Julia source code for the simulations in support of a paper on the applications of the nearly neutral theory from population genetics to cultural evolution. The simulation code is in Julia, while code for producing the plots is written in R. As of July 2019, the code is compatible with Julia v. 1.1 with only one deprecation warnings.
This paper is in progress, and does not yet have a definite title.
- Alden Wright ([email protected]) primary author of the code.
- Cheyenne Laue ([email protected]) first author of the paper.
From Wikipedia
The nearly neutral theory of molecular evolution is a modification of the neutral theory
of molecular evolution that accounts for the fact that not all mutations are either so
deleterious such that they can be ignored, or else neutral. Slightly deleterious mutations
are reliably purged only when their selection coefficient is greater than one divided by
the effective population size. In larger populations, a higher proportion of mutations
exceed this threshold for which genetic drift cannot overpower selection, leading to fewer
fixation events and so slower molecular evolution.
The nearly neutral theory was proposed by Tomoko Ohta in 1973.[1]
This respository includes code for two models: infinite alleles, infinite sites.
To run Julia examples from the command line:
cd src julia run.jl examples/ia_example1 # run infinite alleles model julia run.jl examples/is_example1 # run infinite sites model julia run.jl examples/ia_example1 1 # run infinite alleles model using random number seed 1 julia run.jl examples/is_example1 1 # run infinite sites model using random number seed 1
The file run_tests.sh is a bash script to run all of the examples. The results can be compared with the .csv files in examples/results/.
The top-level results folder includes the R code for producing the plots along with the necessary data.