Phylogenomics and biogeography of palaeognath birds

TitleSupplementary files for phylogenetic, divergence-time, and biogeographic analyses of PalaeognathaeDescriptionThis dataset contains supplementary analysis files and associated code used to reconstruct the evolutionary history of Palaeognathae. The files are organized into three main directories:1. DES analysisContains the code (Code.txt) used for dispersal–extinction–sampling (DES) analyses to investigate historical biogeographic dynamics.2. Divergence time estimationContains input files for divergence-time estimation using MCMCTree under two fossil calibration strategies (Calibration strategies 1 and 2). Each strategy includes separate analyses of mitochondrial and nuclear datasets. The corresponding subdirectories contain the approximate-likelihood files (in.BV), calibrated tree files (calibration_mito.tre), input data (input.txt), and MCMCTree control files (mcmctree.ctl).3. PhylogenyContains files associated with phylogenetic reconstruction using different analytical approaches and substitution models, including weighted ASTRAL (0-wASTRAL), LG4X (1-LG4X), Q.bird (2-Q.bird), partitioned analyses (3-partitioned), LG+C20 (4-LG+C20), and CAT-GTR (5-CAT-GTR).Together, these files document the analytical settings and procedures used in the study and facilitate the reproducibility of the phylogenetic, divergence-time, and historical biogeographic analyses.