Use this link: twoloci.c to download the program.
This program was written recently, but it carries out iterations of gene and genotype frequencies in ways that I started to explore in programs I wrote in the 1960s, initially for my undergraduate honors thesis, which was written in 1964 under the supervision of James F. Crow. It uses the equations for natural selection with constant relative fitnesses in two-locus two-allele diploid genotypes that were first derived by Lewontin and Kojima (Evolution, 1960).
The C program, twoloci.c, iterates genotype frequencies for an infinitely large population with two loci, each of which has two alleles. The alleles at the first locus are A and a, the alleles at the second locus are B and b. The iterations are deterministic, as the infinite population size means that there is no genetic drift. The recombination fraction r can be specified by the user. The initial state of the population is given by entering the initial gene frequencies of A and B, and the initial value of the linkage disequilibrium parameter D.
The user is first asked for the name of the file with the fitnesses. The fitness values are on three lines, each line having three fitnesses separated by blanks. The first line is for AA genotypes, and is the fitnesses for BB, Bb, and bb. The second line is for Aa, the third line is for aa.
Thus a typical fitness file would look like this:
0.7 0.65 0.9 0.8 1.0 0.8 0.9 0.75 0.9
A fitness file for two loci for which there is no interaction between the loci (i.e, where the fitnesses interact multiplicatively) would be
0.64 0.8 0.56 0.8 1.0 0.7 0.72 0.9 0.63
The user specifies how many generations are to be run, and how often the population gene frequencies and D are to be printed out. The prinout for those generations also shows the mean fitness and a + or - indicating whether the mean fitness has increased or decreased since the previous generation.
If your C compiler is GCC, the program can be compiled with the command
gcc -lm twoloci.c -o twoloci
otherwise it may work to type
cc -lm twoloci.c -o twoloci
If the fitnesses are in file fitnesses and are
1.0 1.0 1.01 1.0 1.0 1.0 1.01 1.0 0.0
Then a typical run output will look like this:
Name of file with fitnesses?
fitnesses
BB Bb bb
=========================
AA | 1.000 | 1.000 | 1.010 |
|-------+-------+-------|
Aa | 1.000 | 1.000 | 1.000 |
|-------+-------+-------|
aa | 1.010 | 1.000 | 0.000 |
=========================
initial gene frequencies of A, B?
0.4 0.6
initial D?
-0.01
recombination fraction?
0.2
print every how many generations?
1
how many (more) generations? (0 to restart, -1 to stop)
10
t p(A) p(B) D mean w (increase?)
--- ---- ---- --- ------ -----------
0 0.4000000 0.6000000 -0.0100000 0.9487580
1 0.4219084 0.6338487 -0.0228959 0.9661950 +
2 0.4369957 0.6575943 -0.0295407 0.9752735 +
3 0.4484042 0.6759053 -0.0326589 0.9806127 +
4 0.4575925 0.6909450 -0.0337441 0.9840493 +
5 0.4653215 0.7038407 -0.0336489 0.9864244 +
6 0.4720235 0.7152311 -0.0328759 0.9881645 +
7 0.4779602 0.7255029 -0.0317278 0.9895023 +
8 0.4832992 0.7349026 -0.0303890 0.9905724 +
9 0.4881526 0.7435948 -0.0289721 0.9914563 +
how many (more) generations? (0 to restart, -1 to stop)
-1