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

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.

性染色体对物种界限的形成贡献尤为突出，因其进化速率快于常染色体，且遗传多样性往往更低。其半合子（hemizygous）特性，加之部分类型的选择作用，共同推动了更快的进化分化与更低的遗传多样性。在鸟类中，交配系统、种群瓶颈等其他因素可进一步降低Z连锁位点的有效种群大小（effective population size, Ne），加速分化进程（即Fast-Z效应）。我们针对两种多配性艾草松鸡的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计值进行了对比。正如预期，Z连锁位点的遗传多样性低于常染色体，而种群分化系数（FST）更高。小艾草松鸡（Centrocercus minimus）的Z连锁位点与常染色体的核苷酸多样性（π）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则为0.59。鉴于这些类群的交配系统大概率相近，该比值的跨度范围相对较广。原始数据集的各组雌雄个体数量不均，因此我们选取了数量均衡的缩减数据集：仅包含小艾草松鸡个体，以及来自两个大艾草松鸡亚群的混合个体，重新分析后得到了相似的估计结果：大艾草松鸡为0.54，小艾草松鸡为0.38。本研究进一步证实，在随机交配或单配制的鸟类中，NeZ/NeA（Z连锁位点有效种群大小与常染色体有效种群大小的比值）往往低于理论预期值。小艾草松鸡较低的比值，可能是物种形成过程中Z连锁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，但线粒体分化程度极低。此外，小艾草松鸡的全基因组多样性也更低，因此更严峻的种群历史动态也可能是其比值偏低的原因之一。