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.

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The eupolypods II ferns represent a classic case of evolutionary radiation and, simultaneously, exhibit high substitution rate heterogeneity. These factors have been proposed to contribute to the contentious resolutions among clades within this fern group in multilocus phylogenetic studies. We investigated the deep phylogenetic relationships of eupolypod II ferns by sampling all major families and using 40 plastid genomes, or plastomes, of which 33 were newly sequenced with next-generation sequencing technology. We performed model-based analyses to evaluate the diversity of molecular evolutionary rates for these ferns. Our plastome data, with more than 26,000 informative characters, yielded good resolution for deep relationships within eupolypods II and unambiguously clarified the position of Rhachidosoraceae and the monophyly of Athyriaceae. Results of rate heterogeneity analysis revealed approximately 33 significant rate shifts in eupolypod II ferns, with the most heterogeneous rates (both accelerations and decelerations) occurring in two phylogenetically difficult lineages, that is, the Rhachidosoraceae–Aspleniaceae and Athyriaceae clades. These observations support the hypothesis that rate heterogeneity has previously constrained the deep phylogenetic resolution in eupolypods II. According to the plastome data, we propose that 14 chloroplast markers are particularly phylogenetically informative for eupolypods II both at the familial and generic levels. Our study demonstrates the power of a character-rich plastome data set and high-throughput sequencing for resolving the recalcitrant lineages, which have undergone rapid evolutionary radiation and dramatic changes in substitution rates.

Aim Gondwanan vicariance, boreotropical migration and long‐distance dispersal have been posited as alternative hypotheses explaining the tropical distribution patterns and diversifications in many fern groups. Here, the historical biogeography of Diplazium is reconstructed to evaluate the impact of these biogeographical processes in shaping the modern tropical disjunctions. Location World‐wide with a focus on tropical forest habitats. Methods Divergence times were estimated by analysing nucleotide sequences of seven plastid DNA regions (atpA, atpB, matK, rbcL, rps4, rps4–trnS and trnL–F) from 123 species of Diplazium and its allied genera, using a Bayesian relaxed clock method and three fossil calibrations. The ancestral areas were reconstructed using the likelihood dispersal–extinction–cladogenesis (DEC) approach. Results The crown group of Diplazium was estimated to have originated in Eurasia and undergone an initial diversification in the Northern Hemisphere around 41.7 Ma [95% highest posterior density (HPD): 34–49 Ma] during the Eocene. Two disjunct events between the Old and New World were identified: one in subgenus Diplazium around the Eocene–Oligocene boundary (31.2 Ma, 95% HPD: 25–38 Ma), and the other in subgenus Callipteris during the middle Miocene (12.6 Ma, 95% HPD: 15–23 Ma). Furthermore, Palaeotropical disjunctions in subgenus Callipteris are indicative of multiple dispersal events during the Miocene. Main conclusions The evolutionary history of Diplazium involves a variety of biogeographical scenarios. Early diversification of Diplazium in the Northern Hemisphere during the Eocene corresponds with the migration from Eurasia to North America over land bridges as a member of the boreotropical flora. The current tropical amphi‐Pacific disjunctions in subgenus Diplazium can be better explained by the disruption of boreotropical belt, however, long‐distance dispersal between Eurasia and tropical America cannot be ruled out. Island‐hopping and trans‐Pacific dispersals followed by speciation characterize the disjunctions and diversifications of subgenus Callipteris during the Neogene. Gondwanan vicariance is not supported by any of our results.

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Diplazium and allied segregates (Allantodia, Callipteris, Monomelangium) represent highly diverse genera belonging to the lady‐fern family Athyriaceae. Because of the morphological diversity and lack of molecular phylogenetic analyses of this group of ferns, generic circumscription and infrageneric relationships within it are poorly understood. In the present study, the phylogenetic relationships of these genera were investigated using a comprehensive taxonomic sampling including 89 species representing all formerly accepted segregates. For each species, we sampled over 6000 DNA nucleotides of up to seven plastid genomic regions: atpA, atpB, matK, rbcL, rps4, rps4‐trnS IGS, and trnL intron plus trnL‐trnF IGS. Phylogenetic analyses including maximum parsimony, maximum likelihood and Bayesian methods congruently resolved Allantodia, Callipteris and Monomelangium nested within Diplazium; therefore a large genus concept of Diplazium is accepted to keep this group of ferns monophyletic and to avoid paraphyletic or polyphyletic taxa. Four well‐supported clades and eight robust subclades were found in the phylogenetic topology. Reconstruction of the evolutionary pattern of morphological characters, such as dissections of leaves, petiole/rachis scales, and shapes of sori, recovered some character combinations of systematic value for infrageneric classification. In light of morphological characters and our molecular phylogeny, a re‐defined Diplazium and an infrageneric classification are proposed.

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