Disentangling sources of gene tree discordance in phylogenomic datasets: testing ancient hybridizations in Amaranthaceae s.l.

- The file 'Supplementa_Methods_and_Materials.tar.gz' contains the supplemental methods, figures and tables referenced in the main text - The file 'Homologs.tar.gz' contains the 14584 homolog trees: raw_homologs.tar.gz - trees without any filtering or pruning final_homologs.tar.gz - trees after, monophyletic and paraphyletic grades of the same species masked, deep paralogs prunned, and spurious tips removed. - The file 'Analyses_data.tar.gz' contains the data (alignments and individual gene trees) used for each of the dataset: filtered_transcriptomes.tar.gz - 88 filtered transcriptomes all_13025_orthologs_cln_aln.tar.gz - all the 13025 'monophyletic outgroup' orthologs 105-taxon.tar.gz - 936 alignments and trees of the full 105-taxon analyses 41-taxon.tar.gz - 1242 alignments and trees of the 41-taxon cloudogram 11-taxon-net.tar.gz - 4138 alignments and trees of the 11-taxon(net) used for network analyses 4-taxon.tar.gz - alignments and trees (between 7,756 and 8,793) for each of the 10 4-taxon quartets 11-taxon-tree.tar.gz - 5936 alignments and trees of the 11-taxon(tree) analyses chloroplast.tar.gz - 11-taxon alignment and tree and 76 individual CDS alignment and trees of the plastid analyses