Optimal sampling for pedigree analysis: parameter estimation and genotypic uncertainty

Many problems of sampling strategy arise in pedigree analysis. Although specific questions have been previously considered, there is a need for a general study of the form of the likelihood surface for genetic models. Were genotypes observable, the log-likelihood would have a very simple form. The two classes of factors of genealogical structure affecting general questions of inference are thus those (such as inbreeding or assortive mating) which affect the genotype distribution within a pedigree, and those affecting the extent to which these unobservable genotypes can be inferred from phenotypes. The latter aspect is considered in some detail.