Asplenium sylvaticum (Aspleniaceae), a new fern species from Yungas and Paraná forests, Neotropical region.

A new species of Asplenium L. (Aspleniaceae) is described and illustrated. Asplenium sylvaticum is endemic of the Yungas and Paraná biogeographic provinces in the Southern Cone. The main diagnostic characters for this taxon are: apical pinnae with one to four caudate lobes at the base, similar in size to lateral pinnae, smooth pinnate blades with 18-36 pairs of caudate pinnae and spores with reticulate perispore, winged folds with scarce equinulaes on the margins and the laesurae wide with smooth margin. The new species belongs to the A. serra species complex group, characterised by xeromorphic habit, creeping rhizome and coriaceous fronds with branched scales on both surfaces, and resembles the other species inhabiting in Argentina, A. achalense and A. serra, in overall leaf architecture and shape but differs of the aforementioned species (and the other species of the A. serra complex) by the unique combination of characters of its rhizomatic scales, fronds and spores. A key with the morphological and palynological characters that differentiate A. sylvaticum from the other taxa belonging to the A. serra complex in the South American Cone and Bolivia is given.

Niche and phenotypic differentiation in fern hybrid speciation, a case study of Pteris fauriei (Pteridaceae).

BACKGROUND AND AIMS: Niche differentiation is a crucial issue in speciation. Although it has a well-known role in adaptive processes of hybrid angiosperms, it is less understood in hybrid ferns. Here, we investigate whether an intermediate ecological niche of a fern hybrid is a novel adaptation that provides insights into fern hybrid speciation. METHODS: Pteris fauriei (Pteridaceae) is a natural hybrid fern, occurring in environments between its parent species. The maternal Pteris minor is found in sunny areas, but the habitat of the paternal Pteris latipinna is shady. We combined data from morphology, leaf anatomy and photosynthetic traits to explore adaptation and differentiation, along with measuring the environmental features of their niches. We also performed experiments in a common garden to understand ecological plasticity. KEY RESULTS: The hybrid P. fauriei was intermediate between the parent species in stomatal density, leaf anatomical features and photosynthetic characteristics in both natural habitats and a common garden. Interestingly, the maternal P. minor showed significant environmental plasticity and was more similar to the hybrid P. fauriei in the common garden, suggesting that the maternal species experiences stress in its natural habitats but thrives in environments similar to those of the hybrid. CONCLUSIONS: Based on the similar niche preferences of the hybrid and parents, we propose hybrid superiority. Our results indicate that the hybrid P. fauriei exhibits greater fitness and can compete with and occupy the initial niches of the maternal P. minor. Consequently, we suggest that the maternal P. minor has experienced a niche shift, elucidating the pattern of niche differentiation in this hybrid group. These findings offer a potential explanation for the frequent occurrence of hybridization in ferns and provide new insights into fern hybrid speciation, enhancing our understanding of fern diversity.

A reduced role for water transport during the Cenozoic evolution of epiphytic Eupolypod ferns.

The Cretaceous-Cenozoic expansion of tropical forests created canopy space that was subsequently occupied by diverse epiphytic communities including Eupolypod ferns. Eupolypods proliferated in this more stressful niche, where lower competition enabled the adaptive radiation of thousands of species. Here, we examine whether xylem traits helped shape the Cenozoic radiation of Eupolypod ferns. We characterized the petiole xylem anatomy of 39 species belonging to the Eupolypod I and Eupolypod II clades occupying the epiphytic, hemiepiphytic, and terrestrial niche, and we assessed vulnerability to embolism in a subset of species. The transition to the canopy was associated with reduced xylem content and smaller tracheid diameters, but no differences were found in species vulnerability to embolism and pit membrane thickness. Phylogenetic analyses support selection for traits associated with reduced water transport in Eupolypod 1 species. We posit that in Eupolypod epiphytes, selection favored water retention via thicker leaves and lower stomatal density over higher rates of water transport. Consequently, lower leaf water loss was coupled with smaller quantities of xylem and narrower tracheid diameters. Traits associated with water conservation were evident in terrestrial Eupolypod 1 ferns and may have predisposed this clade toward radiation in the canopy.

Hydathodes in ferns: their phylogenetic distribution, structure and function.

