Discovering Kinship through Small Subsets
In kinship inference, we identify genealogical relationships among organisms. One such problem is sibgroup reconstruction: given a population of same-generation individuals, partition it into sibgroups resulting from mating events. Minimizing the number of matings is NP-hard to approximate, yet a simple heuristic, based on identifying population triplets that can be from the same sibgroup, performs comparably to better than integer programming algorithms in a fraction of the running time. With high probability if we study many loci in the genome, and large populations, our polynomial-time heuristic finds the true sibgroups, assuming a standard probabilistic inheritance model.
KeywordsFailure Probability Simple Heuristic Full Sibling Sibling Relationship Population Member
Unable to display preview. Download preview PDF.
- 3.Wilson, A., Barker, J.: Isolation and characterization of 20 polymorphic microsatellite loci for Scaptodrosophila hibisci. Mol. Ecol. Notes 2, 242–244 (2002)Google Scholar
- 4.Berger-Wolf, T., Sheikh, S., DasGupta, B., Ashley, M., Caballero, I., Chaovalitwongse, W., Putrevu, S.L.: Reconstructing sibling relationships in wild populations. Bioinf. 23(13); Proceedings of ISMB 2007 (2007)Google Scholar
- 6.Conner, J.K.: Personal Communication (2006)Google Scholar
- 8.Devdatt, D., Panconesci, A.: Concentration of measure for the analysis of randomized algorithms. Cambridge Press, New York (2009)Google Scholar
- 12.Jerry, D., Evans, B., Kenway, M., Wilson, K.: Development of a microsatellite DNA parentage marker suite for black tiger shrimp Penaeus monodon. Aquaculture, 542–547 (2006)Google Scholar
- 13.Sheikh, S., Berger-Wolf, T., Khokhar, A., DasGupta, B.: Consensus methods for reconstruction of sibling relationships from genetic data. In: Proceedings of the 4th Workshop on Advances in Preference Handling (2008)Google Scholar
- 14.Sheikh, S., Berger-Wolf, T., Khokhar, A., Caballero, I., Ashley, M., Chaovalitwongse, W., DasGupta, B.: Parsimony-based reconstruction of half-sibling groups. J. Bioinf. and Comp. Biol. (to appear)Google Scholar
- 15.Wang, J.: Sibship reconstruction from genetic data with typing errors. Genetics 166, 1968–1979 (2004)Google Scholar