READ ME Information regarding the files used in the phylogenetic analyses. Four directories: 1. strict - 2 subdirectories; concat/ individual_loci/ In concat/: 4 files - iqtree_strict_commands.txt, supermatrix.phy, partitions.nex, Nephilidae_concat_strict.pdf, and 1 subdirectory output_files/ with the IQTree output files In individual_loci/: 2 subdirectories ASTRAL/ iqtree_runs/ In ASTRAL/: 3 files - best_iqtree_trees.txt, Nephilidae_ASTRAL_strict.iqtree.pdf, strict.iqtree.out.tre In iqtree_runs/: all alignments and output files from the IQTREE runs for each locus 2. loose - 2 subdirectories; concat/ individual_loci/ In concat/: 4 files - iqtree_loose_commands.txt, supermatrix.phy, partitions.nex, Nephilidae_concat_loose.pdf, and 1 subdirectory output_files/ with the IQTree output files In individual_loci/: 2 subdirectories ASTRAL/ iqtree_runs/ In ASTRAL/: 3 files - best_iqtree_trees.txt, Nephilidae_ASTRAL_loose.iqtree.pdf, loose.iqtree.out.tre In iqtree_runs/: all alignments and output files from the IQTREE runs for each locus 3. constrained - 4 files; 1 subdirectory constrained.phy constrained_partitions.txt iqtree_constrained_commands.txt backbone.tre 1 subdirectory output_files/ with the IQTree output files 4. dating - 12 files calibrate.txt - calibration file with info on the nodes and date used in the analysis FcC_supermatrix-loose.fas - FASTA supermatrix groups.txt - file to determine outgroup neph_tree.tre - input tree neph_tree.pdf - PDF of input tree reltime_nucleotide.mao - MEGA commands file timeTree_exactTimes.nwk - output treefile timeTree.tre - dated phylogeny output timeTree.pdf - dated phylogeny output in PDF timeTree_relTimes.nwk - output treefile timeTree_summary.txt - summary file of input commands and files timeTree.txt - dating output information