ddRAD sequencing for Mexican ducks and mallards

Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci, and 172 Z-linked sex chromosome loci. Between the two taxa, Z-linked loci (FST = 0.088) were 5.2 times more differentiated than autosomal DNA (FST = 0.017) but comparable to mtDNA (FST = 0.092). This elevated Z-differentiation deviated from neutral expectations inferred from simulated data that incorporated demographic history and differences in effective population sizes between marker types. Furthermore, 3% of Z-linked loci, compared to <0.1% of autosomal loci, were detected as outlier loci under divergent selection with elevated relative (FST) and absolute (dXY) estimates of divergence. In contrast, the ratio of Z-linked and autosomal differentiation among the seven Mexican duck sampling locations was close to 1:1 (FST = 0.018 for both markers). We conclude that between mallards and Mexican ducks, divergence at autosomal markers is largely neutral, whereas greater divergence on the Z-chromosome (or some portions thereof) is likely the product of selection that has been important in speciation. Our results contribute to a growing body of literature indicating elevated divergence on the Z chromosome and its likely importance in avian speciation.

物种形成是一个连续且动态的过程，对该过程早期阶段的生物类群开展研究，有助于揭示物种形成的潜在机制。绿头鸭（Anas platyrhynchos）与墨西哥鸭（A. [p.] diazi）为两个新近分化的类群，二者存在杂交历史，且分类地位尚存争议。为解析二者的演化历史，本研究开展了基因组扫描，以刻画线粒体DNA（mtDNA）控制区、3523个常染色体位点以及172个Z连锁性染色体位点的遗传多样性与分化模式。两类群间，Z连锁位点的固定分化指数（FST=0.088）较常染色体DNA（FST=0.017）高出5.2倍，但与mtDNA的FST值（0.092）相当。这种升高的Z染色体分化程度，偏离了结合种群历史与不同标记类型有效种群大小差异的模拟数据所推断的中性预期。此外，有3%的Z连锁位点被检测为趋异选择下的异常位点，其相对固定分化指数（FST）与绝对分歧度（dXY）的估计值均显著升高；而常染色体位点中符合该特征的比例不足0.1%。与之形成鲜明对比的是，在7个墨西哥鸭采样种群中，Z连锁位点与常染色体位点的分化程度比值接近1:1（两类标记的FST均为0.018）。本研究结论如下：绿头鸭与墨西哥鸭间，常染色体标记的分化大体呈中性；而Z染色体（或其部分区段）上更高的分化程度，大概率是物种形成过程中发挥作用的选择作用的产物。本研究结果为日益增多的相关研究提供了实证支撑，此类研究均表明Z染色体的分化程度存在升高现象，且其在鸟类物种形成过程中可能具有关键意义。