Bayesian Estimation of Species Divergence Times Integrating Both Fossil and Molecular Information

Lead Research Organisation: University of Bristol


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Technical Summary

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.

Planned Impact

Impact summary and pathways to impact

Accurate estimates of species divergence times are 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 times of viral transmission from one host to another host (such as the host switch of the flu virus) is important for understanding viral transmission dynamics and vitally important for decision making concerning prevention of flu pandemics.

Academic beneficiaries

The main beneficiaries of knowledge arising from this research are scientists working in biodiversity, conservation biology, systematics, evolutionary biology, and virology. The analytical methods and computer software to be developed in this project will allow them to analyze their genetic sequence datasets rigorously, to obtain accurate estimates of divergence times.

We will attend local and international meetings to present our research results. Yang also co-organizes an advanced workshop on Computational Molecular Evolution, partially funded by the Wellcome and the EMBO, which are also relevant venues for publicizing research results from this project.

We will implement the methods and algorithms to be developed in this project in the MCMCTREE program in the PAML software package, and distribute it at its web site, free of charge to academics


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De Baets K (2016) Tectonic blocks and molecular clocks in Philosophical Transactions of the Royal Society B: Biological Sciences

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Donoghue PC (2016) The evolution of methods for establishing evolutionary timescales. in Philosophical transactions of the Royal Society of London. Series B, Biological sciences

Description Our key finding to date has been a test of infinite sites theory using a >20 million nucleotide alignment for 36 species of mammals, which we used to test the hypothesis of the timing of divergence of mammalian ordinal level crown-groups. This unprecedented study had the statistical power to discriminate conclusively among competing models of diversification, corroborating the 'long fuse' model of a post K-Pg diversification of ordinal level crown groups.
Exploitation Route Development of divergence time estimation for forensics and virology Publication in peer-reviewed journal, presentations to academic audiences, and press briefings.
Sectors Education,Healthcare

Title Molecular clock fossil calibration database 
Description A database of fully researched and evidenced fossil calibrations for molecular clock analyses. 
Type Of Material Database/Collection of data 
Year Produced 2014 
Provided To Others? Yes  
Impact There are a number of launch publications associated, it is changing best practice in divergence time estimation, and it fostering links between palaeontologists and molecular biologists. 
Description Conference presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference presentation
Year(s) Of Engagement Activity 2017