BACKGROUND AND AIMS: Ferns are the second largest group of vascular plants and are distributed nearly worldwide. Although ferns have been integrated into some comparative ecological studies focusing on hydathodes, there is a considerable gap in our understanding of the functional anatomy of these secretory tissues that are found on the vein endings of many fern leaves. In this study, we aimed to investigate the phylogenetic distribution, structure and function of fern hydathodes. METHODS: We performed a global review on fern hydathodes and their phylogenetic distribution, carried out an ancestral character state reconstruction, and studied the structure, guttation and elemental composition of salt residues of eight species, and the diurnal patterns of xylem pressure of two species. KEY RESULTS: Hydathodes are known from 1189 fern species, 92 genera and 19 families of 2 orders, Equisetales and Polypodiales. Stochastic character mapping indicated multiple gains and losses of hydathodes at the genus level, occurring especially during the last 50 million years of fern evolution. Hydathodes were located on the adaxial leaf surface and characterized by a cytoplasm-rich, pore-free epidermis, and became functional for several weeks after nearly complete leaf expansion. In two species, positive xylem pressure built up at night, potentially facilitating guttation. Guttation fluid was rich in Ca and often Si, but also contained P, Mg, Na and Al. CONCLUSIONS: Stochastic character mapping and the structural and functional diversity of hydathodes indicate multiple origins, and their presence/absence in closely related taxa implies secondary losses during fern evolution. Positive xylem pressure and high air humidity play an important role as drivers of guttation. Hydathodes may contribute to the regulation of leaf nutrient stoichiometry by the release of excessive compounds and minerals other than waste products, but the presence of essential chemical elements in salt residues also indicates possible leakage.

Stomatal morphology and physiology explain varied sensitivity to abscisic acid across vascular plant lineages.

Abscisic acid (ABA) can induce rapid stomatal closure in seed plants, but the action of this hormone on the stomata of fern and lycophyte species remains equivocal. Here, ABA-induced stomatal closure, signaling components, guard cell K+ and Ca2+ fluxes, vacuolar and actin cytoskeleton dynamics, and the permeability coefficient of guard cell protoplasts (Pf) were analyzed in species spanning the diversity of vascular land plants including 11 seed plants, 6 ferns, and 1 lycophyte. We found that all 11 seed plants exhibited ABA-induced stomatal closure, but the fern and lycophyte species did not. ABA-induced hydrogen peroxide elevation was observed in all species, but the signaling pathway downstream of nitric oxide production, including ion channel activation, was only observed in seed plants. In the angiosperm faba bean (Vicia faba), ABA application caused large vacuolar compartments to disaggregate, actin filaments to disintegrate into short fragments and Pf to increase. None of these changes was observed in the guard cells of the fern Matteuccia struthiopteris and lycophyte Selaginella moellendorffii treated with ABA, but a hypertonic osmotic solution did induce stomatal closure in fern and the lycophyte. Our results suggest that there is a major difference in the regulation of stomata between the fern and lycophyte plants and the seed plants. Importantly, these findings have uncovered the physiological and biophysical mechanisms that may have been responsible for the evolution of a stomatal response to ABA in the earliest seed plants.

Simple and Divided Leaves in Ferns: Exploring the Genetic Basis for Leaf Morphology Differences in the Genus Elaphoglossum (Dryopteridaceae).

Despite the implications leaves have for life, their origin and development remain debated. Analyses across ferns and seed plants are fundamental to address the conservation or independent origins of megaphyllous leaf developmental mechanisms. Class I KNOX expression studies have been used to understand leaf development and, in ferns, have only been conducted in species with divided leaves. We performed expression analyses of the Class I KNOX and Histone H4 genes throughout the development of leaf primordia in two simple-leaved and one divided-leaved fern taxa. We found Class I KNOX are expressed (1) throughout young and early developing leaves of simple and divided-leaved ferns, (2) later into leaf development of divided-leaved species compared to simple-leaved species, and (3) at the leaf primordium apex and margins. H4 expression is similar in young leaf primordia of simple and divided leaves. Persistent Class I KNOX expression at the margins of divided leaf primordia compared with simple leaf primordia indicates that temporal and spatial patterns of Class I KNOX expression correlate with different fern leaf morphologies. However, our results also indicate that Class I KNOX expression alone is not sufficient to promote divided leaf development in ferns. Class I KNOX patterns of expression in fern leaves support the conservation of an independently recruited developmental mechanism for leaf dissection in megaphylls, the shoot-like nature of fern leaves compared with seed plant leaves, and the critical role marginal meristems play in fern leaf development.

