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A Genetic Algorithm for Assigning Individuals to Populations Using Multi-locus Genotyping

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Simulated Evolution and Learning (SEAL 2010)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6457))

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Abstract

This paper reports a genetic algorithm (GA) for individual assignment using multi-locus microsatellite genotyping. Its performance has been compared with existing frequency, Bayesian and distance-based methods using simulated as well as actual data. Simulated data has been generated with SIMCOAL program. Actual data has been generated from genotypes of four cattle breeds from India. The GA showed lower accuracy while assigning individuals from simulated data. Its performance was comparable to that of existing methods using actual data.

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References

  1. Goldberg, D.E.: Genetic algorithms in search, optimization and machine learning. Addison-Wesley, Reading (1989)

    MATH  Google Scholar 

  2. Neilsen, E.E., Hansen, M.M., Bach, L.A.: Looking for a needle in a haystack: discovery of indigenous Atlantic salmon(Salmo salar L.) in stocked populations. Conservation Genetics 2, 219–232 (2001)

    Article  Google Scholar 

  3. Cornuet, J.-M., Piry, S., Luikart, G., Estoup, A., Solignac, M.: New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 153, 1989–2000 (1999)

    Google Scholar 

  4. Guinand, B., Topchy, A., Page, K.S., Burnham-Curtis, M.K., Punch, W.F., Scribner, K.T.: Comparison of likelihood and machine learning methods of individual classification. Journal of Heredity 93(4), 260–269 (2002)

    Article  Google Scholar 

  5. Narayanan, A., Keedwell, E.C., Olsson, B.: Artificial intelligence techniques for bioinformatics. Applied Bioinformatics 1(4), 191–222 (2003)

    Google Scholar 

  6. Guinand, B., Scribner, K.T., Topchy, A., Page, K.S., Punch, W., Burnham-Curtis, M.K.: Sampling issues affecting accuracy of likelihood-based classification using genetical data. Environmental Biology of Fishes 69, 245–259 (2004)

    Article  Google Scholar 

  7. Topchy, A., Scribner, K., Punch, W.: Accuracy-driven loci selection and assignment of individuals. Molecular Ecology Notes 4, 798–800 (2004)

    Article  Google Scholar 

  8. Bhatia, A.K., Basu, S.K.: Implicit elitism in genetic search. In: King, I., Wang, J., Chan, L.-W., Wang, D. (eds.) ICONIP 2006. LNCS, vol. 4234, pp. 781–788. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  9. Piry, S., Alapetite, A., Cornuet, J.-M., Paetkau, D., Baudouin, L., Estoup, A.: GENECLASS2: A software for genetic assignment and first-generation migrant detection. Journal of Heredity 95(6), 536–539 (2004)

    Article  Google Scholar 

  10. Excoffier, L., Novembre, J., Schneider, S.: SIMCOAL: A general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography. Journal of Heredity 91(6), 506–509 (2000)

    Article  Google Scholar 

  11. Mukesh, M., Sodhi, M., Bhatia, S., Mishra, B.P.: Genetic diversity of Indian native cattle breeds as analysed with 20 microsatellite loci. Journal of Animal Breeding and Genetics 121, 416–424 (2004)

    Article  Google Scholar 

  12. Sodhi, M., Mukesh, M., Mishra, B.P., Prakash, B., Ahlawat, S.P.S., Mitkari, K.R.: Evaluation of genetic differentiation in Bos indicus cattle breeds from Marathwada region of India using microsatellite polymorphism. Animal Biotechnogy 16, 1–11 (2005)

    Article  Google Scholar 

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Bhatia, A.K., Sodhi, M., Yadav, D.K., Prakash, B. (2010). A Genetic Algorithm for Assigning Individuals to Populations Using Multi-locus Genotyping. In: Deb, K., et al. Simulated Evolution and Learning. SEAL 2010. Lecture Notes in Computer Science, vol 6457. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-17298-4_39

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  • DOI: https://doi.org/10.1007/978-3-642-17298-4_39

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-17297-7

  • Online ISBN: 978-3-642-17298-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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