Models of Lineage-Specific Rate Variation

December 27, 2013. Unfortunately, because of the conjunction of Revels and winter break, I will not be meeting with Dr. Miller for almost a month! However, most of our work now involves in reading papers online and using computer programs, so the long break time won't be too big of a problem. For a little recap, our goal is to find the divergence time of mycobacterium strains identified in our samples. We are going to construct a tree and calculate the divergence time by using compute program BEAUTi (Bayesian Evolutionary Analysis Utility) and BEAST (Bayesian Evolutionary Analysis Sampling Trees) (very creative names). BEAUti is a program with a graphical user interface for creating an input file for BEAST, which muct be written in XML language. The part that really takes time is deciding which models to use in estimating the divergence time of bacteria. Therefore, what we are doing now is reading journals and previous studies on similar experiments to help us decide our models.

The first type of models introduced here is lineage-specific rate variation. A tutorial mentioned five common models:

• global molecular clock
• local molecular clock
• compound poisson process
• autocorrelated rate
• uncorrelated rate

Sebastián Duchêne's  power point provides simplified explanation of those molecular clock, in which I found very helpful.

Different color represents different rate of substitution. Relaxed clocks include auto- and uncorrelated rates. Credit to S.  Duchene (page 8).

After reading several papers and websites, I decided to try global and local clocks because bacteria evolve quickly in a short period of time. Therefore, the lineage-specific rates variation of different strains are more likely to be same or similar to one and another.

While I am still absorbing more info, I wish everyone happy holidays! I can't believe another year has passed and that I will be graduating in less than 6 months! Nonetheless, I hope to have significant contribution to the bird project before I graduate:)