Human Population Genetics and Genomics ISSN 2770-5005

Human Population Genetics and Genomics 2025;5(4):0006 | https://doi.org/10.47248/hpgg2505040006

Methods Open Access

SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution

Benjamin C. Haller 1 , Chase W. Nelson 2,3 , Murillo F. Rodrigues 4 , Philipp W. Messer 1

  • Department of Computational Biology, Cornell University, Ithaca, NY 14850, USA
  • Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
  • Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
  • Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA

Correspondence: Benjamin C. Haller

Academic Editor(s): Joshua Akey, Carina Schlebusch, Torsten Günther

Received: Aug 29, 2025 | Accepted: Oct 9, 2025 | Published: Oct 15, 2025

This article belongs to the Special Issue

Cite this article: Haller BC, Nelson CW, Rodrigues MF, Messer PW. SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution. Hum Popul Genet Genom. 2025;5(4):0006. https://doi.org/10.47248/hpgg2505040006

Abstract

The reconstruction of human evolutionary history has undergone repeated advances, each made possible by methodological innovations. In recent decades, genetic and genomic data played a central role in the reconstruction of major evolutionary events such as the out-of-Africa migration, and genetic simulations of human evolutionary history have come to play a major role in testing more specific hypotheses including proposed patterns of migration and admixture with archaic hominins. Increasing computational power has allowed human evolutionary history to be modeled at ever-larger scales, but simulations that encompass the complete human genome, including sex chromosomes and mitochondrial DNA, have been difficult due to the lack of support for whole-genome models in commonly used evolutionary simulation frameworks. With the recent introduction of SLiM 5 such simulations are now straightforward to construct, allowing the easy simulation of humans at whole-genome scale under different demographic models and evolutionary dynamics. We here present three versions of a reusable, customizable, open-source SLiM 5 model for simulating the molecular evolution of the full human genome. We also show some simple analyses of results from the model to illustrate its utility. We hope this model, which we have nicknamed “SimHumanity” in jest, will facilitate further progress in the field of human evolutionary simulations.

Keywords

human evolution, whole-genome simulation, full-genome simulation, forward genetic simulation, sex chromosome evolution, individual-based model, agent-based model, SLiM

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