Lycophyte and fern genetic research has accumulated over recent years due to sequencing technology advancement, making nuclear, plastid, and mitochondrial genomes accessible. While early plastid genome research focused on reporting genome structures and sequence characteristics, our current understanding spans comprehensively over structural evolution and phylogenomic analyses. These studies provide us with important insight for understanding the early evolution of vascular plants. Although lycophyte and fern plastid genomes are relatively well understood, this paper summarizes the current understanding of lycophyte and fern plastid genome structure and its variation. Such variation includes large inversions, boundary shifts of repeat regions, gene and intron loss, and some of which could be recognized as synapomorphies of higher taxonomic ranks. We also review RNA editing and long noncoding sequence inserts in plastid genomes, which are prevalent in lycophytes and ferns. However, the origin, mechanism and function of such remain unclear. We also comment on the application, merit and future of plastid phylogenomics.

Lycophytes and ferns display dual life-history traits including a cryptogam (spore) and spermatophyte (vascular bundle) form, which can be attributed to their specific evolutionary history. Among them, epiphytic ferns occupy unique habitats in forests, and their life-history strategies and evolutionary history exhibit close relationships with forest ecosystems. Most epiphytic ferns are capable of clonal growth. However, it is yet unclear how clonal life-history traits affect the adaptation of epiphytic ferns to forest canopies. Here, we review studies of rhizomatous clonal growth of epiphytic ferns, the relationship of fern clonality with ecological adaptation, the clonal forms of ferns, and the evolution of fern clonality. We then discuss the roles of fern clonality in the processes and functions of forest ecosystem and suggest future directions of how to combine fern ecology to global change studies.

Species are not static, but in the process of continuous differentiation and evolution. In this context, reproductive isolation is considered the key to most speciation events. However, species that may be only partially reproductively isolated may disturb our understanding of a species, as stated by ‘The integrative species concept’. In the Flora of China, Chinese Sphaeropteris contains two species, S. brunoniana and S. lepifera. S. brunoniana is thought to be the same species as a Hainan native, S. hainanensis, however, S. hainanensis seems to have differentiated morphologically. This study further explores the genetic relationship between S. brunoniana and its related species by collecting 21 samples from 9 populations for GBS reduced-representation genome sequencing for phylogenetic analysis. Using both genetic and morphological data, our results indicate that S. hainanensis differs genetically from S. brunoniana, but is also morphologically distinct based on leaf characteristics and spore ornamentation. Although the reproductive isolation of the two populations is weak, hybrids are formed in the coastal areas of Guangxi and leaves mimic intermediate morphology between parents. Therefore, our results suggest that S. hainanensis is in the process of speciation due to geographic isolation and suggests to restore its species status. S. brunoniana × hainanensis which the sample from Guangxi should be considered an independent natural hybrid taxon.

Due to wide hybridization and polyploidization, there are numerous species complexes with taxonomic challenges in the fern genus Asplenium. Integrative taxonomy using evidence of morphology, cytology and molecular phylogeny provides one of the best ways for the discovery and delimitation of species. The Asplenium coenobiale complex represents one of the spleenwort complexes, which are morphologically variable and difficult in species delimitation. Owing to the lack of comprehensive sampling and systematic study, the taxonomy of this complex remains unresolved. In this study, we selected representative individuals of this complex covering differences in morphology and geography. We conducted a palynological study to explore reproductive characteristics, and inferred the ploidy level through flow cytometry. Furthermore, based on the phylogenetic evidence from chloroplast and nuclear genomes, we discussed the evolutionary relationship and origin of this complex. Our results showed that: (1) The development of 64 spores within a single normal sporangium is indicative of the ability of sexual reproduction, although abortive sporangia are common in the Asplenium coenobiale complex. (2) Ploidy variation is found in this complex, i.e. A. cornutissimum is diploid, whereas other members are all tetraploid. (3) The maternally inherited chloroplast phylogeny supported four clades within this complex, and this was incongruent with the nuclear phylogeny; therefore, it was inferred that hybridization could be an important driving force during the formation of the complex. Based on our analyses, we conduct a revision to the A. coenobiale complex, i.e. one newly discovered autotetraploid species (A. maguanense sp. nov.), one diploid species (A. cornutissimum), and two allotetraploids with reciprocal origins (A. coenobiale and A. pulcherrimum).

Whole genome duplication is an important driving force to speciation and evolution. Moreover, most existing plants and animals have experienced whole genome duplication in their evolutionary history. As the basal group of the Eupolypods I, Didymochlaena trancatula is the single fern species of Didymochlaenaceae. We performed transcriptome sequencing to detect whole genome duplication (WGD) events by analyzing age distributions built from synonymous substitution rates (Ks). We found that D. trancatula has experienced at least two WGDs during its evolutionary history. We dated the two WGDs at 59-62 million years ago (Mya) and 90-94 Mya, corresponding to Cretaceous-Tertiary (C-T) extinction event and the divergence time of D. trancatula, respectively. Annotation and functional enrichment analysis showed most duplicated genes that were retained are related to environmental regulation, further emphasizing the role that WGDs may play in the adaptive evolution of D. trancatula.

