Bayesian molecular clock dating and the divergence times of angiosperms and primates

The explosive increase of molecular sequence data has produced unprecedented opportunities for addressing a number of evolutionary problems. Specially, the species divergence time estimation is fundamental because our understanding of history of life depends critically on knowledge of the ages of major clades. This thesis explores the use of molecular data (genome-scale datasets), combined with statistical summaries of the fossil record, to date the origin of angiosperms (flowering plants) and the divergence times of its major groups in an attempt to resolve the apparent conflict between the molecular dates and fossil evidence. Moreover, because fossil calibrations are the major source of information for resolving the distances between molecular sequences into estimates of absolute times and absolute rates in molecular clock dating analysis, several strategies for converting fossil calibrations into the prior on times are evaluated. Chapter one introduces the diversity and evolution of angiosperms, reviews the current literature that is based predominantly on systematics, phylogenetics, palaeobotany and plant molecular evolution. In introducing the early evolution of angiosperms this chapter highlights the questions associated with the origin of angiosperms and presents aims of the thesis. Chapter two focuses on molecular clock dating methods. It discusses different approaches for estimating divergence times, with emphasis on Bayesian molecular clock dating methods. Chapter three uses a powerful Bayesian method to analyze a molecular dataset of 83 genes from 644 taxa of vascular plants, combined with a suite of 52 fully-justified fossil calibrations to disentangle the pattern of angiosperm diversification. The results indicate that crown angiosperms originated during the Triassic to the Jurassic interval, long prior to the Cretaceous Terrestrial Revolution. This analysis demonstrates that even though many sources of uncertainty are explored, attempts to control for these factors still do not bring clock estimates and earliest confident fossil occurrences into agreement. A post-Jurassic origin of angiosperms was rejected, supporting the notion of a cryptic early history of angiosperms. The main factors affecting the estimates in this study are also discussed. Subsequently, in chapter four different strategies for summarizing fossil information to construct calibration priors were assessed employing an a priori procedure for deriving accurate calibration densities in Bayesian divergence dating. In general, truncation has a great impact on calibrations so that the effective priors on the calibration node ages after the truncation can be very different from the user-specified calibration densities. The different strategies for generating the effective prior also had considerable impact, leading to very different marginal effective priors. Arbitrary parameters used to implement minimum-bound calibrations were found to have a strong impact upon the prior and posterior of the divergence times. The results highlight the importance of inspecting the joint time prior used by the dating program before any Bayesian dating analysis. Finally, chapter five draws together key finding from chapters three and four, and reviews how this work advances our understanding of the origin and evolution of angiosperms and on molecular clock dating using fossil calibrations. This chapter also highlights new gaps in our understanding of early evolution of angiosperms and in the implementation of fossil calibrations in Bayesian molecular clock dating, and discusses several areas for future research. Overall, this thesis highlights that more room for improvement might lie in refining our knowledge and use of fossil calibrations, the resulting improvements to molecular estimates of timescales will lead to a better understanding of angiosperm evolution. I speculate that these results will also shed light on dating discrepancies in other major clades.