This README.txt file was generated on 11 March, 2022 by Joel Nitta ------------------- GENERAL INFORMATION ----------------- Title of Dataset: Data from: Spatial phylogenetics of Japanese ferns: Patterns, processes, and implications for conservation Author Information Principal Investigator: Joel H. Nitta Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Associate or Co-investigators: Brent D. Mishler, Wataru Iwasaki, Atsushi Ebihara Geographic location of data collection: Japan Information about funding sources or sponsorship that supported the collection of the data: Funding provided in part by the Japan Society for the Promotion of Science (Kakenhi) Grant Number 16H06279 ------------------------------------------------------------------------ SHARING/ACCESS INFORMATION ------------------------------------------------------------------------ Licenses/restrictions placed on the data, or limitations of reuse: CC0 1.0 Universal (CC0 1.0) Recommended citation for the data: Nitta JH, Mishler BD, Iwasaki W, Ebihara A (2022) Data from: Spatial phylogenetics of Japanese ferns: Patterns, processes, and implications for conservation FIXME: add DOI when available Citation for and links to publications that cite or use the data: Nitta JH, Mishler BD, Iwasaki W, Ebihara A (2022) Spatial phylogenetics of Japanese ferns: Patterns, processes, and implications for conservation. American Journal of Botany. FIXME: add DOI, page numbers when available Code for analyzing the data is available on github: ------------------------------------------------------------------------ DATA & FILE OVERVIEW ------------------------------------------------------------------------ File list (filenames, directory structure (for zipped files) and brief description of all data files): - japan_climate.gpkg: Climate data in Japan downloaded from WorldClim database - japan_deer_range.gpkg: Distribution maps of Japanese deer (Cervus nippon) in Japan - japan_ferns_comm_full.csv: Community matrix (species x sites matrix) of native, non-hybrid ferns in Japan, full (unfiltered) dataset - japan_ferns_inext_results.csv: Results of collection curve analysis on fern specimens in Japan - japan_ferns_occ_summary.csv: Summary of specimen data of native, non-hybrid ferns in Japan - japan_ferns_redundancy_by_res: Taxonomic richness, abundance, and redunancy at different spatial resolutions for native, non-hybrid ferns of Japan - japan_ferns_shape_full.gpkg: Location of grid-cells (sites) for native, non-hybrid ferns in Japan, full (unfiltered) dataset - japan_ferns_traits_lucid.csv: Morphological trait data of native, non-hybrid ferns in Japan - japan_map_points.csv: Latitude and longitude of points used to produce a labeled map of Japan - japan_map.gpkg: Map of Japan - japan_protected_areas.gpkg: Protected areas in Japan - testo_sundue_2016_calibrations.csv: Fossil calibration points used for phylogenetic dating analysis - results.zip: Selected analysis results. Files include: - japan_ferns_biodiv.csv: Biodiversity statistics of native, non-hybrid ferns in Japan - japan_ferns_comm.csv: Community matrix (species x sites matrix) of native, non-hybrid ferns in Japan used for biodiversity analysis - japan_ferns_shape.gpkg: Location of grid-cells (sites) for native, non-hybrid ferns in Japan used for biodiversity analysis - japan_ferns_traits.csv: Trait matrix of native, non-hybrid ferns in Japan used for functional biodiversity analysis - japan_ferns_tree_dated.tre: Maximim-likelihood, ultrametric (dated) phylogeny of native, non-hybrid ferns in Japan with clades consisting of identical OTUs collapsed to polytomies - japan_ferns_tree_uncollapsed.tre: Maximim-likelihood, ultrametric (dated) phylogeny of native, non-hybrid ferns in Japan with clades consisting of identical OTUs not collapsed - japan_ferns_tree.tre: Maximim-likelihood phylogeny of native, non-hybrid ferns in Japan Additional data used in analysis not included in current data package: - doi_10.5061_dryad.4362p32__v4.zip: Data including DNA sequences, taxonomy, and breeding system data for native Japanese ferns (Ebihara