The Power of Single-Nucleotide Polymorphisms for Large-Scale Parentage Inference

Abstract

Abstract Likelihood-based parentage inference depends on the distribution of a likelihood-ratio statistic, which, in most cases of interest, cannot be exactly determined, but only approximated by Monte Carlo simulation. We provide importance-sampling algorithms for efficiently approximating very small tail probabilities in the distribution of the likelihood-ratio statistic. These importance-sampling methods allow the estimation of small false-positive rates and hence permit likelihood-based inference of parentage in large studies involving a great number of potential parents and many potential offspring. We investigate the performance of these importance-sampling algorithms in the context of parentage inference using single-nucleotide polymorphism (SNP) data and find that they may accelerate the computation of tail probabilities >1 millionfold. We subsequently use the importance-sampling algorithms to calculate the power available with SNPs for large-scale parentage studies, paying particular attention to the effect of genotyping errors and the occurrence of related individuals among the members of the putative mother–father–offspring trios. These simulations show that 60–100 SNPs may allow accurate pedigree reconstruction, even in situations involving thousands of potential mothers, fathers, and offspring. In addition, we compare the power of exclusion-based parentage inference to that of the likelihood-based method. Likelihood-based inference is much more powerful under many conditions; exclusion-based inference would require 40% more SNP loci to achieve the same accuracy as the likelihood-based approach in one common scenario. Our results demonstrate that SNPs are a powerful tool for parentage inference in large managed and/or natural populations.