This Groh_2021_croc_timesREADME.txt file was generated on 2021-07-27 by SEBASTIAN GROH GENERAL INFORMATION 1. Title of Dataset: Groh_2021_croc_times 2. Author information: A. Principal Investigator Contact Information Name: Sebastian S. Groh Institution: Dpt. of Earth Sciences, University College London Address: Gower Street, London, WC1E 6BT, UK Email: sebastian.groh@ucl.ac.uk; sebastian.s.groh@gmail.com B. Co-investigators Contact Information Name: Paul Upchurch Institution: Dpt. of Earth Sciences, University College London Address: Gower Street, London, WC1E 6BT, UK Email: p.upchurch@ucl.ac.uk Name: Paul M. Barrett Institution: Dpt. of Earth Sciences, Natural History Museum Address: Cromwell Road, London, SW7 5BD, UK Email: p.barrett@nhm.ac.uk Name: Julia J. Day Institution: Dpt. of Genetics, Environment and Evolution, University College London Address: Gower Street, London, WC1E 6BT, UK Email: j.day@ucl.ac.uk 3. Dates of data collection: 2015-04-01 to 2021-02-17, collected in person in museum collections and from online sources (see Groh et al. 2021, "The phylogenetic relationships of neosuchian crocodiles and their implications for the convergent evolution of the longirostrine condition", https://doi.org/10.1093/zoolinnean/zlz117" for more information on how the in person collection took place) 4. Funding sources: Financial support for this study was provided by the London NERC DTP (Ref NE/L002485/1) and the UCL Bogue Fellowship. SHARING/ACCESS INFORMATION 1. Restrictions: please do not reuse the data or code without citation. 2. A previous version of the phylogenetic dataset can be found in Groh, S.S., Upchurch, P., Barrett, P.M. and Day, J.J., 2020. The phylogenetic relationships of neosuchian crocodiles and their implications for the convergent evolution of the longirostrine condition. Zoological Journal of the Linnean Society, 188(2), pp.473-506. 3. Recommended citation for this dataset: Please cite the main paper this dataset is linked to. Groh, S.S., Upchurch, P., Barrett, P.M. and Day, J.J., 2021. How to date a crocodile – estimation of neosuchian emergence dates and a comparison of the performance of four time-scaling methods [under review] DATA & FILE OVERVIEW File List and descriptions Dataset.1: Phylogenetics |- A.Code | |- Groh_2021_croc_times_TNT_Protocol.docx [TNT analysis protocol] |- B.Data (Groh_2021_croc_times_PHYLOGENETICS_DATA.zip) | |- Groh_2021_croc_times_Character_List_Complete.pdf [Complete character list with continuous and discrete characters] | |- Groh_2021_croc_times_Character_List_Rediscretised.pdf [Rediscretised character list with discrete versions of continuous characters where appropriate] | |- Groh_2021_croc_times_complete_dataset.tnt [All character scores for all species when scored from the complete character list] | |- Groh_2021_croc_times_rediscretised_dataset.tnt [All character scores for all species scored from the rediscretised character list] |- C.Results (Groh_2021_croc_times_PHYLOGENETICS_RESULTS.zip) | |- Groh_2021_croc_times_complete_trees.nex [MPTs from the analysis of the complete dataset] | |- Groh_2021_croc_times_rediscretised_trees.nex [MPTs from the analysis of the rediscretised dataset] | |- Groh_2021_croc_times_Stockdale_tree1.nex [Nexus file of the neosuchian part of the Stockdale & Benton 2021 supertree used for analysis] | |- Groh_2021_croc_times_Stockdale_tree2.nex [Nexus file of the neosuchian part of the Stockdale & Benton 2021 supertree used for analysis, with Thalattosuchia removed] | |- Groh_2021_croc_times_Consensus_trees.pdf [Visual representation of the consensus trees from the complete and rediscretised analyses] | |- Groh_2021_croc_times_Synapomorphies.docx [List of synapmorphies for each named clade] | |- Groh_2021_croc_times_Clade_definitions.docx [List of clade definitions in the phylogenetic tree] | |- Groh_2021_croc_times_Changes.pdf [Text summarising the changes in respect to Groh et al. 2021, both to the dataset and in the tree tpologies] Dataset.2: Time-scaling |- A.Code (Groh_2021_croc_times_TIMESCALING_CODE.zip) | |- Groh_2021_croc_times_cal3.txt [R code used for cal3 times] | |- Groh_2021_croc_times_FBD.txt [R code used to extract the ages from the FBD trees] | |- Groh_2021_croc_times_Hedman.txt [R code used for Extended Hedman dating] | |- Groh_2021_croc_times_sGLA.txt [R code