PopG genetic simulation program

version 2.0

January, 2002

The C source code is provided, which can be compiled with the Makefile to produce executable versions for most workstations that have X windows, as well as the CygWin compiler on Windows. A project file is also included which can be used to compile executables for Macintosh using the Codewarrior compiler. However, most people using Windows or Macintosh will not want to recompile the program -- all they need to do is to use the executable that we supply.

Getting PopG

You can fetch PopG using the links below.

• For Windows: win.exe A self-extracting WinZip archive containing the files of the Windows version for Windows 95, 98, NT, 2000, me, xp, and as far as we know all other recent versions of windows.
• For Macintosh: popgmac.sit Macintosh version which can be run on all PowerMacs and later Macs, running under MacOS. It is a Stuffit archive which should be unstuffed as it is transferred; if not, you could use Stuffit Deluxe to unpack it.
• For Linux or Unix: popglinux.tar.gz Linux and Unix version, as a Gnuzip'ed tar archive of the source code and documentation. The executables can easily be created from this (see below).

The documentation

The documentation files are included in the fetchable archives, and consist of this web page. The latest version of it can be read on the Web using this link.

Unpacking the archives

After fetching the archives for Windows, for Mac, or for Linux/Unix, you need to unpack them. Do this:

For Windows

Make sure the popgwin.exe file is in the directory where you want the program to be. The click on it. It will run and unpack itself into a set of files, including this documentation file, the source code files, and the PopG executable.

For Macintosh

When the file popgmac.sit was downloaded, it should have been unpacked into the component files (documentation, source code, and the PopG executable. Make sure these got into the desired directory. If the popgmac.sit archive was transferred without being unpacked, you could unpack it using Stuffit Deluxe.

For Linux or Unix

Put the popglinux.tar.gz file into the directory where you want the program to reside. If your system has the Gnuzip program for unpacking .gz archives, you can run it by typing gunzip popglinux.tar.gz, after which you use tar xvf popglinux.tar

Running the program

To run the program on Linux or Unix systems you should simply type popg while in the proper directory. On Windows or Macintosh systems you simply click (or double-click) on the program icon. The Macintosh version is for PowerMac systems and will not run on older 68k Macintoshes. You can download an older 68k Macintosh version from our web site if you have such a system.

The program uses a random number generator. It should give you a different result every time it is run.

The program opens a window, and there are three menus that you can use to control it. On Windows and Linux/Unix systems the menus are in the upper left of the main window. On Macintoshes they are in the upper left of your desktop window. The windows are File and Run. Most of their menu items can selected using the mouse or else (in the Windows and Macintosh cases) by typing the appropriate character on the keyboard. On Windows systems these are Control characters such as Control-C (holding down the Ctrl key while typing C). On Macintosh systems they are Command characters such as Command-C (holding down the Command key while typing C.

The Run menu

This contains four menu items, Continue, Continue w/, New Run, and Restart.

New Run (Control-N or Command-N)

Initially only New Run is available. It brings up a box with parameter values that can be changed, marking then with the mouse and using backspace and/or delete keys, and typing modified values in. When these are given the desired values, clicking the OK box will dismiss the parameter values and start the run. If at any point you want to restart the run with different parameter values, you can select New Run and you will be given a chance to change the parameters.

Continue w/ (Control-C or Command-C)

This choice continues the run, for the same number of generations as before (which is shown in the menu).

Continue

This continues the run, but presents a box allowing the user to first change the number of generations run in the continuation of the run.

Restart (Control-R or Command-R)

This restarts the run with the same parameter values as before.

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The File menu

This contains four menu items, which may not all be available. They are Save, Print, About and Quit.

Quit (Control-Q or Command-Q)

This is self-explanatory: the program quits.

Print (Control-P or Command-P)

This sends the present image of the graph to the system's print queue. On Windows and Macintosh systems it will present the user with a "print box" in which various options can be selected. On Linux or Unix systems it will send the graph to the system's lpr printing command.

Save (Control-S or Command-S)

This saves the graph as a Postscript file, allowing the user to select the name of the file (the default name is output.ps.

About (Control-A or Command-A)

Displays the program's copyright notice.

Compiling it yourself for Linux or Unix

For Linux or Unix we do not supply an executable program, but you must compile the source code yourself (for Windows and Macintosh this is not necessary as you can simply use the executables we supply). If you want to compile the program yourself on Linux or Unix, instructions are as follows (if, not, you can skip this section).

Download the popg.tar.gz archive using the link given above in the section on Getting PopG. Using the Gunzip archive unpacking program you can unpack it (by the command gunzip popglinux.tar.gz followed by tar xvf popglinux.tar). This will create a directory called popg in your current directory.

