A comprehensive phylogenomic framework for cycads (Cycadales)

Here we present a time-calibrated phylogeny of 346 cycad accessions, covering ≈86% of the 380 accepted species, across all 10 extant genera, inferred from 1,409 single-copy nuclear loci (411,345 amino acid sites) derived from transcriptome and genome data. The maximum likelihood phylogeny was inferred using a partitioned analysis, with branch support assessed via ultrafast bootstrap (UFBoot2), and concordance evaluated using gene concordance factors (gCF) and site concordance factors (sCF), representing gene- and site-level support, respectively. Divergence times were estimated using penalized likelihood (TreePL) with 12 calibration constraints, and 95% confidence intervals were derived from 100 gene-wise bootstrap replicates. Bootstrap support is high (70% of nodes ≥95%), but gene concordance factors are low (median gCF = 3.2%), a pattern consistent with limited phylogenetic signal per locus rather than strong support for alternative topologies. Across all 10 genera, the phylogram recovered a strongly supported generic backbone, confirmed the monophyly of all genera, and provides the first broadly accessible phylogenomic framework for interpreting cycad taxonomy, intergeneric relationships, and evolutionary history. Herein, we provide the phylogram, timetree, all 1,409 gene trees, the concatenated alignment with partition definitions, and associated support, confidence-interval, and calibration data.