Phylogenomics reveal widespread ancient hybridization in the evolution of Lychnophorinae (Vernonieae, Asteraceae)

Data, scripts and figures from "Phylogenomics reveal widespread ancient hybridization in the evolution of Lychnophorinae (Vernonieae, Asteraceae)", under revision in TAXON. This is a copy of the GitHub repository made in 5/15/2025, when it was publicly released. Repository structure: alignments: contains all the aligments used for analyses, separated into phyluce and HybPiper assemblies. assembly_comparisons: this folder contains the R script used to plot figures in the Appendix, with the necessary data files to run it. PDF of the figures are provided. PhyloNetworks: this folder has all the inputs and outputs of all the seven PhyloNetworks analyses. Files are named similarly in each folder, except for the input trees. The scripts folder has a general script that can be used to replicate analysis. The loglik_plot folder has the input and script to produce the plot in Fig 4I. TICR_results has the p-values of all seven tests. QuartetSampling: contains the species tree and concatenated alignment needed to run the QS analysis, plus all the output files. The figtree file was used as basis for Fig 3. tree_comparisons: contains script and data files used to generate the overlayed trees from Fig 2, plus some of the Supplemental Figures. PDFs are provided. trees: contains all trees generated, divided by assembly method.