Recent changes to Forward Simulation

Forward Simulation modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 20:14:05 -0000

Forward Simulation modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 20:13:08 -0000

Forward Simulation modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 19:34:17 -0000

Forward Simulation modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 19:26:48 -0000

--- v1
+++ v2
@@ -3,7 +3,7 @@
 Population with size P₁+P₂ evolves for BURNIN generations in units of 2(P₁+P₂).
 After BURNIN, this population evolves further with the same parameters
 and at _tSpeciation_ splits into two populations with sizes P₁ and P₂.
-These two populations evolve independently for _tSweepStart_ - _tSpeciation generations
+These two populations evolve independently for _tSweepStart_ - _tSpeciation_ generations
 with _m_ individuals per generation migrating from Population 2 to Population 1.
 At _tSweepStart_ selection switches on in Population 1 --- either on a random site
 or on a predefined genome region.

Forward Simulation modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 19:25:37 -0000

Overview

Population with size P₁+P₂ evolves for BURNIN generations in units of 2(P₁+P₂).
After BURNIN, this population evolves further with the same parameters
and at tSpeciation splits into two populations with sizes P₁ and P₂.
These two populations evolve independently for tSweepStart - tSpeciation generations
with _m individuals per generation migrating from Population 2 to Population 1.
At tSweepStart selection switches on in Population 1 --- either on a random site
or on a predefined genome region.

All or only a fraction of sites int this region may be under selection.
Fitness may also be simply 1 if we have none of the alleles in the selected region,
or 1+s if we have any of the alleles in the selected region (regardless of how many
and whether they are homozygous or heterozygous). The user can
specify the dominance parameter h, which will make heterozygote
fitness in both populations to 1+hs. Additionally, two more fitness
options are available. Truncation selection and simple synergistic
epistasis. Truncation selection sets fitness to zero if the number of
mutated sites is larger than a prespecified threshold. Simple
synergistic epistasis models fitness using an additional quadratic
term f = 1+as+bs². The parameters a and b can be specified by
the user.

These two populations evolve for further tTotal - tSweepStart generations
with selection in Population 1 and migration from Population 2 to
Population 1. Populations 1 and/or 2 may start expansion after BURNIN.

All time units are in 2(P₁+P₂) generations.

All evolutionary event times are measured from the end of BURNIN.