| The use of phylogenies in reconstructing evolutionary sequences and inferring patterns from comparative data is addressed with theoretical and empirical studies, the latter emphasizing sympetalous flowering plants. First, assumptions and methods of analyzing character evolution on phylogenies are considered from the standpoint of parsimony-based estimates of ancestral states. The use of weighted step matrices and permutation tests is investigated as a means of quantifying the robustness of hypotheses about whether homoplasy on a phylogeny represents independent gains or losses of a character. Second, macroevolutionary patterns in the distribution of types of flower symmetry among asterid angiosperms are analyzed on a composite "supertree" phylogeny using maximum-likelihood methods that model changes in flower symmetry as a continuous-time Markov process. Hypotheses about directional trends in the evolution of flower symmetry are tested statistically under various assumptions about phylogenetic branch lengths, and inferences about the symmetry of the ancestral asterid flower are compared under parsimony and maximum-likelihood frameworks. Third, a phylogenetic analysis of chloroplast and nuclear genes is presented for Pedicularis , a group of plants in which putatively rampant parallel evolution in the corolla has led to disparate classification systems. Despite conflicting gene trees, several clades corresponding either to previously recognized taxa, or to morphologically distinct groups, are recovered. Evolutionary rates and directionality of change in vegetative and floral characters are compared, and hypotheses of constraint in the evolution of long corolla tubes are tested. Patterns of floral variation are discussed in relation to previously published observational and experimental data on the pollination and reproduction of Pedicularis throughout its range. |
