Error tolerant sibship reconstruction in wild populations

Saad I. Sheikh*, Tanya Y. Berger-Wolf, Mary V. Ashley, Isabel C. Caballero, Wanpracha Chaovalitwongse, Bhaskar DasGupta

Department of Computer Science, University of Illinois at Chicago, 851 S. Morgan (M/C 152), Room 1120 SEO,Chicago, IL 60607. ssheikh@cs.uic.edu

Proc LSS Comput Syst Bioinform Conf. August, 2008. Vol. 7, p. 273-284. Full-Text PDF

*To whom correspondence should be addressed.

Kinship analysis using genetic data is important for many biological applications, including many in conservation biology. Wide availability of microsatellites has boosted studies in wild populations that rely on the knowledge of kinship, particularly sibling relationships (sibship). While there exist many methods for reconstructing sibling relationships, almost none account for errors and mutations in microsatellite data, which are prevalent and affect the quality of reconstruction. We present an error-tolerant method for reconstructing sibling relationships based on the concept of consensus methods. We test our approach on both real and simulated data, with both pre-existing and introduced errors. Our method is highly accurate on almost all simulations, giving over 90% accuracy in most cases. Ours is the first method designed to tolerate errors while making no assumptions about the population or the sampling.