Phylogenomic matrices, tree files, analysis scripts, and result tables for Delphinieae transcriptome phylogenomics

This dataset accompanies manuscript MPE-D-26-00210, “Deep phylogeny, ancestral whole-genome duplication, and gene-family evolution in Delphinieae.” Version 3.0.0 consolidates the base phylogenomic archive and the first-revision reproducibility package and adds the second-round low-BUSCO sample-exclusion sensitivity analyses. The added materials include 8,467 prepared locus alignments and corresponding gene trees for species-tree re-estimation; per-sample duplication-age and paralog-Ks values; original and pruned multi-copy family-tree inputs, strict screening logs, and detailed Tree2GD outputs; curated CYC2 and AGL6 dating inputs; main species-tree dating configurations; and sample-level accession and quality tables. Three ZIP containers hold eight unchanged large input/output archives. The README and SHA-256 manifests document the archive contents and verification steps. Raw transcriptome reads are deposited separately in SRA/DRA, with sample-level accession numbers in Supplementary Table 1.