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.

This study demonstrated that plants respond to the environmental gradient by changing the y-intercepts of the relationship between leaf size-twig size, while keeping the exponent value of the allometric relationship as an invariant constant. The allometric growth in the twig size-leaf size spectrum is related to many other components of plant life history strategy, including the well established life history trade-off between efficiency and safety in the hydraulic transport of water.

Leaves and fine roots are among the most important and dynamic components of terrestrial ecosystems. To what extent plants synchronize their resource capture strategies above- and belowground remains uncertain. Existing results of trait relationships between leaf and root showed great inconsistency, which may be partly due to the differences in abiotic environmental conditions such as climate and soil. Moreover, there is currently little evidence on whether and how the stringent environments of high-altitude alpine ecosystems alter the coordination between above- and belowground. Here we measured six sets of analogous traits for both leaves and fine roots of 139 species collected from Tibetan alpine grassland and Mongolian temperate grassland. N, P and N:P ratio of leaves and fine roots were positively correlated, independent of biogeographic regions, phylogenetic affiliation or climate. In contrast, leaves and fine roots seem to regulate morphological traits more independently. The specific leaf area (SLA)-specific root length (SRL) correlation shifted from negative at sites under low temperature to positive at warmer sites. The cold climate of alpine regions may impose different constraints on shoots and roots, selecting simultaneously for high SLA leaves for rapid C assimilation during the short growing season, but low SRL roots with high physical robustness to withstand soil freezing. In addition, there might be more community heterogeneity in cold soils, resulting in multidirectional strategies of root in resource acquisition. Thus our results demonstrated that alpine climate alters the relationships between leaf and root morphological but not chemical traits.

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