TECHNICAL ADVANCES: A maximum-likelihood relatedness estimator allowing for negative relatedness values

Mol Ecol Resour. 2008 Mar;8(2):256-63. doi: 10.1111/j.1471-8286.2007.01940.x.

Abstract

Previously reported maximum-likelihood pairwise relatedness (r) estimator of Thompson and Milligan (M) was extended to allow for negative r estimates under the regression interpretation of r. This was achieved by establishing the equivalency of the likelihoods used in the kinship program and the likelihoods of Thompson. The new maximum-likelihood (ML) estimator was evaluated by Monte Carlo simulations. It was found that the new ML estimator became unbiased significantly faster compared to the original M estimator when the amount of genotype information was increased. The effects of allele frequency estimation errors on the new and existing relatedness estimators were also considered.