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The Orchidaceae are one of the most species rich and widespread lineages among angiosperms. They have evolved numerous remarkable vegetative and reproductive traits that have allowed them to successfully adapt and diversify into a wide array of environments. More importantly, they have developed several intricate symbiotic relationships with different kinds of organisms (e.g. animals, fungi) that for centuries have attracted the attention of botanists, biologists, amateurs and naturalists. Nevertheless, despite the extensive research done so far on orchid biology and phylogenetics, very little is known about the biotic and environmental variables as well as the evolution of several key traits that seem to be linked with the successful diversification of this lineage. This dissertation is focused on three puzzling aspects of plant evolutionary biology, specifically the phylogenetic incongruence between nuclear and plastid genomes, the evolution of sexual systems, and lineage migration and isolation through time. To address these topics, I chose as a group of study the sub tribe Catasetinae, an orchid lineage including ca. 350 species restricted to the Neotropical region. They show a remarkable set of sexual systems, namely protandry and Environmental Sex Determination (ESD), that were never studied before in a phylogenetic context. My dissertation includes as well a minor part on taxonomic and floristic work devoted to other representative orchid lineages of the Neotropical flora (i.e. Epidendrum and Lepanthes). Based on vegetal material collected during field trips, my taxonomic research resulted in the description of several new species and new chorological reports contributing to the Colombian and Costa Rican Floras. Using a set of nuclear and chloroplast loci obtained from material cultivated at the Botanic Garden Munich and collected during field work in several Latin American countries, I produced a well-supported and insofar the most representatively sampled phylogeny of Catasetinae. While gathering vegetal material, I encountered several complications such as extreme scarcity of individuals and worrisome, extensive bureaucratic administrative processes to obtain collection and research permits that finally undermined my taxon sampling. By studying in detail the Catasetinae internal phylogenetic relationships independently derived from nuclear and plastid loci, I came across several well supported conflicting phylogenetic positions. Most of the traditional phylogenetic methods developed to address these conflicts aim at the inference of a species tree only. In chapter 5, I explored the utility of co-phylogenetic tools (i.e. PACo and ParaFit) to quantify the conflicts between nuclear and plastid genomes. These tools have been largely employed in host-parasite/endosymbiont studies, hence they have the power to assess the contribution of single Operational Terminal Units (OTUs) to the phylogenetic pattern observed. As a result, using the Catasetinae chloroplast and nuclear datasets and extensive simulation… Advisors/Committee Members: Gottschling, Marc (advisor).