Data from: Z chromosome divergence, polymorphism and relative effective population size in a genus of lekking bird

Sex chromosomes contribute disproportionately to species boundaries as they diverge faster than autosomes and often have reduced diversity. Their hemizygous nature contributes to faster divergence and reduced diversity, as do some types of selection. In birds, other factors (mating system and bottlenecks) can further decrease the effective population size of Z-linked loci and accelerate divergence (Fast-Z). We assessed Z-linked divergence and effective population sizes for two polygynous sage-grouse species and compared them to estimates from birds with various mating systems. We found lower diversity and higher FST for Z-linked loci than for autosomes, as expected. The πZ/πA ratio was 0.38 in Centrocercus minimus, 0.48 in Centrocercus urophasianus and 0.59 in a diverged, parapatric population of C. urophasianus, a broad range given the mating system among these groups is presumably equivalent. The full data set had unequal males and females across groups, so we compared an equally balanced reduced set of C. minimus and individuals pooled from both C. urophasianus subgroups recovering similar estimates: 0.54 for C. urophasianus and 0.38 for C. minimus. We provide further evidence that NeZ/NeA in birds is often lower than expected under random mating or monogamy. The lower ratio in C. minimus could be a consequence of stronger selection or drift acting on Z loci during speciation, as this species differs strongly from C. urophasianus in sexually selected characters with minimal mitochondrial divergence. As C. minimus also exhibited lower genomic diversity, it is possible that a more severe demographic history may contribute to its lower ratio.性染色体相较于常染色体，演化分化速率更快且多样性普遍偏低，因此对物种界限的形成贡献远超其基因组占比。其半合子（hemizygous）特性，加之部分类型的选择作用，共同推动了更快的分化进程与更低的多样性水平。在鸟类中，交配系统与瓶颈效应等额外因素可进一步降低Z连锁位点的有效种群大小，加速其分化，即Fast-Z效应。 我们针对两种多配性艾草松鸡物种的Z连锁分化程度与有效种群大小开展了评估，并将结果与不同交配系统鸟类的相关估算值进行了对比。正如理论预期，我们观测到Z连锁位点的核苷酸多样性低于常染色体，而遗传分化指数（FST）则更高。小艾草松鸡（Centrocercus minimus）的Z/常染色体核苷酸多样性比值（πZ/πA）为0.38，大艾草松鸡（Centrocercus urophasianus）为0.48，而大艾草松鸡的一个分化邻域种群的该比值为0.59；尽管这些类群的交配系统大概率一致，该比值却呈现出宽泛的跨度。 完整数据集的各组间雌雄个体数量并不均等，因此我们选取了数量均衡的简化子集：仅包含小艾草松鸡的个体，以及来自两个大艾草松鸡亚群的混合个体，经重新分析得到了相近的估算结果：大艾草松鸡的比值为0.54，小艾草松鸡为0.38。 本研究进一步证实，鸟类的Z连锁有效种群大小与常染色体有效种群大小的比值（NeZ/NeA）通常低于随机交配或一夫一妻制下的理论预期值。小艾草松鸡的该比值更低，这可能是物种形成过程中Z染色体位点受到更强选择作用或遗传漂变的结果——该物种与大艾草松鸡在性选择相关性状上存在显著差异，而线粒体基因组的分化程度却极低。此外，小艾草松鸡的全基因组多样性也更低，因此更剧烈的种群历史动态或许也是导致其NeZ/NeA比值偏低的潜在诱因。