used for sGLA dating] | |- Groh_2021_croc_times_timescaled_trees.txt [R code used to obtain an average timescaled tree from all the methods] |- B.Data (Groh_2021_croc_times_TIMESCALING_DATA.zip) | |- Groh_2021_croc_times_Neosuchia_Times.xlsx [Excel file with all the ages used in the analysis] | |- Groh_2021_croc_times_FBD_Groh.prior.xml [xml file for FBD analysis of the modified Groh et al. 2020 dataset] | |- Groh_2021_croc_times_FBD_Stockdale.prior.xml [xml file for FBD analysis of the Stockdale & Benton 2021 dataset] | |- Groh_2021_croc_times_cal3_inttimesNeosuchia_Groh.txt [interval times for cal3 dating of the modified Groh et al. 2020 dataset] | |- Groh_2021_croc_times_cal3_inttimesNeosuchia_rates.txt [interval times for cal3 rate calibration] | |- Groh_2021_croc_times_cal3_inttimesNeosuchia_Stockdale.txt [interval times for cal3 dating of the Stockdale & Benton 2021 dataset] | |- Groh_2021_croc_times_Hedman_Neosuchia_occurrences_Groh.txt [data file for Extended Hedman analysis of the modified Groh et al. 2020 dataset] | |- Groh_2021_croc_times_Hedman_Neosuchia_occurrences_Stockdale.txt [data file for Extended Hedman analysis of the Stockdale & Benton 2021 dataset] | |- Groh_2021_croc_times_cal3_taxtimesNeosuchia_Groh.txt [taxon times for cal3 dating of the modified Groh et al. 2020 dataset] | |- Groh_2021_croc_times_cal3_taxtimesNeosuchia_Stockdale.txt [taxon times for cal3 dating of the Stockdale & Benton 2021 dataset] | |- Groh_2021_croc_times_cal3_taxtimesNeosuchia_rates.txt [taxon times for cal3 rate calibration] | |- Groh_2021_croc_times_NeosuchiaTimeList_Groh.rdata [Time List in R used for cal3 and sGLA dating the modified Groh et al. 2020 dataset] | |- Groh_2021_croc_times_NeosuchiaTimeList_rates.txt [Time List in R used for cal3 rate calibration] | |- Groh_2021_croc_times_NeosuchiaTimeList_Stockdale.rdata [Time List in R used for cal3 and sGLA dating the Stockdale & Benton 2021 dataset] |- C.Results (Groh_2021_croc_times_TIMESCALING_RESULTS.zip) | |- Groh_2021_croc_times_All_results.xlsx [divergence time estimates for each clade and tree per method including standard deviations] | |- Groh_2021_croc_times_cal3_scaled_Groh.tre [averaged and time scaled tree for the cal3 results of the modified Groh et al. 2020 dataset] | |- Groh_2021_croc_times_cal3_scaled_Stockdale.tre [averaged and time scaled tree for the cal3 results of the Stockdale & Benton 2021 dataset] | |- Groh_2021_croc_times_FBD_scaled_Groh.tre [averaged and time scaled tree for the FBD results of the modified Groh et al. 2020 dataset] | |- Groh_2021_croc_times_FBD_scaled_Stockdale.tre [averaged and time scaled tree for the FBD results of the Stockdale & Benton 2021 dataset] | |- Groh_2021_croc_times_Hedman_scaled_Groh.tre [averaged and time scaled tree for the Extended Hedman results of the modified Groh et al. 2020 dataset] | |- Groh_2021_croc_times_Hedman_scaled_Stockdale.tre [averaged and time scaled tree for the Extended Hedman results of the Stockdale & Benton 2021 dataset] | |- Groh_2021_croc_times_sGLA_scaled_Groh.tre [averaged and time scaled tree for the sGLA results of the modified Groh et al. 2020 dataset] | |- Groh_2021_croc_times_sGLA_scaled_Stockdale.tre [averaged and time scaled tree for the sGLA results of the Stockdale & Benton 2021 dataset] | |- Groh_2021_croc_times_Method_Comparison_G21.xlsm [all node ages from every run from all methods and a statistical comparison of them for the modified Groh et al. 2020 dataset] | |- Groh_2021_croc_times_Method_Comparison_SB21.xlsm [all node ages from every run from all methods and a statistical comparison of them for the Stockdale & Benton 2021 dataset] | |- Groh_2021_croc_times_scaled_tree_figures [all averaged and time-scaled trees plotted against a timescale] | |- Groh_2021_croc_times_variations_results [folder] | | |- Groh_2021_different_outgroup_ages_results [folder with the different results for older and younger Extended Hedman outgroup ages] | | |- Groh_2021_different_vartime_results [folder with the different vartimes used for sGLA and the modified Groh et al. phylogeny] METHODOLOGICAL INFORMATION Methods explained in detail in Groh, S.S., Upchurch, P., Barrett, P.M. and Day, J.J. How to date a crocodile – estimation of neosuchian emergence dates and a comparison of the performance of four time-scaling methods [under review]