Abstract
One of the goals of population genetics is to understand how evolutionary forces shape patterns of genetic variation over time. However, because populations evolve across both time and space, most evolutionary processes also have an important spatial component, acting through phenomena such as isolation by distance, local mate choice, or uneven distribution of resources. This spatial dimension is often neglected, partly due to the lack of tools specifically designed for building and evaluating complex spatiotemporal population genetic models. To address this methodological gap, we present a new framework for simulating spatially-explicit genomic data, implemented in a new R package called slendr (www.slendr.net), which leverages a SLiM simulation back-end script bundled with the package. With this framework, the users can programmatically and visually encode spatial population ranges and their temporal dynamics (i.e., population displacements, expansions, and contractions) either on real Earth landscapes or on abstract custom maps, and schedule splits and gene-flow events between populations using a straightforward declarative language. Additionally, slendr can simulate data from traditional, non-spatial models, either with SLiM or using an alternative built-in coalescent msprime back end. Together with its R-idiomatic interface to the tskit library for tree-sequence processing and analysis, slendr opens up the possibility of performing efficient, reproducible simulations of spatio-temporal genomic data entirely within the R environment, leveraging its wealth of libraries for geospatial data analysis, statistics, and visualization. Here, we present the design of the slendr R package and demonstrate its features on several practical example workflows.
Originalsprog | Engelsk |
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Artikelnummer | e121 |
Tidsskrift | Peer Community Journal |
Vol/bind | 3 |
Antal sider | 24 |
ISSN | 2804-3871 |
DOI | |
Status | Udgivet - 2023 |
Bibliografisk note
Funding Information:FR was supported by a Villum Young Investigator Grant (project no. 00025300), a Novo Nordisk Fonden Data Science Ascending Investigator Award (NNF22OC0076816) and by the European Research Council (ERC) under the European Union's Horizon Europe programme (grant agreements No. 101077592 and 951385). MP was supported by the aforementioned Novo Nordisk Fonden award, as well as a Lundbeck Foundation grant (R302-2018-2155) and a Novo Nordisk Foundation grant (NNF18SA0035006) given to the Lundbeck GeoGenetics Centre. PR was supported by NIH award R01HG010774.
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