Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université Lyon 1, Université de Lyon, Villeurbanne F-69622, France.
Genetics. 2021 Jun 24;218(2). doi: 10.1093/genetics/iyab053.
We propose a method, SDpop, able to infer sex-linkage caused by recombination suppression typical of sex chromosomes. The method is based on the modeling of the allele and genotype frequencies of individuals of known sex in natural populations. It is implemented in a hierarchical probabilistic framework, accounting for different sources of error. It allows statistical testing for the presence or absence of sex chromosomes, and detection of sex-linked genes based on the posterior probabilities in the model. Furthermore, for gametologous sequences, the haplotype and level of nucleotide polymorphism of each copy can be inferred, as well as the divergence between them. We test the method using simulated data, as well as data from both a relatively recent and an old sex chromosome system (the plant Silene latifolia and humans) and show that, for most cases, robust predictions are obtained with 5 to 10 individuals per sex.
我们提出了一种方法，即 SDpop，能够推断出由重组抑制引起的性连锁，这种抑制现象在性染色体中很典型。该方法基于对自然种群中已知性别的个体的等位基因和基因型频率进行建模。它是在分层概率框架中实现的，考虑了不同来源的误差。它允许基于模型中的后验概率进行是否存在性染色体以及检测性连锁基因的统计检验。此外，对于配子同源序列，可以推断每个拷贝的单倍型和核苷酸多态性水平，以及它们之间的差异。我们使用模拟数据以及来自相对较新和较旧的性染色体系统（植物石竹属和人类）的数据对该方法进行了测试，并表明，对于大多数情况，使用每个性别 5 到 10 个个体可以获得稳健的预测。
