Plethodon phylogenomics: Supplementary Material

Plethodon phylogenomics: Supplementary MaterialPhylogenomic trees and supplementary figures and tables for:Phylogenomics of the woodland salamanders (Plethodon): Reticulate evolution and indistinct species boundariesWaldron et al. Molecular Phylogenetics & EvolutionIQ-Tree and wASTRAL#### 'plethodon-cat.treefile' ####Concatenated IQ-Tree analysis of all 198 samples#### 'wASTRAL-plethodon.tree' ####Species tree from wASTRAL with samples assigned to species, phylogroups, or polyphyletic/paraphyletic unitsUltrametric trees#### 'Plethodon-MCMCtree-10Ma.tre' ####Time-calibrated MCMCtree "Figtree" output tree. Includes 95% HPD. *Branch lengths are in units of 10 Ma!Since this file is not readily usable for in most programs for comparative analyses, additional files were prepared below.#### 'plethodon-unpruned.tree' ####Time-calibrated topology taken from 'Plethodon_MCMCtree_10Ma.tre', but with branch units converted to 1 Ma (no HPD included). Can be easily imported into R or other software for comparative analyses.### 'plethodon-pruned.tree' ####Same tree as 'plethodon-unpruned.tree', but intraspecific groups (e.g. phylogroups or polyphyletic samples) were pruned so that each named species is represented by a single tip.Supplementary Figures#### 'All Supplementary Figures.pdf' ####All supplementary figures.Supplementary Tables#### 'Table_S1_sample_info.xlsx' ####Table S1. Sample information, including BioSample accession numbers. Some species names in the Sequence Name and Old Species Name columns reflect names prior to taxonomic revision, and updates are reflected in the New Species Name column (bold). The phylogroup column designates phylogroup membership within species recognized for this study, based on previous phylogeographic studies or on our preliminary phylogenetic analyses. Proportion missing data indicates sample-level missing data in the concatenated matrix of DNA sequences, and the MCMCTree column marks which samples were maintained as representatives for divergence dating of species or phylogroups in MCMCTree. Collection abbreviations: UF = Univeristy of Florida; MVZ = Museum of Vertebrate Zoology; UMMZ = University of Michigan Museum of Zoology; MSB = Museum of Southwestern Biology.#### 'Table_S2_per_locus_statistics.xlsx' ####Table S2. Summary statistics for anchored hybrid enrichment data. Number of taxa includes the number of samples with any data available (i.e. did not have completely missing data).#### 'Table_S3_HyDe_cinereus.xlsx' ####Table S3. Statistically significant hybrid detections from HyDe (after Bonferroni correction) within the cinereus group.#### 'Table_S4_HyDe_wehrlei.xlsx' ####Table S4. Hybrid detection (HyDe) results for the wehrlei-websteri group, sorted by Z-scores. Only significant results after correction for multiple tests are shown.#### 'Table_S5_HyDe_glutinosus.xlsx' ####Table S5. Hybrid detection (HyDe) results for the glutinosus group, sorted by Z-scores. Only significant results after correction for multiple tests are shown.无肺螈属（Plethodon）系统基因组学：补充材料 配套论文为《林地无肺螈（Plethodon）系统基因组学：网状进化与模糊物种界限》，包含系统发育树、补充图表及附表。 论文作者：Waldron等人，刊载于《分子系统发育与进化》（*Molecular Phylogenetics & Evolution*） 所用分析软件：IQ-Tree 与 wASTRAL #### 'plethodon-cat.treefile' #### 所有198个样本的合并式IQ-Tree分析结果树 #### 'wASTRAL-plethodon.tree' #### 基于wASTRAL构建的物种树，样本按物种、演化支（phylogroup）或多系/并系类群进行分组标注 #### 超度量树 #### #### 'Plethodon-MCMCtree-10Ma.tre' #### 经时间校准的MCMCtree（又名Figtree）输出树，包含95%最高后验密度区间（HPD）。*分支长度单位为10百万年（Ma）！* 由于该文件无法直接用于多数比较分析软件，下文提供了适配文件： #### 'plethodon-unpruned.tree' #### 取自'Plethodon_MCMCtree_10Ma.tre'的时间校准拓扑结构，仅将分支长度单位转换为1百万年（未包含HPD区间），可直接导入R或其他软件开展比较分析。 #### 'plethodon-pruned.tree' #### 与'plethodon-unpruned.tree'为同一棵树，但已剪除种内类群（如演化支或多系样本），确保每个命名物种仅对应一个末端分支。 ## 补充图表 #### 'All Supplementary Figures.pdf' #### 全部补充图表 ## 补充附表 #### 'Table_S1_sample_info.xlsx' #### 附表S1：样本信息，包含生物样本库（BioSample）登录号。序列名称列与旧物种名称列中部分物种名称为分类修订前的命名，新物种名称列（加粗字体）为更新后的正式命名。演化支柱列标注了本研究认可的物种内的演化支归属，该标注基于既往系统地理学研究或本研究的初步系统发育分析。缺失数据比例指DNA序列合并矩阵中的样本级缺失数据占比；MCMCTree列标记了在MCMCTree物种或演化支分化定年分析中保留的代表性样本。馆藏缩写说明：UF = 佛罗里达大学；MVZ = 脊椎动物博物馆；UMMZ = 密歇根大学动物学博物馆；MSB = 西南生物学博物馆。 #### 'Table_S2_per_locus_statistics.xlsx' #### 附表S2：锚定杂交富集（anchored hybrid enrichment）数据的汇总统计量。分类单元数量指带有有效数据（即未完全缺失数据）的样本数。 #### 'Table_S3_HyDe_cinereus.xlsx' #### 附表S3：Cinereus类群中经Bonferroni校正后具有统计学显著性的HyDe杂交检测结果。 #### 'Table_S4_HyDe_wehrlei.xlsx' #### 附表S4：Wehrlei-Websteri类群的HyDe杂交检测结果，按Z得分排序，仅展示经多重检验校正后的显著结果。 #### 'Table_S5_HyDe_glutinosus.xlsx' #### 附表S5：Glutinosus类群的HyDe杂交检测结果，按Z得分排序，仅展示经多重检验校正后的显著结果。