The R package ‘glads’ is an individual-based framework for forward demographic, genetic and genomic simulations
The main aim is to simulate the divergence of populations further in time, elucidating genomic patterns that may be generated by a range of demographic and genetic scenarios.
Integrating the program into an Approximate Bayesian Computation (ABC) framework or a similar approach enables the exploration of hypotheses on empirical observations. The framework is valuable for any genotype-phenotype map and any genomic architecture, considering the deterministic and stochastic process for any biological system.
How to cite ‘glads’?
Quilodrán CS, Kristen Ruegg, Sendell-Price AT, Anderson EC, Coulson T, Clegg SM (2020). The multiple population genetic and demographic routes to islands of genomic divergence. Methods in Ecology and Evolution, 11(1), 6-21. https://doi.org/10.1111/2041-210X.13324
Main features of ‘glads’
- Simulation of different types of selection and neutral evolution
- Flexible fitness function for genotype x phenotype x environmental interactions
- Analysis of multiple populations
- Consideration of genomes specificities—for instance, inclusion of genomic regions of high linkage, genes of large effect and multiple polymorphisms
New in the beta version
- Interaction between different populations and taxa
- Populations evolving with different fitness functions
- Easier retrieval of the output at user-defined generations
- Different migration regimes through time
Example of papers using ‘glads’
The following published manuscripts performed computational simulations using ‘glads’. The custom R codes are provided in supporting information.