(r3) Barrick Lab :: ToolsMarkerDivergence

---+ Marker Divergence Experiments

This workflow implements a method for extracting effective beneficial mutation rates (_&mu;_) and selection coefficients (_s_) from marker divergence experiments [[#ReferenceAnchor][&#91;1&#93;]]. This is a way of parameterizing the evolvability of a bacterial strain.

%TOC%

---++ Requirements and Installation

The Perl scripts require the module Math::Random::MT::Auto and its prerequisites for random number generation. They can be installed from [[http://www.cpan.org][CPAN]]. The Math::Random::MT::Auto module has a code component that must be compiled. If you have root access on a  system you can probably install these from the command line as follows:

<code><div style="border-color: grey; border-style: solid; border-width: 1px; padding:1px;">
&nbsp;&gt;sudo perl -MCPAN -e shell<br>
&nbsp;&gt;Password: ********<br>
&nbsp;&gt;install Math::Random::MT::Auto<br>
&nbsp;&nbsp;<i>answer yes to any prompts about installing prerequisites</i>
</div></code>

[[http://www.mathworks.com/][MATLAB]] is required for calculating establishment probabilities.

[[http://www.r-project.org/][R]] is required for fitting marker divergence curves. It should be present in your $PATH, so that Perl scripts can invoke it. 

---++ 1. Fit &alpha; and &tau; Empirical Parameters from Experimental Data

The basic command is:
<code><div style="border-color: grey; border-style: solid; border-width: 1px; padding:1px;">
&nbsp;&gt;marker_divergence_fit.pl -i input.tab > output.fit
</div></code>

---+++ Input File Data Format

The input file is *tab-delimited*. The header row begins with "transfer", and the other columns are labels indicating the name of an experimental time series of marker ratio measurements. Each following row begins with the number of the transfer followed by the marker ratio measurements for that series at that time point. Marker ratios may be given in a variety of formats. Pass the =-m= option followed by =ratio=, =log_ratio=, =log10_ratio= to this script depending on the format of you data values. The default mode is =ratio=.

Portion of an example marker ratio input file:
<code><div style="border-color: grey; border-style: solid; border-width: 1px; padding:1px;">
transfer	exp-1&nbsp;	exp-2&nbsp;	exp-3	<br>
0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;	0.5087	0.5068	0.4990<br>
3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;	0.5000	0.4844	0.5174<br>
6&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;	0.4853	0.5393	0.5115<br>
9&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;	0.4802	0.4862	0.4522<br>
12&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.4884	0.4431	0.5170<br>
15&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.5277	0.5196	0.5266<br>
18&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.4983	0.4638	0.4607<br>
21&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.5221	0.5361	0.5000<br>
</div></code>

---+++ Baseline Correction

If some of your experimental curves do not start at a 1:1 ratio of the neutral marker states, you will also want to pass the =-b= option followed by the number of initial points (not transfers) . The script corrects for the initial marker imbalance by fitting &tau; and &alpha; to a modified equation that accounts for the fact that for a population diverging toward marker state _A_, where _A_ was initially present in less than 50% of the population, the marker ratio will be shifted sooner than in a population where it was initially present in 50% or more of the population.

*Example:*
<code><div style="border-color: grey; border-style: solid; border-width: 1px; padding:1px;">
&nbsp;&gt;marker_divergence_fit.pl -m log_ratio -i input.tab > output.fit
</div></code>
_Corrects for the baseline by taking the average of the first 5 points._

---++ 2. Generate a Table of establishment probabilities with MATLAB.

The population genetics model assumes that each new beneficial mutation that is generated has a certain probability of establishing (not going extinct) during the serial transfer regime of the experiment. A table of these probabilities must be calculated with the MATLAB script.

First, add the directory containing the two ".m" files that come with the distribution to the MATLAB path.

*In MATLAB:*
<code><div style="border-color: grey; border-style: solid; border-width: 1px; padding:1px;">
&nbsp;&gt;&gt;establishment_probability_table(6.64, 5E6, 0.001, 1, 'pr_establishment_T=6.64_No=5E6.tab')
</div></code>

---++ 3. Generate &alpha; and &tau; Values from the Population Genetics Simulation

---+++ 3.1 Generate Simulated Marker Divergence Data for a _&mu;_ and _s_ Combination

---+++ 3.2 Fit &alpha; and &tau; 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
#ReferenceAnchor
   1 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.
   1 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 for providing his raw data to check the results from these tools.
Barrick Lab > ToolList > ToolsMarkerDivergence
Contributors to this topic
JeffreyBarrick
Topic revision: r3 - 2008-09-19 - 16:26:14 - Main.JeffreyBarrick