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 本研究所采用的伪暗果蝇（*D. pseudoobscura*）种组品系。
表S2 暗果蝇（*D. obscura*）种组中发现的转座因子（Transposable Element, TE）：先按是否为已报道转座因子或新发现转座因子排序，再按目级与超家族级分类；传递状态栏用于标注该转座因子家族是否被发现存在跨物种传递现象。
表S3 对角线对比表：用于展示各物种中发现的转座因子家族总数以开展组间对比，括号内标注各物种间共享的新发现转座因子家族数量。
表S4 转座因子与核基因的dN/dS比较分析：本文呈现的dS（同义替换速率）值，将与此前针对对应物种计算得到的核基因dS值进行比对。我们设定判定标准：若某转座因子的dS值低于对应核基因dS值的2.5%分位数，则认为两物种间发生了转座因子跨物种传递事件。对于无可用核基因比较dS值的场景，我们采用伪暗果蝇与目标物种间的dS值进行替代计算。
表S5 各物种比较、各转座因子家族的唯一及共享多态性位点数量，该数据用于绘制图2e中的箱线图（XLSX 153 KB）