Five decades have passed since the proposal of the molecular clock hypothesis, which states that the rate of evolution at the molecular level is constant through time and among species.
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Divergence time estimation may be less accurate and/or precise as a result. In this article, we focus on 2 different methods for specifying the prior on divergence times. Generation of internode times is repeated on different paths within the tree until all nodes have been assigned ages.
A global clock model may appear sensible in these circumstances because it involves fewer parameters and because of lower rate variation due to shorter time scales and similarity of taxa. The first of these is the recursive procedure implemented in the program MULTIDIVTIME (Thorne et al. Time constraints are represented as “hard” maximal and/or minimal bounds on node ages (sensu Yang and Rannala 2006).
The lab files you will need can be downloaded here: BEAST lab zip file. You will need to download it if you are using the cloud as it uses a graphical user interface and thus does not work on the cloud.
You may wish to download it for your own operating system even if you have the ubuntu virtualbox as java creates some difficult behaviour in BEAST on Ubuntu.
Nevertheless, a relaxed clock is often used, possibly because it accommodates both homogenous and heterogenous rates (e.g., Warren et al. The second method for specifying this prior on times uses the birth–death process with species sampling (BDS).
This is implemented in the program MCMCTREE (Rannala and Yang 2007; Yang and Rannala 2006; Yang 2007).
The BEAST tutorials by the creators of the program can be found here There are two older exercises on using BEAST and an additional exercise on how to properly use BEAST* which you can do in your own time.
The “Primates” exercise details how to produced relaxed phylogenies and date with confidence.
Knowledge of their timing can provide valuable insights into the climatic and physical processes that have shaped genetic diversity within species as well as into speciation events. Posterior estimates of divergence times will reflect the prior when sequences are short (and therefore less informative) but should be increasingly influenced by the likelihood as sequence length is increased.