Molecular-Clock Dating Using MrBayes – Seminar and Workshop
- 22 April – Stockholm: 09:30-11:30, Rum 540, Botaniska Institutionen, Stockholms universitet
- 23 April – Uppsala: 13:15-15:15, Lärosal 4, Evolutionsbiologiskt Centrum, Uppsala universitet
Chi Zhang*, Swedish Museum of Natural History, Stockholm
Johan Nylander, BILS/Swedish Museum of Natural History, Stockholm
MrBayes – the most often used software for Bayesian phylogenetic analysis – has included many new features since version 3.2. In this seminar, we will highlight some newly implemented functionality, with focus on the molecular-clock dating capacities of the current version (v.3.2.4). The seminar will consist of two parts, where following a presentation* giving the necessary backrground information, there will be a hands-on tutorial where participants are encouraged to bring their own data (and computers).
There are two approaches on dating using molecular data: node dating and total-evidence dating. Node dating calibrates the internal nodes of the tree by assigning distributions using information from external sources, such as the fossil record. Total-evidence dating uses the morphological data from fossil record and morphological and sequence data from recent organisms together to infer the dates. Several steps involve in Bayesian dating analysis, including data partitioning, node or fossil age calibration, and setting priors for the tree and the molecular clock model. I will describe the available calibration probability distributions, clock tree priors – especially the fossilized birth-death prior for total-evidence dating, and relaxed clock models, through a step-by-step tutorial of MrBayes.
The program (MrBayes v.3.2.4) is available from http://mrbayes.net (alternatively https://sourceforge.net/projects/mrbayes/files/mrbayes)
Participants in the practical part are encouraged to bring their own computers with the software installed from the above mentioned URL’s.