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ABCtoolbox: a versatile toolkit for approximate Bayesian computations

Daniel Wegmann12*, Christoph Leuenberger3, Samuel Neuenschwander4 and Laurent Excoffier12

Author Affiliations

1 Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland

2 Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland

3 Ecole d'ingénieurs de Fribourg, 1705 Fribourg, Switzerland

4 Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland

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BMC Bioinformatics 2010, 11:116  doi:10.1186/1471-2105-11-116

Published: 4 March 2010

Abstract

Background

The estimation of demographic parameters from genetic data often requires the computation of likelihoods. However, the likelihood function is computationally intractable for many realistic evolutionary models, and the use of Bayesian inference has therefore been limited to very simple models. The situation changed recently with the advent of Approximate Bayesian Computation (ABC) algorithms allowing one to obtain parameter posterior distributions based on simulations not requiring likelihood computations.

Results

Here we present ABCtoolbox, a series of open source programs to perform Approximate Bayesian Computations (ABC). It implements various ABC algorithms including rejection sampling, MCMC without likelihood, a Particle-based sampler and ABC-GLM. ABCtoolbox is bundled with, but not limited to, a program that allows parameter inference in a population genetics context and the simultaneous use of different types of markers with different ploidy levels. In addition, ABCtoolbox can also interact with most simulation and summary statistics computation programs. The usability of the ABCtoolbox is demonstrated by inferring the evolutionary history of two evolutionary lineages of Microtus arvalis. Using nuclear microsatellites and mitochondrial sequence data in the same estimation procedure enabled us to infer sex-specific population sizes and migration rates and to find that males show smaller population sizes but much higher levels of migration than females.

Conclusion

ABCtoolbox allows a user to perform all the necessary steps of a full ABC analysis, from parameter sampling from prior distributions, data simulations, computation of summary statistics, estimation of posterior distributions, model choice, validation of the estimation procedure, and visualization of the results.