Using clock and phylogeny-based approaches to understand vertebrate diversification

Abstract

The mechanisms underlying vertebrates’diversification and evolutionary success, particularly the timing and driving forces of key evolutionary transitions, remain controversial and poorly understood. In this work, I applied both molecular clock and phylogenetic methods, integrating molecular, morphological and fossil occurrence data to study the timeline and pattern of diversification in two major vertebrate lineages: teleosts and placental mammals. First, I studied the impact of a whole genome duplication event (3R-WGD) on the diversification of teleosts. I estimated the 3R-WGDtohave occurred in the early–middle Permian, consistent with previous inferences based on a fossil-based proxy for genome size. My result also revealed substantial temporal lags between the 3R-WGD and radiations of teleosts, providing evidence for testing debated hypotheses regarding the mechanisms linking both events. Subsequently, I applied a novel strategy that integrates all available fossil occurrence data to establish node calibrations for dating the phylogenomic tree of placental mammals. My research yields a more precise timescale that supports the Long Fuse model, suggesting that the origin and interordinal diversification of placentals occurred in the Late Cretaceous. Finally, I explored the origin and diversification of placentals (crown eutherians) from a morphological perspective to assess whether evidence from the current fossil record is strong enough to confidently rule out their existence in the Cretaceous. I developed a rigorous framework for identifying crown eutherians and applied it to evaluate putative Cretaceous fossils. My results revealed that high morphological similarity, combined with the fragmented fossil record, obscures the identification of early crown eutherians but that it is not possible to reject their existence in the Cretaceous among the known fossil record. My work demonstrates that in studying the mechanisms and patterns of vertebrate diversification, fossil, molecular, and morphological data constitute complementary lines of evidence, whose integration can lead to a more holistic understanding.

Date of Award	20 Jan 2026
Original language	English
Awarding Institution	University of Bristol
Supervisor	Davide Pisani (Supervisor) & Philip C J Donoghue (Supervisor)