Triadic IBD coefficients and applications to estimating pairwise relatedness

Genetical Research - Tập 89 Số 3 - Trang 135-153 - 2007
Jinliang Wang1
1Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY UK

Tóm tắt

SummaryKnowledge 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 therbetween 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 ofrestimates (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 ofrfor related dyads, and that incorporating a model of typing errors in the TL method improvesrestimates 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, offeringrestimates with a RMSE that is substantially smaller than the five commonly used moment estimators and the dyadic likelihood method.

Từ khóa


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Thông tin
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Genetical Research

Tập 89 Số 3

135-153

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