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SibPublic

Research in Sibling Reconstruction

Introduction

Falcons and other birds of prey are extremely secretive about their lives. Sharks are hard to catch and study because they live in water. Cowbirds leave eggs in other birdsí nests and let them raise the cowbird chicks. A female oak tree can have acorns from many male trees, some growing very far away. One of the things common to all these species is that it is difficult to study their mating system. It is even difficult to identify which animals or plants are siblings. Yet, this simple fact is necessary for conservation, animal management, and understanding of evolutionary mechanisms.

Lemon Sharks Image

Our team has developed an efficient computational method for reconstruction of sibling relationships from genetic data geared especially to wild populations. Now, given a genetic sample of the individuals from the same generation, we can identify full siblings without any information on the parents. Unlike other methods, ours does not assume anything about the data beyond the simple Mendelian laws of inheritance and does not require any a priori knowledge about the population. Our method reconstructs the known sibling groups exactly on data from such diverse species as cod, shrimp, flies, and radishes. Biologists now can use our method to find out more about the mating systems of falcons and sharks. Moreover, they can do it by just taking the genetic sample from the chicks in the nests or the young shark in shallow waters, without having to chase the parents across the sky and the ocean.

We can also use our method when parents of one gender are known to estimate the number of parents of the other gender necessary to produce all the offspring. Our team has found the smallest number of fathers that would have to pollinate a female oak tree to explain the genetics of all the acorns. Even this very modest (but mathematically rigorous) bottom line showed that male oak pollen travels a lot further to get to a female tree than biologists thought was possible.

Our Group:

Alumni:

Funding:

  • NSF IIS-0612044, Collaborative Research: SEI: Computational Methods for Kinship Reconstruction,
(T.Y. Berger-Wolf, co-PIs: M. V. Ashley, B. DasGupta, W. Chaovalitwongse)
  • NSF CAREER Award IIS-0747369 "Computational Tools for Population Biology" (T.Y. Berger-Wolf)

Publications

  • S. I. Sheikh, T. Y. Berger-Wolf, Ashfaq Khokhar, Isabel C. Caballero, Mary V. Ashley, Wanpracha Chaovalitwongse and B. DasGupta
Combinatorial Reconstruction of Half-Sibling Groups
Proceedings of the 8th Annual International Conference on Computational Systems Biology (CSB 2009) (to appear, also invited to JBCB) PDF
  • M. Ashley, T. Berger-Wolf, W. Chaovalitwongse, B. DasGupta, A Khokhar, S. Sheikh
On Approximating An Implicit Cover Problem in Biology
Proceedings of 5th International Conference on Algorithmic Aspects of Information and Management 2009 PDF
  • W. Chaovalitwongse, C-A Chou, T. Y. Berger-Wolf, B. DasGupta, S. Sheikh, M. V. Ashley, I. C. Caballero.
New Optimization Model and Algorithm for Sibling Reconstruction from Genetic Markers
INFORMS Journal of Computing (to appear) PDF
  • M. Ashley, T. Berger-Wolf, P. Berman, W. Chaovalitwongse, B. DasGupta, and M.-Y. Kao.
On Approximating Four Covering and Packing Problems
Journal of Computer and System Science 75(5) PDF
  • M. V. Ashley, I. C. Caballero, W. Chaovalitwongse, B. DasGupta, P. Govindan, S. Sheikh and T. Y. Berger-Wolf.
KINALYZER, A Computer Program for Reconstructing Sibling Groups
Molecular Ecology Resources 9(4) PDF
  • S. I. Sheikh, T. Y. Berger-Wolf, M. V. Ashley, I. C. Caballero, W. Chaovalitwongse, and B. DasGupta
Error Tolerant Sibship Reconstruction in Wild Populations
Proceedings of the 7th Annual International Conference on Computational Systems Bioinformatics
(CSB), August 2008, Stanford, CA. PDF
  • S. I. Sheikh, T. Y. Berger-Wolf, A. A. Khokhar, and B. DasGupta
Consensus Methods for Reconstruction of Sibling Relationships from Genetic Data
Proceedings of the AAAI Multidisciplinary Workshop on Advances in Preference Handling
(MPREF), July 2008, Chicago, IL PDF
  • T.Y. Berger-Wolf, S.I. Sheikh, B. DasGupta, M.V. Ashley, I.C. Caballero, W. Chaovalitwongse, S.L. Putrevu
Reconstructing Sibling Relationships in Wild Populations
Bioinformatics, 23(13) and Proceedings of ISMB/ECCB 2007, Vienna, Austria, 2007. PDF
  • Chaovalitwongse, W., T.Y. Berger-Wolf, B. DasGupta, and M. V. Ashley.
Set covering approach for reconstruction of sibling relationships
Optimization Methods and Software (Special Issue on Systems Analysis, Optimization and Data Mining in Biomedicine),
22(1), Feb 2007, 11--24. PDF
  • S. Sheikh, T. Y. Berger-Wolf, W. Chaovalitwongse, B. DasGupta, and M. Ashley.
Reconstructing Sibling Relationships from Microsatellite Data
European Conf. on Computational Biology (ECCB), Jan 2007, Eilat, Israel PDF
  • T.Y. Berger-Wolf, Bhaskar DasGupta, Wanpracha Chaovalitwongse and Mary V. Ashley.
Combinatorial Reconstruction of Sibling Relationships
Proceedings of the 6th International Symposium on Computational Biology and Genome Informatics
(CBGI 05), Utah, July 21 - 26, 2005, pp. 1252-1255 PDF
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Page last modified on February 12, 2013, at 10:57 AM