README_data.txt

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
<joelnitta@gmail.com>

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

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SHARING/ACCESS INFORMATION

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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:
<https://github.com/joelnitta/japan_ferns_spatial_phy>

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DATA & FILE OVERVIEW

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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
    <https://datadryad.org/stash/dataset/doi:10.5061/dryad.4362p32>. 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 <https://figshare.com/s/87b8ec102303bf9f3212>. MD5 checksum
    26b95c283eec6529c71b252a47d3a06c FIXME: replace with DOI when
    available

Checksums are 32-byte MD5 hashes generated with tools::md5sum() in R.

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METHODOLOGICAL INFORMATION

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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
(<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 (FTOL v0.0.1; Nitta et al., in
prep.; <https://github.com/fernphy/ftol/>). 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 (2022)
Spatial phylogenetics of Japanese ferns: Patterns, processes, and
implications for conservation. American Journal of Botany. FIXME: add
DOI, page numbers when available

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DATA-SPECIFIC INFORMATION

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japan_deer_range.gpkg: Distribution maps of Japanese deer (Cervus
nippon) in Japan. Raw data were downloaded from the Japan Ministry of
the Environment
(<https://www.biodic.go.jp/biodiversity/activity/policy/map/map14/index.html>).
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

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japan_climate.gpkg: Climate data in Japan downloaded from WorldClim
database (<https://worldclim.org/data/v1.4/formats.html>). 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

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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

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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
(<http://www.biodic.go.jp/trialSystem/EN/shpddl.html>)

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

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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

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japan_ferns_traits_lucid.csv: Morphological trait data of native,
non-hybrid ferns in Japan, originally formatted for Lucid dichotomous
key software (<https://www.lucidcentral.org/>). For more information on
codes used for scoring of traits, see
<https://help.lucidcentral.org/lucid/scoring-the-key/>

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

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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
<https://github.com/joelnitta/japan_ferns_spatial_phy/blob/main/R/geocode.R>

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

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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
(<https://www.gsi.go.jp/kankyochiri/gm_japan_e.html>). All polygons were
combined into a single polygon and CRS set to JGD2000 using code
available at
<https://github.com/joelnitta/japan_ferns_spatial_phy/blob/main/R/process_raw_data.R>.

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

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japan_protected_areas.gpkg: Spatial of protected areas in Japan in
GeoPackage format. Original spatial data downloaded from the Japan
Ministry of the Environment
(<https://www.biodic.go.jp/biodiversity/activity/policy/map/map17/index.html>)
and Ministry of Land, Infrastructure, Transport and Tourism
(<https://nlftp.mlit.go.jp/ksj/gml/datalist/KsjTmplt-A45.html>).
Categorization of protected areas generally followed
(**Kusumoto2017?**): 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
<https://github.com/joelnitta/japan_ferns_spatial_phy/blob/main/R/process_raw_data.R>

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

------------------------------------------------------------------------

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.
<https://doi.org/10.1007/s10265-019-01137-3>.

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.
<https://doi.org/gdskcx>.

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. <https://doi.org/10.1093/molbev/msu300>.

Smith, Stephen A, and Brian C. O'Meara. 2012. "treePL: Divergence Time
Estimation Using Penalized Likelihood for Large Phylogenies."
*Bioinformatics* 28 (20): 2689--90.
<https://doi.org/10.1093/bioinformatics/bts492>.

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.
<https://doi.org/10.1016/j.ympev.2016.09.003>.