Additional file 2: of Extensive exchange of transposable elements in the Drosophila pseudoobscura group

Table S1. D. pseudoobscura species group lines used in this study. Table S2. TEs found in D. obscura group. Sorted by if they are previously discovered or novel, then by Order and super family. Transmission states if the TE family is found to transfer between species. Table S3. Diagonal table showing the total number of TE families found in each species for comparison. In brackets, the number of novel TE families found shared between species. Table S4. Comparisons of dN/dS between TEs and nuclear genes. The dS values presented here are compared to the dS values of nuclear genes between the given species calculated previously. We considered a transfer event between two species to have occurred if the TE dS value is less than the 2.5th percentile for nuclear genes. For instances where no dS for nuclear comparisons are available, we used the dS between D. pseudoobscura and the species of interest. Table S5. Number of unique and shared polymorphic sites for each species comparison, for each TE family, used in the boxplots in Fig. 2e. (XLSX 153 kb)

表S1 本研究使用的拟暗果蝇（*Drosophila pseudoobscura*）种组品系。
表S2 暗果蝇（*Drosophila obscura*）种组中发现的转座子（Transposable Element, TE）家族，先按是否为已报道类型或新发现类型排序，随后按目（Order）与超家族（superfamily）分类。传播状态字段用以标注该TE家族是否被证实存在跨物种转移现象。
表S3 对角线比对表格，用于对比各物种中鉴定到的TE家族总数，括号内标注各物种对间共享的新发现TE家族数量。
表S4 转座子与核基因的dN/dS值比对分析。本文呈现的dS值将与此前针对对应物种计算得到的核基因dS值进行对比。我们设定判定标准：当某TE家族的dS值低于对应物种核基因dS值的2.5百分位数时，即可认为该TE在两个物种间发生了水平转移事件。对于无可用核基因比对dS值的情况，我们采用拟暗果蝇（*Drosophila pseudoobscura*）与目标物种的dS值作为替代计算依据。
表S5 针对各物种比对组合、各TE家族的唯一多态性位点与共享多态性位点数量，该数据集用于绘制图2e中的箱线图。（XLSX 格式，文件大小153 KB）