Spore morphology is diverse and complex in ferns, thus serving as an important indicator of taxonomy. In conjunction, morphological traits and phylogeny are used to study taxonomy and recent character evolution. This study analyzes the evolution of spore ornamentation in once-pinnate maidenhair ferns (Adiantum) using scanning electron microscopy and ancestral state reconstruction. Our results show that there are five ornamental types in once-pinnate maidenhair ferns: psilate, scabrate, granulate, verrucate and tuberculate. The ancestral state of spore ornamentation in Adiantum is probably tuberculate, with verrucate ornamentation possibly deriving from tuberculate. We suggest that spore ornamentation evolved from simple to complex in Adiantum. In other words, the more evolutionary species, will with a more complex spore ornamentation.

Fern oogenesis is a vital process in sexual reproduction, yet Polypodia II oogenesis has not been studied. This paper studies sexual reproduction oogenesis of Macrothelypteris torresiana of Polypodiaceae. Our findings document oogenesis and egg movement throughout sexual reproduction. The appearance of egg envelope, the formation of fertilization pore and nuclear evaginations during the development of Macrothelypteris torresiana are similar to other pteridophytes in eupolypods, and are significantly different from those of the primitive basal groups in leptosporangiates. This indicates that Macrothelypteris torresiana may be a evolutionary fern. Based on the characteristics of the egg envelope and the fertilization pore, we infer that primitive leptosporangiates evolved into polypods after passing through gleicheniales and cyatheales.

Ferns are a group of plants with a long history, and thus they provide important experimental materials in scientific studies. This study analyzes all papers that describe “fern”, “lycophyte”, “pteridophyte” and “pteridophyta” in the Web of Science database published from January 1 ^st, 2000 to December 31 ^st, 2018. Our four main results were: (1) After 2000, the number of scientific papers about ferns increased rapidly, with a significant increase after 2006. Today, the number of studies annually exceeds 600. (2) Since 2010, interdisciplinary fern research has become more common, in contrast to the fern-specific studies that were more common before 2010. (3) China has become a major leader in the number of fern and lycophyte publications. (4) Finally, there still needs some efforts for Chinese researchers in the following time. With the four above conclusions, our research review highlights new opportunities and directions for research related to ferns and serves as a guide fern researchers in China.

Field investigation and herbarium specimen information revealed that 261 species of lycophytes and ferns, belonging to 72 genera and 26 families were found in Mountain Mufu. It was characterized by Dryopteris-Asplenium flora with strong transiting distribution from east to west. The species richness was the highest (224 species) in Mount Lushan and the species density (2.09 species/km ²) was the highest in Mount Mufu. Besides Dryopteris included 29 species, Asplenium, Lepisorus and Selaginella were more abundant in Mount Lushan, Mount Jiugong and Mount Mufu, respectively. It shared only 95 common species among these three mountains, and the phenomena of neo-endemic genera and species was obvious. There were high restrictions on differentiation of genera and species in this area, which showed that monotypic family/genus and depauperate family/genus account for more than 60% of the total families and 80% of the total genera. The ratios of tropical elements to temperate elements (R/T) were 2.6 and 2.3 at the family and the generic level with tropical elements. Compared with the mountains in the same latitude zone, the R/T value at generic level in the junction zone of mid-subtropics and north subtropics was between 2.18-2.36. The R/T value was 0.2 at specific level with obvious temperate elements, which was an important component of the temperate flora of Luoxiao Mountains. The flora of lycophytes and ferns in this area was closely related to the flora of East and South China, showing the intersection of the two floristic components.

Species cataloguing is the basis for understanding their biodiversity. In the study, the diversity and geographical distribution of lycophytes and ferns in the Loess Plateau have been analyzed by utilizing published monographs, the current literature, and Herbaria specimens’ information. Following the order system from Flora of China, families and genera are classified relying on the latest research update on molecular taxonomy in this paper. Data analysis shows that the Loess Plateau is diverse with 165 species, 2 subspecies, 5 varieties, 42 genera and 18 families of lycophytes and ferns, which including 35 species endemic to China (20.35% of total species). The top five families are Pteridaceae (29 species, including subspecies and varieties), Dryopteridaceae (28 species), Polypodiaceae (19 species), Athyriaceae (16 species), and Aspleniaceae (16 species). The top six genera are Asplenium (16 species), Dryopteris (15 species), Polystichum (12 species), Woodsia (11 species), Selaginella (10 species), and Lepisorus (10 species). No rare and endangered plants, or endemic genera to China are contained. According to the ecological type, lycophytes and ferns are divided into 4 categories in the Loess Plateau, including terrestrial (112 species), lithophytes (75 species), epiphytes (18 species), and hydrophytes (3 species). The species of terrestrial or lithophytes are rich to 89.53% of the total species in this area. While the lycophytes and ferns of the Loess Plateau are located at the current geographical distribution edge, the distributions found in this study are consistent with our current understanding of lycophytes and ferns in China.