A flexible forward simulator for populations subject to selection and demography

Abstract

This article introduces a new forward population genetic simulation program that can efficiently generate samples from populations with complex demographic histories under various models of natural selection. The program (SFS_CODE) is highly flexible, allowing the user to simulate realistic genomic regions with several loci evolving according to a variety of mutation models (from simple to context-dependent), and allows for insertions and deletions. Each locus can be annotated as either coding or non-coding, sex-linked or autosomal, selected or neutral, and have an arbitrary linkage structure (from completely linked to independent).

Availability: The source code (written in the C programming language) is available at http://sfscode.sourceforge.net, and a web server (http://cbsuapps.tc.cornell.edu/sfscode.aspx) allows the user to perform simulations using the high-performance computing cluster hosted by the Cornell University Computational Biology Service Unit.

Fig. 1.

The basic life cycle that takes place every generation. Each individual in the population is generated from a male and female chosen from the parental population with probabilities given by their relative fitness in their sex (only necessary for diploid and allo/autotetraploid populations, as haploid populations are simulated asexually). The new individuals are then able to migrate among populations. The gametes of the new populations then undergo recombination and mutation (both at Poisson rates) before being passed on to the next generation. Note that circles represent females, squares represent males and different colors indicate different haplotypes.