Examples

Selection and dominance

Population expansion

[Victor Spirin]

Selection and Dominance

The user can specify selection coefficient s and dominance h parameters. The fitness of heterozygotes is 1 + hs ( h = 0 for recessive, 0.5 for codominant and 1 for dominant). Values below 0 and above 1 are for underdominance and overdominance. Default value of h is set to 0.5. The fitness of homozygotes is 1 + s.

To set dominance parameter to 0.75, for example, add --dominance 0.75


FS -N P 1 10000 -N P 2 10000 -B 1.0 -TS 0.002 -TW 0.002 -TE 0.01 -t 4e-4 -r 4e-4 -L 100000 -s 159 --selectionCoeff 1000 --selectionStartSite 49700 --selectionEndSite 50300 -n 1000 1000 --outputTime 0.001 0.0025 0.005 0.0075 -o ssw21 -Tg P 2 0.00 0.01 P 1 0.00 0.01 --dominance 0.75


Specifying --selectionStartSite and --selectionEndSite is essential. If the selection acts on the entire genome, these two parameters should be set to 0 and genomeLength L. By default, if these two parameters are not specified, the selection will act on only one site. This site will be chosen after BURNIN and will be the closest to L/2 polymorphic site. This is the sample command line to see sweep on one site:


FS -N P 1 10000 -N P 2 10000 -B 1.0 -TS 0.002 -TW 0.002 -TE 0.01 -t 4e-4 -r 4e-4 -L 100000 -s 159 --selectionCoeff 1000 -n 1000 1000 --outputTime 0.001 0.0025 0.005 0.0075 -o ssw21 -Tg P 2 0.00 0.01 P 1 0.00 0.01 --dominance 0.75


Population Expansion


FS -N P 1 10000 -N P 2 10000 -B 1.0 -TS 0.002 -TW 0.002 -TE 0.01 -t 4e-4 -r 4e-4 -L 100000 -s 159 --selectionCoeff 1000 --selectionStartSite 49700 --selectionEndSite 50300 --fitnessBoolOR -n 1000 1000 --outputTime 0.001 0.0025 0.005 0.0075 -o ssw21 -Tg P 2 0.00 0.01 P 1 0.00 0.01


The expansion part is -Tg P 1 0.00 0.01 P 2 0.00 0.01. Six arguments after -Tg are mandatory. P₁ starts expanding at 0.00 after BURNIN and expands at a rate 1.01 every generation (0.01 corresponds to this 1% growth). Same with P₂.