DGS-9d.EXE
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(Drift-Geneflow-Selection simulation program version 9d; April 1995)
This program allows simulation of evolution at multiple (up to 300) polymorphic loci (2 alleles) in multiple (up to 100) populations in any wanted number of generations. While this program was primarily designed for simulation of qualitative genetic differentiation between populations, the large number of polymorphic loci allowed may make it useful also for simulation of the adaptation process of an additive quantitative trait. Epistasis and mutations are not provided. Otherwise, the evolutionary regime is under full user control:
- genetic drift (separate, different, and randomly varying population sizes)
- gene flow (two-way, may be different for all pairs of populations)
- selection (separate setting for each genotype at each locus in each population)
The start situation can be set in any detail (i.e., allele frequencies at each locus in each population). This is very convenient for "What-if" analyses in situations where base-line data exist, and one wants to examine possible genetic (evolutionary) outcomes of various scenarios
(various combinations of genetic drift, gene flow, selection, and generations). This level of user control is enabled via four ASCII data files which can be created with a word processor or DOS-editor and given by the user at the program's prompt. The structures of the four files are examplified below, showing sample ASCII input files for a simulation study involving 8 variable loci in 8 populations. The order of the populations, loci and alleles is the same in all files (i.e., "O1", "B1", ... "F1").
1) - a "start" file w/allele frequencies (2 alleles) at each variable locus in each population (sample file: "LAKS8")
8 8 0 2
2 2 2 2 2 2 2 2
"O1" .935 .065 1.00 0.00 1.00 0.00 .389 .611 .991 .009 .981 .019 .472 .528 1.00 0.00 ( This is also the
"B1" .900 .100 1.00 0.00 1.00 0.00 .460 .540 1.00 0.00 .990 .010 .370 .630 1.00 0.00 format for input
"S1" .792 .208 .993 .007 1.00 0.00 .507 .493 1.00 0.00 1.00 0.00 .565 .435 1.00 0.00 in the analytical
"M1" 1.00 0.00 1.00 0.00 1.00 0.00 .571 .429 1.00 0.00 1.00 0.00 .534 .466 1.00 0.00 programs:
"N1" .929 .071 1.00 0.00 1.00 0.00 .500 .500 .979 .021 1.00 0.00 .528 .472 1.00 0.00 DG27A.EXE,
"A1" .979 .021 1.00 0.00 1.00 0.00 .289 .711 .997 .003 1.00 0.00 .360 .640 1.00 0.00 DG100A.EXE, &
"T1" .903 .097 1.00 0.00 1.00 0.00 .462 .538 .989 .011 1.00 0.00 .392 .608 .998 .020 GSA.EXE)
"F1" .764 .236 1.00 0.00 1.00 0.00 .543 .457 1.00 0.00 1.00 0.00 .361 .639 1.00 0.00
2) - a file with fitness coefficients for each genotype at each locus (columns) in each population (rows). In this example all fitnesses (except locus 8 in «F1») are set to 1 (sample file: "W88N"):
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 .6 1 .9
3) - a file with a data matrix describing the number of genetically effective immigrants which each population gives to each of the others, and how many it gets from each of the others (sample file: "FLOW8"):
0 10 10 10 10 10 10 1150 Note that the matrix is 8 populations x 8 populations,
10 0 10 10 10 10 10 500 e.g., the left-to-right diagonal of "0"s represents
10 10 0 10 10 10 10 75 zero "self-immigration".
10 10 10 0 10 10 10 15
10 10 10 10 0 10 10 2150 The values here mimic a regime in which 7 populations ("O1"-"T1")
10 10 10 10 10 0 10 625 with restricted gene flows(mN=10)receive large proportions (m=1/3 when
10 10 10 10 10 10 0 6000 when related to population sizes; cf point 4)of immigrants from one
0 0 0 0 0 0 0
captive stock giving off lots of escapees).
4) - a file containing the effective sizes (w/ standard deviation) of the populations (the Sds are here arbitrarily set to
10% in all populations). (sample file: "SIZE8"):
2300 , 0.10
1000 , 0.10
150 , 0.10
30 , 0.10
4300 , 0.10
1250 , 0.10
12000 , 0.10
40 , 0.10
Creating of input files can be eased by using the support programs Pcreate.exe («Start» population description), Wcreate.exe (Fitness coefficient matrix) and Fcreate.exe (gene flow matrix). Once created, parameters in these «standardized» files are easily taylored to any need by a word processor.
After the program har read in the parameters of the simulation from the data files and run through the chosen number of generations, the results (end allele frequencies at each locus in each population) are written to a data file (user named ) with the same format as the "start file". This "end file" may of course be used as "start" of a new simulation with different parameters, or it may be analysed with the
"analytical programs" ( DG27A.EXE, DG100A.EXE, GSA.EXE, MD-2.EXE
).
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