DOI: 10.5061/dryad.4362p32
title: Data from: An update and reassessment of fern and lycophyte diversity data in the Japanese Archipelago

description: The fern and lycophyte flora of Japan comprising 721 native taxa
 (including subspecies and varieties) plus 371 interspecific hybrids was
 reassessed using a nearly comprehensively sampled distribution map at
 10 km resolution vouchered by 216,687 specimens, up-to-date
 cytotaxonomic information covering 74% of the taxa, and an rbcL sequence
 dataset covering 97.9% of the taxa. Spatial distribution of
 species richness and phylogenetic diversity was visualized.
 Apomixis was observed in 11.0% of the native taxa whose reproductive modes
 are known. The number of sexually reproducing polyploid taxa (n = 199) is
 less than sexual diploids (n = 241), and 30 of them are evidently
 allopolyploid, in contrast with the low number of possible autopolyploids
 (n = 4). Apomictic taxa were found to have smaller latitudinal ranges than
 sexual taxa or taxa with multiple reproductive modes. A
 morphological character dataset in Lucid format is provided for taxonomic
 identification of the native taxa.
description: 2_grid_cells_all.csv: List of 10 km x 10 km grid-cells for Japan ("secondary grid-cells"). ESM1. A list of native fern and lycophyte taxa (species, subspecies and varieties; 721 taxa total) in Japan accepted in this study: Taxon ID refers to that in FernGreenList ver.1.0.1 (http://www.rdplants.org/gl/). Unless otherwise noted, rbcL GenBank accession numbers are those used in Ebihara et al. (2010). Asterisks after accession numbers indicate newly generated sequences by this study. Voucher information only provided for newly generated sequences. Information on reproductive modes, ploidy levels and leaf seasonality follow those in Ebihara et al. (2016, 2017), and only records based on material collected in Japan are used. For reproductive mode, irregular meiosis is not considered, 0 = no information, 1 = sexual, 2 = apomictic and 3 = sexual + apomictic. ESM1.csv ESM2. A list of fern and lycophyte herbarium specimens from Japan used to generate the 10 km grid cell distribution maps in Ebihara et al. (2016, 2017): A single specimen is cited per taxon per grid cell for all native taxa including species, subspecies, varieties, and hybrids (1090 taxa total). A small number of corrections on identification and location after publication of Ebihara et al. (2016, 2017) were applied, but new findings (e.g., new species and new records) made during the same period are not reflected. Taxon ID refers to that in FernGreenList ver. 1.0.1 (http://www.rdplants.org/gl/). Secondary grid code refers to “Basic Grid Square Codes” defined by the statistics Bureau of Japan (http://www.stat.go.jp/english/data/mesh/05.html). Grid cells at the secondary partition level (ca. 100 km2) are used, and coordinates of their center points are listed. Herbarium acronyms follow Index Herbariorum (http://sweetgum.nybg.org/science/ih/) but the following abbreviations are used for those not listed in Index Herbariorum; Gifu: Gifu Prefectural Museum; Gunma: Gunma Museum of Natural History; Iwate: Iwate Prefectural Museum; Kobe: Kobe University; Kurashiki: Kurashiki Museum of Natural History; Miyajima: Miyajima Natural Botanical Garden, Hiroshima University, Niigata: Niigata University; Sendai City Wild Plants Garden; Tochigi: Tochigi Prefectural Museum; Yamaguchi: Yamaguchi Prefectural Museum; Yokohama; Yokohama City Children’s Botanical Garden; Yokosuka: Yokosuka City Museum. All the listed specimens were seen by the authors except for a part of Isoëtes specimens which are cited from Takamiya et al. (1997). ESM2.csv ESM3. JpFernKeys ver. 1.0: An interactive key file for identification of all the native fern and lycophyte taxa (species, subspecies and varieties) in Japan plus a few common naturalized species for the software Lucid v3.3 (free edition) available at http://www.lucidcentral.com The data are excerpts from matrices of morphological characters included in Ebihara (2016, 2017). Measurements are based on ten fertile herbarium specimens per taxon collected in Japan which were selected randomly with a few exceptions for taxa bearing large fronds (e.g., tree ferns). For some rare taxa with less than ten specimens available, those collected outside Japan were used. ESM3.zip FernGreenListV1.01E.xls: List of Japanese ferns and lycophytes species including<br> scientific name, endemic status, conservation status, and other taxonomic data (English version).<br> Originally downloaded from http://www.rdplants.org/gl/FernGreenListV1.01.xls on 2019-07-17. japan_pterido_rbcl_cipres.zip: Output of Bayesian analysis of Japanese pteridophyte<br> rbcL data matrix (rbcl_mrbayes.nex) using MrBayes v 3.2.6 downloaded from the CIPRES cluster. Contains<br> the following files:<br>     - infile.nex: Input NEXUS file used for analysis (same as rbcl_mrbayes.nex)<br>     - infile.nex.con.tre: Consensus tree. Tip names same as accession names in JpFern_rbcl.txt.<br>     - infile.nex.mcmc: Mcmc run diagnostics<br>     - infile.nex.parts: Specification of clades or splits<br>     - infile.nex.run1.p: Parameter samples<br>     - infile.nex.run2.p: Parameter samples<br>     - infile.nex.run1.t: Tree samples<br>     - infile.nex.run2.t: Tree samples<br>     - infile.nex.trprobs: Sampled trees and their probabilities<br>     - infile.nex.tstat: Tree statistics<br>     - infile.nex.vstat: Branch length statistics<br>     - paramfile.txt: Parameters used by CIPRES<br>     - stdout.txt STDOUT: written by CIPRES during run JpFern_rbcl.txt: DNA alignment of the plastid rbcL gene in PHYLIP format of Japanese ferns and lycophytes<br> (706 taxa, 1205 sites). Alignment constructed using MAFFT. ppgi_taxonomy.csv: Pteridophyte Phylogeny I working group taxonomic system for pteridophytes at the genus<br> level and above (Pteridophyte Phylogeny Group I, 2016). rbcl_mrbayes.nex: NEXUS file used for phylogenetic analysis of Japanese fern<br> and lycophyte taxa with MrBayes.