Search

Dryopteris sect. Diclisodon is a small section of ferns with about 12 species mainly distributed in East Asia. Here, we carried out morphological and phylogenetic analyses of this section. A new species from southwest China, D. gaoligongensis, is described and illustrated. Dryopteris gaoligongensis resembles D. indonesiana and D. sparsa, but differs by having a creeping rhizome and large 4-pinnate fronds. We also show that D. glabrior Ching & Z.Y. Liu is a distinct species; however, because it is a later homonym of D. glabrior Copeland, it should be renamed D. renchangiana. We conclude that a species previously known as D. nitidula, also an illegitimate homonym, should be recognized with a new name, D. sinonepalensis. We resolve the phylogenetic position of D. yoroii as sister to other sampled species of D. sect. Diclisodon. Our phylogenetic analyses confirm the distinctiveness of D. gaoligongensis, D. renchangiana, and D. sinonepalensis. A key to species of D. sect. Diclisodon in China is provided.

Comprising about 82% of the extant fern species diversity, Polypodiales are generally believed to have diversified in the Late Cretaceous. We estimated the divergence times of Polypodiales using both penalized likelihood and Bayesian methods, based on a dataset consisting of 208 plastomes representing all 28 families and 14 fossil constraints reflecting current interpretations of fossil record. Our plastome phylogeny recovered the same six major lineages as a recent nuclear phylogeny, but the position of Dennstaedtiineae was different. The present phylogeny showed high resolution of relationships among the families of Polypodiales, especially among those forming the Aspleniineae. The divergence time estimates supported the most recent common ancestor of Polypodiales and its closest relative dating back to the Triassic, establishment of the major lineages in the Jurassic, and a likely accelerated radiation during the late Jurassic and the Early Cretaceous. The estimated divergence patterns of Polypodiales and angiosperms converge to a scenario in which their main lineages were established simultaneously shortly before the onset of the Cretaceous Terrestrial Revolution, and further suggest a pre-Cretaceous hidden history for both lineages. The pattern of simultaneous diversifications shown here elucidate an important gap in our understanding of the Terrestrial Revolution that shaped today's ecosystems.

Cytidine-to-uridine (C-to-U) RNA editing is common in coding regions of organellar genomes throughout land plants. In most cases RNA editing alters translated amino acids or creates new start codons, potentially confounds phylogenetic reconstructions. In this study, we used the spike moss genus Selaginella (lycophytes), which has the highest frequency of RNA editing, as a model to test the effects of extreme RNA editing on phylogenetic reconstruction. We predicted the C-to-U RNA editing sites in coding regions of 18 Selaginella plastomes, and reconstructed the phylogenetic relationships within Selaginella based on three data set pairs consisted of plastome or RNA-edited coding sequences, first and second codon positions, and translated amino acid sequences, respectively. We predicted between 400 and 3100 RNA editing sites of 18 Selaginella plastomes. The numbers of RNA editing sites in plastomes were highly correlated with the GC content of first and second codon positions, but not correlated with the GC content of plastomes as a whole. Contrast phylogenetic analyses showed that there were substantial differences (e.g., the placement of clade B in Selaginella) between the phylogenies generated by the plastome and RNA-edited data sets. This empirical study provides evidence that extreme C-to-U RNA editing in the coding regions of organellar genomes alters the sequences used for phylogenetic reconstruction, and might even confound phylogenetic reconstruction. Therefore, RNA editing sites should be corrected when plastid or mitochondrial genes are used for phylogenetic studies, particularly in those lineages with abundant organellar RNA editing sites, such as hornworts, quillworts, spike mosses, and some seed plants.

Neocheiropteris palmatopedata (Baker) Christ is an endangered fern species endemic to southwest China. In this study, we sequenced the complete plastid genome of N. palmatopedata. The gene order and structure of the N. palmatopedata plastome are similar to those published plastomes in Polypodiales. The complete plastome is 153,344 bp in length, and the GC content is 42.1%. The plastome comprises 113 unique genes (83 protein-coding genes, 29 tRNA genes and four rRNA genes).

