Vines in the Neotropics: Phylogenomics, Biogeography and Systematics in Passion Flowers (Passiflora Subgenus Decaloba Section Decaloba)

With 600 species, Passiflora is a large, morphologically complex and broadly distributed genus in Passifloraceae that represents a major challenge to scientists interested in understanding the evolutionary history of tropical vines. Passiflora has been divided into subgenera, super sections and sections. One of the most enigmatic and species-rich (~120 spp.) groups in Passiflora is section Decaloba, which occurs in the Neotropics and is particularly diverse in Andean montane forests. In this study, we used phylogenomic and population genomic approaches to investigate the evolutionary history, biologeography, species boundaries, and taxonomy of Passiflora section Decaloba. We sampled herbarium specimens, extracted DNA, and employed a high-throughput DNA sequencing technique called 2b-RAD to generate DNA sequence data for phylogenetic and population genetic analyses. In the first chapter, we reconstructed the phylogeny and biogeographic history for this section and found that section Decaloba originated in Central America around 10.4 Ma, and then dispersed to South America across the Panama isthmus, where it diversified and later colonized the Caribbean and lowland South America. In the second chapter we reconstructed the phylogeny and analyzed the population genetic structure and morphology of a challenging clade in section Decaloba, the “alnifolia group,” to understand how the lineages correspond to the current taxonomy of the group. We discovered that the “alnifolia group” likely represents a rapid radiation, that patterns of genetic variation do not correspond to described species, and that several species need a new circumscription. The third chapter used the results from the previous two chapters as the basis for a taxonomic treatment that included nomenclatural changes and new species circumscriptions. Among the most important taxonomic changes was the synonymy of 4 species from the “alnifolia group”. Overall, the use of herbarium specimens and a rad-seq approach provided a well-resolved phylogeny that allowed us to generate the first phylogenetic framework for Passiflora section Decaloba, helped elucidate major biogeographic patterns in the genus, as well as patterns of population genetic structure and morphological variation. This approach may be useful for future studies that aim to elucidate the evolutionary relationships among broadly distributed, highly diverse, and poorly accessible groups of plants