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Lycophytes are an ancient clade of the non-flowering vascular plants with chromosome numbers that vary from tens to hundreds. They are an excellent study system for examining whole-genome duplications (WGDs), or polyploidization, in spore-dispersed vascular plants. However, a lack of genome sequence data limits the reliable detection of very ancient WGDs, small-scale duplications (SSDs), and recent WGDs. Here, we integrated phylogenomic analysis and the distribution of synonymous substitutions per synonymous sites (Ks) of the transcriptomes of 13 species of lycophytes to identify, locate, and date multiple WGDs in the lycophyte family Lycopodiaceae. Additionally, we examined the genus Phlegmariurus for signs of genetic discordance, which can provide valuable insight into the underlying causes of such conflict (e.g., hybridization, incomplete lineage sorting, or horizontal gene transfer).We found strong evidence that two WGD events occurred along the phylogenetic backbone of Lycopodiaceae, with one occurring in the common ancestor of extant Phlegmariurus (Lycopodiaceae) approximately 22–23 million years ago (Mya) and the other occurring in the common ancestor of Lycopodiaceae around 206–214 Mya. Interestingly, we found significant genetic discordance in the genus Phlegmariurus, indicating that the genus has a complex evolutionary history. This study provides molecular evidence for multiple WGDs in Lycopodiaceae and offers phylogenetic clues to the evolutionary history of Lycopodiaceae.

Fenghwaia, a new monotypic genus, along with the new species Fenghwaia gardeniicarpa, is described from Guangdong Province, China. The combined features of inferior ovary, cylindrical drupaceous fruits and orbicular and dorsiventrally-compressed seeds with an elongate and pronounced basal appendage make the new genus significantly different from other genera of the family. In addition, its pollen morphology also showed great similarity to other species of this stenopalynous family. The molecular phylogenetic analysis, based on nuclear ribosomal internal transcribed spacer (ITS) and plastid trnL-F intron spacer (trnL-F) DNA sequence data from the new genus and the other 375 species representing 58 genera of Rhamnaceae, indicates that Fenghwaia is nested within the ‘rhamnoid’ group and sister to the tribe Rhamneae and then both sister to the tribe Maesopsideae. A taxonomic classification key to the ‘rhamnoid’ group is provided, based on morphological characters. A global conservation assessment is also performed and classifies Fenghwaia gardeniicarpa as Near Threatened (NT).

Begonia danxiaensis, a new tuberous species of Begonia, is described and illustrated, and supported by morphological and molecular evidences. It belongs to Begonia sect. Diploclinium and is endemic to the Danxia landforms of both Jiangxi and Hunan provinces, China. The morphological similarity between the new species and its similar taxa were compared and discussed. The new species is assigned to Vulnerable (VU) according to the IUCN Red List Categories and Criteria.

Begonia yizhouensis, a new species in Begonia sect. Coelocentrum (Begoniaceae) from Guangxi of China, is described and illustrated. Morphologically, it is similar to the adjacently distributed B. luochengensis, but clearly separated by its waxy leaves with glabrous or sometimes sparsely puberulous surfaces, larger variation in leaf color and maculation along the main veins, white to pinkish-white flowers and late flowering. Furthermore, molecular phylogenetic analysis indicated B. yizhouensis was a monophyletic lineage and was sister with B. luochengensis. The relationship of the new species and other similar species is also discussed. This new species is endemic to limestone hills in Guangxi and is assessed as “Endangered” (EN) according to the IUCN Red List Categories and Criteria. Additionally, morphological and molecular evidence for B. yishanensis not being synonymous with B. porteri is presented.

A new diploid species of marattioid ferns, Angiopteris sugongii Gui L. Zhang, J.Y. Xiang & Ting Wang (Marattiaceae), with ascending rhizomes, once pinnate to bipinnate laminae and marginal long sori, is identified and characterized from Southeast Yunnan, China. The distinctiveness between the new species and three relatives, A. itoi, A. bipinnata and A. sparsisora, are presented in detail, and a key to 11 species with once pinnate, or once pinnate to bipinnate laminae of Angiopteris in China is provided. Currently, there are three populations with 30 individuals in Daweishan National Nature Reserve and we suggest A. sugongii should be categorized as Critically Endangered (CR) species according to the criteria of IUCN. The discovery of this new species not only provides an important evidence for understanding the evolution of Angiopteris (sen. lat.), but also gives us a key insight into origin of species in the genus.

Dryopteris wulingshanensis, a new species growing on limestone in the Wulingshan Mountains, Hunan, China, is described and illustrated. This species is most similar to D. jishouensis and D. gymnophylla on general morphological traits, such as the form of scales, rhizome and sori, but differs by the number of vascular bundles at the base of the petiole, length to width ratio of lamina, stalk length of basal pinnae, division of the lamina, apex form of the pinnule and habitat. Moreover, molecular phylogenetic analysis using the chloroplast rbcL gene suggested that D. wulingshanensis, as the sister group of D. jishouensis, is a monophyletic clade. According to its restricted geographic range, small populations and few individuals, D. wulingshanensis should be considered endangered, according to the IUCN Red List criteria.

Epiphytic ferns have been found to flourish after angiosperms dominated forest communities, and they play important roles in rainforest canopies. How do epiphytic ferns adapt to tropical rainforest canopy habitats? At present, we know little about the molecular mechanism underlying this adaptation. Asplenium nidus is a well-known epiphytic fern that is closely related to the terrestrial species Asplenium komarovii. Here, RNA-seq and comparative transcriptomic analyses were performed to explore the underlying basis of the adaptation of A. nidus to extreme environments. A total of 44.04 and 44.57 Mb clean reads were obtained from A. nidus and A. komarovii, respectively, and they were assembled into 89,741 and 77,912 unigenes. Functional annotation showed that 52,305 (58.28% of the total genes for A. nidus) and 45,938 (58.96% of the total genes for A. komarovii) unigenes were annotated in public databases. Genes involved in stress responses and photosynthesis were found to have undergone positive selection in A. nidus. Compared to A. komarovii, transcription factors related to stress response, leaf development, and root development were found to be considerably expanded in A. nidus, especially in the ANR1 subclade of MADS-box family genes which played roles in lateral root development. This study improves our understanding of the adaptation of A. nidus to epiphytic habitats by forming unique strategies.

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.