Data from: Ant-plant interactions evolved through increasing interdependence

Dryad Supplementary File 1. Exclude terms used in NCBI queries for Formicidae accessions.Dryad_Supplementary_File_1_excludes_terms.docxDryad Supplementary File 2. Alignment used to infer Formicidae ML tree.Dryad Supplementary File 2. Alignment used to infer Formicidae ML tree.Dryad_Supplementary_File_2_infile.txtPartition file used in Formicidae ML tree inference.Partition file used in Formicidae ML tree inference.Dryad_Supplementary_File_3_part.txtDryad Supplementary File 4. ML phylogeny of Formicidae.Dryad Supplementary File 4. ML phylogeny of Formicidae.Dryad_Supplementary_File_4_RAxML_bipartitions.result.ladderized.dropped.treDryad Supplementary File 5. treePL configuration file (with prime function) used.Dryad Supplementary File 5. treePL configuration file (with prime function) used.Dryad_Supplementary_File_5_prime_configfile_185.txtDryad Supplementary File 6. treePL configuration file (with cross validation) used.Dryad Supplementary File 6. treePL configuration file (with cross validation) used.Dryad_Supplementary_File_6_cv_configfile_185.txtDryad Supplementary File 7. Time-calibrated maximum-likelihood phylogeny of 1731 ant species and associated Aculeata outgroup taxa.Dryad Supplementary File 7. Time-calibrated maximum-likelihood phylogeny of 1731 ant species and associated Aculeata outgroup taxa.Dryad_Supplementary_File_7_ML_TREE_treepl_185.treDryad Supplementary File 8. List of valid ant species derived from AntWiki.Dryad Supplementary File 8. List of valid ant species derived from AntWiki.Dryad_Supplementary_File_8_AntWiki_Valid_Species_w_fossils_mymods.csvDryad Supplementary File 9. List of valid ant species assigned to alternate genera.Dryad Supplementary File 9. List of valid ant species assigned to alternate genera.Dryad_Supplementary_File_9_Genus.probs.mods.csvDryad_Supplementary_File_10_richness_modifier_10nov2016.28nov2016Dryad Supplementary File 10. R script used to modify richness estimates of ant genera.Dryad Supplementary File 11. Higher-level taxonomy of vascular plant genera used in analyses.Dryad Supplementary File 11. Higher-level taxonomy of vascular plant genera used in analyses.Dryad_Supplementary_File_11_df.for.constraint.10860.clean.csvDryad Supplementary File 12. Constraint tree derived from higher-level taxonomy which was used to infer vascular plant phylogeny.Dryad Supplementary File 12. Constraint tree derived from higher-level taxonomy which was used to infer vascular plant phylogeny.Dryad_Supplementary_File_12_constraint.10860.treDryad Supplementary File 13. Partition file used to infer vascular plant phylogeny.Dryad Supplementary File 13. Partition file used to infer vascular plant phylogeny.Dryad_Supplementary_File_13_Streptophytina_by_genus_partitions.part.reduced.reducedDryad Supplementary File 14. Constrained ML phylogeny of vascular plants.Dryad Supplementary File 14. Constrained ML phylogeny of vascular plants.Dryad_Supplementary_File_14_ExaML_result.higher_cons_10860_ML_TREE_rerooted.treDryad Supplementary File 15. Genera dropped from the vascular plant ML phylogeny.Dryad Supplementary File 15. Genera dropped from the vascular plant ML phylogeny.Dryad_Supplementary_File_15_bl.lengths.drops.10860.csvDryad Supplementary File 16. Constrained ML phylogeny of vascular plants after genera in file genera removed.Dryad Supplementary File 16. Constrained ML phylogeny of vascular plants after genera in file genera removed.Dryad_Supplementary_File_16_ExaML_result.higher_cons_10860_ML_TREE_rerooted_clean.treDryad Supplementary File 17. Time-scaled phylogeny of plant genera based on age estimates in Magallón et al. (2013).Dryad Supplementary File 17. Time-scaled phylogeny of plant genera based on age estimates in Magallón et al. (2013).Dryad_Supplementary_File_17_1_1382193753_Magallon_etal_five_11Feb13.nexorg_woaligntax_ladderized_DATED_namesupdatedforcongruification.treDryad Supplementary File 18. treePL file used to time-scale vascular plant phylogeny.Dryad Supplementary File 18. treePL file used to time-scale vascular plant phylogeny.Dryad_Supplementary_File_18_ExaML_result.higher_cons_10860_ML_TREE_rerooted_clean_treepl_smooth_0.000001.txtDryad Supplementary File 19. Time-calibrated maximum-likelihood phylogeny of 10785 vascular plant genera.Dryad Supplementary File 19. Time-calibrated maximum-likelihood phylogeny of 10785 vascular plant genera.Dryad_Supplementary_File_19_ExaML_result.higher_cons_10860_ML_TREE_rerooted_clean_treepl_smooth_0.000001.treDryad Supplementary File 20. Time-calibrated maximum-likelihood phylogeny of 1731 ant species. Outgroup taxa removed and tree ladderizedDryad Supplementary File 20. Time-calibrated maximum-likelihood phylogeny of 1731 ant species. Outgroup taxa removed and tree ladderizedML_TREE_treepl_185_outsdroppeds.ladderized.increasing.treDryad_Supplementary_File_21_BAMM_controlfileDryad_Supplementary_File_21_bamm_controlfilebamm_controlfile_25m.10nov2016_medusa.txtDryad_Supplementary_File_22_BAMM_chain_swap_infoDryad_Supplementary_File_22_BAMM_chain_swap_infochain_swap_medusa.txtDryad_Supplementary_File_23_BAMM_event_dataDryad_Supplementary_File_23_BAMM_event_dataevent_data_medusa.txtDryad_Supplementary_File_24_sampling_fractions_usedDryad_Supplementary_File_24_sampling_fractions_usedfor.bamm.w.global.10nov2016.txtDryad_Supplementary_File_25_BAMM_mcmc_outfileDryad_Supplementary_File_25_BAMM_mcmc_outfilemcmc_out_medusa.txtDryad_Supplementary_File_26_BAMM_run_info_outfileDryad_Supplementary_File_26_BAMM_run_info_outfilerun_info_medusa.txtDryad_Supplementary_File_27_Rsave_file_containing_results_of_correlated_trait_evolutionDryad_Supplementary_File_27_Rsave_file_containing_results_of_correlated_trait_evolutionall.linked.pp.RsaveDryad_Supplementary_File_28_Plant_TraitsDryad Supplementary File 28 Plant Traitsall.merged.tree.clean.csv