Inferring population history with DIYABC: a user-friendly approach to Approximate Bayesian Computation

TL;DR

DIYABC is a user-friendly software tool that enables biologists to perform complex population history inferences using Approximate Bayesian Computation, accommodating multiple populations, admixtures, and size changes.

Contribution

It introduces a flexible, customizable ABC-based program allowing detailed population history inference beyond simple scenarios.

Findings

Successfully analyzed simulated data with complex scenarios.

Applied to real data demonstrating practical utility.

Provided estimates of evolutionary parameters with bias and precision measures.

Abstract

Genetic data obtained on population samples convey information about their evolutionary history. Inference methods can extract this information (at least partially) but they require sophisticated statistical techniques that have been made available to the biologist community (through computer programs) only for simple and standard situations typically involving a small number of samples. We propose here a computer program (DIYABC) for inference based on Approximate Bayesian Computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples. Such scenarios involve any combination of population divergences, admixtures and stepwise population size changes. DIYABC can be used to compare competing scenarios, estimate parameters for one or more scenarios, and compute bias and precision measures for a given scenario and known values of parameters (the current version applies to unlinked microsatellite data). This article describes key methods used in the program and provides its main features. The analysis of one simulated and one real data set, both with complex evolutionary scenarios, illustrates the main possibilities of DIYABC