This _Readme_Medeiros_etal_2022_DATASET.txt file was generated on 2022-04-18 by ALINE MEDEIROS GENERAL INFORMATION 1. Title of Dataset: Does Genome Size Increase with Water Depth in Marine Fishes? 2. Author Information A. Principal Investigator Contact Information Name: Ricardo Betancur-R Institution: The University of Oklahoma Address: Email: ricardo.betancur@ou.edu B. Associate or Co-investigator Contact Information Name: Aline P. M. Medeiros Institution: Universidade Federal da Paraiba Address: Email: alinepaivamm@gmail.com 3. Date of data collection (approximate date): 2019-08-06 4. Data collection: Genomesize.com & NCBI SHARING/ACCESS INFORMATION 1. Links to publications that cite or use the data: http://genomesize.com/ DATA & FILE OVERVIEW 1. File List: _Readme_Medeiros_etal_2022_DATASET.txt Code_Evolution_ToDryad.R FigS2_TimeCalibratedPhylogeny.pdf
Databases.xlsx _Alignments.phy _B17_Backbone.tre _B17GB_CalibratedTree_2454spp.nex Carangaria_Phase1_1.csv Carangaria_Phase1_2.csv Carangaria_Phase1_3.csv Carangaria_Phase1_4.csv Carangaria_Phase1_5.csv Carangaria_Phase1_6.csv EEA71_B17GB_Spp.csv EEA71_B17GB_Spp.tre EEA71_R18Sim_Spp_100_trees_SppNodeLength.csv EEA71_R18Sim_Spp_100_trees_SppNodeLength.tre EEA71_R18Sim_Spp_100_trees.tre EEA71_R18Sim_Spp.csv EEA71_Spp_B17GB_trial1.csv EEA71_Spp_B17GB_trial2.csv EEA71_Spp_B17GB_trial3.csv EEA71_Spp_B17GB_trial4.csv EEA71_Spp_B17GB_trial5.csv EEA71_Spp_B17GB_trial6.csv EEA71_Spp_B17GB_trial7.csv EEA71_Spp_B17GB_trial8.csv EEA71_Spp_B17GB_trial9.csv EEA71_Spp_B17GB_trial10.csv EEA71_Spp_B17GB_trial11.csv EEA71_Spp_B17GB_trial12.csv EEA71_Spp_B17GB_trial13.csv EEA71_Spp_B17GB_trial14.csv EEA71_Spp_B17GB_trial15.csv EEA71_Spp_B17GB_trial16.csv EEA71_Spp_B17GB_trial17.csv EEA71_Spp_B17GB_trial18.csv EEA71_Spp_B17GB_trial19.csv EEA71_Spp_B17GB_trial20.csv EEA71_Spp_B17GB_trial21.csv EEA71_Spp_B17GB_trial22.csv EEA71_Spp_B17GB_trial23.csv EEA71_Spp_B17GB_trial24.csv EEA71_Spp_R18Sim_trial1.csv EEA71_Spp_R18Sim_trial2.csv EEA71_Spp_R18Sim_trial3.csv EEA71_Spp_R18Sim_trial4.csv EEA71_Spp_R18Sim_trial5.csv EEA71_Spp_R18Sim_trial6.csv EEA71_Spp_R18Sim_trial7.csv EEA71_Spp_R18Sim_trial8.csv EEA71_Spp_R18Sim_trial9.csv EEA71_Spp_R18Sim_trial10.csv EEA71_Spp_R18Sim_trial11.csv EEA71_Spp_R18Sim_trial12.csv EEA71_Spp_R18Sim_trial13.csv EEA71_Spp_R18Sim_trial14.csv EEA71_Spp_R18Sim_trial15.csv EEA71_Spp_R18Sim_trial16.csv EEA71_Spp_R18Sim_trial17.csv EEA71_Spp_R18Sim_trial18.csv EEA71_Spp_R18Sim_trial19.csv EEA71_Spp_R18Sim_trial20.csv EEA71_Spp_R18Sim_trial21.csv EEA71_Spp_R18Sim_trial22.csv EEA71_Spp_R18Sim_trial23.csv EEA71_Spp_R18Sim_trial24.csv Pelagiaria_Phase1_1.csv