ArticleMolecular ecology resources2019
Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes.
Article in Molecular ecology resources, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 139 papers.
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Who cites it
139 citing papers in PubMed.
- Characterizing the detectable and invisible fractions of genomic loci under balancing selection.Molecular biology and evolution · 2026Article
- Blocks of Identity by Descent Reveal the Dual Role Played by Reef Fish Larvae for Retention and Dispersal.Molecular ecology · 2026Article
- Polygenic and monogenic adaptation drive evolutionary rescue at different magnitudes of environmental change.The Journal of heredity · 2026Article
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- Comparing ARG Inference Methods Under Transmission of Reproductive Success: Tree Imbalance Matters.Genome biology and evolution · 2026Article
- Phylogenetically Diverse Introgression Drives Subtle Population Structure in Pacific Rockfishes.Molecular ecology · 2026Article
- MixedUpParents: A New and Improved Method for Genetic Parentage Assignment in Admixed Populations.Molecular ecology resources · 2026Article
- Article
- Genetic Footprints of Seasonal Fluctuating Selection: A Comparison With Established Selection Forms.Genome biology and evolution · 2026Article
- e3SIM: Epidemiological-ecological-evolutionary simulation framework for genomic epidemiology.Methods in ecology and evolution · 2026Article
- Summary statistics and approximate bayesian computation are comparable to convolutional neural networks for inferring times to fixation.bioRxiv : the preprint server for biology · 2026Article
- Estimating the Reduction in Genetic Diversity from Background Selection under Non-equilibrium Demography and Partial Selfing.Molecular biology and evolution · 2026Article
- Contemporary hybridization among Arabis floodplain species creates opportunities for adaptation.The New phytologist · 2026Article
- Tracing the evolutionary histories of ultra-rare variants using variational dating of large ancestral recombination graphs.bioRxiv : the preprint server for biology · 2026Article
- Likelihoods for a general class of ARGs under the SMC.Genetics · 2026Article
- SLiM 5: Eco-evolutionary Simulations Across Multiple Chromosomes and Full Genomes.Molecular biology and evolution · 2026Article
- On the robustness of Bayesian inference of gene flow to intragenic recombination and natural selection.Molecular biology and evolution · 2026Article
- Human ancestries simulation and inference: a review of ancestral recombination graph-based approaches.Frontiers in bioinformatics · 2026Review
- Article
- The promise and challenge of spatial inference with the full ancestral recombination graph under Brownian motion.G3 (Bethesda, Md.) · 2025Article
79 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
There is an increasing demand for evolutionary models to incorporate relatively realistic dynamics, ranging from selection at many genomic sites to complex demography, population structure, and ecological interactions. Such models can generally be implemented as individual-based forward simulations, but the large computational overhead of these models often makes simulation of whole chromosome sequences in large populations infeasible. This situation presents an important obstacle to the field that requires conceptual advances to overcome. The recently developed tree-sequence recording method (Kelleher, Thornton, Ashander, & Ralph, 2018), which stores the genealogical history of all genomes in the simulated population, could provide such an advance. This method has several benefits: (1) it allows neutral mutations to be omitted entirely from forward-time simulations and added later, thereby dramatically improving computational efficiency; (2) it allows neutral burn-in to be constructed extremely efficiently after the fact, using "recapitation"; (3) it allows direct examination and analysis of the genealogical trees along the genome; and (4) it provides a compact representation of a population's genealogy that can be analysed in Python using the msprime package. We have implemented the tree-sequence recording method in SLiM 3 (a free, open-source evolutionary simulation software package) and extended it to allow the recording of non-neutral mutations, greatly broadening the utility of this method. To demonstrate the versatility and performance of this approach, we showcase several practical applications that would have been beyond the reach of previously existing methods, opening up new horizons for the modelling and exploration of evolutionary processes.
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