and Nitta 2019) downloaded from . MD5 checksum 4ae5355c524ab47336d3fe56bf7aa440 - ftol_data_release_v0.0.1.zip: Fern Tree of Life project global DNA alignment and phylogenetic tree (Nitta et al., in prep.) downloaded from . MD5 checksum 26b95c283eec6529c71b252a47d3a06c FIXME: replace with DOI when available Checksums are 32-byte MD5 hashes generated with tools::md5sum() in R. ------------------------------------------------------------------------ METHODOLOGICAL INFORMATION ------------------------------------------------------------------------ Description of methods used for collection/generation of data: A list of native, non-hybrid fern specimens housed at the herbarium of the Museum of Science and Nature, Japan was converted to a community data matrix at four grain sizes (square grid-cells spanning Japan, each 10, 20, 30, or 40 km per side). The 20 km degree grain size was selected for further analysis based on redundancy (ratio of number of specimens to number of taxa per cell). All taxon names are based on the Green List (; English version available at ). Traits were measured on each species as described in Ebihara and Nitta (2019). Phylogenetic analysis was conducted with maximum likelihood in IQ-TREE v1.6.12 (Nguyen et al. 2015) by combining plastid rbcL sequences of each taxon with a globally sampled data matrix (FTOL v0.0.1; Nitta et al., in prep.; ). Next, dating analysis was carried out using treePL v1.0 (Smith and O'Meara 2012) with 26 fossil calibration points after Testo and Sundue (2016). The dated phylogeny was then trimmed to include Japanese taxa only. The community matrix, traits, and phylogeny were used to analyze spatial patterns of phylogenetic diversity and endemism. Data files were generated from raw data (not included here) using scripts available at , in particular . For full methods, see Nitta JH, Mishler BD, Iwasaki W, Ebihara A (2022) Spatial phylogenetics of Japanese ferns: Patterns, processes, and implications for conservation. American Journal of Botany. FIXME: add DOI, page numbers when available ------------------------------------------------------------------------ DATA-SPECIFIC INFORMATION ------------------------------------------------------------------------ japan_deer_range.gpkg: Distribution maps of Japanese deer (Cervus nippon) in Japan. Raw data were downloaded from the Japan Ministry of the Environment (). The data include range maps based on three types of data: range of Japanese deer surveyed in 1978, range surveyed in 2003, and estimated range inferred from a model including snow cover and forest type based on the 2003 survey data. Only estimated range with < 0.10 movement cost was included. Number of variables: 2 Number of cases/rows: 3 Coordinate reference system: JGD2000 Variable list: - range: Source of range data. '1978' = 1978 survey, '2003' = 2003 survey, 'estimated' = range estimated from model based on 2003 survey data - geom: Vector describing shape and position of range polygon Missing data codes: No missing data. MD5 checksum: 27c0b6e9b3d01803f4ee5b1a51c9f291 ------------------------------------------------------------------------ japan_climate.gpkg: Climate data in Japan downloaded from WorldClim database (). Raw data were downloaded at the 2.5 minute scale. The intersection of the raw climate data with 20 km × 20 km grid-cells (japan_ferns_shape_full.gpkg) were identified, then average value for each climatic variable was calculated for each grid-cell. Number of variables: 5 Number of cases/rows: 73836 Coordinate reference system: JGD2000 Variable list: - temp: Mean annual temperature, in units of 10 * degrees celsius (BIO1) - temp_season: Temperature seasonality (standard deviation ×100) (BIO4) - precip: Annual precipitation (mm) (BIO12) - precip_season: Precipitation seasonality (coefficient of variation) (BIO15) - geom: Vector describing shape and position of grid-cell Missing data codes: No missing data. MD5 checksum: 18072eafeb15e24933a92ad0792c66b0 ------------------------------------------------------------------------ japan_ferns_comm_full.csv: Community matrix (species x sites matrix) of native, non-hybrid ferns in Japan. Sites correspond to 20 km x 20 km grid-cells covering Japan. For location of grid-cells, see japan_ferns_shape_full.gpkg. Full dataset including all grid-cells (none excluded due to low redundancy). Number of variables: 674 Number of cases/rows: 1377 Variable list: - grids: Name of grid-cell. - Other columns: Each column is named for a Japanese fern taxon. Values indicate number of specimens that were observed in each grid-cell for that taxon. Missing data codes: No missing data. MD5 checksum: dec21fea32840c0ad464d913a5bb2a12 ------------------------------------------------------------------------ japan_ferns_inext_results.csv: Output from running iNEXT (Hsieh, Ma, and Chao 2016) on specimen data of native, non-hybrid ferns in Japan. iNEXT estimates diversity (here, species richness) and sampling completeness based on interpolation and extrapolation from the original data. Number of variables: 9 Number of cases/rows: 40 Variable list: - m: Sample size (number of individuals) - method: Method used to estimate diversity - order: Diversity order of Hill number (here 0, equivalent to species richness) - qD: Estimated diversity - qD.LCL: Lower 95% confidence limit on estimated diversity - qD.UCL: Upper 95% confidence limit on estimated diversity - SC: Estimated sampling completeness - SC.LCL: Lower 95% confidence limit on sampling completeness - SC.UCL: Upper 95% confidence limit on sampling completeness Missing data codes: No missing data. MD5 checksum: c13234b7a531bbb9539a0f60a5ca8c24 ------------------------------------------------------------------------ japan_ferns_occ_summary.csv: Summary of raw specimen data for native, non-hybrid ferns of Japan. Raw specimen data consists of one row per specimen, with species name, latitude, longitude, and collection date (raw specimen data not included here). Raw data were filtered to remove duplicate specimens and specimens that occurred outside of the second-degree mesh (approximately 10 km sq grid-cell) map of Japan () Number of variables: 3 Number of cases/rows: 4 Variable list: - dataset: Dataset name. 'occ_point_data_ferns_unfiltered' indicates data includes all specimens, 'occ_point_data_ferns' indicates data only includes specimens after filtering - variable: Variable. 'n_taxa' indicates number of taxa, 'n_specimens' indicates number of specimens - value: Value corresponding to each variable Missing data codes: No missing data. MD5 checksum: 7dc8f58056b9a13386a4fc2ffc7ae17a ------------------------------------------------------------------------ japan_ferns_redundancy_by_res.csv: Results of testing binning raw specimen data of native, non-hybrid ferns of Japan into grid-cells at different resolutions. Sampling redundancy is a metric of sampling completeness, calculated as 1 - (richness/abundance). Number of variables: 5 Number of cases/rows: 7048 Variable list: - res: Degree of resolution (grid-cell side length), from 10 to 40 km (in m) - grids: Name of grid-cell - richness: Number of taxa occurring in grid-cell - abundance: Number of specimens occurring in grid-cell - redundancy: Redundancy (measure of sampling completeness) Missing data codes: No missing data. MD5 checksum: 2dc6a1efa94eb3265ca270f30fceedfa ------------------------------------------------------------------------ japan_ferns_shape_full.gpkg: Location of grid-cells (sites) for native, non-hybrid ferns in Japan in GeoPackage format. Compiled from raw specimen data by binning specimens into 20 km × 20 km grid-cells across Japan. Full dataset including all grid-cells (none excluded due to low redundancy). Number of variables: 5 Number of cases/rows: 1377 Coordinate reference system: Mollweide (+proj=moll +lon_0=135) Variable list: - grids: Name of grid-cell - richness: Number of taxa occurring in grid-cell - abundance: Number of specimens occurring in grid-cell - redundancy: Redundancy (measure of sampling completeness) - geom: Vector describing shape and position of grid-cell Missing data codes: No missing data. MD5 checksum: 02be6ea548a880e99b0a09a46a347ef1 ------------------------------------------------------------------------ japan_ferns_traits_lucid.csv: Morphological trait data of native, non-hybrid ferns in Japan, originally formatted for Lucid dichotomous key software (). For more information on codes used for scoring of traits, see Number of variables: 436 Number of cases/rows: 675 Variable list: 'taxon' indicates taxon name. Other columns correspond to traits. If the column name includes 'number' it is numeric, otherwise categorical. Categorical trait codes as follows: - 0 = absent - 1 = common - 2 = rare - 3 = uncertain - 4 = common and misinterpreted - 5 = rare and misinterpreted - 6 = not scoped Numeric trait data formatted as a series of numbers separated by colons (':'), unless missing (0 or 3). For example, 1:9.4:12:14:16. The starting '1:' does not mean anything. The next series of numbers correspond to the outside minimum, normal minimum, normal maximum and outside maximum. For example, a plant leaf may normally be in the range of 4-5 cm, but sometimes as low as 2 cm or as high as 6 cm. This would be written 1:2:4:5:6. Missing data codes: '0' indicates trait is missing; '3' indicates uncertain. MD5 checksum: f0fdb678e38fa19a650140af9d4c1d06 ------------------------------------------------------------------------ japan_map_points.csv: Latitude and longitude of points used to produce a labeled map of Japan. Some points were originally generated using script at Number of variables: 5 Number of cases/rows: 17 Variable list: - query: Name of point of interest - lat: Latitude - lon: Longitude - lat_end: Ending latitude (only for features that are lines, not points) - lon_end: Ending longitude (only for features that are lines, not points) Missing data codes: No data entered between commas in CSV. MD5 checksum: 17e92adffd7daa40b26494ae680fd4cb ------------------------------------------------------------------------ japan_map.gpkg: Map of land area of Japan. Raw data downloaded from Geospatial Information Authority of Japan under the Creative Commons Attribution License v4.0 (). All polygons were combined into a single polygon and CRS set to JGD2000 using code available at . Number of variables: 1 Number of cases/rows: 1 Variable list: - geom: Vector describing shape and position of land area polygon Missing data codes: No missing data. MD5 checksum: 8eb5006bb8cf550ae7ebaaabe9cc2705 ------------------------------------------------------------------------ japan_protected_areas.gpkg: Spatial of protected areas in Japan in GeoPackage format. Original spatial data downloaded from the Japan Ministry of the Environment () and Ministry of Land, Infrastructure, Transport and Tourism (). Categorization of protected areas generally followed Kusumoto et al. (2017): either "high" (no human activities allowed at all) or "medium" status (some economic activities allowed by permit); other areas not meeting these criteria or not including plants were not considered. Any overlapping areas within the same protection level were combined, and any areas overlapping between "medium" and "high" were considered only "high." Code used to categorize areas available at Number of variables: 2 Number of cases/rows: 2 Coordinate reference system: JGD2000 Variable list: - status: Protection status ('high' or 'medium') - geom: Vector describing shape and position of protected area polygon Missing data codes: No missing data. MD5 checksum: 8b2294626115e9d40fc957945b312674 ------------------------------------------------------------------------ testo_sundue_2016_calibrations.csv: Fossil calibration points used for phylogenetic dating analysis with treePL (Smith and O'Meara 2012), based on Testo and Sundue (2016). MRCA = "most recent common ancestor." Number of variables: 9 Number of cases/rows: 27 Variable list: - Clade: Name of clade - Stem_Crown: Type of node. 'crown' (node corresponding to MRCA of extant taxa only) or 'stem' (node corresponding to split between MRCA of extant taxa and its sister) - Fossil: Name of fossil - Age: Age of fossil - Age_type: Type of age. 