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.

Developmental programmes in the evolution of Equisetum reproductive morphology: a hierarchical modularity hypothesis.

Background: The origin of the Equisetum strobilus has long been debated and the fossil record has played an important role in these discussions. The paradigm underlying these debates has been the perspective of the shoot as node-internode alternation, with sporangiophores attached at nodes. However, fossils historically excluded from these discussions (e.g. Cruciaetheca and Peltotheca ) exhibit reproductive morphologies that suggest attachment of sporangiophores along internodes, challenging traditional views. This has rekindled discussions around the evolution of the Equisetum strobilus, but lack of mechanistic explanations has led discussions to a stalemate. Scope: A shift of focus from the node-internode view to a perspective emphasizing the phytomer as a modular unit of the shoot, frees the debate of homology constraints on the nature of the sporangiophore and inspires a mechanism-based hypothesis for the evolution of the strobilus. The hypothesis, drawing on data from developmental anatomy, regulatory mechanisms and the fossil record, rests on two tenets: (1) the equisetalean shoot grows by combined activity of the apical meristem, laying down the phytomer pattern, and intercalary meristems responsible for internode elongation; and (2) activation of reproductive growth programmes in the intercalary meristem produces sporangiophore whorls along internodes. Conclusions: Hierarchical expression of regulatory modules responsible for (1) transition to reproductive growth; (2) determinacy of apical growth; and (3) node-internode differentiation within phytomers, can explain reproductive morphologies illustrated by Cruciaetheca (module 1 only), Peltotheca (modules 1 and 2) and Equisetum (all three modules). This model has implications - testable by studies of the fossil record, phylogeny and development - for directionality in the evolution of reproductive morphology ( Cruciaetheca - Peltotheca - Equisetum ) and for the homology of the Equisetum stobilus. Furthermore, this model implies that sporangiophore development is independent of node-internode identity, suggesting that the sporangiophore represents the expression of an ancestral euphyllophyte developmental module that pre-dates the evolution of leaves.

Morphometric and mechanical characteristics of Equisetum hyemale stem enhance its vibration.

MAIN CONCLUSION: The order of the internodes, and their geometry and mechanical characteristics influence the capability of the Equisetum stem to vibrate, potentially stimulating spore liberation at the optimum stress setting along the stem. Equisetum hyemale L. plants represent a special example of cellular solid construction with mechanical stability achieved by a high second moment of area and relatively high resistance against local buckling. We proposed the hypothesis that the order of E. hyemale L. stem internodes, their geometry and mechanical characteristics influence the capability of the stem to vibrate, stimulating spore liberation at the minimum stress setting value along the stem. An analysis of apex vibration was done based on videos presenting the behavior of an Equisetum clump filmed in a wind tunnel and also as a result of excitation by bending the stem by 20°. We compared these data with the vibrations of stems of the same size but deprived of the three topmost internodes. Also, we created a finite element model (FEM), upon which we have based the 'natural' stem vibration as a copy of the real object, 'random' with reshuffled internodes and 'uniform', created as one tube with the characters averaged from all internodes. The natural internode arrangement influences the frequency and amplitude of the apex vibration, maintaining an equal stress distribution in the stem, which may influence the capability for efficient spore spreading.

Equisetum thermale sp. nov. (Equisetales) from the Jurassic San Agustín hot spring deposit, Patagonia: anatomy, paleoecology, and inferred paleoecophysiology.

PREMISE OF THE STUDY: Dated molecular phylogenies suggest a Cenozoic origin for the crown group of Equisetum. but compression fossil equisetaleans that are morphologically indistinguishable from extant Equisetum and recently discovered anatomically preserved examples strongly suggest an earlier Mesozoic initial diversification. METHODS: In situ samples of Equisetum thermale sp. nov. from the Upper Jurassic San Agustín hot spring deposit were collected and studied with the use of polished blocks, thin sections, and light microscopy. KEY RESULTS: Equisetum thermale exhibits all the morphological and anatomical characteristics of the extant crown group Equisetum. It shows a mixture of features present in the two extant subgenera, e.g., superficial stomata typical of subgenus Equisetum allied with infrequently ramifying stems typical of subgenus Hippochaete. This appears to ally E. thermale with the least derived extant species in the genus Equisetum bogotense (sister species to the two subgenera). Its association of hydromorphic and xeromorphic characters allowed it to grow as an emergent aquatic in physically and chemically stressed geothermally influenced wetlands, where it formed dense monospecific stands. Equisetum thermale, because it is preserved in situ with intact anatomy, provides clear paleoecological, biological, plus inferred paleoecophysiological evidence of adaptations known in extant species. CONCLUSIONS: As the earliest unequivocal member of the genus, E. thermale supports the hypothesis of a Mesozoic origin. Its inferred tolerance of a similar range of stresses (e.g., high salinity, alkalinity, and heavy metal concentrations) to that seen in extant Equisetum suggests early evolution and subsequent maintenance of ecophysiological innovations in the genus.

