DATA PACKAGE FROM SUN ET AL (ANNALS OF BOTANY) Phylogenomic analyses of the East Asian endemic Abelia (Caprifoliaceae) shed insights into the temporal and spatial diversification history with widespread hybridization This package contains the data and software outputs (i.e. fasta filtes, alignments, trees, etc). Part 1. File called. Data_part_1.tar.gz 1_alignments. Unaligned fasta files (*.fa), MAFFT aligned fasta files (*.aln), and Cleaned alignments with Phyx (*.aln-cln) 2_trees. RAxML bipartition labeled trees (*.tre), and boostrapt trees (*.trees) from each of the alignments of 1_alignments. 3_masked_mono_para_tips. Trees from 2_trees with masked monophyletic and grades of the same species. 4_masked_spurious_tips. Trees from 3_masked_mono_para_tips with spurious tips removed with TreeShrink. Some *.txt files represent the tips removed byTreeShrink. Empty *.txt means that TreeShrink did not remove any tip from that tree. 5_orthologs 1_final_orthologs. MO orthologs pruned from trees of 4_masked_spurious_tips. 2_fasta_files_from_orthologs. Individual fasta file from the MO orthologs (*.fa) 3_fasta_to_tree. MAFFT aligned fasta files (*.aln), and Cleaned alignments with Phyx (*.aln-cln), RAxML bipartition labeled trees (*.tre), and boostrapt trees (*.trees) from each of MO fasta file. 4_concatenated_alignments. Concatenated alignments of the individual clean alignments of 3_fasta_to_tree 6_Analyses ASTRAL. ASTRAL species trees from all trees from 5_orthologs/3_fasta_to_tree. Iqtree. IQ-TREE tree from the alignment of 4_concatenated_alignments. Phylonet 12_taxa_E48 1_fasta_to_tree. Alignments and RAxML trees from the 12-taxa reduced data set. 2_rooted_trees. Rooted trees from 1_fasta_to_tree. 3_Phylonet. Phylonet results from MPL analyses from 1-5 hybridization events. 15_taxa 1_fasta_to_tree. Alignments and RAxML trees from the 15-taxa reduced data set. 2_rooted_trees. Rooted trees from 1_fasta_to_tree. 3_Phylonet. Phylonet results from MPL analyses from 1-5 hybridization events. QS QS_Abelia_Astral. QuartetSampling results fo the ASTRAL tree. QS_Abelia_IQtree. QuartetSampling results fo the cpDNA tree QS_Abelia_cpDNA. QuartetSampling results fo the RAxML tree cpDNA. Chloroplast alignment and inferred tree with Iqtree. If you have any question about data in Data_part_1.tar.gz, please do not hesitate to contact Diego F. Morales-Briones at dfmoralesb@gmail.com Part 2. File called. Data_part_2.tar.gz divertime_chroloplast. This folder contains the XML input and nexus files output of the divergence time estimation with BEAST for the cpDNA data. divertime_nuclear. This folder contains the XML input and nexus files output of the divergence time estimation with BEAST for the nuclear data. ancestral_area_reconstructions. This folder contain the tre input of the ancestral area reconstructions for the nuclear data. Ecological_niche_modelling. This folder contains the csv input and asc files output of the ecological niche modelling. If you have any question about data in Data_part_2.tar.gz, please do not hesitate to contact Qing-Hui Sun at 378618006@qq.com or Huafeng Wang at hfwang@hainanu.edu.cn