Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.

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BackgroundMolecular phylogenetic investigations have revolutionized our understanding of the evolutionary history of ferns—the second-most species-rich major group of vascular plants, and the sister clade to seed plants. The general absence of genomic resources available for this important group of plants, however, has resulted in the strong dependence of these studies on plastid data; nuclear or mitochondrial data have been rarely used. In this study, we utilize transcriptome data to design primers for nuclear markers for use in studies of fern evolutionary biology, and demonstrate the utility of these markers across the largest order of ferns, the Polypodiales.Principal FindingsWe present 20 novel single-copy nuclear regions, across 10 distinct protein-coding genes: ApPEFP_C, cryptochrome 2, cryptochrome 4, DET1, gapCpSh, IBR3, pgiC, SQD1, TPLATE, and transducin. These loci, individually and in combination, show strong resolving power across the Polypodiales phylogeny, and are readily amplified and sequenced from our genomic DNA test set (from 15 diploid Polypodiales species). For each region, we also present transcriptome alignments of the focal locus and related paralogs—curated broadly across ferns—that will allow researchers to develop their own primer sets for fern taxa outside of the Polypodiales. Analyses of sequence data generated from our genomic DNA test set reveal strong effects of partitioning schemes on support levels and, to a much lesser extent, on topology. A model partitioned by codon position is strongly favored, and analyses of the combined data yield a Polypodiales phylogeny that is well-supported and consistent with earlier studies of this group.ConclusionsThe 20 single-copy regions presented here more than triple the single-copy nuclear regions available for use in ferns. They provide a much-needed opportunity to assess plastid-derived hypotheses of relationships within the ferns, and increase our capacity to explore aspects of fern evolution previously unavailable to scientific investigation.

Convergent evolution driven by adaptation to arid habitats has made It difficult to identify monophyletic taxa in the cheilanthoid ferns. Dependence on distinctive, but potentially bomoplastic characters, to define majcr clades has resulted in a taxonomic conundrum: all of the largest cheilanthoid genera have been shown to be polyphyletic. Here we reconstruct the first comprehensive phylogeny of the strictly New World cheilanthoid genus Argyrochosma. We use our reconstruction to examine the evolution of farina (powdery leaf deposits), which has played a prominent role in tbe circum.scription of cheilanthoid genera. Our data indicate that Argyrochosma comprises two major monophyletic groups: one exclusively non-farinose and the other primarily farinose. Within the latter gioup, there has been at least one evolutionary reversal (loss) of farina and the development of major chemical variants tbat characterize specific clades. Our phylogenetic hypothesis, in combination with spore data and chromosome counts, also provides a critical context for addressing the prevalence of polyploidy and apomixis within the genus. Evidence from these datasets provides testable hypotheses regarding reticulate tvolution and suggests the presence of several previously undetected taxa oí Argyrochosma.