Abstract
Previous techniques for estimating quantitative genetic parameters, such as heritability in populations where exact relationships are unknown but are instead inferred from marker genotypes, have used data from individuals on a pairwise level only. At this level, families are weighted according to the number of pairs within which each family appears, hence by size rather than information content, and information from multiple relationships is lost. Estimates of parameters are therefore not the most efficient achievable. Here, Markov chain Monte Carlo techniques have been used to partition the population into complete sibships, including, if known, prior knowledge of the distribution of family sizes. These pedigrees have then been used with restricted maximum likelihood under an animal model to estimate quantitative genetic parameters. Simulations to compare the properties of parameter estimates with those of existing techniques indicate that the use of sibship reconstruction is superior to earlier methods, having lower mean square errors and showing nonsignificant downward bias. In addition, sibship reconstruction allows the estimation of population allele frequencies that account for the relationships within the sample, so prior knowledge of allele frequencies need not be assumed. Extensions to these techniques allow reconstruction of half sibships when some or all of the maternal genotypes are known.
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Selected References
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- Kuhner M. K., Yamato J., Felsenstein J. Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics. 1995 Aug;140(4):1421–1430. doi: 10.1093/genetics/140.4.1421. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lynch M. Estimation of relatedness by DNA fingerprinting. Mol Biol Evol. 1988 Sep;5(5):584–599. doi: 10.1093/oxfordjournals.molbev.a040518. [DOI] [PubMed] [Google Scholar]
- Lynch M., Ritland K. Estimation of pairwise relatedness with molecular markers. Genetics. 1999 Aug;152(4):1753–1766. doi: 10.1093/genetics/152.4.1753. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Mousseau T. A., Roff D. A. Natural selection and the heritability of fitness components. Heredity (Edinb) 1987 Oct;59(Pt 2):181–197. doi: 10.1038/hdy.1987.113. [DOI] [PubMed] [Google Scholar]
- Thomas S. C., Pemberton J. M., Hill W. G. Estimating variance components in natural populations using inferred relationships. Heredity (Edinb) 2000 Apr;84(Pt 4):427–436. doi: 10.1046/j.1365-2540.2000.00681.x. [DOI] [PubMed] [Google Scholar]
- Thompson E. A. The estimation of pairwise relationships. Ann Hum Genet. 1975 Oct;39(2):173–188. doi: 10.1111/j.1469-1809.1975.tb00120.x. [DOI] [PubMed] [Google Scholar]
- Yang Z., Rannala B. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method. Mol Biol Evol. 1997 Jul;14(7):717–724. doi: 10.1093/oxfordjournals.molbev.a025811. [DOI] [PubMed] [Google Scholar]