Data from: A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica
Authors/Creators
- 1. University of Tokyo
- 2. National Museum of Nature and Science
- 3. University of California, Berkeley
Description
Floristic surveys are crucial to the conservation of biodiversity, but the vast majority of such surveys are limited to listing species names, and few take into account the evolutionary history of species. Here, we combine classical taxonomic and molecular phylogenetic (DNA barcoding) approaches to catalog the biodiversity of pteridophytes (ferns and lycophytes) of the Nectandra Cloud Forest Reserve, Costa Rica. Surveys were carried out over three field seasons (2008, 2011, and 2013), resulting in 176 species representing 69 genera and 22 families of pteridophytes. Our literature survey of protected areas in Costa Rica shows that Nectandra has an exceptionally diverse pteridophyte flora for its size. Plastid rbcL was selected as a DNA barcode marker and obtained for >95% of pteridophyte taxa at this site. Combined molecular and morphological analyses revealed two previously undescribed taxa that appear to be of hybrid origin. The utility of rbcL for species identification was assessed by calculating minimum interspecific distances and found to have a failure rate of 18%. Finally we compared the distribution of minimum interspecific rbcL distances with two other areas that have been the focus of pteridophyte molecular surveys: Japan and Tahiti. The comparison shows that Nectandra is more similar to Japan than Tahiti, which may reflect the biogeographic history of these floras.
Notes
Files included:
• costa_rica_richness.csv: Data on species richness of pteridophytes in protected areas in Costa Rica.
• cyatheaceae_rbcL.fasta: Aligned rbcL sequences of family Cyatheaceae from the Nectandra Cloud Forest Reserve, Costa Rica and all available sequences on GenBank in FASTA format.
• cyatheaceae_rbcL.tre: Phylogenetic tree of family Cyatheaceae from the Nectandra Cloud Forest Reserve, Costa Rica and all available rbcL sequences on GenBank in Newick format.
• grammitidoideae_rbcL.fasta: Aligned rbcL sequences of subfamily Grammitidoideae from the Nectandra Cloud Forest Reserve, Costa Rica and all available sequences on GenBank in FASTA format.
• grammitidoideae_rbcL.tre: Phylogenetic tree of subfamily Grammitidoideae from the Nectandra Cloud Forest Reserve, Costa Rica and all available rbcL sequences on GenBank in Newick format.
• JNG4254.fasta: DNA sequence in FASTA format of rbcL gene from Amauropelta atrovirens (C. Chr.) Salino & T.E. Almeida (Nitta 2237).
• nectandra_gb_template.sbt: Plain text file (submit-block object) containing metadata related to GenBank submission.
• nectandra_DNA_accessions.csv: DNA accession numbers and specimen accession numbers of pteridophytes from the Nectandra Cloud Forest Reserve, Costa Rica.
• nectandra_rbcL.fasta: Newly generated rbcL sequences of pteridophytes from the Nectandra Cloud Forest Reserve, Costa Rica in FASTA format.
• nectandra_rbcL.phy: Aligned rbcL sequences of pteridophytes from the Nectandra Cloud Forest Reserve, Costa Rica in PHYLIP format.
• nectandra_rbcL.treefile: Phylogenetic tree of pteridophytes from the Nectandra Cloud Forest Reserve, Costa Rica in Newick format.
• nectandra_specimens.csv: Specimen data of pteridophytes from the Nectandra Cloud Forest Reserve, Costa Rica collected by Joel Nitta.
• ppgi_taxonomy.csv: Taxonomic system of Pteridophyte Phylogeny Group I (2016) for pteridophytes at the genus level and above.
• seqids.txt: Newly assigned GenBank accession numbers for sequences generated by this project.
For details, see README file.
Funding provided by: Japan Society for the Promotion of Science
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001691
Award Number: 15K07204
Funding provided by: Nectandra Institute*
Crossref Funder Registry ID:
Award Number:
Funding provided by: Alan R. Smith Fern Research and Curation Fund*
Crossref Funder Registry ID:
Award Number:
Funding provided by: Nectandra Institute
Crossref Funder Registry ID:
Funding provided by: Alan R. Smith Fern Research and Curation Fund
Crossref Funder Registry ID:
Files
costa_rica_richness.csv
Files
(2.2 MB)
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Additional details
Related works
- Is supplemented by
- 10.5061/dryad.df59g (DOI)
- 10.5061/dryad.4362p32 (DOI)