Double reduction estimation and equilibrium tests in natural autopolyploid populations
Double reduction estimation and equilibrium tests in natural autopolyploid populations
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DOI：
10.1111/biom.13722
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发表时间：
2022-07-26
期刊：
影响因子：
1.9
通讯作者：
Gerard, David
中科院分区：
文献类型：
--
作者：
Gerard, David
许多生物信息学管道包括平衡测试。二倍体的检测方法已经得到了很好的研究和广泛的应用，但是将这些方法扩展到同源多倍体却受到了双重减数分裂的阻碍，即在减数分裂过程中姐妹染色单体片段共迁移到同一配子中。虽然平衡测试的障碍，双减少率是在自己的权利感兴趣的数量，因为他们提供了关于同源多倍体生物体的减数分裂行为的见解。在这里，我们开发的程序（i）测试平衡，同时考虑到双重减少，和（ii）估计双重减少率给定的平衡。要做到这一点，我们采取两种方法：一种可能性的方法，和一种新的U-统计量最小化的方法，我们表明推广经典的平衡卡方检验二倍体。对于小样本和不确定的基因型，我们进一步开发了一个自助程序的基础上，我们的U-统计量来测试的均衡。我们验证我们的方法模拟和真实的数据。
Many bioinformatics pipelines include tests for equilibrium. Tests for diploids are well studied and widely available, but extending these approaches to autopolyploids is hampered by the presence of double reduction, the comigration of sister chromatid segments into the same gamete during meiosis. Though a hindrance for equilibrium tests, double reduction rates are quantities of interest in their own right, as they provide insights about the meiotic behavior of autopolyploid organisms. Here, we develop procedures to (i) test for equilibrium while accounting for double reduction, and (ii) estimate the double reduction rate given equilibrium. To do so, we take two approaches: a likelihood approach, and a novel U-statistic minimization approach that we show generalizes the classical equilibrium chi(2) test in diploids. For small sample sizes and uncertain genotypes, we further develop a bootstrap procedure based on our U-statistic to test for equilibrium. We validate our methods on both simulated and real data.