A comparative phylogenetic analysis of the reticulate radiation of Eucalyptus

Abstract

In this thesis dissertation, my aim was to employ a range of tools from comparative phylogenetics and phylogenomics to provide insights into the macroevolutionary processes involved in Eucalyptus species diversity. I combined ecological morphological and phylogenetic data to investigate Eucalyptus adaptation to drought at the macroevolutionary scale. Additionally, I analysed reference-guided datasets of single-copy orthologs in two young rapid radiations of Eucalyptus with contrasting species diversity: sect. Adnataria and Exsertaria. In those clades, I undertook phylogenetic analyses, evaluated the extent of discordance, its cause and predictors. In Chapter II, I undertook a macroevolutionary study to understand the large-scale drought adaptation in eucalypts, using species metrics of drought-associated morphologies, climate-origins and relative drought sensitivity for more than 500 species of eucalypts. In Chapter III, my research focused on sections Exsertaria and Adnataria (10-5 Mya), two recently diverged lineages that differ in species diversity. In Chapter IV, I investigate the molecular processes causing gene tree discordance and phylogeny incongruence in sect. Exsertaria and Adnataria Across my thesis chapters, I found that drought sensitivity is phylogenetically constrained in eucalypts, with environmental and lineage-specific variation of traits involved in drought response. I determined that the evolution of the recent sections Exsertaria and Adnataria cannot be represented by a bifurcating phylogeny tree. The species trees reconstructed with different phylogenetic approaches were discordant and disagree with the established taxonomy. In the molecular phylogenies of those clades, while many branches showed high bootstrap support, the concordance factors showed no support for the reconstructed or alternative topologies. I provided fundamental insights into the underlying molecular processes causing clade-wide gene tree discordance in both sect. Exsertaria and Adnataria, although the latter showed much higher levels of interspecific admixture. The outcomes provide essential understanding on Eucalyptus species biology and phylogenetics providing avenues for exploration of the role of incomplete lineage sorting and hybrid introgression in providing species with putatively adaptive ancestral variants for drought adaptation.

Date of Thesis submission	2024
Original language	English
Awarding Institution	Western Sydney University
Supervisor	Paul Rymer (Supervisor), Rose Andrew (Supervisor), Justin Borevitz (Supervisor) & Collin Ahrens (Supervisor)