Bayesian Estimation of Species Divergence Times Integrating Fossil and Molecular Information

If our genes accumulate changes over time at a constant rate, the genetic distance between two species, measured by the number of changes accumulated, will be proportional to the time of species divergence. Thus molecules can serve as a clock, keeping time of species divergence by the accumulated changes. If fossil records or geological events can be used to assign an absolute geological time to a species divergence event on the phylogenetic tree, one can convert all calculated genetic distances into absolute geological times. This rationale for molecular clock dating has recently been extended to deal with local variation in evolutionary rate. Critical to molecular dating is the use of fossil information to calibrate the clock. In this project, we will develop statistical models and computer programs to analyze fossil and molecular data to accurately represent and incorporate the information in the fossil record in molecular dating analysis. The new methods will be applied to analyze datasets to estimate divergence times among mammals and to date viral transmission events.

Two major improvements have recently been made to molecular clock dating methods: (i) relaxation of the clock assumption through local-clock models and (ii) incorporation of uncertainties in fossil calibrations. Nevertheless, representation of errors and uncertainties in the fossil record in a molecular dating analysis remains a challenging task. In this project, we will use models of clade divergences, fossil preservation and discovery, and morphological character evolution to derive statistical distributions of divergence times, which will be used as calibration densities for molecular clock dating. We will develop new models to describe the change in the evolutionary rate. The new models and methods will be applied to large datasets to date divergences among mammals and to date the host-switching events of the influenza virus.

Accurate estimation of species divergence times is important to assessing the current biodiversity, and the impact of geological and environmental changes on biodiversity. The research results from this project will thus be useful for providing advice on decision making concerning biodiversity management and conservation policies.

Knowledge of absolute times of divergence between viral subtypes and of viral transmissions across species boundaries (such as the host switch of the flu virus from birds to humans) is important for understanding viral transmission and evolutionary dynamics. Such information may be useful to advise on public-health decisions and prevention of flu pandemics.