Superrepellency of underwater hierarchical structures on Salvinia leaf.

Biomimetic superhydrophobic surfaces display many excellent underwater functionalities, which attribute to the slippery air mattress trapped in the structures on the surface. However, the air mattress is easy to collapse due to various disturbances, leading to the fully wetted Wenzel state, while the water filling the microstructures is difficult to be repelled to completely recover the air mattress even on superhydrophobic surfaces like lotus leaves. Beyond superhydrophobicity, here we find that the floating fern, Salvinia molesta, has the superrepellent capability to efficiently replace the water in the microstructures with air and robustly recover the continuous air mattress. The hierarchical structures on the leaf surface are demonstrated to be crucial to the recovery. The interconnected wedge-shaped grooves between epidermal cells are key to the spontaneous spreading of air over the entire leaf governed by a gas wicking effect to form a thin air film, which provides a base for the later growth of the air mattress in thickness synchronously along the hairy structures. Inspired by nature, biomimetic artificial Salvinia surfaces are fabricated using 3D printing technology, which successfully achieves a complete recovery of a continuous air mattress to exactly imitate the superrepellent capability of Salvinia leaves. This finding will benefit the design principles of water-repellent materials and expand their underwater applications, especially in extreme environments.

Are stomata in ferns and allies sluggish? Stomatal responses to CO2 , humidity and light and their scaling with size and density.

Fast stomatal reactions enable plants to successfully cope with a constantly changing environment yet there is an ongoing debate on the stomatal regulation mechanisms in basal plant groups. We measured stomatal morphological parameters in 29 fern and allied species from temperate to tropical biomes and two outgroup angiosperm species. Stomatal dynamic responses to environmental drivers were measured in 16 ferns and the two angiosperms using a gas-exchange system. Principal components analyses were used to further reveal the structure-function relationships in stomata. We show a > 10-fold variation for stomatal opening delays and 20-fold variation for stomatal closing delays in ferns. Across species, stomatal responses to vapor pressure deficit (VPD) were the fastest, while light and [CO2 ] responses were slower. In most cases the outgroup species' reaction speeds to changes in environmental variables were similar to those of ferns. Correlations between stomatal response rate and size were apparent for stomatal opening in light and low [CO2 ] while not evident for closing reactions and changes in VPD. No correlations between stomatal density and response speed were observed. Together, this study demonstrates different mechanisms controlling stomatal reactions in ferns at different environmental stimuli, which should be considered in future studies relating stomatal morphology and function.

A novel approach for the metric analysis of fern fronds: Growth and architecture of the Mesozoic fern Weichselia reticulata in the light of modern ferns.

The architecture of primary and secondary pinnae of the fossil fern Weichselia reticulata (C. Stokes et Webb) Fontaine is studied based on 28 large specimens from the upper Barremian La Huérguina Formation of the fossil locality Las Hoyas, Cuenca, Spain. The study of the specimens is performed through a morphometric analysis consisting in a reformulation of the Branching Algorithms method of shape description including measurements (insertion angle, distance between pinnae, first segment length and rachis width) and ratios (interval ratio, branching ratio and tapering ratio). A protocol to relocate isolated fragments of fossil pinnae is also established using the interval ratio (distance between pinnae/ previous distance between pinnae) and insertion angle of the pinnae. All specimens show a similar architecture, having elliptic primary pinnae with a sinuous apically tapering primary rachis and triangular secondary pinnae with pinnules of different morphologies. The analysis of the architecture allows to propose that the position of the frond was plagiotropic and that the frond growth was basiplastic for the petiole head and acroplastic for the primary pinnae. The metric method is applied to explore the architecture of four living fern species (Angiopteris evecta (Forst.) Hoffm., Matonia pectinata R.Br., Sphaeropteris cooperi (F.Muell.) R.M.Tryon, and Woodwardia unigemmata (Makino) Nakai). Weichselia architecture results extremely ordered and regular in comparison with the primary pinnae variation of the living species.

Order-level fern plastome phylogenomics: new insights from Hymenophyllales.

