BackgroundFerns, originated about 360 million years ago, are the sister group of seed plants. Despite the remarkable progress in our understanding of fern phylogeny, with conflicting molecular evidence and different morphological interpretations, relationships among major fern lineages remain controversial.ResultsWith the aim to obtain a robust fern phylogeny, we carried out a large-scale phylogenomic analysis using high-quality transcriptome sequencing data, which covered 69 fern species from 38 families and 11 orders. Both coalescent-based and concatenation-based methods were applied to both nucleotide and amino acid sequences in species tree estimation. The resulting topologies are largely congruent with each other, except for the placement of Angiopteris fokiensis, Cheiropleuria bicuspis, Diplaziopsis brunoniana, Matteuccia struthiopteris, Elaphoglossum mcclurei, and Tectaria subpedata.ConclusionsOur result confirmed that Equisetales is sister to the rest of ferns, and Dennstaedtiaceae is sister to eupolypods. Moreover, our result strongly supported some relationships different from the current view of fern phylogeny, including that Marattiaceae may be sister to the monophyletic clade of Psilotaceae and Ophioglossaceae; that Gleicheniaceae and Hymenophyllaceae form a monophyletic clade sister to Dipteridaceae; and that Aspleniaceae is sister to the rest of the groups in eupolypods II. These results were interpreted with morphological traits, especially sporangia characters, and a new evolutionary route of sporangial annulus in ferns was suggested. This backbone phylogeny in ferns sets a foundation for further studies in biology and evolution in ferns, and therefore in plants.

The infrageneric relationships and taxonomy of the largest fern genus, Asplenium (Aspleniaceae), have remained poorly understood. Previous studies have focused mainly on specific species complexes involving a few or dozens of species only, or have achieved a large taxon sampling but only one plastid marker was used. In the present study, DNA sequences from six plastid markers (atpB, rbcL, rps4, rps4-trnS, trnL and trnL-F) of 1030 accessions (616 of them newly sequenced here) representing c. 420 species of Asplenium (60% of estimated species diversity), 16 species of Hymenasplenium, three Diplaziopsidaceae, and four Rhachidosoraceae were used to produce the largest genus-level phylogeny yet for ferns. Our major results include: (i) Asplenium as broadly circumscribed is monophyletic based on our inclusion of representatives of 32 of 38 named segregate genera; (ii) 11 major clades in Asplenium are identified, and their relationships are mostly well-resolved and strongly supported; (iii) numerous species, unsampled in previous studies, suggest new relationships and numerous cryptic species and species complexes in Asplenium; and (iv) the accrued molecular evidence provides an essential foundation for further investigations of complex patterns of geographical diversification, speciation and reticulate evolution in this family.

Ferns that evolved from 400 million years ago show various functional traits and ecological strategies in extant species, over 80% of which belong to the youngest order Polypodiales. How the functional traits and strategies of ferns have changed during their evolutionary history remains unexplored. Here, we measured functional traits that are sensitive to environmental light and water availability in 345 fern species across fern phylogeny, and reconstructed their evolutionary histories. We found that ferns, mainly Polypodiales, have developed diversified functional traits in response to forest environments. Terrestrial species, especially Thelypteridaceae and Athyriaceae in eupolypods II, since the late Jurassic period, have shown decreased leaf mass per area (LMA) and area‐based leaf nitrogen (Narea), but increased mass‐based leaf nitrogen (Nmass) compared with early‐derived polypods. Epiphytic species, mainly those in Polypodiaceae, have shown reductions in Nmass and individual leaf area (Area) since the late Cretaceous period. The adaption of functional traits of Polypodiales to forest environment may have played a crucial role in fern radiation since the late Jurassic period. Integrative analysis of functional traits, especially numerical ones, may shed new light on plant evolution.

The northwest region of Yunnan province (southwest China), belonging to the Pan-Himalaya, is a hotspot of biodiversity. We report Stegnogramma leptogrammoides from Yunnan as a new discovery for China. This species was identified based on morphological comparison with the type specimens of all similar species, and DNA barcoding was performed to obtain additional evidence. As it was previously recorded to be endemic to Sikkim, the new record provides a case for confirming floristic affinities between Sikkim and Yunnan within the Pan-Himalaya at the species level.

Because synonymy treatment traditionally relies on morphological judgments, it usually causes many problems in species delimitation and in the biodiversity catalogue. For example, Diplopterygium simulans, which belongs to the Gleicheniaceae family, has been considered to be synonymous with D. glaucum or D. giganteum based mainly on the morphology of its pinna rachis and blade. In the absence of molecular evidence, these revisions remain doubtful. DNA barcoding, which is considered to be a powerful method for species-level identification, was employed to assess the genetic distance among 9 members of the Diplopterygium genus. The results indicate that D. simulans is an independent species rather than a synonymy of D. glaucum or D. giganteum. Moreover, phylogenetic analysis uncovered the sisterhood of D. simulans and D. cantonense, which is supported by their geographical distributions and morphological traits. Incorrect synonymy treatment is prevalent in the characterization of biological diversity, and our study proposes a convenient and effective method for validating synonym treatments and discovering cryptic species.