SLiM 5.0 Enables First Whole-Genome Simulations for Human Evolution Studies

A new model named SimHumanity, utilizing the recently released SLiM 5.0 evolutionary simulation framework, is set to revolutionize the study of human evolution by enabling comprehensive whole-genome simulations. Announced by Razib Khan on social media, the project leverages SLiM 5.0's advanced capabilities to model the intricate genetic processes of human populations at an unprecedented scale. This development marks a significant step forward in understanding complex evolutionary dynamics.

SLiM 5.0, an open-source framework developed by the Messer Lab, introduces a major extension allowing simulations across multiple chromosomes and full genomes, including sex chromosomes and mitochondrial DNA. Previously, such detailed whole-genome modeling was challenging due to the intrinsic limitations of existing simulation tools. The new version overcomes this by supporting up to 256 chromosomes, each with various types and inheritance patterns, and introduces the term "haplosome" for individual chromosome copies.

The SimHumanity model, as described in a bioRxiv preprint, provides a reusable and customizable platform designed specifically for human evolutionary history. It facilitates testing specific hypotheses about human demographic models, migration patterns, and interactions with archaic hominins. This capability is crucial for researchers aiming to reconstruct major evolutionary events, such as the out-of-Africa migration, with greater accuracy and detail.

Whole-genome evolutionary simulations are increasingly vital for population genetics, offering a powerful means to interpret vast genomic datasets. They allow scientists to disentangle the effects of demographic changes from natural selection, analyze structural variations, and understand the impact of mutational biases across the entire human genome. Such simulations are instrumental in developing and testing methods for analyzing large-scale sequence data, providing insights into the genetic basis of human-specific traits and diseases.

The Messer Lab, known for its contributions to population genetics and evolutionary biology, has continuously refined SLiM to address the growing complexity of research questions. SLiM's flexibility, powered by its Eidos scripting language and graphical user interface (SLiMgui), allows for modeling diverse scenarios from selective sweeps to gene drive dynamics. The SimHumanity project, built upon SLiM 5.0, exemplifies the framework's capacity to push the boundaries of evolutionary research, offering a robust tool for future discoveries in human genetics.