Bayesian tests for random mating in polyploids
Bayesian tests for random mating in polyploids
复制标题
DOI：
10.1111/1755-0998.13856
复制
发表时间：
2023-08-14
影响因子：
7.7
通讯作者：
Gerard，David
中科院分区：
文献类型：
--
作者：
Gerard，David
哈迪-温伯格比例（Hardy-Weinberg ratio， HWP）常用于评估随机配对的假设。然而，在自多倍体中，具有两套以上同源染色体的生物体，HWP和随机交配是不同的假设，需要不同的统计检验方法。目前，检测自多倍体随机交配的唯一方法(1)严重依赖于渐近近似，(2)假设基因型是已知的，忽略了基因型的不确定性。此外，这些方法都是频率论的，因此不具备贝叶斯分析的优点，包括易于解释、合并先验信息和null下的一致性。在这里，我们提出了贝叶斯方法来测试随机配对，把贝叶斯分析的好处带到这个问题上。我们的贝叶斯方法也(i)不依赖于渐近近似，适用于小样本量，以及（ii）通过基因型可能性选择性地解释基因型不确定性。我们在模拟中验证了我们的方法，并在两个真实数据集上证明了随机交配测试如何比HWP测试（在自然群体中）和孟德尔分离测试（在实验S1群体中）更有助于检测基因分型错误。我们的方法在综合R档案网络https://cran.r‐project.org/package=hwep上的hwepr软件包2.0.2版中实现。
Hardy–Weinberg proportions (HWP) are often explored to evaluate the assumption of random mating. However, in autopolyploids, organisms with more than two sets of homologous chromosomes, HWP and random mating are different hypotheses that require different statistical testing approaches. Currently, the only available methods to test for random mating in autopolyploids (i) heavily rely on asymptotic approximations and (ii) assume genotypes are known, ignoring genotype uncertainty. Furthermore, these approaches are all frequentist, and so do not carry the benefits of Bayesian analysis, including ease of interpretability, incorporation of prior information, and consistency under the null. Here, we present Bayesian approaches to test for random mating, bringing the benefits of Bayesian analysis to this problem. Our Bayesian methods also (i) do not rely on asymptotic approximations, being appropriate for small sample sizes, and (ii) optionally account for genotype uncertainty via genotype likelihoods. We validate our methods in simulations and demonstrate on two real datasets how testing for random mating is more useful for detecting genotyping errors than testing for HWP (in a natural population) and testing for Mendelian segregation (in an experimental S1 population). Our methods are implemented in Version 2.0.2 of thehwepR package on the Comprehensive R Archive Network https://cran.r‐project.org/package=hwep.