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Dryad Supplementary File 1. Exclude terms used in NCBI queries for Formicidae accessions.
Dryad_Supplementary_File_1_excludes_terms.docx
Dryad 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.txt
Partition file used in Formicidae ML tree inference.
Partition file used in Formicidae ML tree inference.
Dryad_Supplementary_File_3_part.txt
Dryad Supplementary File 4. ML phylogeny of Formicidae.
Dryad Supplementary File 4. ML phylogeny of Formicidae.
Dryad_Supplementary_File_4_RAxML_bipartitions.result.ladderized.dropped.tre
Dryad 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.txt
Dryad 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.txt
Dryad 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.tre
Dryad 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.csv
Dryad 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.csv
Dryad_Supplementary_File_10_richness_modifier_10nov2016.28nov2016
Dryad 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.csv
Dryad 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.tre
Dryad 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.reduced
Dryad 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.tre
Dryad 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.csv
Dryad 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.tre
Dryad Supplementary File 17. Time-scaled phylogeny of plant genera based on age estimates in Magall\u00f3n et al. (2013).
Dryad Supplementary File 17. Time-scaled phylogeny of plant genera based on age estimates in Magall\u00f3n et al. (2013).
Dryad_Supplementary_File_17_1_1382193753_Magallon_etal_five_11Feb13.nexorg_woaligntax_ladderized_DATED_namesupdatedforcongruification.tre
Dryad 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.txt
Dryad 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.tre
Dryad Supplementary File 20. Time-calibrated maximum-likelihood phylogeny of 1731 ant species. Outgroup taxa removed and tree ladderized
Dryad Supplementary File 20. Time-calibrated maximum-likelihood phylogeny of 1731 ant species. Outgroup taxa removed and tree ladderized
ML_TREE_treepl_185_outsdroppeds.ladderized.increasing.tre
Dryad_Supplementary_File_21_BAMM_controlfile
Dryad_Supplementary_File_21_bamm_controlfile
bamm_controlfile_25m.10nov2016_medusa.txt
Dryad_Supplementary_File_22_BAMM_chain_swap_info
Dryad_Supplementary_File_22_BAMM_chain_swap_info
chain_swap_medusa.txt
Dryad_Supplementary_File_23_BAMM_event_data
Dryad_Supplementary_File_23_BAMM_event_data
event_data_medusa.txt
Dryad_Supplementary_File_24_sampling_fractions_used
Dryad_Supplementary_File_24_sampling_fractions_used
for.bamm.w.global.10nov2016.txt
Dryad_Supplementary_File_25_BAMM_mcmc_outfile
Dryad_Supplementary_File_25_BAMM_mcmc_outfile
mcmc_out_medusa.txt
Dryad_Supplementary_File_26_BAMM_run_info_outfile
Dryad_Supplementary_File_26_BAMM_run_info_outfile
run_info_medusa.txt
Dryad_Supplementary_File_27_Rsave_file_containing_results_of_correlated_trait_evolution
Dryad_Supplementary_File_27_Rsave_file_containing_results_of_correlated_trait_evolution
all.linked.pp.Rsave
Dryad_Supplementary_File_28_Plant_Traits
Dryad Supplementary File 28 Plant Traits
all.merged.tree.clean.csv
", "type": { "id": "notes", "title": { "de": "Anmerkungen", "en": "Notes" } } } ], "creators": [ { "affiliations": [ { "name": "Field Museum of Natural History" } ], "person_or_org": { "family_name": "Nelsen", "given_name": "Matthew P.", "name": "Nelsen, Matthew P.", "type": "personal" } }, { "affiliations": [ { "name": "Field Museum of Natural History" } ], "person_or_org": { "family_name": "Ree", "given_name": "Richard H.", "name": "Ree, Richard H.", "type": "personal" } }, { "affiliations": [ { "name": "Field Museum of Natural History" } ], "person_or_org": { "family_name": "Moreau", "given_name": "Corrie S.", "name": "Moreau, Corrie S.", "type": "personal" } } ], "description": "Ant\u2013plant 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\u2013plant 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.", "publication_date": "2018-12-10", "publisher": "Zenodo", "related_identifiers": [ { "identifier": "10.1073/pnas.1719794115", "relation_type": { "id": "iscitedby", "title": { "de": "Wird zitiert von", "en": "Is cited by" } }, "scheme": "doi" } ], "resource_type": { "id": "dataset", "title": { "de": "Datensatz", "en": "Dataset" } }, "rights": [ { "description": { "en": "CC0 waives copyright interest in a work you've created and dedicates it to the world-wide public domain. Use CC0 to opt out of copyright entirely and ensure your work has the widest reach." }, "icon": "cc-cc0-icon", "id": "cc0-1.0", "props": { "scheme": "spdx", "url": "https://creativecommons.org/publicdomain/zero/1.0/legalcode" }, "title": { "en": "Creative Commons Zero v1.0 Universal" } } ], "subjects": [ { "subject": "Coevolution" } ], "title": "Data from: Ant-plant interactions evolved through increasing interdependence" }, "parent": { "access": { "owned_by": { "user": "90070" } }, "communities": { "default": "734b6452-1f40-4db0-b218-08ab1d568b7f", "entries": [ { "access": { "member_policy": "open", "members_visibility": "public", "record_submission_policy": "open", "review_policy": "open", "visibility": "public" }, "children": { "allow": false }, "created": "2020-02-04T14:03:17.992421+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "id": "734b6452-1f40-4db0-b218-08ab1d568b7f", "links": {}, "metadata": { "curation_policy": "

The Dryad collection in Zenodo contains datasets mirrored from the Dryad Digital Repository. If you want your dataset to appear here, submit it through https://datadryad.org. No other datasets will be accepted.

", "description": "Dryad is an international open-access repository of research data, especially data underlying scientific and medical publications. Dryad is a curated general-purpose repository that makes data discoverable, freely reusable, and citable.", "organizations": [ { "id": "00x6h5n95" } ], "page": "

Dryad is a community-governed open data publishing and curation repository. Through Dryad and Zenodo's partnership, Zenodo hosts a preservation copy of Dryad datasets, available through this Zenodo Community. For more information or to access the original published datasets, visit https://datadryad.org.

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