Exploring evolutionary rates and patterns of diversification across the Tree of Life

Abstract

My thesis provides substantial insight into evolutionary processes across the Tree of Life. I have analysed the geological record as well as phenotypic traits and genomes from extant organisms to better understand the processes of diversification and change. I begin by challenging the notion that the diversification of flowering plants was intimately linked to a contemporaneous diversification of pollinating insects. This evolutionary event, which propelled flowering plants to dominate terrestrial landscapes, may instead have been bolstered by unique environmental factors, and by insect pollinators that were primed by previous interaction with seed plants. I then examine the tempo of evolution for many diverse taxa by inferring evolutionary rates. I first validate and assess five methods for detecting evolutionary rate correlations between molecular sequences and morphological traits, using a comprehensive simulation study with thousands of replicate data sets. After determining the most statistically accurate and powerful methods, I apply these methods to diverse taxa from the eukaryote Tree of Life. This spans groups including, but not limited to, worms, tetrapods, fish, insects, plants, and parasites. In doing so, I uncover powerful evidence for decoupled evolutionary rates of molecules and morphology across all groups tested, demonstrating the disparate mechanisms that govern the evolution of morphology, which is under the constraint of natural selection, and molecules, which exhibit more stochastic evolution. Finally, I analyse evolutionary rates in land plant genomes, testing the link between rates in the three genomic compartments of land plants (nucleus, chloroplast, and mitochondrion). In this chapter I demonstrate that there is a shared evolutionary rate between the genomic compartments in land plants – effectively extending the hypothesis of 'mitonuclear covariation' from animals to plants.