Phylogenomic studies of the monocot sister orders Pandanales and Dioscoreales

The sister orders Pandanales and Dioscoreales are the last two major clades of monocots that remain to be examined in depth using phylogenomic approaches. Previous studies produced basic phylogenetic outlines for both orders, but left multiple higher-order relationships unresolved, including precise placements of non-photosynthetic mycoheterotrophic lineages. Species-level relationships in the Dioscorea yams, the largest Dioscoreales genus, are also poorly known despite the economic importance of this clade. Here I develop and apply phylogenomic methods to reconstruct the evolutionary histories of Pandanales, Dioscoreales and Dioscorea, using the resulting frameworks to address various phylogenetic and evolutionary hypotheses in each group. I employed a bi-organellar phylogenomic approach to resolve higher-order relationships in Pandanales, with mostly strong support. Mitogenomes are generally slowly evolving, but nevertheless permit inference of well-supported relationships. They also exhibit sporadic order-wide rate accelerations that are decoupled from plastome rate variation. I estimated clade ages to address several biogeographic hypotheses, and uncovered plastome structural variants that may define individual families. In Dioscoreales, I used plastid phylogenomic data and morphology to infer higher-order relationships. The molecular analyses resolve higher-order relationships, but are complicated by extreme substitution rate elevation observed in several mycoheterotrophic lineages. Nevertheless, my analyses confirm the non-monophyly of Burmanniaceae and Dioscoreaceae as currently circumscribed in angiosperm classification schemes. An updated morphological data set supports the local phylogenetic placement of several mycoheterotrophic genera for which plastid data are lacking, and ancestral-state reconstructions predict morphological synapomorphies relevant to the revision of family-level classification schemes. For phylogenomic studies of Dioscorea, I developed a customized bait panel comprising 260 low-to-single-copy nuclear genes. I assessed the utility of the panel with a pilot taxon sampling, supplemented with transcriptome data, that comprises representatives of all major Dioscorea clades, including multiple crop yams. The panel enables resolution of phylogenetic relationships at both deep and recent scales in Dioscorea, mostly with strong support, and provides insights into relationships between crop plants and putative crop wild relatives. Overall, my dissertation offers new insights into a broad diversity of evolutionary questions, made possible by resolution here of recalcitrant phylogenetic relationships in Pandanales, Dioscoreales and the Dioscorea yams.Science, Faculty ofBotany, Department ofGraduat