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.