Evolution of floral regulatory genes in the Lamiales

The genetic regulation of floral development is remarkably conserved among flowering plants (angiosperms) despite dramatic differences in floral morphology. This apparent conflict between conserved genetic regulation of development despite large scale morphological diversification is a common theme among plants and animals that naturally leads to the question of how regulatory genes contribute to evolution. One commonly cited mechanism involves gene duplication, whereby duplicate regulatory genes provide source material for evolution. However, the role of selection in this process is unclear. In this dissertation, I first explore the use of evolutionary models to test hypotheses regarding how selection acts among genes. Using computer simulations, fixed-sites models are shown to have significant power to detect differences in the non-synonymous to synonymous substitution ratio (o, an index of selection pressure) among even highly constrained genes. Likelihood ratio tests of these models should be interpreted cautiously, however, as the chi 2 approximation is biased in some cases.;Next, I investigate duplication of floral regulatory genes in the Lamiales. Homologs of three genes that interact during floral development and regulate floral induction (FLO), boundary specification (FIM), and organ identity (DEF) in the model species Antirrhinum majus were cloned from taxa representing several evolutionary lineages of Lamiales. Phylogenetic analyses of homologs support simultaneous duplication of FLO and DEF after divergence with the lineage leading to A. majus, consistent with whole genome duplication resulting in functional duplicates conserved among several families that separated 30 to 50 million years ago. Phylogenetic analyses of FIM homologs are inconclusive regarding duplication and copy number in Lamiales.;I then use codon substitution models to study the role of selection in the evolution of FLO and DEF duplicates in Lamiales. These models show that o increases following duplication for one (FLO) or both (DEF) duplicates due to relaxed purifying selection rather than positive selection and that changes are distinct among different functional domains. These patterns suggest preservation of FLO and DEF duplicates via a sub-functionalization type mechanism, consistent with the view that duplicate regulatory genes contribute to evolution primarily through cis-regulatory changes rather than adaptive evolution of protein-coding domains.;This dissertation includes co-authored material.