in subst. at 4 fold degenerate sites or 3rd position (general synonymous relative to 1-2nd pos.) HyPhy.docs, overall dS increase in Physalis relative to Solanum; overall increase in dN in Physalis?). In Chapter III, I explore the genetics of a putative S-locus polymorphism in three previously uncharacterized species of Papaveraceae native to California. Analyses of putative S-allele sequences from A. munita , P. californicus and Romneya coulteri sampled from natural populations have shown that each harbors substantial genetic polymorphism homologous to stylar S-alleles from Papaver rhoeas. These genes appear to be expressed only in female reproductive tissues as expected for stylar S-locus products. In A. munita and P. californicus, greenhouse crosses among full sibs with matching putative S-genotypes usually don't result in seed set while crosses among individuals with non-matching genotypes almost always do. In addition, potential duplications at or near this locus have been detected in diploid P. californicus. Contrary to other well known SI systems, allelic genealogies from Papaveraceae show a general pattern of monophyletic clustering according to species. Genealogies of these species' S-alleles and those from newly sequenced Papaver alleles show general patterns of monophyletic clustering. The reduced levels of trans-specific polymorphism may be explained by founder events or population bottlenecks in each of the species, though other possibilities must also be considered. We also employ maximum likelihood models to estimate positive selection among putative alleles from these taxa