Pelagiaria_Phase1_2.csv Pelagiaria_Phase1_3.csv Pelagiaria_Phase1_4.csv Pelagiaria_Phase1_5.csv Pelagiaria_Phase1_6.csv Perciformes_Phase1_1.csv Perciformes_Phase1_2.csv Perciformes_Phase1_3.csv Perciformes_Phase1_4.csv Perciformes_Phase1_5.csv Perciformes_Phase1_6.csv Zeiogadaria_Phase1_1.csv Zeiogadaria_Phase1_2.csv Zeiogadaria_Phase1_3.csv Zeiogadaria_Phase1_4.csv Zeiogadaria_Phase1_5.csv Zeiogadaria_Phase1_6.csv B17GB_AllSpp_v2_648spp.tre B17GB_AllSpp_v2_651spp_outgroups.tre B17GB_AllSpp_v2_SppNodeLength.tre Carangaria_RRPP_ARtree.tre Carangaria_RRPP_R18.tre Database_R18Gen.csv Gobiaria_B17GB.tre Gobiaria_R18Gen.tre Labriformes_B17GB.tre Labriformes_R18Gen.tre Lutjaniformes_B17GB.tre Lutjaniformes_R18Gen.tre Lutjaniformes_RiconTree_RaxML_Pruned.tre Ovalentaria_B17GB.tre Ovalentaria_R18Gen_pruned_SppNodeLength.tre Ovalentaria_R18Gen.tre Pelagiaria_B17GB.tre Pelagiaria_R18Gen.tre Perciformes_B17GB.tre Perciformes_R18Gen.tre PGLS_AllSpp_B17GB_v2_648spp_trial1.csv PGLS_AllSpp_B17GB_v2_648spp.csv PGLS_AllSpp_B17GB_v2_648spp.nex PGLS_AllSpp_B17GB_v2_mvmorph.csv PGLS_AllSpp_B17GB_v2_SppNodeLength_mvmorph.csv PGLS_AllSpp_B17GB_v2_SppNodeLength.csv PGLS_AllSpp_B17GB_v2_SppNodeLength.nex PGLS_AllSpp_R18Gen_592spp_SppNodeLength_mvmorph.csv PGLS_AllSpp_R18Gen_592spp_SppNodeLength_mvmorph.nex PGLS_AllSpp_R18Gen_594spp_mvmorph.csv PGLS_AllSpp_R18Gen_594spp_mvmorph.nex PGLS_AllSpp_R18Gen_594spp.csv PGLS_AllSpp_R18Gen_594spp.nex PGLS_AllSpp_R18Gen_trial1_594spp.csv PGLS_AllSpp_R18Gen_trial1_594spp.nex PGLS_Carangaria_B17GB.csv PGLS_Carangaria_B17GB.nex PGLS_Carangaria_R18Gen.csv PGLS_Carangaria_R18Gen.nex PGLS_Carangaria_R18Sim_tree69.nex PGLS_Carangaria_R18Sim.csv PGLS_Gobiaria_B17GB.csv PGLS_Gobiaria_B17GB.nex PGLS_Gobiaria_R18Gen.csv PGLS_Gobiaria_R18Gen.nex PGLS_Labriformes_B17GB.csv PGLS_Labriformes_B17GB.nex PGLS_Labriformes_R18Gen.csv PGLS_Labriformes_R18Gen.nex PGLS_Lutjaniformes_B17GB.csv PGLS_Lutjaniformes_B17GB.nex PGLS_Lutjaniformes_R18Gen.csv PGLS_Lutjaniformes_R18Gen.nex PGLS_Lutjaniformes_Rincon.csv PGLS_Ovalentaria_B17GB.csv PGLS_Ovalentaria_B17GB.nex PGLS_Ovalentaria_R18Gen_SppNodeLength.csv PGLS_Ovalentaria_R18Gen_SppNodeLength.nex PGLS_Ovalentaria_R18Gen.csv PGLS_Ovalentaria_R18Gen.nex PGLS_Pelagiaria_B17GB.csv PGLS_Pelagiaria_B17GB.nex PGLS_Pelagiaria_R18Gen.csv PGLS_Pelagiaria_R18Gen.nex PGLS_Perciformes_B17GB.csv PGLS_Perciformes_B17GB.nex PGLS_Perciformes_R18Gen.csv PGLS_Perciformes_R18Gen.nex PGLS_Spariformes_B17GB.csv PGLS_Spariformes_B17GB.nex PGLS_Spariformes_R18Gen.csv PGLS_Spariformes_R18Gen.nex PGLS_Syngnatharia_B17GB.csv PGLS_Syngnatharia_B17GB.nex PGLS_Syngnatharia_R18Gen.csv