Supplemental Material for Huang et al., 2018

Parentage analysis is an important method, used widely in zoological and ecological studies. Current mathematical models of parentage analyses usually assume that a population has a uniform genetic structure and that mating is panmictic. In a natural population, the geographic or social structure of a population, and/or non-random mating, usually leads to a genetic structure and results in genotypic frequencies deviating from those expected under the Hardy-Weinberg Equilibrium (HWE). In addition, in the presence of null alleles, an observed genotype represents one of several possible true genotypes. The true father of a given offspring may thus be erroneously excluded in parentage analyses, or may have a low or negative LOD score. Here we present a new mathematical model to estimate parentage that includes simultaneously the effects of inbreeding, null alleles and negative amplification. The influences of these three factors on previous model are evaluated by Monte-Carlo simulations and empirical data, and the performance of our new model is compared under controlled conditions. We found that for both simulated and empirical data, our new model outperformed other methods in many situations. We make available our methods in a new, free software package entitled PARENTAGE. This can be downloaded via http://github.com/huangkang1987/parentage.