'min' for minimum age, or 'fixed' for fixed age - Citation: Citation for the fossil - taxon_1: Name of first taxon that is used to identify MRCA - taxon_2: Name of second taxon that is used to identify MRCA - note: Notes, in particular explaining any differences with Testo and Sundue (2016) Missing data codes: No data entered between commas in CSV. MD5 checksum: 60a5bf932a5b9039b5caf61567d172d0 ------------------------------------------------------------------------ japan_ferns_biodiv.csv (contained in "results.zip"): Biodiversity statistics of native, non-hybrid ferns and environmental variables in Japan. Biodiversity metrics calculated as described in Nitta et al. 2022. Climatic (temperature and preciptation) variables calculated as described for japan_climate.gpkg. Includes three rows with missing data and one outlier for % apomixis that were removed prior to spatial modeling analysis. Number of variables: 28 Number of cases/rows: 1239 Variable list: - grids: Name of grid-cell - lat: Latitude of grid-cell centroid - long: Longitude of grid-cell centroid - abundance: Number of specimens occurring in grid-cell - richness: Number of taxa occurring in grid-cell - fd_obs_z: Z-score (standard effect size) of observed functional diversity (FD) - pd_obs_z: Z-score of observed phylogenetic diversity (PD) - pe_obs_z: Z-score of observed phylogenetic endemism (PE) - rfd_obs_z: Z-score of observed relative FD - rpd_obs_z: Z-score of observed relative PD - richness_obs_p_upper: Richness percentile - fd_obs_p_upper: FD percentile - pd_obs_p_upper: PD percentile - pe_obs_p_upper: PE percentile - pd_signif: Significance of PD compared to null distribution, two-sided test at alpha 0.05 - rpd_signif: Significance of RPD compared to null distribution, two-sided test at alpha 0.05 - fd_signif: Significance of FD compared to null distribution, two-sided test at alpha 0.05 - rfd_signif: Significance of RFD compared to null distribution, two-sided test at alpha 0.05 - pe_signif: Significance of PE compared to null distribution, two-sided test at alpha 0.05 - taxonomic_cluster: Membership in cluster based on taxonomic distances - phylo_cluster: Membership in cluster based on phylogenetic distances - endem_type: Endemism type determined by CANAPE - lat_area: Area of 1-degree latitudinal band around grid-cell - temp: Annual mean temperature, in units of degrees celsius * 10 - temp_season: Temperature seasonality - precip: Annual precipitation, measured in mm - precip_season: Precipitation seasonality - percent_apo: Percent apomictic taxa Missing data codes: No data entered between commas in CSV. MD5 checksum: 17428c0be8a75689b922e37ef645ab3a ------------------------------------------------------------------------ japan_ferns_comm.csv (contained in "results.zip"): Community matrix (species x sites matrix) of native, non-hybrid ferns in Japan used for biodiversity analysis. Same as japan_ferns_comm_full.csv, but grid-cells with redundancy <0.1 (indicating under-sampling) excluded. Number of variables: 673 Number of cases/rows: 1239 Variable list: - grids: Name of grid-cell. - Other columns: Each column is named for a Japanese fern taxon. Values indicate number of specimens that were observed in each grid-cell for that taxon. Missing data codes: No missing data. MD5 checksum: 8b725b25553121021806e987fbe1c8e1 ------------------------------------------------------------------------ japan_ferns_shape.gpkg (contained in "results.zip"): Location of grid-cells (sites) for native, non-hybrid ferns in Japan used for biodiversity analysis. Same as japan_ferns_shape_full.gpkg, but grid-cells with redundancy <0.1 (indicating under-sampling) excluded. Number of variables: 5 Number of cases/rows: 1239 Coordinate reference system: JGD2000 Variable list: - grids: Name of grid-cell - richness: Number of taxa occurring in grid-cell - abundance: Number of specimens occurring in grid-cell - redundancy: Redundancy (measure of sampling completeness) - geom: Vector describing shape and position of grid-cell Missing data codes: No missing data. MD5 checksum: 51fe654173b1cc916b6ec5279ce58094 ------------------------------------------------------------------------ japan_ferns_traits.csv (contained in "results.zip"): Trait matrix of native, non-hybrid ferns in Japan used for functional biodiversity analysis. Number of variables: 78 Number of cases/rows: 675 Variable list: 'taxon' indicates taxon name. Other columns correspond to traits. 