Pradopteris, a new genus of neotropical ferns (Dryopteridaceae)
Data files
Mar 18, 2026 version files 336.16 KB
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Alignments.zip
333.60 KB
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README.md
2.56 KB
Abstract
Pradopteris, a new genus of dryopteroid fern, is described based on evidence from phylogeny and morphology. The genus is entirely Neotropical and closely related to Cyclodium, Olfersia, and Polybotrya. It contains three species: P. obtusa sp. nov., P. ochropteroides and P. macrostegia. A key is provided to distinguish the genus from closely related ones, and its three species are treated taxonomically, each being given full synonymy, typification, descriptions, habitats, elevations, discussions, specimens examined, distribution maps, and illustrations. Lectotypes are designated for Nephrodium macrostegium and N. popayense.
Dataset DOI: 10.5061/dryad.f1vhhmhb0
Description of the data and file structure
This dataset includes multispecies alignments for 376 target-capture loci used for phylogenetic analyses by Moran et al. (in review) to characterize the phylogenetic position of a new genus of ferns, Pradopteris (Dryopteridaceae). Alignments are for 376 loci sequenced using the GoFlag 408 probe set on Illumina HiSeq and Element AVITI platforms. Read trimming and quality assessment were performed on the raw-read pairs to remove adapters, low-quality bases, and reads less than 15 nucleotides in length. Sequences were then assembled using a reference sequence derived from 1KP transcriptome data (One Thousand Plant Transcriptomes Initiative 2019) for Polystichum acrostichoides (Michx.) Schott and Polypodium glycyrrhiza D.C. Eaton. Individual reads were mapped to the reference file and then contigs were assembled using de novo assembly.
Files and variables
File: Alignments.zip
Description: This compressed archive includes 376 single-locus alignment files in FASTA format. Indels are coded with "-"; sample names and metadata associated with Sequence Read Archive BioProject PRJNA1426427
Code/software
The alignment files can be viewed using a text editor or any sequence visualizing software, such as Mesquite or Geneious.
Read trimming and quality assessment were performed on the raw-read pairs using fastp to remove adapters, low-quality bases, and reads less than 15 nucleotides in length. HybPiper (v. 2.3.2) was used to assemble sequences using a reference sequence derived from 1KP transcriptome data (One Thousand Plant Transcriptomes Initiative 2019) for Polystichum acrostichoides (Michx.) Schott and Polypodium glycyrrhiza D.C. Eaton. BWA was used to map individual reads to the reference file, followed by SPAdes for de novo contig assembly. HybPiper’s intronerate option was selected to recover flanking intron regions and used to generate supercontigs.
Following assembly, all loci that contained sequences for fewer than six samples were removed. Sequences for the remaining loci were aligned using MAFFT v. 7.525 and all columns with more than 50% missing data were trimmed using trimAI.
Access information
Other publicly accessible locations of the data:
- Raw sequence data used to generate these alignments can be accessed on the NCBI Sequence Read Archive under BioProject PRJNA1426427