The generic classification of the Thelypteridaceae has been the subject of much controversy. Proposed taxonomic systems have varied from recognizing more than 1000 species in the family within the single genus Thelypteris, to systems favoring upwards of 30 genera. Insights on intrafamilial relationships have been gained from recent phylogenetic studies, especially for the Neotropics; however, in the most recent classification, 10 of 30 recognized genera are either non-monophyletic or untested. In the present study, we sequenced 407 nuclear loci for 621 samples, representing all recognized genera and approximately half the known species diversity. Our phylogenomic results, coupled with morphological study, provide a foundation for a new generic classification. Our recently recognized monophyletic genera demonstrate greater geographic coherence than previous taxonomic concepts suggested. Additionally, our results demonstrate that certain morphological characters, such as frond division, are evolutionarily labile, and are thus inadequate for defining genera.

These data include an 407-locus alignment file, a partition file, a maximum likelihood phylogeny annotated with ultrafast bootstrap support values, gene- and site concordance factors created in IQ-Tree, and a pseudocoalescent tree created in ASTRAL, annotated with local posterior probabilities. A spreadsheet includes specimen data for the 621 vouchers used in the phylogenomic analysis of the Thelypteridaceae, and pipeline and post-processing scripts. The data were generated by the GoFlag Consortium. GoFlag (Genealogy of Flagellate Plants) is an NSF-funded project (DEB 1541506) based at the University of Florida, Field Museum, and University of Arizona. Project personnel include (at UF): J. Gordon Burleigh, Emily Sessa, Stuart McDaniel, Christine Davis, Pavlo Antonenko, Sarah Carey, Lorena Endara, Weston Testo; (at Field): Matt von Konrat, Eve Gaus; (at UA): Hong Cui. 

Please see Breinholt et al. 2020 for more detailed methods. The raw reads are available on the NCBI Sequence Read Archive Bioproject 646399. The trees are easily viewed using FigTree, and the alignment and partition file are formatted to use with IQ-Tree, ASTRAL or other similar software. The supplementary methods folder contains ReadMe files and scripts.