AlleleA1 Manual

Drift
A a
Selection
Mutation
A a
Migration
AlleleA1
Software for Evolutionary Analysis
http://www.prenhall.com/freeman
AlleleA1 2.0 © 2003 by Jon C. Herron
AlleleA1 is free. You may give it to anyone you like, so long as you distribute it as a stand-alone
application and include this manual along with it. You may not sell it. You may not include it in
a collection with other software, regardless of whether you are selling the collection or giving it
away.
I make no warranties or guarantees about the quality of AlleleA1, or the accuracy of the
simulations it runs. Use it in good health, but at your own risk.
If you have comments or suggestions, please send them to me at herronjc@attbi.com.

Introduction
AlleleA1 simulates evolution at a single locus in an ideal population of

imaginary organisms. The locus of interest has 2 alleles: A1 and A2. The user
enters values for parameters controlling selection, mutation, migration, genetic
drift, and inbreeding. As the simulation runs, the software plots a graph showing
the frequency of allele A1 over time.
The equations AlleleA1 uses are presented in Chapters 5 and 6 of Evolutionary

Analysis, 2e.
Using AlleleA1
Setting the Parameters

Set the parameters by entering values in the boxes in the AlleleA1 window. For
example, to set the initial frequency of allele A1 to 0.01, double click in the box
labeled Starting frequency of allele A1, then type 0.01.
Running the Simulation

Run the simulation by going to the Simulation menu and selecting Run, by
pressing command-R, or by clicking on the Run button.
Setting the Number of Generations

By default, the simulation will run for 500 generations. You can select a different
number of generations by using the popup menu at the lower right corner of the
graph. Click on the small black triangle, and hold the button down. Then move
the cursor to the number of generations you want.
Setting the Graph Line Mode

By default, the graph will clear itself at the start of each run. To overlay the graph
for a new run onto the graph for the previous run, click on the Multiple radio
button under Graph lines at the bottom right of the AlleleA1 window.
Setting the Graph Line Color

To change the color of the graph line for your next run, click on the color you
want in the palette at the lower right of the AlleleA1 window. The currently
selected color is shown in the larger rectangle to the left of the palette. If you
select Auto, the software will automatically cycle through all eight colors.
Clearing the Graph

To clear the graph, but leave the parameters unchanged, go to the Simulation
menu and select Clear, or press command-K, or click on the Clear button.
Restoring All Settings To Their Default Values

To clear the graph and restore all settings to their default values, go to the
Simulation menu and select Reset, or press command-D, or click on the Reset
button.
The Parameters
Starting frequency of allele A1

As it's name suggests, this parameter controls the frequency of allele A1 at the
start of the simulation. The frequency of allele A2 is determined automatically by
subtraction. The starting frequency of allele A1 should not be less than zero or
greater than one.
Fitness of genotypes A1A1, A1A2, and A2A2

These parameters determine the relative fitnesses of the three genotypes (that is,
the relative probability that an individual of each genotype will survive to
reproduce). The fitnesses should be positive, but otherwise all that matters is
their values relative to each other.
Mutation rates
These parameters determine the rate at which copies of allele A1 turn into allele
A2 and vice versa. The mutation rates should not be less than zero or greater than
one.
Fraction of migrants
This parameter controls the fraction of individuals in each generation that are
migrants newly arrived from another population. The fraction of migrants
should not be less than zero or greater than one.
Frequency of allele A1 in the source population

This parameter controls the frequency of allele A1 among the newly arrived
migrants. It should not be less than zero or greater than one.
Population size
By default, the population size is infinite, and the population evolves according
to a deterministic equation. Entering a positive integer for the population size
makes the population finite. Each generation, the allele frequencies are
determined by sampling from the previous generation's gene pool.
Coefficient of inbreeding
This parameter, also known as F, determines the probability that an individual's
two alleles are identical by descent from a common ancestor. A value of 0
represents outbreeding; a value of 1 represents selfing. F should not be less than
zero or greater than one.
Advanced Features
Graphing frequencies other than that of allele A1

On the allele frequency graph in the AlleleA1 window, a popup menu under the
Y-axis label will let you select other frequencies to plot.
Saving the data from a simulation

At the upper right of the AlleleA1 window there is a small disclosure triangle.
Clicking on the triangle will reveal a table on the upper right. As you run a
simulation, AlleleA1 fills this table with data. At the end of the run, you can
select rows in the table, copy the data, and paste them into a spreadsheet or text
file.
Graphing mean fitness and ∆Fr(A1) for your model

At the upper right of the AlleleA1 window there is a small disclosure triangle.
Clicking on the triangle will reveal additional graphs on the lower right. These
show the mean fitness for your population and the change from one generation
to the next in the frequency of allele A1, both as functions of the frequency of
allele A1.

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Drift

AlleleA1 2.0 © 2003 by Jon C. Herron

If you have comments or suggestions, please send them to me at herronjc@attbi.com.

AlleleA1 simulates evolution at a single locus in an ideal population of

The equations AlleleA1 uses are presented in Chapters 5 and 6 of Evolutionary

Setting the Parameters

Running the Simulation

Setting the Number of Generations

Setting the Graph Line Mode

Setting the Graph Line Color

Clearing the Graph

Restoring All Settings To Their Default Values

Starting frequency of allele A1

Fitness of genotypes A1A1, A1A2, and A2A2

Frequency of allele A1 in the source population

Graphing frequencies other than that of allele A1

Saving the data from a simulation

Graphing mean fitness and ∆Fr(A1) for your model

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