PopG genetic simulation program

version 3.3

October, 2008

Getting PopG

You can fetch PopG using the links below.

• For Windows: popgwin.exe A self-extracting zip archive containing the files of the Windows version for Windows 95, 98, NT, 2000, me, xp, Vista and as far as we know all other recent versions of windows.
• For Mac OS X: popgosx.dmg A Mac OS X version which can be run on any version of Mac OS X as a Universal native-mode executable. It is a .dmg "disk image" file.
• For Linux: popglinux.tar.gz Linux version, as a Gnuzip'ed tar archive of the executables and documentation.

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 folder 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 and the PopG executable. These will be in a folder (directory) called PopG_3.3

For Mac OS X

After the disk image has been downloaded, you should click on it to mount it. A new folder should open showing the contents of the disk image. It will have a folder (directory) PopG_3.3 with documentation, an icon graphic, and the PopG executable). Copy the PopG_3.3 folder to some other place on your system, outside of the disk image (such as your desktop). Do not try to use it inside the disk image.

For Linux or Unix

Put the popglinux.tar.gz file into the folder where you want the program to reside and do tar xvfz popglinux.tar.gz. This will create a folder (directory) called PopG_3.3 that contains these files.

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 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 Mac OS 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 w/, Continue, 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. If you want to change some of the parameter values, use New Run instead.

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, Mac OS X or Mac OS 9 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 as a Postscript file 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

Most people will not have to compile the program themselves, and thus they won't need a C compiler for it. But if you want to modify the program, or if you want to port it to a different version of Unix, you will need to compile the program. If you don't need to do any of these, you can just use the executables that we distribute.

If you do need to compile the program, first download from our site the appropriate source code archive, and make sure it is extracted into a folder. Instructions for downloading and compiling the source code are available on our server, where you will find a web page with those instructions. There are downloadable files that contain source code, compiling instructions, and compilation support files for Windows, for Linux and Unix systems, and for Mac OS 9 and Mac OS X systems. After you download the correct source code archive, use your browser to read the compiling.html web page in the main source code folder. It contains instructions for compiling in each of these operating systems.

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 ten 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? How is that migration rate affected by the population size?
• 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?

Credits

PopG was written by Joe Felsenstein, Hisashi Horino, Sean Lamont, Bill Alford, Mark Wells, Mike Palczewski, Doug Buxton, and Elizabeth Walkup. 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, and Doug Buxton modified the program to the 3.0 version and prepared the executables for different operating systems. Elizabeth Walkup improved the X windows interaction and prepared version 3.3.

Copyright notice

Copyright 1993-2008. 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 @ gs.washington.edu