Simulated dataset

The uploaded files contain gene trees generated under three distinct topological scenarios. Each archive includes trees simulated under five transfer rates (0.1%, 0.4%, 0.7%, 1%, and 2%). All gene trees meet the following criteria: (1) each subgeneric clade is monophyletic and includes at least four extant species; and (2) each species is constrained to a maximum of 10 gene leaf nodes. 2v2.zip, 3v3.zip, 3v4.zip The uploaded file Poaceae_case.zip contains the following materials related to the Poaceae RI detection: (1) Manully_scignificant_gene_tree: A folder containing gene trees in the Poaceae RI detection. (2) Poaceae_config.txt: The configuration file used as input for the analysis. (3) Poaceae_tree_V16.out.consistance.significant: A list of significant ancient introgression events. (4) Poaceae_tree_V16.out.consistance.significant.all.out: A list of both significant ancient and recent introgression events. (5) Poaceae_tree_V16.out.consistance.significant.gene.list: A gene list corresponding to the significant results. (6) Poaceae_tree_V16.out.consistance.significant.OG.node.nwk: Tree structures of each OG-like group showing significant gene flow events. (7) Poaceae_tree_V16.out.OG.node. nwk and Poaceae_tree_V16.out. p_value: Respectively, the tree structures of each OG-like group for all detected gene flow events, and the statistical assessment distinguishing incomplete lineage sorting (ILS) from introgression.本次上传的文件包含基于三种不同拓扑场景生成的基因树。每个压缩包均包含在五种基因转移速率（0.1%、0.4%、0.7%、1%和2%）下模拟得到的基因树。所有基因树均满足以下两项标准：(1) 每个亚属支系均为单系群，且包含至少4个现生物种；(2) 每个物种最多对应10个基因叶节点。涉及的压缩包包括2v2.zip、3v3.zip、3v4.zip。 上传文件Poaceae_case.zip包含以下与禾本科渐渗检测相关的材料：(1) 手动筛选的显著基因树文件夹：内含用于禾本科渐渗检测的基因树；(2) Poaceae_config.txt：本次分析所用的输入配置文件；(3) Poaceae_tree_V16.out.consistance.significant：显著古代渐渗事件列表；(4) Poaceae_tree_V16.out.consistance.significant.all.out：涵盖显著古代与近代渐渗事件的完整列表；(5) Poaceae_tree_V16.out.consistance.significant.gene.list：与显著检测结果对应的基因列表；(6) Poaceae_tree_V16.out.consistance.significant.OG.node.nwk：展示每个类直系同源基因簇类群显著基因流事件的树结构；(7) Poaceae_tree_V16.out.OG.node.nwk与Poaceae_tree_V16.out.p_value：前者为所有检测到的基因流事件对应的每个类直系同源基因簇类群的树结构，后者为区分不完全谱系分选（Incomplete Lineage Sorting）与渐渗的统计评估结果。