PREMISE OF THE STUDY: Filmy ferns (Hymenophyllales) are a highly specialized lineage, having mesophyll one-cell layer thick and inhabiting particularly shaded and humid environments. The phylogenetic placement of Hymenophyllales has been inconclusive, and while over 87 whole fern plastomes have been published, none was from Hymenophyllales. To better understand the evolutionary history of filmy ferns, we sequenced the first complete plastome for this order. METHODS: We compiled a phylogenomic plastome data set encompassing all 11 fern orders, and reconstructed phylogenies using different data types (nucleotides, codons, and amino acids) and partition schemes (codon positions and loci). To infer the evolution of fern plastome organization, we coded plastome features, including inversions, inverted repeat boundary shifts, gene losses, and tRNA anticodon sequences as characters, and reconstructed the ancestral states for these characters. KEY RESULTS: We discovered a suite of novel, Hymenophyllales-specific plastome structures that likely resulted from repeated expansions and contractions of the inverted repeat regions. Our phylogenetic analyses reveal that Hymenophyllales is highly supported as either sister to Gleicheniales or to Gleicheniales + the remaining non-Osmundales leptosporangiates, depending on the data type and partition scheme. CONCLUSIONS: Although our analyses could not confidently resolve the phylogenetic position of Hymenophyalles, the results here highlight the danger of drawing conclusions from "all-in" phylogenomic data set without exploring potential inconsistencies in the data. Finally, our first order-level reconstruction of fern plastome structural evolution provides a useful framework for future plastome research.

Assessing the evolutionary history of the fern family Dipteridaceae (Gleicheniales) by incorporating both extant and extinct members in a combined phylogenetic study.

PREMISE OF THE STUDY: Dipteridaceae is a lineage of ferns that has existed from the early Mesozoic and is known for its extensive fossil record. By integrating information from all described extant and extinct genera into a single phylogenetic study, this paper aims to examine the taxonomy of the group on a whole and explore character evolution within the lineage across time. METHODS: A morphological matrix of 51 characters was developed for 72 species (43 extinct and 29 extant) based on published information. Morphological characters were combined with nucleotide sequences for four chloroplast genes (rbcL, atpA, atpB, and rps4) for extant taxa, and combined parsimony analyses were conducted to infer evolutionary trends in the group. KEY RESULTS: Dipteridaceae was found to be monophyletic and characterized by highly anastomosing minor veins forming a meshwork of areoles with free-included veinlets. Based on our analyses, we recognize six previously described genera (i.e., Goeppertella, Thaumatopteris, Clathropteris, Digitopteris, Dipteris, and Cheiropleuria) and one new genus (i.e., Sewardalea). Fossils currently described as Dictyophyllum, Kenderlykia, Hausmannia, and Protorhipis are ambiguously placed on the tree and are recognized as possibly unnatural morphogenera. CONCLUSIONS: Overall, the evolutionary trend in Dipteridaceae has been toward increasing complexity in the venation pattern and laminal fusion. Only the Hausmannia-type frond with dichotomizing primary veins and relatively fused lamina persisted in the later part of the Mesozoic to the present. Within the crown group, we see evidence of re-radiation of frond forms in Dipteris and Cheiropleuria.

Bioinspired 3D Printable Soft Vacuum Actuators for Locomotion Robots, Grippers and Artificial Muscles.

Continued technological progress in robotic systems has led to more applications where robots and humans operate in close proximity and even physical contact in some cases. Soft robots, which are made of highly compliant and deformable materials, provide inherent safety features unlike conventional robots that are made of stiff and rigid components. Soft robotics is a rapidly developing field exploiting biomimetic design principles, novel sensor and actuation concepts, and advanced manufacturing techniques. In this study, we propose novel 3D printable soft vacuum actuators that are inspired by the sporangium of fern trees. These actuators that are directly manufactured using commercial and affordable fused deposition modeling 3D printers offer many advantages such as high actuation speed (5.54 Hz), long lifetime (123,000 cycles), large payload to weight ratio (∼26), and significant output forces (∼16 N). The behavior of these actuators is accurately predicted, and their performance is optimized using finite element modeling. Furthermore, diverse robotic applications such as locomotion robots (a walking robot moving with an average forward speed of vf = 3.54 cm/s, and a hopping robot called Gongaroo hopping with an average speed of vf = 3.75 cm/s), grippers, and artificial muscles have been established and activated using the new soft actuation concept. Finally, to demonstrate the modularity of the proposed actuation concept, soft actuators with multiple degrees of freedom and variable length are established using a series of 3D printable vacuum hinges.