Reasons for the presence or absence of convective (pressurized) ventilation in the genus Equisetum.

• The very high rates of convective ventilation reported recently in Equisetum telmateia (up to 120 cm(3) min(-1); internal wind speed, 10 cm s(-1)) prompted this study of a further eight species for the presence or absence of convection and the possible reasons for this. • Convection rates were examined in relation to anatomical pathways, internal resistance to applied pressurized gas flow and stomata. • Only species with interconnecting cortical aerenchyma in branches (when present), shoots and rhizomes induced convection. Rapid humidity-induced convection (HIC) occurred in E. palustre (up to 13 cm(3) min(-1)), with slower rates in E. × schaffneri and E. ramosissimum (≤ 6 and 3 cm(3) min(-1), respectively). Excised shoots of E. hyemale and E. fluviatile showed the potential for HIC (≤ 0.5 and 0.15 cm(3) min(-1), respectively), but not into the rhizomes. High rates were linked to low internal gas flow resistance. No convection was detected in E. scirpoides, E. sylvaticum or E. arvense due to the extremely high resistance to pressure flow, for example, from intercalary meristems and, in the last two, to nonaerenchymatous branches. • Of the nine Equisetum species studied so far, four showed through-flow convection; the other species must rely solely on diffusion for underground aeration in wet soils.

Record rates of pressurized gas-flow in the great horsetail, Equisetum telmateia. Were Carboniferous Calamites similarly aerated?

Significant pressurized (convective) ventilation has been demonstrated in some flowering wetland plants, for example water-lilies and reeds, but not previously in nonflowering plants. Here we investigated convective flows in the great horsetail, Equisetum telmateia, and the possibility that convections aerated the massive rhizomes of the Calamites, extinct giant horsetails of the Carboniferous. Convection in E. telmateia was examined in relation to induction sites, anatomical pathways, relative humidity (RH), external wind-speed, diurnal effects, rhizome resistance and pressure-gradients. A mathematical model, incorporating Calamite aeration anatomy, was applied in assessing potentials for convective aeration. Individual shoots of E. telmateia generated extremely high rates of humidity-induced convection: < or = 120 cm(3) min(-1) (internal wind-velocity: 10 cm s(-1)) with rates proportional to branch numbers and 1/RH. Flows passed through branches, stem and rhizome via low-resistance lacunae (vallecular canals) and vented via stubble. Stomata supported internal pressures up to 800 Pa. Anatomically, E. telmateia resembles the Calamites and modelling predicted possible flows of 70 l min(-1) per Calamite tree. This is the first demonstration of significant convective flow in a nonflowering species, indicating that plant ventilation by a type of 'molecular gas-pump' may date back 350 million yr or more. Stomatal form and low-resistance pathways may facilitate high flow rates.

Modelling primary and secondary growth processes in plants: a summary of the methodology and new data from an early lignophyte.

A mathematical method, based on polar coordinates that allow modelling of primary and secondary growth processes in stems of extant and fossil plants, is summarized and its potential is discussed in comparison with numerical methods using digitizing tablets or electronic image analysing systems. As an example, the modelling of tissue distribution in the internode of an extant sphenopsid (Equisetum hyemale) is presented. In the second half of the paper we present new data of a functional analysis of stem structure and biomechanics of the early lignophyte Tetraxylopteris schmidtii (Middle Devonian) using the polar coordinate method for modelling the tissue distribution in stems of different ontogenetic age. Calculations of the mechanical properties of the stems, based on the modelling of the tissue arrangement, indicate that there is no increase in structural bending modulus throughout the entire development of the plant. The oldest ontogenetic stage has a significantly smaller bending elastic modulus than the intermediate ontogenetic stage, a 'mechanical signal', which is not consistent with a self-supporting growth form. These results, and the ontogenetic variations of the contributions of different stem tissues to the flexural stiffness of the entire stem, are discussed in the evolutionary context of cambial secondary growth.