DOI: 10.5061/dryad.ft4sn88
title: Data from: Ant-plant interactions evolved through increasing interdependence

description: Ant–plant interactions are diverse and abundant and include classic models
 in the study of mutualism and other biotic interactions. By estimating a
 time-scaled phylogeny of more than 1,700 ant species and a time-scaled
 phylogeny of more than 10,000 plant genera, we infer when and how
 interactions between ants and plants evolved and assess their
 macroevolutionary consequences. We estimate that ant–plant interactions
 originated in the Mesozoic, when predatory, ground-inhabiting ants first
 began foraging arboreally. This served as an evolutionary precursor to the
 use of plant-derived food sources, a dietary transition that likely
 preceded the evolution of extrafloral nectaries and elaiosomes.
 Transitions to a strict, plant-derived diet occurred in the Cenozoic, and
 optimal models of shifts between strict predation and herbivory include
 omnivory as an intermediate step. Arboreal nesting largely evolved from
 arboreally foraging lineages relying on a partially or entirely
 plant-based diet, and was initiated in the Mesozoic, preceding the
 evolution of domatia. Previous work has suggested enhanced diversification
 in plants with specialized ant-associated traits, but it appears that for
 ants, living and feeding on plants does not affect ant diversification.
 Together, the evidence suggests that ants and plants increasingly relied
 on one another and incrementally evolved more intricate associations with
 different macroevolutionary consequences as angiosperms increased their
 ecological dominance.
description: 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