A global plastid phylogeny uncovers extensive cryptic speciation in the fern genus Hymenasplenium (Aspleniaceae).

The fern genus Hymenasplenium (Aspleniaceae) is one of the two genera in the family. It is generally recognized among modern pteridologists. However, its infrageneric relationships and species diversity have been unclear and controversial. The molecular studies so far have had small taxon and character sampling. In the present study, DNA sequences of six plastid markers of 158 accessions representing ca. 40 out of ca. 50 known species of Hymenasplenium, and 16 species of Asplenium were used to infer a phylogeny with maximum likelihood, Bayesian inference, and maximum parsimony approaches. Our major results include: (1) Hymenasplenium as currently defined is strongly supported as monophyletic; (2) three major clades representing early splits in Hymenasplenium are identified, with the Old World species being strongly supported as monophyletic; it is ambiguous if the New World species are monophyletic; (3) extensive cryptic speciation in the Old World is discovered demonstrating the complexity of evolution of the genus; and (4) six strongly or moderately supported subclades in the Old World clade are revealed, differing from one another in molecular, morphological, and geographical features.

Rates of molecular evolution in tree ferns are associated with body size, environmental temperature, and biological productivity.

Variation in rates of molecular evolution (heterotachy) is a common phenomenon among plants. Although multiple theoretical models have been proposed, fundamental questions remain regarding the combined effects of ecological and morphological traits on rate heterogeneity. Here, we used tree ferns to explore the correlation between rates of molecular evolution in chloroplast DNA sequences and several morphological and environmental factors within a Bayesian framework. We revealed direct and indirect effects of body size, biological productivity, and temperature on substitution rates, where smaller tree ferns living in warmer and less productive environments tend to have faster rates of molecular evolution. In addition, we found that variation in the ratio of nonsynonymous to synonymous substitution rates (dN/dS) in the chloroplast rbcL gene was significantly correlated with ecological and morphological variables. Heterotachy in tree ferns may be influenced by effective population size associated with variation in body size and productivity. Macroevolutionary hypotheses should go beyond explaining heterotachy in terms of mutation rates and instead, should integrate population-level factors to better understand the processes affecting the tempo of evolution at the molecular level.

Are rates of species diversification and body size evolution coupled in the ferns?

PREMISE OF THE STUDY: Understanding the relationship between phenotypic evolution and lineage diversification is a central goal of evolutionary biology. To extend our understanding of the role morphological evolution plays in the diversification of plants, we examined the relationship between leaf size evolution and lineage diversification across ferns. METHODS: We tested for an association between body size evolution and lineage diversification using a comparative phylogenetic approach that combined a time-calibrated phylogeny and leaf size data set for 2654 fern species. Rates of leaf size change and lineage diversification were estimated using BAMM, and rate correlations were performed for rates obtained for all families and individual species. Rates and patterns of rate-rate correlation were also analyzed separately for terrestrial and epiphytic taxa. KEY RESULTS: We find no significant correlation between rates of leaf area change and lineage diversification, nor was there a difference in this pattern when growth habit is considered. Our results are consistent with the findings of an earlier study that reported decoupled rates of body size evolution and diversification in the Polypodiaceae, but conflict with a recent study that reported a positive correlation between body size evolution and lineage diversification rates in the tree fern family Cyatheaceae. CONCLUSIONS: Our findings indicate that lineage diversification in ferns is largely decoupled from shifts in body size, in contrast to several other groups of organisms. Speciation in ferns appears to be primarily driven by hybridization and isolation along elevational gradients, rather than adaptive radiations featuring prominent morphological restructuring. The exceptional diversity of leaf morphologies in ferns appears to reflect a combination of ecophysiological constraints and adaptations that are not key innovations.

Integrated taxonomy of the Asplenium normale complex (Aspleniaceae) in China and adjacent areas.