Neocheiropteris palmatopedata (Baker) Christ is an endangered fern species endemic to southwest China. In this study, we sequenced the complete plastid genome of N. palmatopedata. The gene order an...

Studies on chloroplast genomes of ferns and lycophytes are relatively few in comparison with those on seed plants. Although a basic phylogenetic framework of extant ferns is available, relationships among a few key nodes remain unresolved or poorly supported. The primary objective of this study is to explore the phylogenetic utility of large chloroplast gene data in resolving difficult deep nodes in ferns. We sequenced the chloroplast genomes from Cyrtomium devexiscapulae (Koidz.) Ching (eupolypod I) and Woodwardia unigemmata (Makino) Nakai (eupolypod II), and constructed the phylogeny of ferns based on both 48 genes and 64 genes. The trees based on 48 genes and 64 genes are identical in topology, differing only in support values for four nodes, three of which showed higher support values for the 48-gene dataset. Equisetum L. was resolved as the sister to the Psilotales-Ophioglossales clade, and Equisetales-Psilotales-Ophioglossales clade was sister to the clade of the leptosporangiate and marattioid ferns. The sister relationship between the tree fern clade and polypods was supported by 82% and 100% bootstrap values in the 64-gene and 48-gene trees, respectively. Within polypod ferns, Pteridaceae was sister to the clade of Dennstaedtiaceae and eupolypods with a high support value, and the relationship of Dennstaedtiaceae-eupolypods was strongly supported. With recent parallel advances in the phylogenetics of ferns using nuclear data, chloroplast phylogenomics shows great potential in providing a framework for testing the impact of reticulate evolution in the early evolution of ferns.

DNA barcoding is a fast-developing technique to identify species by using short and standard DNA sequences. Universal selection of DNA barcodes in ferns remains unresolved. In this study, five plastid regions (rbcL, matK, trnH-psbA, trnL-F and rps4-trnS) and eight nuclear regions (ITS, pgiC, gapC, LEAFY, ITS2, IBR3_2, DET1, and SQD1_1) were screened and evaluated in the fern genus Adiantum from China and neighboring areas. Due to low primer universality (matK) and/or the existence of multiple copies (ITS), the commonly used barcodes matK and ITS were not appropriate for Adiantum. The PCR amplification rate was extremely low in all nuclear genes except for IBR3_2. rbcL had the highest PCR amplification rate (94.33%) and sequencing success rate (90.78%), while trnH-psbA had the highest species identification rate (75%). With the consideration of discriminatory power, cost-efficiency and effort, the two-barcode combination of rbcL+ trnH-psbA seems to be the best choice for barcoding Adiantum, and perhaps basal polypod ferns in general. The nuclear IBR3_2 showed 100% PCR amplification success rate in Adiantum, however, it seemed that only diploid species could acquire clean sequences without cloning. With cloning, IBR3_2 can successfully distinguish cryptic species and hybrid species from their related species. Because hybridization and allopolyploidy are common in ferns, we argue for including a selected group of nuclear loci as barcodes, especially via the next-generation sequencing, as it is much more efficient to obtain single-copy nuclear loci without the cloning procedure.

Adiantum consists of about 150-200 species mostly with a pantropical distribution, yet the classifications of Adiantum have been based primarily on regional studies. Confounding the clarity of reconstructing the evolutionary history of Adiantum is that previous molecular phylogenetic studies suggest that a separate and distinctive clade, the vittarioids, may be derived from within Adiantum. Five plastid markers (atpA, atpB, rbcL, trnL-F and rps4-trnS) are employed to assess the monophyly of Adiantum, and construct the molecular phylogeny of Chinese Adiantum. Our analyses support the monophyly of Adiantum. All temperate Adiantum species form a clade nested within the pantropical grade, suggesting a tropical origin of Adiantum. Six main clades are supported within Chinese Adiantum, which are only partially consistent with Lin's classification of the genus. Series Caudata is polyphyletic with series Gravesiana nested within one subgroup of series Caudata. The prolonged whip-like stolon at the apex of the fronds is the defining character for series Caudata, but it may have evolved multiple times. Adiantum reniforme with the simple fronds is sister to series Venusta, which has a decompound lamina with many flabellate to cuneate segments. Series Veneri-capilliformia is not monophyletic, with A. capillus-veneris sister to series Flabellulata except for A. diaphanum, and A. edentulum sister to series Pedata. Series Flabellulata is biphyletic with A. diaphanum nested within the pantropical grade. The phylogeny suggests that convergent evolution in frond architecture has occurred in Adiantum.

