Marshall T C, Slate J, Kruuk L E, Pemberton J M
Institute of Cell, Animal and Population Biology, University of Edinburgh, UK.
Mol Ecol. 1998 May;7(5):639-55. doi: 10.1046/j.1365-294x.1998.00374.x.
Paternity inference using highly polymorphic codominant markers is becoming common in the study of natural populations. However, multiple males are often found to be genetically compatible with each offspring tested, even when the probability of excluding an unrelated male is high. While various methods exist for evaluating the likelihood of paternity of each nonexcluded male, interpreting these likelihoods has hitherto been difficult, and no method takes account of the incomplete sampling and error-prone genetic data typical of large-scale studies of natural systems. We derive likelihood ratios for paternity inference with codominant markers taking account of typing error, and define a statistic delta for resolving paternity. Using allele frequencies from the study population in question, a simulation program generates criteria for delta that permit assignment of paternity to the most likely male with a known level of statistical confidence. The simulation takes account of the number of candidate males, the proportion of males that are sampled and gaps and errors in genetic data. We explore the potentially confounding effect of relatives and show that the method is robust to their presence under commonly encountered conditions. The method is demonstrated using genetic data from the intensively studied red deer (Cervus elaphus) population on the island of Rum, Scotland. The Windows-based computer program, CERVUS, described in this study is available from the authors. CERVUS can be used to calculate allele frequencies, run simulations and perform parentage analysis using data from all types of codominant markers.
利用高度多态的共显性标记进行父权推断在自然种群研究中变得越来越普遍。然而，即使排除无关雄性的概率很高，通常也会发现多个雄性在基因上与每个测试后代相匹配。虽然存在各种方法来评估每个未排除雄性的父权可能性，但迄今为止，解释这些可能性一直很困难，而且没有一种方法考虑到自然系统大规模研究中典型的不完整抽样和易出错的遗传数据。我们推导了考虑分型错误的共显性标记父权推断的似然比，并定义了一个用于解决父权问题的统计量δ。使用所研究种群的等位基因频率，一个模拟程序生成δ的标准，从而能够在已知的统计置信水平下将父权分配给最有可能的雄性。该模拟考虑了候选雄性的数量、被抽样雄性的比例以及遗传数据中的缺口和错误。我们探讨了亲属可能产生的混淆效应，并表明该方法在常见条件下对其存在具有稳健性。使用来自苏格兰拉姆岛经过深入研究的马鹿（Cervus elaphus）种群的遗传数据对该方法进行了验证。本研究中描述的基于Windows的计算机程序CERVUS可从作者处获得。CERVUS可用于计算等位基因频率、运行模拟并使用来自所有类型共显性标记的数据进行亲权分析。
