Source-linked AI summary
SLiM: Simulating Evolution with Selection and Linkage
Philipp W. Messer
TL;DR
The paper addresses simulation of linked selection at chromosome-wide scale. SLiM uses fitness-proportional parent choice, recombination, and new mutations; it achieves substantially shorter runtimes than SFS CODE and supports chromosome-scale simulations.
Problem
The paper addresses simulation of linked selection at chromosome-wide scale.
Method
SLiM draws parents in proportion to fitness, then generates gametes by recombining parental chromosomes and adding new mutations.
Results
Five to ten times shorter simulation times than SFS CODE are reported across scenarios.
Takeaways & Limitations
SLiM’s computational efficiency enables simulations spanning entire eukaryotic chromosomes in reasonably large populations.
Takeaways & Limitations
The reported runtime example assumes u = 10−8, r = 1 cM/Mb, a 5% functional density, and an exponential DFE with 2Ns = −10.
Abstract
from arXiv · showhide
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 and chromosomal structure, and user-defined recombination maps.