DOI: 10.5061/dryad.3630t8j
title: Data from: Using text-mined trait data to test for cooperate-and-radiate co-evolution between ants and plants

description: Mutualisms may be “key innovations” that spur lineage diversification by
 augmenting niche breadth, geographic range, or population size, thereby
 increasing speciation rates or decreasing extinction rates. Whether
 mutualism accelerates diversification in both interacting lineages is an
 open question. Research suggests that plants that attract ant mutualists
 have higher diversification rates than non-ant associated lineages. We ask
 whether the reciprocal is true: does the interaction between ants and
 plants also accelerate diversification in ants, i.e. do ants and plants
 cooperate-and-radiate? We used a novel text-mining approach to determine
 which ant species associate with plants in defensive or seed dispersal
 mutualisms. We investigated patterns of lineage diversification across a
 recent ant phylogeny using BiSSE, BAMM, and HiSSE models. Ants that
 associate mutualistically with plants had elevated diversification rates
 compared to non-mutualistic ants in the BiSSE model, with a similar trend
 in BAMM, suggesting ants and plants cooperate-and-radiate. However, the
 best-fitting model was a HiSSE model with a hidden state, meaning that
 diversification models that do no account for unmeasured traits are
 inappropriate to assess the relationship between mutualism and ant
 diversification. Against a backdrop of diversification rate heterogeneity,
 the best-fitting HiSSE model found that mutualism actually decreases
 diversification: mutualism evolved much more frequently in rapidly
 diversifying ant lineages, but then subsequently slowed diversification.
 Thus, it appears that ant lineages first radiated, then cooperated with
 plants.
description: All_Terms_SpeciesPlant mutualist trait information for all text-mined species.Species_Domatia_DataTrait information for domatia for all text-mined species.Species_EFN_DataTrait information for extrafloral nectaries (EFN) for all text-mined species.Species_Seed_Dispersal_DataTrait information for seed dispersal for all text-mined species.Species_Food_Body_DataTrait information for food bodies for all text-mined species.Species_DEF_pruned_dataTrait information for pruned list of species for defense mutualisms (included traits are domatia, extrafloral nectaries, and food bodies).Species_SD_pruned_dataTrait information for pruned list of species for seed dispersal mutualisms (included trait is seed dispersal only).Plant_Mutualist_Trait_DataPlant mutualist trait information for all text-mined species (file formatted for BAMM analysis).Pruned Species TreeOriginal species tree is 'Supplementary File 20' from Dryad data package: Nelsen MP, Ree RH, Moreau CS (2018) Data from: Ant-plant interactions evolved through increasing interdependence. Dryad Digital Repository. https://doi.org/10.5061/dryad.ft4sn88.2, associated with the publication Nelsen MP, Ree RH, Moreau CS (2018) Ant-plant interactions evolved through increasing interdependence. Proceedings of the National Academy of Sciences of the United States of America 115 (48) 12253-12258. https://doi.org/10.1073/pnas.1719794115. We pruned the 1731 species to 795 species to match the trait information, resulting in our file Pruned Species Tree (Newick_Species_Tree).Newick_Species_Treepreprocess_abstractsCode used to format abstracts for text-mining.scan_abstractsCode used to text-mine abstracts.scan_all_abstracts.pySpringer API ScriptScript used to obtain abstracts.BAMM_Plant_MutualistScript for BAMM analysis.BAMM_PlantMutualist.RBAMM_STRAPPOutput of STRAPP analysis.event_data_species_1Event data required for BAMM analysis.mcmc_out_species_1MCMC data required for BAMM analysis.BiSSE_Plant_MutualistScript for BiSSE model.BiSSE_PlantMutualist.Rmcmcbisse_species_all_dataMCMC output from BiSSE model.mcmcbisse_species_all_dataOutput from BiSSE model.HiSSE_DEFScript for HiSSE model run on defense mutualisms.HiSSE_Defense.RHiSSE_SDScript for HiSSE model run on seed dispersal mutualisms.HiSSE_Seed_Dispersal.RHiSSE_Plant_MutualistScript for HiSSE model run on all traits (plant mutualist category).HiSSE_PlantMutualist.R