SLiM: simulating evolution with selection and linkage

Abstract

SLiM is an efficient forward population genetic simulation designed for studying the effects of linkage and selection on a chromosome-wide scale. The program can incorporate complex scenarios of demography and population substructure, various models for selection and dominance of new mutations, arbitrary gene structure, and user-defined recombination maps.

Keywords: background selection; genetic hitchhiking; population genetic simulation.

Figure 1

(A) Illustration of SLiM’s core algorithm for a scenario with two subpopulations. In each generation, a new set of offspring is created from the individuals in the previous generation. Parents are drawn with probabilities proportional to their fitness. Gametes are generated by recombining parental chromosomes and adding new mutations. Migration is modeled by choosing parents from the source subpopulation. (B) Comparison of runtimes and peak resident set size memory requirements between SLiM and SFS_CODE for different evolutionary scenarios. In each column, one of the four parameters L, N, u, and r was varied, while the others were kept constant at their respective base values (L = 5 Mbp, N = 500, u = 10⁻⁹, and r = 10⁻⁸). Simulations were run for 10N generations. Data points show the observed runtimes and memory requirements averaged over 10 simulation runs.