Go into this popg directory. Type make which will cause the system compiler to compile the program, creating an executable called popg. If this does not work, try to modify the compiling command and switches in the Makefile which controls the compilation process. The resulting executable (popg) can display on any X terminal or X-capable workstation.

Compiling the program for Windows or for Macintosh

This will generally not be necessary, as we have supplied the already-compiled executables for these systems, and you can simply run those. Only if you want to modify the program somehow should you attempt this.

Windows

We supply a Makefile which can be used with the Cygwin Gnu C++ compiler, which is a Windows port of the Gnu C++ compiler. The Makefile in the Windows distribution is called Makefile (the Linux/Unix Makefile is called Makefile.unix in that distribution).

Macintosh

We supply a project file for the Metrowerks Codewarrior 7 compiler. You can run the compiler and load this project file to prepare for compiling the programs.

Simulating with PopG

This program simulates the evolution of random-mating populations with two alleles, arbitrary fitnesses of the three genotypes, an arbitrary mutation rate, an arbitrary rate of migration between the replicate populations, and finite population size.

The programs simulate eight simultaneously evolving populations with you specifying the population size, the fitnesses of the three genotypes, the mutation rates in both directions (from A to a and from a to A), and the initial gene frequency. They also ask for a migration rate among all the populations, which will make their gene frequencies more similar to each other. Much of the time (but not always!) you will want to set this migration rate to zero. In most respects the program is self-explanatory.

When you make a menu selection that causes the program to run, a graph of the gene frequencies of the A allele in each of the populations will be drawn in the window. Note that the window can be resized, and the graph should adjust to this. There will also be a dashed curve that shows what the gene frequencies would be in an infinite population (one with no genetic drift). The graph can be printed using the Print option of the File menu, or saved to a Postscript file using the Save option in that menu.

Note that once the plot of the gene frequency curves reaches the right-hand side of the graph, the program prints there the number of populations that fixed for the A allele (ended up with a frequency of 1.0) and the number that lost this allele.

The program can simulate a wide variety of cases, and you should explore some of these. Here are some suggestions:

• Try cases with no mutation, no migration, and all fitnesses 1.0 so that there is no selection. Does genetic drift in a population of size 1000 accomplish roughly the same changes in 1000 generations as genetic drift in a population of size 100 does in 100 generations? By running a largish number of populations, can you check whether the probability that an allele is fixed by genetic drift is equal to its initial frequency in the populations?
• Try a case with no mutation or migration, with the A allele favored by natural selection (with fitness of the AA genotype set highest and fitness of the aa genotype set lowest). Start with a small frequency of A. Is it always fixed? If one starts with a single copy of the allele, how does the probability that A is fixed compare with the selection coefficient favoring it in the heterozygote (compared to the fitness of the aa genotype? Is this fixation probability larger than the one you would get with the same initial frequency with no selection.
• Try overdominance (Aa having the highest fitness). Does the gene frequency converge towards an equilibrium? Why does it vary from this equilibrium frequency? How large do the selection coefficients have to be to cause the gene frequency to stay away from fixation or loss for large amounts of time?
• Try underdominance (Aa having the lowest fitness). Is there a starting gene frequency that will result in some populations heading for fixation, and others heading for loss? If you add a small amount of migration, what will happen? if you add a small amount of mutation in both directions?
• With migration but no selection or mutation, how much migration is needed to make the gene frequency curves be quite similar to each other? How much is needed to make them all end up at the same gene frequency?
• With mutation but no migration or selection, how much mutation is needed to cause the gene frequencies to converge on a mutational equilibrium gene frequency? How does this value relate to the population size?
• If an allele is selected against, can you set up mutation rates that will maintain it at low frequency in the population?

PopG was written by Joe Felsenstein, Hisashi Horino, Sean Lamont, Bill Alford, Mark Wells, and Mike Palczewski. I wrote the original version of the program. Hisashi and Sean did the screen graphics for IBM PC and the first part of the Postscript printing system. Bill greatly improved and expanded the Postscript printing and the X windows graphics. Mark Wells did the original Macintosh version. Mike Palczewski greatly improved the Windows, Macintosh and X Windows graphical user interface.

Copyright notice

Copyright 1993-2002. University of Washington and Joseph Felsenstein. All rights reserved. Permission is granted to reproduce, perform, and modify this program. Permission is granted to distribute or provide access to this program provided that this copyright notice is not removed, this program is not integrated with or called by any product or service that generates revenue, and that your distribution of this program is free. Any modified versions of this program that are distributed or accessible shall indicate that they are based on this program. Educational institutions are granted permission to distribute this program to their students and staff for a fee to recover distribution costs. Permission requests for any other distribution of this program should be directed to license@u.washington.edu.

email:   joe@genetics.washington.edu