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oai:figshare.com:article/19474316 2026-10-02T05:30:06Z category_24280 item_type_3 month_year_10_2026

Fern Tree of Life (FTOL) input data Joel Nitta (9653195) Santiago Ramírez-Barahona (3252120) Eric Schuettpelz (4448305) Wataru Iwasaki (235369) Evolutionary biology not elsewhere classified ferns phylogeny Evolutionary Biology 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. 2022-03-31T06:43:56Z Dataset Dataset 10.6084/m9.figshare.19474316.v11 https://figshare.com/articles/dataset/Fern_Tree_of_Life_FTOL_input_data/19474316 CC0