SimHumanity

SLiM scripts for full-human-genome evolutionary simulations

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This repository contains scripts and data associated with the publication:

Haller, B.C., Nelson, C.W., Rodrigues, M.F., and Messer, P.W. (2025). SimHumanity: Using SLiM 5.0 to run full-genome simulations of human evolution.

In particular, it contains:

• README.md : this file

• LICENSE : specifying the license for this repository

• model1_foundation.slim : the first version of the SimHumanity model presented in the paper (Code Sample 1)

• model1_foundation_FIGURE.slim : an extended version of model1_foundation.slim that adds plotting code that produces Fig. 1

• model2_demography.slim : the second version of the SimHumanity model presented in the paper (Code Sample 2)

• model2_demography_FIGURE.slim : an extended version of model2_demography.slim that adds plotting code that produces Fig. 2

• model2_demography_WITH_NEUTRAL.slim : a modified version of model2_demography.slim that includes neutral mutations

• model2_sweeps.R : an R script that explores the sweep data generated by model 2; not used in the publication

• model3_treeseq.slim : the third version of the SimHumanity model presented in the paper (Code Sample 3)

• model3_treeseq_FIGURE.slim : an extended version of model3_treeseq.slim for the pipeline that produces Fig. 3

• model3_analysis.py : a Python script that performs recapitation and neutral mutation overlay for the trees archive produced by model3_treeseq_FIGURE.slim, leading to Fig. 3

• model3_figure.py : a Python script that uses the trees archive produced by model3_analysis.py to produce Fig. 3

• environment.yml : environment information for the Python scripts

• stdpopsim extraction : a folder containing genetic structure data for all chromosomes except the mtDNA, together with scripts and materials for extracting that genetic structure data from stdpopsim

• mtDNA info : a folder containing genetic structure data for the mtDNA chromosome, together with info about how we obtained that data from the NCBI Reference Sequence we used

The trees archives simhumanity_trees and simhumanity_trees_RO are not provided in this repository, due to their size. They can be downloaded separately from the links given in the manuscript.

If you have questions, please contact the corresponding author(s) for the paper.