The molecular clock hypothesis has become a powerful tool in evolutionary biology, making it possible to use molecular sequences to estimate the geological ages of species divergence events. With recent advances in Bayesian clock dating methodology and the explosive accumulation of genetic sequence data, molecular clock dating has found widespread applications, from tracking virus pandemics, to studying the macroevolutionary process of speciation and extinction, to estimating a timescale for Life on Earth. 

This workshop will cover molecular dating of phylogenies with Bayesian methods on genome-scale datasets. A brief introduction will be followed by a hands-on tutorial for Bayesian divergence time estimates on phylogenomic data using MCMCTree (PAML). The hands-on tutorial will be based on the book chapter Bayesian molecular clock dating using genome-scale datasets* and its tutorial.

Participants are encouraged to attend Mario's seminar the day before: Bayesian molecular clock-dating of phylogenies: fossils, genomes and uncertainty.

Topics

• Divergence time estimation with MCMCTree (PAML)
• Assessing convergence of the MCMC and summarising result
• Tree visualization
• Divergence time with approximate likelihood calculation for complete genomes
• Case study: Divergence time estimation of Primates

Workshop schedule

• 9:15pm-10:15 Introduction and tutorial.
• 10:15-10:45 Morning tea break
• 10:45-12:30  Hands-on tutorial.

Target audience

Students and researchers interested or performing molecular dating analysis with phylogenomic data.

Prerequisites 

• Practical knowledge of the command line interface in Unix or Windows.
• Basics of phylogenetics and interpretation of phylogenetic trees. For example, having used software (IQtree, RAxML, Beast, mrbayes) to estimate a phylogeny.
• Basic knowledge of R and R Studio (both optional).

Required software

• Participants are required to bring their own laptop to the workshop with the following software installed: 
• MCMCtree and BASEML which are part of the PAML software package for phylogenetic analysis. Make sure MCMCtree and BASEML are in your system’s path variable as explained here.
• FigTree a graphical viewer of phylogenetic trees
• Tracer a graphical viewer of MCMC traces

Note: Please install and test the programs in advance. Our ability to help with installation problems during the workshop will be very limited.

Recommended reading

• *dos Reis M, Z. Yang. 2019. Bayesian molecular clock dating using genome-scale datasets. In Anisimova M, ed. Evolutionary Genomics: Statistical and Computational Methods. Springer, New York.
• dos Reis, M., P.C.J. Donoghue, Z. Yang. 2016. Bayesian molecular clock dating of species divergences in the genomics era. Nature Reviews Genetics 17:71-80. 

Registration

The workshop is free, but participation is on a first-come, first-served basis (30 participants max) and will close on Friday 28 February. Please register here.

Organisers

Hermes E. Escalona  (Australian National Insect Collection, CSIRO) and Minh Bui (Research School of Computer Science, Australian National University).