The Asplenium normale D. Don complex comprises several taxa that are either diploid or tetraploid. The tetraploids are assumed to have originated from diploid ancestors by relatively recent autopolyploidization or allopolyploidization. Some of the diploids are readily recognized morphologically but most of the taxa have until now been placed into a single species. However, phylogenetic studies have challenged this treatment and emphasized the notion that the taxonomic treatment of this complex needs to be revised. An integrative taxonomic approach was employed to delimit species in the complex using cytological, morphological, and DNA sequence data. Initially, we employed a diploid first approach to establish a robust taxonomic framework. Special efforts were made to collect and identify the diploid progenitors of each polyploid lineage identified in the plastid DNA based phylogenetic hypothesis. A total of six distinct diploid species were identified. The distinctive nature of the six diploids is strongly supported by sequence differences in plastid DNA and nuclear loci, as well as by the results of morphometric analysis. Diagnostic morphological characters were identified to distinguish the six diploid species, resulting in their revised taxonomy, which includes two novel species, namely, Asplenium normaloides and A. guangdongense. Further studies to strengthen the taxonomic classification of all of the tetraploid taxa are warranted.

A total-evidence phylogeny of the lady fern genus Athyrium Roth (Athyriaceae) with a new infrageneric classification.

The lady fern genus Athyrium represents one of the most diversified lineages in Athyriaceae with about 160-220 known species, and is notorious for its taxonomic difficulty. Despite progress in recent phylogenetic studies involving this genus, it still lacks a modern systematic and taxonomic update using integrative analyses of molecular and morphological evidence based on a broad species sampling. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the genus to date based on a total-evidence approach, covering all formerly accepted segregates within the athyrioid ferns. We sampled up to eight plastid markers and 20 morphological characters for each species. Our analyses, including maximum parsimony, maximum likelihood and Bayesian inference, yield a robust phylogenetic framework. We find that Athyrium is not monophyletic by recovering Athyrium skinneri and A. alpestre nested with Anisocampium and Cornopteris respectively while Pseudocystopteris is included in Athyrium. Furthermore, eight well-resolved clades and two isolated species within Athyrium are found in the phylogenetic topology, which can be also characterized by morphological synapomorphies from traits of petioles, leaves, sori and spores. In the interest of recognizing monophyletic taxa with morphological synapomorphies, we agree with the inclusion of Pseudocystopteris in Athyrium as proposed in previous studies, but treat Anisocampium and Cornopteris as separate genera. We further propose to resurrect a monotypic Pseudathyrium to accommodate A. alpestre. Based on morphological characters and molecular phylogeny, a new infrageneric classification system of Athyrium is proposed which subdivided it into ten sections, and one New-World species A. skinneri is transferred into Anisocampium.

High endemism and stem density distinguish New Caledonian from other high-diversity rainforests in the Southwest Pacific.

Background and Aims: The biodiversity hotspot of New Caledonia is globally renowned for the diversity and endemism of its flora. New Caledonia's tropical rainforests have been reported to have higher stem densities, higher concentrations of relictual lineages and higher endemism than other rainforests. This study investigates whether these aspects differ in New Caledonian rainforests compared to other high-diversity rainforests in the Southwest Pacific. Methods: Plants (with a diameter at breast height ≥10 cm) were surveyed in nine 1-ha rainforest plots across the main island of New Caledonia and compared with 14 1-ha plots in high-diversity rainforests of the Southwest Pacific (in Australia, Fiji, Papua New Guinea and the Solomon Islands). This facilitated a comparison of stem densities, taxonomic composition and diversity, and species turnover among plots and countries. Key Results: The study inventoried 11 280 stems belonging to 335 species (93 species ha-1 on average) in New Caledonia. In comparison with other rainforests in the Southwest Pacific, New Caledonian rainforests exhibited higher stem density (1253 stems ha-1 on average) including abundant palms and tree ferns, with the high abundance of the latter being unparalleled outside New Caledonia. In all plots, the density of relictual species was ≥10 % for both stems and species, with no discernible differences among countries. Species endemism, reaching 89 % on average, was significantly higher in New Caledonia. Overall, species turnover increased with geographical distance, but not among New Caledonian plots. Conclusions: High stem density, high endemism and a high abundance of tree ferns with stem diameters ≥10 cm are therefore unique characteristics of New Caledonian rainforests. High endemism and high spatial species turnover imply that the current system consisting of a few protected areas is inadequate, and that the spatial distribution of plant species needs to be considered to adequately protect the exceptional flora of New Caledonian rainforests.

Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns.

Background: Ferns, 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. Results: With 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. Conclusions: Our 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.