'frond_width,' 'stipe_length,' 'number_pinna_pairs' are numeric; others are binary (0 or 1) Missing data codes: Missing data coded as 'NA.' MD5 checksum: 58cd40120c19b27bea373bdf51288e70 ------------------------------------------------------------------------ japan_ferns_tree.tre (contained in "results.zip"): Maximim-likelihood phylogeny of native, non-hybrid ferns in Japan in newick format inferred with maximum likelihood IQ-TREE v1.6.12 (Nguyen et al. 2015). Values at nodes are bootstrap support values calculated using 1000 replicates of ultrafast bootstrap (Nguyen et al. 2015). Number of tips: 663 Missing data codes: No missing data. MD5 checksum: 325a292834bdcbf21304dabab1e1c0ac ------------------------------------------------------------------------ japan_ferns_tree_dated_uncollapsed.tre (contained in "results.zip"): Maximim-likelihood, ultrametric (dated) phylogeny of native, non-hybrid ferns in Japan in newick format. Tree dated using treePL v1.0 (Smith and O'Meara 2012) with 26 fossil calibration points after Testo and Sundue (2016). Values at nodes are bootstrap support values calculated using 1000 replicates of ultrafast bootstrap (Nguyen et al. 2015). Clades consisting of identical OTUs not collapsed. Number of tips: 663 Missing data codes: No missing data. MD5 checksum: 036247fc001951541a0e1170d6291cab ------------------------------------------------------------------------ japan_ferns_tree_dated.tre (contained in "results.zip"): Maximim-likelihood, ultrametric (dated) phylogeny of native, non-hybrid ferns in Japan in newick format. Tree dated using treePL v1.0 (Smith and O'Meara 2012) with 26 fossil calibration points after Testo and Sundue (2016). Values at nodes are bootstrap support values calculated using 1000 replicates of ultrafast bootstrap (Nguyen et al. 2015). Clades consisting of identical sequences have been collapsed to polytomies with zero branch length between OTUs. Number of tips: 663 Missing data codes: No missing data. MD5 checksum: 4f62ad63f894d5702acb803a34db6143 ------------------------------------------------------------------------ CHANGE LOG 2022-03-11 - Use Mollweide projection for grid-cells - Don't include targets cache (move to ) - Fix spelling errors in README text - Fix missing '1:' in LUCID trait data example - Fix description of rows with missing data in japan_ferns_biodiv.csv - Automate generation of plain text file 2021-09-22 - Generate this README file. ------------------------------------------------------------------------ REFERENCES Ebihara, Atsushi, and Joel H. Nitta. 2019. "An Update and Reassessment of Fern and Lycophyte Diversity Data in the Japanese Archipelago." *Journal of Plant Research* 132 (6): 723--38. . Hsieh, T. C., K. H. Ma, and Anne Chao. 2016. "iNEXT: An R Package for Rarefaction and Extrapolation of Species Diversity (Hill Numbers)." *Methods in Ecology and Evolution* 7 (12): 1451--56. . Kusumoto, Buntarou, Takayuki Shiono, Masashi Konoshima, Atsushi Yoshimoto, Takayuki Tanaka, and Yasuhiro Kubota. 2017. "How Well Are Biodiversity Drivers Reflected in Protected Areas? A Representativeness Assessment of the Geohistorical Gradients That Shaped Endemic Flora in Japan." *Ecological Research* 32 (3): 299--311. . Nguyen, Lam-Tung, Heiko A. Schmidt, Arndt von Haeseler, and Bui Quang Minh. 2015. "IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies." *Molecular Biology and Evolution* 32 (1): 268--74. . Smith, Stephen A, and Brian C. O'Meara. 2012. "treePL: Divergence Time Estimation Using Penalized Likelihood for Large Phylogenies." *Bioinformatics* 28 (20): 2689--90. . Testo, Weston L., and Michael A Sundue. 2016. "A 4000-Species Dataset Provides New Insight into the Evolution of Ferns." *Molecular Phylogenetics and Evolution* 105: 200--211. .