The data included here are used in a pipeline that (mostly) automatically generates a maximally sampled fern phylogenetic tree based on plastid sequences in GenBank (https://github.com/fernphy/ftol).

The first step is to download the latest release of GenBank data from the NCBI GenBank FTP site (https://ftp.ncbi.nlm.nih.gov/genbank/) and use it to create a local database of fern sequences. This is done with custom R scripts contained in https://github.com/fernphy/ftol, in particular setup_gb.R (https://github.com/fernphy/ftol/blob/main/R/setup_gb.R).

Next, a set of reference FASTA files for 79 target loci (one per locus; ref_aln.tar.gz) is generated. These include 77 protein-coding genes based on a list of 83 genes (Wei et al. 2017) that was filtered to only genes that show no evidence of duplication, plus two spacer regions (trnL-trnF and rps4-trnS). Each FASTA file in ref_aln.tar.gz includes one representative (longest) sequence per avaialable fern genus. This is done with prep_ref_seqs_plan.R (https://github.com/fernphy/ftol/blob/main/prep_ref_seqs_plan.R).

Sequences matching the target loci are then extracted from each accession in the local database using the FASTA files contained in ref_aln.tar.gz as references with the “Reference_Blast_Extract.py” script of superCRUNCH (Portik and Wiens 2020).

The extracted sequences are aligned with MAFFT (Katoh et al. 2002), phylogenetic analysis is done using IQ-TREE (Nguyen et al. 2015) and divergence times estimated with treePL (Smith and O’Meara 2012).

For additional methodological details, see:

Nitta JH, Schuettpelz E, Ramírez-Barahona S, Iwasaki W. 2022. An open and continuously updated fern tree of life. Frontiers in Plant Sciences 13 https://doi.org/10.3389/fpls.2022.909768.

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...

GreenList is lists of names of Japanese wild plants primarily intended for use on the national Red List. The previous version of a list of ferns and lycophytes (FernGreenList ver. 1.01; Ebihara et al., 2017) is available as a part of supplementary data of the study by Ebihara & Nitta (2019) at https://doi.org/10.5061/dryad.4362p32.
Since the publication of the previous version six years ago, the number of species to be added to the list has gradually increased. In addition, accelerated publication activities of taxonomic revision in a global scale have resulted in changes to scientific names of Japanese species. Therefore, we compiled an updated version of the FernGreenList.

WorldFerns and WorldPlants are synonymic checklists of the vascular plants of the world (including ferns and lycophytes). The data set has been compiled – independently from other catalogues - over the last 40 years by starting from the basic data of the Kew Index and the Index Filicum. These names (initially over 1 million) have been subsequently cross-checked against local or regional floras, checklists, monographies and treatments. Large subsets of the database have been cross-checked by experts for certain groups. In the current status almost all names have been verified, and distribution data, newer checklists and/or floras are available for almost all countries and regions. Over the years, about 400,000 names have been added to the basic subset, leading to a total of 1,380,000 names for all families. Only a small subset (about 50,000 names) of mostly old, unverified and unassignable (“unplaced”) names have been deliberately omitted. Newly described taxa are added on a regular basis through data exchange with IPNI. Special attention is given to arranging the genera in correct phylogenetic sequence, by inclusion of the most important phylogenetic papers and monographies. The linear sequence of genera can be seen on the original website worldplants.de.

As of 2023, almost all countries and regions have recent checklists or floras of reasonable quality and completeness, and over 90 % of geographical distribution is probably known. Some remaining large gaps have been closed by the recent completion of checklists for Brazil and India. Remaining regions with some data deficiencies are parts of Malesia and Central Africa (the two Congos), and for some states of former Yugoslavia the distribution is not yet fully broken down.

WorldFerns is proud to be the main data source for the new Pteridophyte Phylogeny Group initiative “PPG-II”, starting 2023. Results from this continuing revision of the WorldFerns catalogue by almost 300 experts worldwide are subsequently back-integrated in the existing dataset and almost immediately available.

