This readme file was generated on 2022-09-10 by Chris Muir GENERAL INFORMATION Title of Dataset: How important are functional and developmental constraints on phenotypic evolution? An empirical test with the stomatal anatomy of flowering plants Author/Principal Investigator Information Name: Christopher D. Muir ORCID: 0000-0003-2555-3878 Institution: University of Hawaiʻi at Mānoa Address: 2538 McCarthy Mall EDM 216 Honolulu, HI 96822 Email: cdmuir@hawaii.edu SHARING/ACCESS INFORMATION Licenses/restrictions placed on the data: No licenses/restrictions on processed data The ropenstomata R package contains raw data distributed under an MIT license Links to other publicly accessible locations of the data: Raw stomatal anatomical data: https://github.com/cdmuir/ropenstomata Processed data: https://github.com/cdmuir/stomata-independence Links/relationships to ancillary data sets: References to original stomatal anatomical data sets are provided in Table A5 of the Muir et al. (2022) and in the ropenstomata R package. The GBOTB.extended mega-tree came from V.phylomaker (https://onlinelibrary.wiley.com/doi/10.1111/ecog.04434) Sequence data came from GenBank Plant and Fungal sequences database division (https://www.ncbi.nlm.nih.gov/genbank/htgs/divisions/) Genome size data came from the Angiosperm DNA C-values database (https://cvalues.science.kew.org/) Recommended citation for this dataset: To cite ropenstomata in publications use: Muir CD. 2022. ropenstomata: An Open Stomatal Database. https://github.com/cdmuir/ropenstomata. DATA & FILE OVERVIEW File List: stomatal-anatomy.csv - raw stomatal anatomical data from ropenstomata stomatal-anatomy-metadata.csv - metadata on raw stomatal anatomical data from ropenstomata plant-c-value.csv - raw data on plant C-value downloaded from the Angiosperm DNA C-values database trimmed-data.csv - trimmed data set of species found on phylogeny trimmed-phylogeny.new - trimmed phylogeny of species with stomatal anatomical data in newick format phylogenetic-contrasts.csv - phylogenetically independent contrasts used in final analyses Relationship between files: The column "resolved_name" in trimmed-data.csv matches the tip names in trimmed-phylogeny.new. The column "tree_node" in phylogenetic-contrasts.csv refers to the node in trimmed-phylogeny.new The columns "sp1" and "sp2" match "resolved_name" in trimmed-data.csv matches the tip names in trimmed-phylogeny.new DATA-SPECIFIC INFORMATION FOR: stomatal-anatomy.csv Number of variables: 7 Number of rows: 5842 Variable List: source_id, taxonomic ID in original source, Genus species trait, trait ID, {"abaxial_stomatal_density_mm2" , "abaxial_stomatal_length_um", "abaxial_stomatal_width_um", "adaxial_stomatal_density_mm2", "adaxial_stomatal_length_um", "adaxial_stomatal_width_um", "abaxial_pore_length_um" "adaxial_pore_length_um"} mu, mean trait value, um or mm^2 n, sample size, 1 sd, trait standard deviation, um or mm^2 source, original source, first-author_first-word_year se, trait standard error of the mean, um or mm^2 Missing data codes: NA DATA-SPECIFIC INFORMATION FOR: stomatal-anatomy-metadata.csv Number of variables: 7 Number of rows: 38 Variable List: source, original source, first-author_first-word_year taxa, taxomic group studies, open-ended location, location of data in source, tableX or figureX density_unit, unit of stomatal density in source, open-ended length_unit, unit of stomatal length in source, open-ended sample_size, sample size, 1 notes, usage notes, open-ended Missing data codes: NA DATA-SPECIFIC INFORMATION FOR: plant-c-value.csv Number of variables: 9 Number of rows: 1033 Variable List: family, plant family genus, plant genus species, plant species subspecies, plant subspecies chromostome_number_2n, 2N chromosome number, 1 ploidy_level_x, Ploidy level, 1 dna_amount_1c_pg, 1C DNA amount, pg c_value_reference, reference c_value_note, note Missing data codes: NA DATA-SPECIFIC INFORMATION FOR: trimmed-data.csv Number of variables: 27 Number of rows: 638 Variable List: resolved_name, resolved taxonomic name family, plant family source, original source, first-author_first-word_year source_id, taxonomic ID in original source, Genus species abaxial_stomatal_density_mm2, abaxial stomatal density, mm^2 adaxial_stomatal_density_mm2, adaxial stomatal density, mm^2 abaxial_stomatal_length_um, abaxial stomatal length, um adaxial_stomatal_length_um, adaxial stomatal length, um phy_name, tip label in original phylogeny grass, is species a grass, boolean c, morphological constant used to calculate m for gmax, unitless h, morphological constant used to calculate m for gmax, unitless j, morphological constant used to calculate m for gmax, unitless m, morphological constant used to calculate gmax, unitless b, biophysical constant used to calculate gmax, mol / m / s abaxial_stomatal_area_um2, abaxial stomatal area, um^2 adaxial_stomatal_area_um2, adaxial stomatal area, um^2 abaxial_gmax, abaxial maximum stomatal conductance, mol / m^2 / s adaxial_gmax, abaxial maximum stomatal conductance, mol / m^2 / s abaxial_fs, abaxial fraction of epidermal area allocated to stomata, unitless adaxial_fs, adaxial fraction of epidermal area allocated to stomata, unitless genus, plant genus subspecies, plant subspecies chromostome_number_2n, 2N chromosome number, 1 ploidy_level_x, Ploidy level, 1 c_value_reference, reference c_value_note, note dna_amount_2c_pg, 2C DNA amount, pg Missing data codes: NA DATA-SPECIFIC INFORMATION FOR: phylogenetic-contrasts.csv Number of variables: 18 Number of rows: 236 Variable List: tree_node, node in trimmed phylogeny, 1 pair_age, divergence time between sp1 and sp2, millions of year sp1, resolved name species 1, Genus_species sp2, resolved name species 2, Genus_species All other columns are the log10-difference between sp1 and sp2 for the trait given by the column name Missing data codes: NA