{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T21:26:00Z","timestamp":1791494760559,"version":"4.3.4"},"posted":{"date-parts":[[2025,8,11]]},"group-title":"Evolutionary Biology","reference-count":43,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,8,11]],"date-time":"2025-08-11T00:00:00Z","timestamp":1754870400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"award":["R01HG012473"],"award-info":[{"award-number":["R01HG012473"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R35GM152242"],"award-info":[{"award-number":["R35GM152242"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,8,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>Evolutionary simulations of multiple chromosomes, even up to the scale of full-genome simulations, are becoming increasingly important in population genetics and evolutionary ecology. Unfortunately, the popular simulation framework SLiM has always been intrinsically limited to simulations of a single diploid chromosome. Modeling multiple chromosomes of different types, such as sex chromosomes, has always been cumbersome even with scripting, presenting a substantial barrier to the development of full-genome simulations. Here we present SLiM 5, a major extension of SLiM\u2019s capabilities for simulating multiple chromosomes. Modeling up to 256 chromosomes is now possible, and each chromosome may belong to any of a wide variety of types \u2013 not just autosomes (diploid and haploid), but also sex chromosomes (X, Y, Z, and W), haploid mitochondrial and chloroplast DNA, and more. This new functionality is integrated across all of SLiM, including not only the mechanics of reproduction and inheritance, but also input and output of multi-chromosome data in formats like VCF, and tree-sequence recording across multiple chromosomes. New recipes in the SLiM manual demonstrate these new features, and SLiM\u2019s graphical modeling environment, SLiMgui, has been extended in many ways for the visualization of multi-chromosome models. These new features will open new horizons and enable a heightened level of realism for full-genome simulations.<\/jats:p>","DOI":"10.1101\/2025.08.07.669155","type":"posted-content","created":{"date-parts":[[2025,8,11]],"date-time":"2025-08-11T21:50:13Z","timestamp":1754949013000},"source":"Crossref","is-referenced-by-count":14,"title":["SLiM 5: Eco-evolutionary simulations across multiple chromosomes and full genomes"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1874-8327","authenticated-orcid":false,"given":"Benjamin C.","family":"Haller","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9459-6866","authenticated-orcid":false,"given":"Peter L.","family":"Ralph","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8453-9377","authenticated-orcid":false,"given":"Philipp W.","family":"Messer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025081311000711000_2025.08.07.669155v1.1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.54967"},{"issue":"3","key":"2025081311000711000_2025.08.07.669155v1.2","doi-asserted-by":"crossref","first-page":"e1006517","DOI":"10.1371\/journal.pgen.1006517","article-title":"Evolved genetic and phenotypic differences due to mitochondrial-nuclear interactions","volume":"13","year":"2017","journal-title":"PLoS Genetics"},{"key":"2025081311000711000_2025.08.07.669155v1.3","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.genet.35.102401.090231"},{"key":"2025081311000711000_2025.08.07.669155v1.4","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.05.038"},{"key":"2025081311000711000_2025.08.07.669155v1.5","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2000.0556"},{"issue":"1","key":"2025081311000711000_2025.08.07.669155v1.6","doi-asserted-by":"crossref","first-page":"58","DOI":"10.2174\/138920210790218007","article-title":"Simulation of genes and genomes forward in time","volume":"11","year":"2010","journal-title":"Current Genomics"},{"issue":"10","key":"2025081311000711000_2025.08.07.669155v1.7","doi-asserted-by":"crossref","first-page":"e1002905","DOI":"10.1371\/journal.pgen.1002905","article-title":"The many landscapes of recombination in Drosophila melanogaster","volume":"8","year":"2012","journal-title":"PLoS Genetics"},{"key":"2025081311000711000_2025.08.07.669155v1.8","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1099"},{"key":"2025081311000711000_2025.08.07.669155v1.9","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-018-0108-x"},{"key":"2025081311000711000_2025.08.07.669155v1.10","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2014.08.006"},{"key":"2025081311000711000_2025.08.07.669155v1.11","doi-asserted-by":"publisher","DOI":"10.1111\/mec.13339"},{"issue":"2","key":"2025081311000711000_2025.08.07.669155v1.12","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1111\/1755-0998.12968","article-title":"Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes","volume":"19","year":"2019","journal-title":"Molecular Ecology Resources"},{"key":"2025081311000711000_2025.08.07.669155v1.13","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msw211"},{"key":"2025081311000711000_2025.08.07.669155v1.14","doi-asserted-by":"publisher","DOI":"10.1101\/418657"},{"key":"2025081311000711000_2025.08.07.669155v1.15","doi-asserted-by":"publisher","DOI":"10.1086\/723601"},{"key":"2025081311000711000_2025.08.07.669155v1.16","unstructured":"Haller, B.C. , Nelson, C.W. , and Messer, P.W. 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