Systematics of Cactaceae Juss.: phylogeny, cpDNA evolution, and classification, with emphasis on the genus Mammillaria Haw

The Cactaceae is a family of New World dicotyledonous angiosperms noted for its ecogeographic significance and highly specialized vegetative features adapted to arid environments. Generic limits and phylogenetic relationships between taxa of this family have been in a state of flux, hindering evolutionary studies. In this thesis original DNA sequence data from the multiple chloroplast regions for 157 species of Cactaceae, Portulacaceae, Basellaceae, Halophytaceae, and Didieraceae are analyzed using maximum parsimony, minimum evolution, and Bayesian methods to reconstruct phylogenetic relationships, and shed light on the tempo and mode of Cactaceae evolution. The seemingly abrupt appearance of novel adaptations marking the origin of new taxa at relatively higher rank has intrigued biologists even before Darwin. In Cactaceae, major morphological disjunctions between leafy and leafless cacti have been difficult to explain. Evidence of lineage specific increases in the rate of accumulation of nucleotide replacements is presented here based on Bayesian analyses of three protein-coding chloroplast genes. The first increase in evolutionary rate, occurring soon after the origin of the family, is discussed in the context of aridity as a stimulus to quantum evolution. A much more recent rate increase was observed in the derived genus Mammillaria. Mammillaria, the largest genus of Cactaceae, has historically been viewed as the main lineage in a complex of small and micro genera sharing tuberculate podaria and complex taxonomy. This study also investigates "What is a Mammilllaria?" To circumscribe a monophyletic Mammillaria and clarify several small genera, most type species of the Mammillaria complex were sampled and character sampling was expanded to include four intergenic spacer regions and three Group II chloroplast introns in addition to the 3- gene coding data set. In contrast to previous molecular studies in Cactaceae, the broad sampling of taxa and characters used here provided sufficient resolution and confidence in results to allow revision of the suprageneric classification based on chloroplast phylogeny. A nomenclaturally sensitive approach has been used in producing an explicitly phylogenetic revision of classification.