AbstractPremise of the study: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data. Methods: Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35877 bp), along with rigorous alignment, orthology inference and model selection. Key results: Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ∼200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data. Conclusions: Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies. Usage notesMrBayes_configAndResultsNexus datafile (alignment), MrBayes commands, and resulting parameter and tree log files.alignments_andTrees_v5Nexus files (alignments) for each locus, with their corresponding maximum likelihood tree.add_genbankNums_toVouchertablePython script to extract the genBank numbers from the list supplied by NCBI (in response to a sequin submission) and format them into an accession-by-locus table.add_node_numbers_to_treePython script to print a version of an input phylogeny with the nodes annotated with their node number. (So that, e.g., the nodes can be matched to their divergence time estimates, etc.)append_metadata_tofasta_forSequinA python script that goes through a single-locus alignment and matches each taxon in that alignment with the corresponding metadata, which it adds in a Sequin block to the alignment file. For automating the production of Sequin submission to GenBank in cases where there are many loci, each with different combinations of taxa.nexusToNewickPython script to convert a bunch of tree files from nexus to newick format.summarizing_supportR script to summarize support values across analyses. Computes average node support, does t- and z-tests to examine whether average support differs across analyses/whether support for particular nodes differs.

The goal of the FTOL project is to generate a maximally sampled phylogenetic tree for all extant fern species. It will be continuously updated as new data become available. Each release of the tree and associated metadata has a version number available on the project github repository (https://github.com/fernphy/ftol). The current data release includes GenBank accessions with allowed dates from 1980-01-01 to 2020-06-30.For more information, see README file.This repository only contains FTOL v0.0.1. For more recent versions, see https://fernphy.github.io/

This layer provides a transformation of environmental layer to best predict fern compositional turnover. Generalized Dissimilarity Modelling was used to produce a model of biotic composition in relationship to environment and biogeography. This model was used to transform and scale environmental layers to predict community composition. These transformed environmental layers can be used to predict commmunity composition changes, and to classify New Zealand into areas of similar biotic composition. The biotic data used for this model include all fern taxa from NVS recce data and estimated community compositions from pollen data.

The expansion of angiosperm-dominated forests in the Cretaceous and early Cenozoic had a profound effect on terrestrial biota by creating novel ecological niches. The majority of modern fern lineages are hypothesized to have arisen in response to this expansion, particularly fern epiphytes that radiated into the canopy. Recent evidence, however, suggests that epiphytism does not correlate with increased diversification rates in ferns, calling into question the role of the canopy habitat in fern evolution. To understand the role of the canopy in structuring fern community diversity, we investigated functional traits of fern sporophytes and gametophytes across a broad phylogenetic sampling on the island of Moorea, French Polynesia, including > 120 species and representatives of multiple epiphytic radiations. While epiphytes showed convergence in small size and a higher frequency of non-cordate gametophytes, they showed greater functional diversity at the community level relative...

One of the two data files contains occurrence and abundance information for Adiantum and Lindsaea fern species in 1215 sampling units distributed across Amazonia. The other data file contains metadata and soil base cation concentration values. Explanations of the data columns are in the README.txt file.

A fern survey was done of the plots established by under MRCE funding to assess controls on primary productivity along an elevational gradient. The control plots (CP), fertilized plots (FP) and plots where only leaf litter (ll) was removed at El Verde were survey and all ferns present in the plots listed, mapped and measured in Fall of 1995, several years after the initial fertilization and leaf litter treatment had been applied. The objective was to determine the extent to which the fern flora had been affected by the treatments.

This database is supplementary material of the article "Diversity of ferns and lycophytes in Brazil" published in the Journal Rodriguésia in 2015 (DOI: 10.1590 / 2175-7860201566410).

Premise of the study: Relationships of leaf size and shape (physiognomy) with climate have been well characterized for woody non-monocotyledonous angiosperms (dicots), allowing the development of models for estimating paleoclimate from fossil leaves. More recently, petiole width of seed plants has been shown to scale closely with leaf mass. By measuring petiole width and leaf area in fossils, leaf mass per area (MA) can be estimated and an approximate leaf life span inferred. However, little is known about these relationships in ferns, a clade with a deep fossil record and with the potential to greatly expand the applicability of these proxies. Methods: We measured the petiole width, MA, and leaf physiognomic characters of 179 fern species from 188 locations across six continents. We applied biomechanical models and assessed the relationship between leaf physiognomy and climate using correlational approaches. Key results: The scaling relationship between area-normalized petiole width and MA differs between fern fronds and pinnae. The scaling relationship is best modeled as an end-loaded cantilevered beam, which is different from the best-fit biomechanical model for seed plants. Fern leaf physiognomy is not influenced by climatic conditions. Conclusions: The cantilever beam model can be applied to fossil ferns. The lack of sensitivity of leaf physiognomy to climate in ferns argues against their use to reconstruct paleoclimate. Differences in climate sensitivity and biomechanical relationships between ferns and seed plants may be driven by differences in their hydraulic conductivity and/or their differing evolutionary histories of vein architecture and leaf morphology.