PGLS_Syngnatharia_R18Gen.nex PGLS_Tetraodontiformes_B17GB.csv PGLS_Tetraodontiformes_B17GB.nex PGLS_Tetraodontiformes_R18Gen.csv PGLS_Tetraodontiformes_R18Gen.nex PGLS_Zeiogadaria_B17GB.csv PGLS_Zeiogadaria_B17GB.nex PGLS_Zeiogadaria_R18Gen.csv PGLS_Zeiogadaria_R18Gen.nex R18Gen_592spp_SppNodeLength.tre R18Gen_594spp.tre R18Gen_trial1_594spp.tre Spariformes_B17GB.tre Spariformes_R18Gen.tre Syngnatharia_B17GB.tre Syngnatharia_R18Gen.tre Tetraodontiformes_B17GB.tre Tetraodontiformes_R18Gen.tre Zeiogadaria_B17GB.tre Zeiogadaria_R18Gen.tre PGLS_AllSpp_R18Sim_705_spp_SppNodeLength_100_trees.tre PGLS_AllSpp_R18Sim_705_spp_SppNodeLength_mvmorph.csv PGLS_AllSpp_R18Sim_705_spp_SppNodeLength.csv PGLS_AllSpp_R18Sim_708_spp_100_trees.tre PGLS_AllSpp_R18Sim_708spp_1tree.tre PGLS_AllSpp_R18Sim_SppNodeLength.csv PGLS_AllSpp_R18Sim_tree69.nex PGLS_AllSpp_R18Sim_trial1.csv PGLS_AllSpp_R18Sim.csv PGLS_Gobiaria_R18Sim_tree69.nex PGLS_Gobiaria_R18Sim.csv PGLS_Labriformes_R18Sim_tree69.nex PGLS_Labriformes_R18Sim_trial1.csv PGLS_Labriformes_R18Sim.csv PGLS_Lutjaniformes_R18Sim_tree69.nex PGLS_Lutjaniformes_R18Sim.csv PGLS_Ovalentaria_R18Sim_SppNodeLength.csv PGLS_Ovalentaria_R18Sim_tree69.nex PGLS_Ovalentaria_R18Sim.csv PGLS_Pelagiaria_R18Sim_tree69.nex PGLS_Pelagiaria_R18Sim.csv PGLS_Perciformes_R18Sim_tree69.nex PGLS_Perciformes_R18Sim.csv PGLS_Spariformes_R18Sim_tree69.nex PGLS_Spariformes_R18Sim.csv PGLS_Syngnatharia_R18Sim_tree69.nex PGLS_Syngnatharia_R18Sim.csv PGLS_Tetraodontiformes_R18Sim_tree69.nex PGLS_Tetraodontiformes_R18Sim.csv PGLS_Zeiogadaria_R18Sim_tree69.nex PGLS_Zeiogadaria_R18Sim.csv R18Sim_AllTrees_Carangaria.tre R18Sim_AllTrees_Gobiaria.tre R18Sim_AllTrees_Labriformes.tre R18Sim_AllTrees_Lutjaniformes.tre R18Sim_AllTrees_Ovalentaria_SppNodeLength.tre R18Sim_AllTrees_Ovalentaria.tre R18Sim_AllTrees_Pelagiaria.tre R18Sim_AllTrees_Perciformes.tre R18Sim_AllTrees_Spariformes.tre R18Sim_AllTrees_Syngnatharia.tre R18Sim_AllTrees_Tetraodontiformes.tre R18Sim_AllTrees_Zeiogadaria.tre 2. Relationship between files: Files that have identical names were used to run the same analysis (ex. to run a PGLS analysis it is necessary two files: .csv & .tre ) DATA-SPECIFIC INFORMATION FOR FILES: 1. Predictor variable used in analyses ('labels in datasets'): i. Categorical: depth ('Habitat', 'Depth_200' & 'Depth_600') ii. Continuous: depth in meters ('DepthMax' & 'DepthRange') 2. Response variables used in the analyses: i. Continuous: genome size in megabases ('Average_GenomeSizeMb') 3. Missing data codes: n/a 4. Specialized formats or other abbreviations used: i. Phylogenetic trees in nexus (.nex) and Newick (.tre) formats