An earlier known species originally assigned to Asplenium from China, A. pubirhizoma Ching & Z.Y.Liu, is transferred to Hymenasplenium to form H. pubirhizoma (Ching & Z.Y.Liu) K.W.Xu & Li Bing Zhang, comb. nov.

Polystichum has often been treated as a sub-cosmopolitan genus of 180-230 species (i.e., Polystichum s.l.), but several segregate genera, such as Cyrtogonellum, Cyrtomidictyum, Cyrtomium, Phanerophlebia, and Sorolepidium, have been recognized in various treatments. Together, these genera constitute the polystichoid ferns. We used a data set of 47 species of the polystichoid ferns and three outgroups, including new rbcL sequences for six species in Asia, to address their phylogeny. Maximum-parsimony (MP) and Bayesian inference analyses were performed. The polystichoid ferns were resolved to include four major clades, the tropical American Phanerophlebia clade, the Cyrtomium s.s. clade, the Polystichum s.s. clade, and an eastern Asian clade containing Cyrtomium subser. Balansana, Cyrtogonellum, three sections of Polystichum, and Cyrtomidictyum (the BCPC clade). The Cyrtomium s.s. clade included 15 species of the genus but excluded subser. Balansana. The Polystichum s.s. clade was resolved as being monophyletic with relatively low bootstrap support, as long as Sorolepidium is included in Polystichum. The overall topology retrieved by the Bayesian analysis was similar to that of the MP tree, but generally had higher internal support. Based on the molecular phylogeny, three sections of Polystichum s.l., i.e., sect. Sphaenopolystichum, sect. Haplopolystichum, and sect. Crucifilix, may be more closely related to other members of the BCPC group. The eastern Asian BCPC group shared once-pinnate fronds, except for Polystichum sect. Sphaenopolystichum. Morphologically, once-pinnate leaf dissection and reticulate venation appear to be ancestral in the polystichoid ferns.

Cyrtomium (Dryopteridaceae) is an Asiatic genus comprising about 40 species characterized by having anastomosing veins that form areolae with included veinlets. Twelve chromosome counts representing 11 taxa were made in the present study. The chromosome numbers of six species endemic to China are reported for the first time: C. uniseriale, 2n = 164; C. guizhouense, 2n = 82; C. shingianum, n = 82, 2n = c.164; C. chingianum, 2n = 164; C. urophyllum, 2n = 82 and C. aequibasis, 2n = 123. The results were used to show that (1) C. uniseriale should be reduced to varietal status under C. balansae; (2) subseries Balansana is not closely related to any other Cyrtomium species and should be separated from Cyrtomium; and (3) C. guizhouense and C. lonchitoides are basal groups when subseries Balansana is not considered. These results were also supported by morphology. A high level of differentiation is a distinct characteristic in Cyrtomium. The genus has two reproductive types: sexual and apogamous. Sexual species are distributed mostly in China. Southwestern China is a modern diversity centre of Cyrtomium, with 80.6% of known species occurring there. Many species are endemic, most of which are sexual tetraploids or apogamous triploids. Both the apogamous reproductive type and polyploid species are adaptions to limestone habitats. (c) 2006 The Linnean Society of London.

The chromosome numbers and karyomorphology of 14 Chinese species of the genus Parnassia were in- vestigated. The chromosome numbers of 11 species were reported for the first time. The report of 2n=48 for P. monochrofolia Franch was new to the Chinese species of the genus. There are about 30 species cytologically studied up to now. From the available data, the species of Parnassia with the basic chromosome numbers of x=7, 8 and 9 were found in China and the Himalayas, in which the more species with x=9, as well as mainly in western N America, while x=8 was only found in eastern N. America. