This README_PRICE_ETAL_2022_DATA.txt file was generated on 2022-03-10 by Benjamin D. Blanchard GENERAL INFORMATION 1. Title of Dataset: Phylogenomics and fossil data inform the systematics and geographic range evolution of a diverse Neotropical ant lineage 2. Author Information Corresponding Investigator Name: Dr. Benjamin D. Blanchard Institution: Field Museum of Natural History Email: bblanchard@fieldmuseum.org Co-investigator 1 Name: Dr. Shauna Price Institution: Loyola University Chicago Co-investigator 2 Name: Dr. Scott Powell Institution: George Washington University Co-investigator 3 Name: Dr. Bonnie Blaimer Institution: Museum für Naturkunde Co-investigator 4 Name: Dr. Corrie Moreau Institution: Cornell University ESA Editorial Office: 3 Park Place, Suite 307, Annapolis, MD 21401-3722, USA. Editorial Office Phone: 1-301-731-4535. 3. Date of data collection: 2016-2021 4. Geographic location of data collection: Argentina, Bolivia, Brazil, Cayman Islands, Costa Rica, Dominican Republic, Ecuador, French Guiana, Guyana, Honduras, Jamaica, Mexico, Nicaragua, Panama, Paraguay, Peru, Surinama, United States of America, Venezuela 5. Funding sources that supported the collection of the data: Field Museum of Natural History, National Science Foundation 6. Recommended citation for this dataset: Price, S.L., et al. 2022. Phylogenomics and fossil data inform the systematics and geographic range evolution of a diverse Neotropical ant lineage. Insect Systematics and Diversity, 6(1):9. DATA & FILE OVERVIEW 1. Description of dataset These data were generated to infer a phylogeny of Cephalotes turtle ants using genome-wide data (ultraconserved elements) and to infer the impact of land bridge formation on diversification in this group. 2. File List: File 1 Name: UCEmatrix_phyluce_mafft-nexus-edge-trimmed-clean-75p.phylip File 1 Description: Aligned UCE matrix for 136 Cephalotes and outgroup taxa produced using the program "phyluce" File 2 Name: contigs_trimmed_unfiltered_136taxa.zip File 2 Description: Raw unfiltered contigs for 136 Cephalotes and outgroup taxa File 3 Name: contigs_trimmed_filtered_136taxa.zip File 3 Description: Contigs for 136 taxa after quality filtering File 4 Name: BioGeoBEARS File 4 Description: Folder containing necessary files for biogeographic range inference in BioGeoBEARS File 5 Name: BAMM File 5 Description: Folder containing necessary files for diversification rate inference in BAMM File 6 Name: TreeFiles File 6 Description: Folder containing output phylogenetic trees for inferences using MrBayes, MCMCTree, ASTRAL, and RAxML File 7 Name: ACSrange_71320_101taxa File 7 Description: Presence/absence of each species included in the phylogeny in each biogeographic region File 8 Name: CorrRates_FiveRunsCombined_Newick_tipdropped.tre File 8 Description: Time-scaled phylogeny from MCMCTree, with only one tip per species and those with biogeographic data included File 9 Name: timeperiods.txt File 9 Description: File to set time ranges corresponding to full closure of the Isthmus of Panama, the beginning of the formation of the Isthmus, and the putative temporary GAARlandia land bridge File 10 Name: manual_dispersal_multipliers.txt File 10 Description: Relative probability of dispersal between each geographic region in each time period set by the "timeperiods.txt" file File 11 Name: GeographicRangeInference_BioGeoBEARS_Rscript.R File 11 Description: R script for running the biogeographic range inference analyses File 12 Name: MCMCTree_NUMBERtaxa_FiveRunsCombined_newick.tre File 12 Description: Time-scaled phylogeny from MCMCTree File 13 Name: event_data.txt File 13 Description: Event data file produced by BAMM File 14 Name: BAMM_Cephalotes_RScript.R File 14 Description: R script for running functions in the R package BAMMtools File 15 Name: mcmc_out.txt File 15 Description: Output MCMC data from BAMM run File 16 Name: control.txt File 16 Description: BAMM configuration file File 17 Name: myPriors.txt File 17 Description: Priors block identified by setBAMMpriors function in the R package BAMMtools File 18 Name: MrBayes_run1212comb.tree File 18 Description: Bayesian phylogeny inferred with two independent runs using MrBayes File 19 Name: MCMCTree_CorrRates_FiveRunsCombined_FigTree.tre File 19 Description: Time-scaled phylogeny from MCMCTree File 20 Name: ASTRAL_Cephalotes1239loci_bootstrap_consensus.tre File 20 Description: Consensus tree from ASTRAL File 21 Name: RAxML_bipartitions-SW_partitioned_ratehet.500bs.tre File 21 Description: Maximum likelihood phylogeny with bootstrap support inferred using RAxML METHODOLOGICAL INFORMATION See the Materials and Methods section of the associated open-access article: https://doi.org/10.1093/isd/ixab023 DATA-SPECIFIC INFORMATION FOR: UCEmatrix_phyluce_mafft-nexus-edge-trimmed-clean-75p.phylip 1. Number of variables: N/A 2. Number of cases/rows: 136 3. Variable List: N/A 4. Missing data codes: ? 5. Abbreviations used: N/A 6. Other relevant information: Cleaned and aligned UCE data, phylip-formated with 136 samples and a total dataset length of 995,575 base pairs DATA-SPECIFIC INFORMATION FOR: contigs_trimmed_unfiltered_136taxa.zip 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List: N/A 4. Missing data codes: N/A 5. Abbreviations used: N/A 6. Other relevant information: Zip file containing 2,514 UCE contig files DATA-SPECIFIC INFORMATION FOR: contigs_trimmed_filtered_136taxa.zip 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List: N/A 4. Missing data codes: N/A 5. Abbreviations used: N/A 6. Other relevant information: Zip file containing 1,327 UCE contig files DATA-SPECIFIC INFORMATION FOR: BioGeoBEARS 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List: N/A 4. Missing data codes: N/A 5. Abbreviations used: N/A 6. Other relevant information: DATA-SPECIFIC INFORMATION FOR: BAMM 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List: N/A 4. Missing data codes: N/A 5. Abbreviations used: N/A 6. Other relevant information: DATA-SPECIFIC INFORMATION FOR: TreeFiles 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List: N/A 4. Missing data codes: N/A 5. Abbreviations used: N/A 6. Other relevant information: DATA-SPECIFIC INFORMATION FOR: ACSrange_71320_101taxa 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List: N/A 4. Missing data codes: N/A 5. Abbreviations used: A = Antilles geographic region C = Central American geographic region S = South American geographic region 6. Other relevant information: 0 = Present 1 = Absent DATA-SPECIFIC INFORMATION FOR: CorrRates_FiveRunsCombined_Newick_tipdropped.tre 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List: N/A 4. Missing data codes: N/A 5. Abbreviations used: N/A 6. Other relevant information: Phylogenetic tree with 101 terminals DATA-SPECIFIC INFORMATION FOR: timeperiods.txt 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List: N/A 4. Missing data codes: N/A 5. Abbreviations used: N/A 6. Other relevant information: DATA-SPECIFIC INFORMATION FOR: manual_dispersal_multipliers.txt 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List: N/A 4. Missing data codes: N/A 5. Abbreviations used: A = Antilles geographic region C = Central American geographic region S = South American geographic region 6. Other relevant information: DATA-SPECIFIC INFORMATION FOR: GeographicRangeInference_BioGeoBEARS_Rscript.R 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List: N/A 4. Missing data codes: N/A 5. Abbreviations used: N/A 6. Other relevant information: DATA-SPECIFIC INFORMATION FOR: MCMCTree_NUMBERtaxa_FiveRunsCombined_newick.tre 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List: N/A 4. Missing data codes: N/A 5. Abbreviations used: N/A 6. Other relevant information: Newick-formatted phylogeny with 102 terminals DATA-SPECIFIC INFORMATION FOR: event_data.txt 1. Number of variables: 8 2. Number of cases/rows: 8 3. Variable List: generation leftchild rightchild abstime lambdainit lambdashift muinit mushift 4. Missing data codes: N/A 5. Abbreviations used: N/A 6. Other relevant information: DATA-SPECIFIC INFORMATION FOR: BAMM_Cephalotes_RScript.R 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List: N/A 4. Missing data codes: N/A 5. Abbreviations used: N/A 6. Other relevant information: DATA-SPECIFIC INFORMATION FOR: mcmc_out.txt 1. Number of variables: 6 2. Number of cases/rows: 6 3. Variable List: generation N_shifts logPrior logLik eventRate acceptRate 4. Missing data codes: N/A 5. Abbreviations used: N/A 6. Other relevant information: DATA-SPECIFIC INFORMATION FOR: control.txt 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List: N/A 4. Missing data codes: N/A 5. Abbreviations used: N/A 6. Other relevant information: DATA-SPECIFIC INFORMATION FOR: myPriors.txt 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List: N/A 4. Missing data codes: N/A 5. Abbreviations used: N/A 6. Other relevant information: DATA-SPECIFIC INFORMATION FOR: MrBayes_run1212comb.tree 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List: N/A 4. Missing data codes: N/A 5. Abbreviations used: N/A 6. Other relevant information: NEXUS-formatted phylogeny with 105 terminals DATA-SPECIFIC INFORMATION FOR: MCMCTree_CorrRates_FiveRunsCombined_FigTree.tre 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List: N/A 4. Missing data codes: N/A 5. Abbreviations used: N/A 6. Other relevant information: NEXUS-formated phylogeny with 102 terminals DATA-SPECIFIC INFORMATION FOR: ASTRAL_Cephalotes1239loci_bootstrap_consensus.tre 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List: N/A 4. Missing data codes: N/A 5. Abbreviations used: N/A 6. Other relevant information: Newick-formatted phylogeny with 105 terminals DATA-SPECIFIC INFORMATION FOR: RAxML_bipartitions-SW_partitioned_ratehet.500bs.tre 1. Number of variables: N/A 2. Number of cases/rows: N/A 3. Variable List: N/A 4. Missing data codes: N/A 5. Abbreviations used: N/A 6. Other relevant information: Newick-formatted phylogeny with 136 terminals