The use of plastome data to infer phylogenies, systematics and biogeography of Vochysiaceae

This dissertation comprises three chapters that explored relevant questions in modern biology and biodiversity in order to understand better the tree of life and the patterns and processes that affect diversity. The first chapter is an analytical approach to the use of plastid genes in phylogenetic analyses. The study system was the rosid clade, which comprises a third of all species of flowering plants. Analyses indicated that phylogenetic signal varies across plastid genes and that the exploration of different frameworks of phylogenetic inference, including the multispecies coalescent method, can be used to explore regions of the tree that may be controversial. Among the samples used in this chapter, there were species representing genera of Vochysiaceae. The second chapter investigated the systematics and historical biogeography of Vochysiaceae. Due to a sparse fossil record available for Vochysiaceae, analyses were performed at the ordinal level using fossils from other myrtalean families to date the phylogeny. Two analyses of historical biogeography were performed at the ordinal (global scale) and at family level focusing on the Neotropical Vochysiaceae (continental scale). The most recent common ancestor of Vochysiaceae occurred in both Africa and South America when they were contiguous during the Cretaceous and after the separation of the continents the lineage experienced an intense reduction in range. The Cerrado was recovered as the ancestral range for almost all extant genera of South American Vochysiaceae, with the exception of Vochysia for which the Amazon was the ancestral area. The third chapter focused on Vochysia itself, the largest genus of Vochysiaceae and presented a comprehensive investigation of the systematics, historical biogeography, and diversification dynamics. The historical biogeography considered Neotropical biomes at a fine scale compared to the areas used in the second chapter and corroborated the findings from the second chapter. Within Vochysia there were multiple independent events of colonization to biomes that surround the Amazon and multiple events of habitat switches, whereas switches in habit and hydrologic regimes were less frequent. There was one shift of diversification in Vochysiaceae in the lineage that gave rise to most extant Vochysia species.