Data from: Detecting the footprints of divergent selection in oaks with linked markers

Genome scans are increasingly used to study ecological speciation, providing a useful genome-wide perspective on divergent selection in the presence of gene flow. Here, we compare current approaches to detect footprints of divergent selection in closely related species. We analyzed 192 individuals from two interfertile European temperate oak species using 30 genomic microsatellites from eight linkage groups. These markers present little intraspecific differentiation and can be used in combination to assign individual genotypes to species. We first show that different outlier detection tests give somewhat different results, possibly due to model constraints. Second, using linkage information for these markers, we further characterize the signature of divergent selection in the presence of gene flow. In particular, we show that recombination estimates for regions with outlier markers are lower than those for a control region, in line with a prediction from ecological speciation theory. Most importantly, we show that analyses at the haplotype level can distinguish between truly divergent (bi-directional) selection and positive selection in one of the two species, offering a new and improved method for characterizing the speciation process.

基因组扫描（Genome scans）正日益应用于生态物种形成（ecological speciation）研究，为存在基因流（gene flow）情境下的歧化选择（divergent selection）提供了极具价值的全基因组视角。本研究针对近缘物种，对比了当前用于检测歧化选择分子痕迹的各类方法。我们选取欧洲温带栎两个可互育物种的192份个体样本，利用来自8个连锁群（linkage groups）的30个基因组微卫星（microsatellites）标记开展分析。此类标记的种内分化程度极低，可通过组合使用将个体基因型划归至对应物种。首先，本研究证实不同的异常位点检测检验（outlier detection tests）所得结果存在一定差异，该差异可能源于模型约束。其次，借助此类标记的连锁信息，我们进一步解析了存在基因流情境下的歧化选择特征信号。具体而言，我们发现携带异常位点标记的区域的重组率估算值低于对照区域，这与生态物种形成理论的预测相符。最为关键的是，本研究证实基于单倍型水平（haplotype level）的分析可区分真正的歧化选择（双向选择，bi-directional selection）与两个物种其中之一的正选择（positive selection），为物种形成过程的解析提供了一种全新且更优化的方法。