Usage Notes Leaf mass, leaf area, petiole width, and leaf physiognomic measurements of globally distributed ferns (Appendices S1a, S1b)Peppe et al_Appendices.xlsxFern images from Baylor University HerbariumZipped folder with images of ferns from Baylor Herbarium. Folder also includes ReadMe file and image key.Baylor ferns.zipFern images from Queensland HerbariumZipped folder with images of ferns from Queensland Herbarium. Folder also includes ReadMe file and image key.Queensland ferns.zipFern images from Te Papa HerbariumZipped folder with images of ferns from Te Papa Herbarium at the Museum of New Zealand Te Papa Tongarewa. Folder also includes ReadMe file and image key.Te Papa ferns (2).zipFern images from US National Herbarium (part 1)Zipped folder with images of ferns from USNH. Folder also includes ReadMe file and image key.USNH ferns_1.zipFern images from US National Herbarium (part 2)Zipped folder with images of ferns from USNH. Folder also includes ReadMe file and image key.USNH ferns_2.zipFern images from Waikato HerbariumZipped folder with images of ferns from Waikato Herbarium. Folder also includes ReadMe file and image key.Waikato ferns.zip

A list of native, non-hybrid fern specimens mostly 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 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 (http://www.rdplants.org/gl/; English version available at https://datadryad.org/stash/dataset/doi:10.5061/dryad.4362p32).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 (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 https://github.com/joelnitta/japan_ferns_spatial_phy, in particular https://github.com/joelnitta/japan_ferns_spatial_phy/blob/main/R/process_raw_data.R.For full methods, see Nitta JH, Mishler BD, Iwasaki W, Ebihara A (2021) Spatial phylogenetics of Japanese ferns: Patterns, processes, and implications for conservation https://doi.org/10.1101/2021.08.26.457744

Research on fern ecology has gained attention in the last decade, yet there is a paucity of information on the comparison of ferns communities across continents. This study focused on comparing the ferns community assemblages in some tropical forests of Malaysia and Nigeria, thereby assessing the patterns of species richness (SR) and phylogenetic diversity(PD) in relation to the bioclimatic drivers across the continents. The diversity and taxonomic compositions of ferns were assessed using 180 plots of 10 m x 10 m in each country. The species richness and other diversity indices were determined using the combined forests data for each country and for the individual forests. Also, the phylogenetic diversity of the ferns was assessed using the genus-based molecular sequences downloaded from the GeneBank. The patterns of the ferns SR and PD in the two countries as driven by some bioclimatic factors were evaluated using the regression analysis. The observed and rarefied–extrapolated fern sp...

Ferns, with about 12,000 species, are the second most diverse lineage of vascular plants after angiosperms. They have been the subject of numerous molecular phylogenetic studies, resulting in the publication of trees for every major clade and DNA sequences from nearly half of all species. Global fern phylogenies have been published periodically, but as molecular systematics research continues at a rapid pace, these become quickly outdated. Here, we develop a mostly automated, reproducible, open pipeline to generate a continuously updated fern tree of life (FTOL) from DNA sequence data available in GenBank. Our tailored sampling strategy combines whole plastomes (few taxa, many loci) with commonly sequenced plastid regions (many taxa, few loci) to obtain a global, species-level fern phylogeny with high resolution along the backbone and maximal sampling across the tips. We use a curated reference taxonomy to resolve synonyms in general compliance with the community-driven Pteridophyte Phylogeny Group I classification. The current FTOL includes 5,582 species, an increase of ca. 40% relative to the most recently published global fern phylogeny. Using an updated and expanded list of 51 fern fossil constraints, we find estimated ages for most families and deeper clades to be considerably older than earlier studies. FTOL and its accompanying datasets, including the fossil list and taxonomic database, will be updated on a regular basis and are available via a web portal (https://fernphy.github.io) and R packages, enabling immediate access to the most up-to-date, comprehensively sampled fern phylogeny. FTOL will be useful for anyone studying this important group of plants over a wide range of taxonomic scales, from smaller clades to the entire tree. We anticipate FTOL will be particularly relevant for macroecological studies at regional to global scales and will inform future taxonomic systems with the most recent hypothesis of fern phylogeny.

