Inferring past demographic changes from contemporary genetic data: A simulation-based evaluation of the ABC methods implemented in diyabc.

Abstract

Inferring the demographic history of species and their populations is crucial to understand their contemporary distribution, abundance and adaptations. The high computational overhead of likelihood-based inference approaches severely restricts their applicability to large data sets or complex models. In response to these restrictions, approximate Bayesian computation (ABC) methods have been developed to infer the demographic past of populations and species. Here, we present the results of an evaluation of the ABC-based approach implemented in the popular software package diyabc using simulated data sets (mitochondrial DNA sequences, microsatellite genotypes and single nucleotide polymorphisms). We simulated population genetic data under five different simple, single-population models to assess the model recovery rates as well as the bias and error of the parameter estimates. The ability of diyabc to recover the correct model was relatively low (0.49): 0.6 for the simplest models and 0.3 for the more complex models. The recovery rate improved significantly when reducing the number of candidate models from five to three (from 0.57 to 0.71). Among the parameters of interest, the effective population size was estimated at a higher accuracy compared to the timing of events. Increased amounts of genetic data did not significantly improve the accuracy of the parameter estimates. Some gains in accuracy and decreases in error were observed for scaled parameters (e.g., Ne μ) compared to unscaled parameters (e.g., Ne and μ). We concluded that diyabc-based assessments are not suited to capture a detailed demographic history, but might be efficient at capturing simple, major demographic changes.