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bioRxiv · 10.1101/2025.09.30.679676

Bridging forward-in-time and coalescent simulations using pyslim

Gopalan, S.·Rodrigues, M. F.·Ralph, P. L.·Haller, B. C.
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Abstract

Ancestral Recombination Graphs (ARGs) provide an expressive and compact way to represent genetic variation data generated by simulations embedded within its genealogical history, and it can dramatically speed up simulations. The fact that the ARG records genealogical as well as genomic information opens up the possibility for a number of new analysis and simulation techniques. Here, we aim to introduce the reader to this deep source of information as produced by the forwards simulator SLiM. SLiM records the ARG using the tree sequence format, which can be manipulated using the tskit and pyslim python packages. We first describe the information that SLiM records in the tree sequence, then provide several examples that use the tree sequence as a format to losslessly pass population states between simulators: recapitation of a forwards simulation with coalescent simulation; initiation of a forwards simulation using the results of a coalescent simulation; and parallelization of simulations, first across branches of a phylogenetic tree, and then across the populations of parasites infecting different hosts.

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Gopalan, S., Rodrigues, M. F., Ralph, P. L., Haller, B. C.. 2025-10-01. Bridging forward-in-time and coalescent simulations using pyslim. https://doi.org/10.1101/2025.09.30.679676

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