In the context of parentage assignment using genomic markers, key issues are genotyping errors and an absence of parent genotypes because of sampling, traceability or genotyping problems. Most likelihood-based parentage assignment software programs require a priori estimates of genotyping errors and the proportion of missing parents to set up meaningful assignment decision rules. We present here the R package APIS, which can assign offspring to their parents without any prior information other than the offspring and parental genotypes, and a user-defined, acceptable error rate among assigned offspring. Assignment decision rules use the distributions of average Mendelian transmission probabilities, which enable estimates of the proportion of offspring with missing parental genotypes. APIS has been compared to other software (CERVUS, VITASSIGN), on a real European seabass (Dicentrarchus labrax) single nucleotide polymorphism data set. The type I error rate (false positives) was lower with APIS than with other software, especially when parental genotypes were missing, but the true positive rate was also lower, except when the theoretical exclusion power reached 0.99999. In general, APIS provided assignments that satisfied the user-set acceptable error rate of 1% or 5%, even when tested on simulated data with high genotyping error rates (1% or 3%) and up to 50% missing sires. Because it uses the observed distribution of Mendelian transmission probabilities, APIS is best suited to assigning parentage when numerous offspring (>200) are genotyped. We have demonstrated that APIS is an easy-to-use and reliable software for parentage assignment, even when up to 50% of sires are missing.

中文翻译：

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APIS：能够容忍父母失踪的自适应父母身分推断软件。

在使用基因组标记进行亲子鉴定的情况下，关键问题是基因分型错误和由于采样，可追溯性或基因分型问题而导致的亲本基因型缺失。大多数基于可能性的育儿分配软件程序都需要对基因分型错误和失去父母的比例进行先验估计，以建立有意义的分配决策规则。我们在这里介绍了R包APIS，它可以将后代分配给其父母，而无需任何先验信息，除了后代和父母的基因型，以及用户定义的可接受的错误率。分配决策规则使用平均孟德尔传播概率的分布，从而可以估计具有缺失的父母基因型的后代的比例。APIS已与其他软件（CERVUS，VITASSIGN）进行了比较，真实的欧洲鲈鱼（Dicentrarchus labrax）单核苷酸多态性数据集上。APIS的I型错误率（假阳性）比其他软件要低，尤其是在缺少父母基因型的情况下，但真正的阳性率也较低，除非理论排斥力达到0.99999。总体而言，即使在具有高基因分型错误率（1％或3％）和高达50％缺失父本的模拟数据上进行测试，APIS所提供的分配也可以满足用户设置的1％或5％可接受的错误率。因为它使用了观察到的孟德尔传播概率分布，所以当对多个后代（> 200）进行基因分型时，APIS最适合分配亲本。我们已经证明，即使丢失了多达50％的父亲，APIS还是一种易于使用且可靠的用于育儿分配的软件。