Thoroughly sampled phylogenies are the foundation of modern evolutionary research. With the continuous growth of DNA sequences in GenBank, it is now possible to assemble maximally sampled phylogenies for nearly any study group. However, as sequences rapidly accumulate, any such phylogeny will become quickly outdated. Furthermore, many sequences in GenBank are mis-identified or poorly annotated, so producing a high-quality phylogeny is not straightforward.

Here, we develop a mostly automated, reproducible, open pipeline to generate a continuously updated phylogeny of ferns (Polypodiopsida) from data in GenBank. Our sampling strategy combines whole plastomes (few taxa, many loci) with commonly sequenced plastid regions (many taxa, few loci) to obtain a global, species-level fern tree of life (FTOL) with high resolution along the backbone and maximal sampling across the tips. We use a curated reference taxonomy in combination with a newly developed R package, ‘taxastand’, to resolve synonyms and remove erroneous accessions.

The current FTOL includes 5,582 species, or nearly half of extant fern diversity (ca. 12,000 species). FTOL and its accompanying datasets will be updated on a regular basis and are available via a web portal (https://fernphy.github.io) and R packages, enabling immediate access to the most up-to-date, comprehensively sampled fern phylogeny.