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Triadic IBD coefficients and applications to estimating pairwise relatedness

  • JINLIANG WANG (a1)
Summary
Summary

Knowledge of the genetic relatedness among individuals is essential in diverse research areas such as behavioural ecology, conservation biology, quantitative genetics and forensics. How to estimate relatedness accurately from genetic marker information has been explored recently by many methodological studies. In this investigation I propose a new likelihood method that uses the genotypes of a triad of individuals in estimating pairwise relatedness (r). The idea is to use a third individual as a control (reference) in estimating the r between two other individuals, thus reducing the chance of genes identical in state being mistakenly inferred as identical by descent. The new method allows for inbreeding and accounts for genotype errors in data. Analyses of both simulated and human microsatellite and SNP datasets show that the quality of r estimates (measured by the root mean squared error, RMSE) is generally improved substantially by the new triadic likelihood method (TL) over the dyadic likelihood method and five moment estimators. Simulations also show that genotyping errors/mutations, when ignored, result in underestimates of r for related dyads, and that incorporating a model of typing errors in the TL method improves r estimates for highly related dyads but impairs those for loosely related or unrelated dyads. The effects of inbreeding were also investigated through simulations. It is concluded that, because most dyads in a natural population are unrelated or only loosely related, the overall performance of the new triadic likelihood method is the best, offering r estimates with a RMSE that is substantially smaller than the five commonly used moment estimators and the dyadic likelihood method.

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*Corresponding author. Telephone: +44 20 74496620. Fax: +44 20 75862870. e-mail: jinliang.wang@ioz.ac.uk
References
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Aparicio J. M., Ortego J. & Cordero P. J. (2006). What should we weigh to estimate heterozygosity, alleles or loci? Molecular Ecology 15, 46594665.
Blouin M. S. (2003). DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends in Ecology and Evolution 18, 503511.
Bonin A., Bellemain E., Eidesen P. B., Pompanon F., Brochmann C. & Taberlet P. (2004). How to track and assess genotyping errors in population genetics studies. Molecular Ecology 13, 32613273.
Csilléry K., Johnson T., Beraldi D., Clutton-Brock T. H., Coltman D., Hansson B., Spong G. & Pemberton J. (2006). Performance of marker-based relatedness estimators in natural populations of outbred vertebrates. Genetics 173, 20912101.
Hamilton W. D. (1964). The genetical evolution of social behaviour: I and II. Journal of Theoretical Biology 7, 152.
Harris D. L. (1964). Genotypic covariances between inbred relatives. Genetics 50, 13191348.
Jacquard A. (1972). Genetic information given by a relative. Biometrics 28, 11011114.
Li C. C., Weeks D. E. & Chakravarti A. (1993). Similarity of DNA fingerprints due to chance and relatedness. Human Heredity 43, 4552.
Lynch M. (1988). Estimation of relatedness by DNA fingerprinting. Molecular Biology and Evolution 5, 584599.
Lynch M. & Ritland K. (1999). Estimation of pairwise relatedness with molecular markers. Genetics 152, 17531766.
Lynch M. & Walsh J. B. (1998). Genetics and analysis of Quantitative Traits. Sunderland, MA: Sinauer Associates.
Malécot G. (1948). Les Mathématiques de l'hérédité. Paris: Masson et Cie.
Milligan B. G. (2003). Maximum-likelihood estimation of relatedness. Genetics 163, 11531167.
Morrissey M. B. & Wilson A. J. (2005). The potential costs of accounting for genotypic errors in molecular parentage analyses. Molecular Ecology 14, 41114121.
Oliehoek P. A., Windig J. J., van Arendonk J. A. M. & Bijma P. (2006). Estimating relatedness between individuals in general populations with a focus on their use in conservation programs. Genetics 173, 483496.
Pompanon F., Bonin A., Bellemain E., & Taberlet P. (2005). Genotyping errors: causes, consequences and solutions. Nature Reviews Genetics 6, 847859.
Press W. H., Teukolsky S. A., Vetterling W. T. & Flannery B. P. (1996). Numerical Recipes in Fortran 90, 2nd edn. Cambridge: Cambridge University Press.
Queller D. C. & Goodnight K. F. (1989). Estimating relatedness using molecular markers. Evolution 43, 258275.
Ritland K. (1996). Estimators for pairwise relatedness and inbreeding coefficients. Genetical Research 67, 175186.
Ritland K. (2000). Marker-inferred relatedness as a tool for detecting heritability in nature. Molecular Ecology 9, 11951204.
Ritland K. (2005). Multilocus estimation of pairwise relatedness with dominant markers. Molecular Ecology 14, 31573165.
Thomas S. C. (2005). The estimation of genetic relationships using molecular markers and their efficiency in estimating heritability in natural populations. Philosophical Transactions of the Royal Society of London, Series B 360, 14571467.
Thomas S. C., Pemberton J. M. & Hill W. G. (2000). Estimating variance components in natural populations using inferred relationships. Heredity 84, 427436.
Thompson E. A. (1974). Gene identities and multiple relationships. Biometrics 30, 667680.
Van de Casteele T., Galbusera P. & Matthysen E. (2001). A comparison of microsatellite-based pairwise relatedness estimates. Molecular Ecology 10, 15391549.
Wang J. (2002). An estimator for pairwise relatedness using molecular markers. Genetics 160, 12031215.
Wang J. (2004 a). Sibship reconstruction from genetic data with typing errors. Genetics 166, 19631979.
Wang J. (2004 b) Estimating pairwise relatedness from dominant genetic markers. Molecular Ecology 13, 31693178.
Wang J. (2006). Informativeness of genetic markers for pairwise relationship and relatedness inference. Theoretical Population Biology 70, 300321.
Weir B. S. (1996). Genetic Data Analysis II. Sunderland, MA: Sinauer Associates.
Weir B. S., Anderson A. D., and Hepler A. B. (2006). Genetic relatedness analysis: modern data and new challenges. Nature Reviews Genetics 7, 771780.
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Genetics Research
  • ISSN: 0016-6723
  • EISSN: 1469-5073
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