This dataset provides information about the number of properties, residents, and average property values for Fern Way cross streets in Nehalem, OR.

MrBayes_configAndResultsNexus datafile (alignment), MrBayes commands, and resulting parameter and tree log files.alignments_andTrees_v5Nexus files (alignments) for each locus, with their corresponding maximum likelihood tree.add_genbankNums_toVouchertablePython script to extract the genBank numbers from the list supplied by NCBI (in response to a sequin submission) and format them into an accession-by-locus table.add_node_numbers_to_treePython script to print a version of an input phylogeny with the nodes annotated with their node number. (So that, e.g., the nodes can be matched to their divergence time estimates, etc.)append_metadata_tofasta_forSequinA python script that goes through a single-locus alignment and matches each taxon in that alignment with the corresponding metadata, which it adds in a Sequin block to the alignment file. For automating the production of Sequin submission to GenBank in cases where there are many loci, each with different combinations of taxa.nexusToNewickP...

About this dataset

Context

The dataset tabulates the data for the Fern, Wisconsin population pyramid, which represents the Fern town population distribution across age and gender, using estimates from the U.S. Census Bureau American Community Survey (ACS) 2019-2023 5-Year Estimates. It lists the male and female population for each age group, along with the total population for those age groups. Higher numbers at the bottom of the table suggest population growth, whereas higher numbers at the top indicate declining birth rates. Furthermore, the dataset can be utilized to understand the youth dependency ratio, old-age dependency ratio, total dependency ratio, and potential support ratio.

Key observations

• Youth dependency ratio, which is the number of children aged 0-14 per 100 persons aged 15-64, for Fern, Wisconsin, is 22.2.
• Old-age dependency ratio, which is the number of persons aged 65 or over per 100 persons aged 15-64, for Fern, Wisconsin, is 140.3.
• Total dependency ratio for Fern, Wisconsin is 162.5.
• Potential support ratio, which is the number of youth (working age population) per elderly, for Fern, Wisconsin is 0.7.

Content

When available, the data consists of estimates from the U.S. Census Bureau American Community Survey (ACS) 2019-2023 5-Year Estimates.

Age groups:

• Under 5 years
• 5 to 9 years
• 10 to 14 years
• 15 to 19 years
• 20 to 24 years
• 25 to 29 years
• 30 to 34 years
• 35 to 39 years
• 40 to 44 years
• 45 to 49 years
• 50 to 54 years
• 55 to 59 years
• 60 to 64 years
• 65 to 69 years
• 70 to 74 years
• 75 to 79 years
• 80 to 84 years
• 85 years and over

Variables / Data Columns

• Age Group: This column displays the age group for the Fern town population analysis. Total expected values are 18 and are define above in the age groups section.
• Population (Male): The male population in the Fern town for the selected age group is shown in the following column.
• Population (Female): The female population in the Fern town for the selected age group is shown in the following column.
• Total Population: The total population of the Fern town for the selected age group is shown in the following column.

Good to know

Margin of Error

Data in the dataset are based on the estimates and are subject to sampling variability and thus a margin of error. Neilsberg Research recommends using caution when presening these estimates in your research.

Custom data

If you do need custom data for any of your research project, report or presentation, you can contact our research staff at research@neilsberg.com for a feasibility of a custom tabulation on a fee-for-service basis.

Inspiration

Neilsberg Research Team curates, analyze and publishes demographics and economic data from a variety of public and proprietary sources, each of which often includes multiple surveys and programs. The large majority of Neilsberg Research aggregated datasets and insights is made available for free download at https://www.neilsberg.com/research/.

Recommended for further research

This dataset is a part of the main dataset for Fern town Population by Age. You can refer the same here

No description is available. Visit https://dataone.org/datasets/farshid25.45.1 for complete metadata about this dataset.

This dataset provides information about the number of properties, residents, and average property values for Dancing Fern cross streets in Sequatchie, TN.