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.

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.

Three datasets: species_abundance_data, species_traits, and environmental_data. The three datasets were collected in the Fortuna Forest Reserve (8°45′ N, 82°15′ W) and Palo Seco Protected Forest (8°45′ N, 82°13′ W) located in western Panama. The two reserves support humid to super-humid rainforests, according to Holdridge (1947). The species_abundance_data and species_traits datasets were collected across 15 subplots of 25 m2 in 12 one-hectare permanent plots distributed across the two reserves. The subplots were spaced 20 m apart along three 5 m wide transects, each 30 m apart. Please read Prada et al. (2017) for details on the environmental characteristics of the study area. Prada CM, Morris A, Andersen KM, et al (2017) Soils and rainfall drive landscape-scale changes in the diversity and functional composition of tree communities in a premontane tropical forest. J Veg Sci 28:859–870. https://doi.org/10.1111/jvs.12540

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...

Modern ferns diversified simultaneously with the rise of angiosperms. This pattern is arguably the consequence of ecological opportunities presented by shady and moist habitats that emerged with the advent of angiosperm dominated habitats. This hypothesis was tested by applying phylogenetic comparative methods that investigated the role of shaded habitats in fern diversification across 1397 fern species from 37 families. Our results showed a significant positive correlation between the occupancy of shaded habitats and diversification rates across the phylogeny of ferns compared to those of open habitats with high sunlight. Tests evaluating false correlations using hidden state speciation and extinction corroborated this result. Since the onset of the Angiosperm Terrestrial Revolution, the diversification rates of shade-dwelling ferns has exceeded those of sun-dwelling ferns. Synthesis: Our findings support the hypothesis that shaded habitats created by the flourishing of angio..., , , # Shaded habitats have higher rates of fern diversification

https://doi.org/10.5061/dryad.qz612jmr7

Description of the data and file structure

The data included phylogenetic trees at both the species level (all_5582.tre) and family level (family_37.tre), light habitat data (sp_1397.csv), epiphytic habitat data (sp_4078.csv), species containing both light and epiphytic information (sp_1339.csv), BAMM analysis output for all fern species (event_data_2.5_5582.txt), and the corresponding R script (codes.txt).

Files and variables

File: data_ferns.zip

Description: All of our data and code are included in the zip file. The details are as follows:

• all_5582.tre: Phylogenetic tree of 5,582 fern species, constructed by Nitta et al. (2022).
• family_37.tre: Phylogenetic tree of 37 families used in our study for PGLS analysis.
• family_37.csv: Diversification rates estimated using both stem and crown ages, ...

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 dataset supports an investigation into the temporal dynamics of speciation and dispersal in ferns (Polypodiopsida) across the American tropics. It includes 378,115 georeferenced occurrence records compiled from GBIF, cleaned and taxonomically standardised using the 'CoordinateCleaner' and 'taxastand' R packages. Species were matched to a time-calibrated phylogenetic tree comprising 5850 fern species, from which 56 clades predominantly distributed in the American tropics were retrieved. These clades encompass 1530 species coded for presence/absence across nine biogeographically defined regions and a global category. Using biogeographical stochastic mapping (BSM) in BioGeoBEARS, we estimated the frequency and type of biogeographic events (e.g., dispersal, extinction, speciation) across 1-million-year time slices. The dataset also includes lineage-through-time (LTT) counts, regional species pool compositions at four time points (0, 5, 10, and 30 Ma), and pairwise compositional similar...

Ferns, as a large and biodiverse group, significantly contribute to the vascular plant diversity of the lowland tropical forests of Brunei Darussalam, Borneo. These forests encompass three main types: Mixed Dipterocarp Forest (MDF), Peat Swamp Forest (PSF), and Heath Forest (HF). This study aims to describe and compare fern communities in these three forest types, focusing on species richness, diversity, and the identification of indicator species. Additionally, it investigates the environmental factors that shape these communities. We conducted fieldwork in 48 plots across Brunei's lowland forests. We identified fern species and abundance through a visual census and analyzed environmental parameters, including soil pH, organic matter (OM) content, nutrient availability, and soil texture. The results showed 83 fern species, with MDF having the most (57 species). Peat Swamp and HFs had similar fern species richness (33 and 34 species, respectively). Our environmental analy..., , # Dryad dataset

Dataset DOI: 10.5061/dryad.0k6djhbd3

Description of the data and file structure

The data were collected as part of a field study on fern communities in lowland tropical forests of Brunei Darussalam, Borneo. The aim of the study was to assess fern species diversity, identify potential indicator species, and investigate how environmental factors and forest types influence community composition. Fieldwork was conducted across 48 plots representing three different forest types, where all fern individuals were recorded, identified, and assigned to life form categories. In each plot, a set of environmental variables was also measured to evaluate species–environment relationships.

Files and variables

File: 01_Species_abundance_plots.csv

Description:
This file contains fern species composition and abundance data from 48 forest plots. Each row corresponds to a fern species, while each column represents a plot. Values indica...,

Ferns evolved from 400 million years ago show various functional traits and ecological strategies in extant species, and over 80% of them belong to the youngest order Polypodiales. How the functional traits and strategies of ferns have changed during their evolutionary history remains unexplored. Here, we measured functional traits that sensitive to environmental light and water availability of 345 fern species across the fern phylogeny, and reconstructed their evolutionary histories. We found that ferns, mainly Polypodiales, have developed diversified functional traits in response to forest environments. Terrestrial species, especially Thelypteridaceae and Athyriaceae in eupolypods II, showed decreased leaf mass per area (LMA) and area-based leaf nitrogen (Narea) but increased mass-based leaf nitrogen (Nmass) than early-derived polypods since the late Jurassic. Epiphytic species, mainly those in Polypodiaceae, showed reductions in Nmass and individual leaf area (Area) since the late Cr...

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.

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

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

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...

This dataset provides information on the exact day and site where spores of 121 taxa of ferns and lycopos were collected for the Index Seminum (seed exchange catalogue) of the Botanic Garden of the University of Coimbra, between 1926 and 2013. Spores were collected from spontaneous and cultivated individuals across Portugal, including both native and introduced taxa. The database consists of 3,383 curated records with information on the species, or infraspecific taxa (including authority), and the day and site where spores were collected. All records are georeferenced and provided with a confidence interval for the collection site.

Ferns originated about 360 million years ago is the sister group of seed plants. Despite remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidences and different morphological interpretations, relationships among major fern lineages remain controversial.

With the aim to obtain a robust fern phylogeny, we carried large scale phylogenomic analysis using high-quality transcriptome sequencing data which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotides and amino acids sequences in species tree estimation. Among the mainly consistent and strongly supported cladograms, coalescent-based method using nucleotides sequence yielded the most robust cladogram.

Our result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships new to the current view of fern phylogeny, including that Psilotaceae and Ophioglossaceae form a monophyletic clade which is sister to Marattiaceae; Gleicheniaceae and Hymenophyllaceae form a monophyletic clade which is sister to Dipteridaceae; and that Aspleniaceae is sister to the rest groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangia annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants.

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...

Thirteen fern species are reported for the first time for Brazil. Among the new records, eight are from Acre state (Cyathea subincisa, Cyclodium trianae, Elaphoglossum stenophyllum, Hypoderris brauniana, Pleopeltis stolzei, Thelypteris arcana, Thelypteris comosa, Thelypteris valdepilosa), two are from Pará state (Polypodium flagellare, Tectaria heracleifolia), one from Minas Gerais state (Alsophila salvinii), one from Ceará state (Campyloneurum costatum) and one from Bahia state (Thelypteris rolandii). Part of the species shows a disjunct occurrence or illustrates floristic relations between Brazilian and Andean Mountains or Central American Mountains.

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.

Fern (Pteridophyta) specimens deposited in Toyama Science Museum

Cold tolerance strategies in plants vary from structural to biochemical. Many temperate tree fern taxa are marcescent—retaining whorls of dead fronds encircling the upper trunk—or develop short or prostrate trunks possibly to insulate against cold temperatures that might detrimentally affect their trunks and growing crowns. We asked the following questions: (1) do global growth patterns traits of temperate taxa relate to environmental factors associated with latitude (a proxy for seasonality and frost tolerance) and elevation (a proxy for temperature), (2) do growth patterns of tree ferns in New Zealand vary along a temperature related gradient, and (3) do marcescent tree fern skirts insulate the growing crown from sub-zero temperatures? We review the global and regional distributions of these structural and morphological traits within Cyatheales. Further, we assess the patterns of tree fern marcescence, and other traits potentially associated with cold tolerance (no trunk, prostrate, s..., Global distribution of growth forms We reviewed the descriptive literature on tree ferns to identify, where possible (skirts are not a frequently described trait), the global proportion and distribution of tree ferns with marcescent skirts and/or prostrate taxa. We conducted a literature search using the Google Scholar (https://scholar.google.com), Scopus (www.scopus.com) and ISI Web of Science (www.isiknowledge.com) databases with the search terms [“tree fern†OR “tree-fern†OR "treefern"] and [“skirt*†OR “collar†OR “marcescen* OR “attached necromass†OR “prostrate†]. To identify taxa from America we also used Google Scholar to search in Spanish and Portuguese using ["helecho* aborescente†, OR “helecho* arbóreos†AND “falda†] and [“samabaia†AND “saia†]. Finally we checked for the presence of skirts as a recorded trait in the Botanical Information and Ecology Network (BIEN; https://bien.nceas.ucsb.edu/bien/biendata/) database. The geographic distribution and elevation data of all ext..., , # Marcescence and prostrate growth in tree ferns are adaptations to cold tolerance

https://doi.org/10.5061/dryad.tx95x6b7f

Description of the data and file structure

The treefern_skirts.zip file contains an RStudio project with all the data and code required to reproduce our analyses. Open the treefern_skirts.rproj file and ensure that you have the required packages/versions.

Files and variables

File: treefern_skirts.zip

Description:Â

The ./data/ folder contains all data for the project.

The ./data/global.csv contains the dataset put together for the global review of treefern growth forms, alongside temp.csv which has all of the GBIF records of treefern occurrences globally. We could not supply these data, as they are protected by CC, and so requires direct download from GBIF. Initially, we reviewed the descriptive literature on tree ferns to identify, where possible (skirts are not a frequently described trait),...