Marker Divergence Experiments
This workflow implements a method for extracting effective beneficial mutation rates (
μ) and selection coefficients (
s)from marker divergence experiments
[1]. This is a way of parameterizing the evolvability of a bacterial strain.
Requirements and Installation
The Perl scripts require the module Math::Random::MT::Auto and its prerequisites. They can be installed from
CPAN. The Math::Random::MT::Auto module has a code component that must be compiled. On many systems you can install these from the command line as follows:
>sudo perl -MCPAN -e shell
>Password: ********
>install Math::Random::MT::Auto
answer yes to any prompts about installing prerequisites
1. Fit α and τ Empirical Parameters from Experimental Data
2. Generate a Table of establishment probabilities with MATLAB.
3. Generate α and τ Values from a Population Genetics Simulation
3.1 Generate Simulated Data for a μ and s Combination
3.2 Fit α and τ Empirical Parameters from Experimental Data
3.3 Helper Script: Automating this Step
4 Determine the Effective Parameters where Simulations and Experimental Data Produce the Same Distributions of Empirical Parameters
References
- Hegreness, M., Shoresh, N., Hartl, D., and Kishony, R. (2006) An equivalence principle for the incorporation of favorable mutations in asexual populations. Science 311, 1615-1617.
- Wahl, L.M., and Gerrish, P.J. (2001) The probability that beneficial mutations are lost in populations with periodic bottlenecks. Evolution 55, 2606-2610.
Acknowledgments
Many thanks to Noam Shoresh for extensive discussions that made it possible for me to reproduce his methods and providing his raw data to check the results from these tools.