DOI: 10.5061/dryad.bnzs7h477
title: Data from: A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica

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 &gt;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.
description: Surveys of pteridophytes (i.e., ferns and lycophytes) were
 carried out over three field seasons (January 2008, 2011, and 2013; 37
 days total) at the Nectandra Cloud Forest Reserve, Costa Rica. Most
 specimens were collected along trails through the reserve. Epiphytes were
 collected from fallen trees or tree branches, or up to 2 m on tree trunks.
 Permits for collection were obtained from the Costa Rican government
 (SINAC No. 04941 and Cites 2014-CR 1006/SJ (#S 1045)). The first set of
 voucher specimens was deposited at UC, with duplicates at CR, GH, and TI.
 Herbarium codes follow Thiers (2020). Leaf tissue was preserved on silica
 gel for DNA extraction. Spores of selected taxa were observed with a
 standard compound light microscope. DNA was extracted
 with the DNEasy plant mini kit following the manufacturer’s protocol
 (Qiagen). One species per taxon was sampled for morphologically distinct
 taxa, and up to five specimens per taxon for taxa that are more difficult
 to identify using standard keys and morphological characters. The plastid
 <em>rbcL</em> gene was amplified using PCR primers and
 thermocycler settings of Schuettpelz and Pryer (2007). PCR products were
 purified with Exo-STAR enzyme (GE Healthcare) and sequenced using the Big
 Dye Terminator v3.1 Cycle Sequencing Kit (ThermoFisher) with two internal
 primers, ESRBCL654R and ESRBCL628F (Schuettpelz and Pryer 2007) in
 addition to the amplification primers. The resulting AB1 trace files were
 imported into Geneious (Kearse et al. 2012), assembled into contigs, and
 the consensus sequences exported in FASTA format. A multi-sequence
 alignment was generated using MAFFT (Katoh et al. 2002), and a
 phylogenetic tree inferred using IQ-TREE with automatic model selection
 (Nguyen et al. 2015). For a small number of genera that were not supported
 as monophyletic in the original phylogenetic analysis (Cyathea and
 Lellingeria), all available <em>rbcL</em> sequences for
 closely related taxa (at the family or subfamily level, respectively) were
 downloaded from GenBank, aligned in combination with the newly generated
 sequences from Nectandra with MAFFT, and a phylogenetic tree inferred
 using FastTree on default settings (Price, Dehal, and Arkin 2009,
 2010). Molecular analysis was performed under permits
 R-CM-RN-001-2014-OT-CONAGEBIO and R-CM-RN-002-2017-OT-CONAGEBIO.
 For additional methodological details, see Nitta JH, Ebihara A,
 Smith AR (in press, PLOS ONE) For full list of
 references, see README.txt
description: Files included:<br> •    costa_rica_richness.csv: Data on
 species richness of pteridophytes in protected areas in Costa
 Rica.<br> •    cyatheaceae_rbcL.fasta: Aligned
 <em>rbcL</em> sequences of family Cyatheaceae from the
 Nectandra Cloud Forest Reserve, Costa Rica and all available sequences on
 GenBank in FASTA format.<br> •    cyatheaceae_rbcL.tre: Phylogenetic
 tree of family Cyatheaceae from the Nectandra Cloud Forest Reserve, Costa
 Rica and all available <em>rbcL</em> sequences on GenBank in
 Newick format.<br> •    grammitidoideae_rbcL.fasta: Aligned
 <em>rbcL</em> sequences of subfamily Grammitidoideae from the
 Nectandra Cloud Forest Reserve, Costa Rica and all available sequences on
 GenBank in FASTA format.<br> •    grammitidoideae_rbcL.tre:
 Phylogenetic tree of subfamily Grammitidoideae from the Nectandra Cloud
 Forest Reserve, Costa Rica and all available <em>rbcL</em>
 sequences on GenBank in Newick format.<br> •    JNG4254.fasta: DNA
 sequence in FASTA format of <em>rbcL</em> gene from
 <em>Amauropelta atrovirens </em>(C. Chr.) Salino &
 T.E. Almeida (<em>Nitta 2237</em>).<br> •  
  nectandra_gb_template.sbt: Plain text file (submit-block object)
 containing metadata related to GenBank submission.<br> •  
  nectandra_DNA_accessions.csv: DNA accession numbers and specimen
 accession numbers of pteridophytes from the Nectandra Cloud Forest
 Reserve, Costa Rica.<br> •    nectandra_rbcL.fasta: Newly generated
 <em>rbcL</em> sequences of pteridophytes from the Nectandra
 Cloud Forest Reserve, Costa Rica in FASTA format.<br> •  
  nectandra_rbcL.phy: Aligned <em>rbcL</em> sequences of
 pteridophytes from the Nectandra Cloud Forest Reserve, Costa Rica in
 PHYLIP format.<br> •    nectandra_rbcL.treefile: Phylogenetic tree
 of pteridophytes from the Nectandra Cloud Forest Reserve, Costa Rica in
 Newick format.<br> •    nectandra_specimens.csv: Specimen data of
 pteridophytes from the Nectandra Cloud Forest Reserve, Costa Rica
 collected by Joel Nitta.<br> •    ppgi_taxonomy.csv: Taxonomic
 system of Pteridophyte Phylogeny Group I (2016) for pteridophytes at the
 genus level and above.<br> •    seqids.txt: Newly assigned GenBank
 accession numbers for sequences generated by this project.
 For details, see README file.