Data for: A comprehensive phylogenomic framework for cycads (Cycadales

This dataset underpins the article “A comprehensive phylogenomic framework for cycads (Cycadales)”. It contains the phylogenomic data used to infer a species-level framework for Cycadales based on 1,409 single-copy nuclear loci sampled from 346 cycad accessions and Ginkgo biloba as outgroup. The deposit includes the concatenated alignment, partition definitions, the maximum-likelihood phylogram, the time-calibrated tree with 95% confidence intervals, the full set of individual gene trees, calibration constraints, bootstrap confidence interval summaries, and a tip-label mapping file documenting nomenclatural updates between original source labels and the labels used in the deposited analyses. Files:- concatenated_alignment.fasta.gz: concatenated amino acid alignment (347 taxa, 411,345 sites)- partition_file.txt: gene partition boundaries for the concatenated alignment- ML_tree_combined_support.nexus: maximum-likelihood phylogram with bootstrap, gene concordance factor, and site concordance factor support- timetree_with_95CI.nexus: time-calibrated phylogeny with node ages and 95% confidence intervals- combined_gene_trees.treefile: all 1,409 individual gene trees- fossil_calibrations.txt: TreePL calibration constraints- CI_summary.tsv: bootstrap confidence intervals for dated nodes- current_tip_labels.csv: mapping between original source labels and corrected labels used in the deposited files- README.txt: file descriptions and methods summary Taxonomy and nomenclature follow the World List of Cycads. In cases where source labels were corrected, synonymized, or retained as taxonomically uncertain, those changes are documented in current_tip_labels.csv.