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Open Access Software

SMARTPOP: inferring the impact of social dynamics on genetic diversity through high speed simulations

Elsa G Guillot and Murray P Cox*

Author Affiliations

Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University Palmerston North, New Zealand

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BMC Bioinformatics 2014, 15:175  doi:10.1186/1471-2105-15-175

Published: 9 June 2014

Abstract

Background

Social behavior has long been known to influence patterns of genetic diversity, but the effect of social processes on population genetics remains poorly quantified – partly due to limited community-level genetic sampling (which is increasingly being remedied), and partly to a lack of fast simulation software to jointly model genetic evolution and complex social behavior, such as marriage rules.

Results

To fill this gap, we have developed SMARTPOP – a fast, forward-in-time genetic simulator – to facilitate large-scale statistical inference on interactions between social factors, such as mating systems, and population genetic diversity. By simultaneously modeling genetic inheritance and dynamic social processes at the level of the individual, SMARTPOP can simulate a wide range of genetic systems (autosomal, X-linked, Y chromosomal and mitochondrial DNA) under a range of mating systems and demographic models. Specifically designed to enable resource-intensive statistical inference tasks, such as Approximate Bayesian Computation, SMARTPOP has been coded in C++ and is heavily optimized for speed and reduced memory usage.

Conclusion

SMARTPOP rapidly simulates population genetic data under a wide range of demographic scenarios and social behaviors, thus allowing quantitative analyses to address complex socio-ecological questions.

Keywords:
Population genetics; Mating systems; Forward-in-time simulation