dfuse and simadmix

dfuse and simadmix are programs for the simulation of hybridization and admixture. They are variants of the same model and implement forward-in-time simulations of populations of diploid individuals, ancestry of their complete genomes based on modeling junctions, and the effects of finite population size, migration, and selection on genomic composition. Statistics on simulated genomes from dfuse

simadmix

simadmix considers hybridization in a single deme, with recurrent migration of gametes possible from parental species, and various models of selection and genetic architectures of fitness. This code and slight variants of it were the basis for analyses in the following papers. The model is described to varying extents in these papers. The code was written in standard C by Alex Buerkle, requires the GNU Scientific Library, and runs reasonably fast.

Source code: simadmix.tgz Posted on 15 June 2015. Code last modified in 2011.

Most of the code (the core of modeling junctions) was initially written for a different purpose and for a project that never saw the light of day (understanding how chromosomal rearrangements would affect species barriers). Six or seven years later I was able to dust it off and put it to good use. The core of the code was validated against analytical theory for neutral evolution as described in Buerkle and Rieseberg 2008.

  • Gompert, Z. and C. A. Buerkle. 2012. bgc: Software for Bayesian estimation of genomic clines. Molecular Ecology Resources 12: 1168–1176. (article)
  • Gompert, Z., T. L. Parchman, and C. A. Buerkle. 2012a. Genomics of isolation in hybrids. Philosophical Transactions of the Royal Society, B: 367: 439–450. (article)
  • Gompert, Z. and C. A. Buerkle. 2011b. Bayesian estimation of genomic clines. Molecular Ecology 20: 2111–2127. (article)
  • Gompert, Z. and C. A. Buerkle. 2010. introgress: a software package for mapping components of isolation in hybrids. Molecular Ecology Resources 10: 378–384. (article)
  • Gompert, Z. and C. A. Buerkle. 2009. A powerful regression-based method for admixture mapping of isolation across the genome of hybrids. Molecular Ecology 18: 1207–1224. (article)
  • Buerkle, C. A. and L. H. Rieseberg. 2008. The rate of genome stabilization in homoploid hybrid species. Evolution 62: 266–275. (article)

dfuse

dfuse adds an important spatial component to the modeling and allows a flexible number of demes in which hybridization occurs, separate consideration of demes adjacent to parental species, and much more complex models and a very flexible specification of the genetic architecture of fitness. Doro Lindtke (d.lindtke@sheffield.ac.uk) wrote these modifications to the simadmix code and the description of the model and results of her analyses were published in Evolution (Lindtke and Buerkle 2015). Again, compiling and running the code requires the GNU Scientific Library.

Lindtke, D. and C. A. Buerkle. 2015. The genetic architecture of hybrid incompatibilities and their effect on barriers to introgression in secondary contact. Evolution 69: 1987–2004. (article)
Statistics on simulated genomes from dfuse
  • Source code: dfuse.tgz Posted on 15 June 2015. Code last modified in 2015.
  • Brief documentation of dfuse usage: notes.pdf.
  • Perl and R scripts to run dfuse and calculate statistics

Terms of use

The simadmix and dfuse software is available for use under the GNU Public License (GPL). This means it is free to use. You are encouraged to download the source code, review it, and improve it. If you use parts of the code in software of your own, you are required to give your users the same rights that were granted to you under the GPL.

Note that under the GPL, the software is distributed without warranty.