Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0)

By Jean-Marie Cornuet, Virgine Ravigné, Arnaud Estoup. BMC Bioinformatics, 2010

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BackgroundApproximate Bayesian computation (ABC) is a recent flexible class of Monte-Carlo algorithms increasingly used to make model-based inference on complex evolutionary scenarios that have acted on natural populations. The software DIYABC offers a user-friendly interface allowing non-expert users to consider population histories involving any combination of population divergences, admixtures and population size changes. We here describe and illustrate new developments of this software that mainly include (i) inference from DNA sequence data in addition or separately to microsatellite data, (ii) the possibility to analyze five categories of loci considering balanced or non balanced sex ratios: autosomal diploid, autosomal haploid, X-linked, Y-linked and mitochondrial, and (iii) the possibility to perform model checking computation to assess the "goodness-of-fit" of a model, a feature of ABC analysis that has been so far neglected.ResultsWe used controlled simulated data sets generated under evolutionary scenarios involving various divergence and admixture events to evaluate the effect of mixing autosomal microsatellite, mtDNA and/or nuclear autosomal DNA sequence data on inferences. This evaluation included the comparison of competing scenarios and the quantification of their relative support, and the estimation of parameter posterior distributions under a given scenario. We also considered a set of scenarios often compared when making ABC inferences on the routes of introduction of invasive species to illustrate the interest of the new model checking option of DIYABC to assess model misfit.ConclusionsOur new developments of the integrated software DIYABC should be particularly useful to make inference on complex evolutionary scenarios involving both recent and ancient historical events and using various types of molecular markers in diploid or haploid organisms. They offer a handy way for non-expert users to achieve model checking computation within an ABC framework, hence filling up a gap of ABC analysis. The software DIYABC V1.0 is freely available at http://www1.montpellier.inra.fr/CBGP/diyabc.

Subfields: Genetics, Statistics and Probability

View Paper: https://www.semanticscholar.org/paper/cddf9c625a33f86ad6d7b728a0b03392f896f744

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Citations in the corpus

abc: an R package for approximate Bayesian computation (ABC) (2011, methodology): “…problems have already been developed in these fields (Anderson et al. 2005; Hickerson et al. 2007; Cornuet et al. 2008; Jobin & Mountain 2008; Tallmon et al. 2008; Lopes et al. 2009; Thornton 2009; Bray et al. 2010; Cornuet et al. 2010; Liepe et al. 2010; Wegmann et al. 2010; Huang et al. 2011).”
Reliable ABC model choice via random forests (2014, methodology): “…of a similar type (although based on PCA) as well as computation for each summary statistics and for each model of the probabilities of the observed values in the prior distributions have been proposed by Cornuet et al. (2010) and are already automatically provided by the DIYABC software.”
Reconstructing routes of invasion using genetic data: why, how and so what? (2010, background): “…account balanced or unbalanced sex ratios: autosomal diploid, autosomal haploid, X-linked, Y-linked and mitochondrial, and (iii) the possibility to proceed model checking computation to assess the ‘goodnessof-fit’ of a model, a much-neglected facet of ABC analysis (Cornuet et al. 2010; DIYABC V1.”
Bayesian computation: a summary of the current state, and samples backwards and forwards (2015, methodology): “…genetics, model choice and hypotheses validation is presumably the primary motivation for using ABC methods as exempliﬁed in Belle et al. (2008), Cornuet et al. (2010), Excofﬁer et al. (2009), Ghirotto et al. (2010), Guillemaud et al. (2009), Leuenberger and Wegmann (2010), Patin et al. (2009),…”
The global spread of Harmonia axyridis (Coleoptera: Coccinellidae): distribution, dispersal and routes of invasion (2011, methodology): “Interestingly, new DIYABC analyses of microsatellite data, taking into account the above genetic structure within the native range, indicated that populations from western Asia also contributed in a significant manner to the invasive bridgehead population located in eastern North America (E. Lombaer”