Using Phylogenomic Data to Untangle the Patterns and Timescale of Flowering Plant Evolution

Abstract

Angiosperms are one of the most dominant groups on Earth, and have fundamentally changed global ecosystem patterns and function. Therefore, unravelling their evolutionary history is key to understanding how the world around us was formed, and how it might change in the future. In this thesis, I use genome-scale data to investigate the evolutionary patterns and timescale of angiosperms at multiple taxonomic levels, ranging from angiosperm-wide to genus-level data sets. I begin by using the largest combination of taxon and gene sampling thus far to provide a novel estimate for the timing of angiosperm origin in the Triassic period. Through a range of sensitivity analyses, I demonstrate that this estimate is robust to many important components of Bayesian molecular dating. I then explore tactics for phylogenomic dating using multiple molecular clocks. I evaluate methods for estimating the number and assignment of molecular clock models, and strategies for partitioning molecular clock models in analyses of multigene data sets. I also demonstrate the importance of critically evaluating the precision in age estimates from molecular dating analyses. Finally, I assess the utility of plastid data sets for resolving challenging phylogenetic relationships, focusing on Pimelea Banks & Sol. ex Gaertn. Through analysis of a multigene data set, sampled from many taxa, I provide an improved phylogeny for Pimelea and its close relatives. I then generate a plastome-scale data set for a representative sample of species to further refine the Pimelea phylogeny, and characterise discordant phylogenetic signals within their chloroplast genomes. The work in this thesis demonstrates the power of genome- scale data to address challenging phylogenetic questions, and the importance of critical evaluation of both methods and results. Future progress in our understanding of angiosperm evolution will depend on broader and denser taxon sampling, and the development of improved phylogenetic methods.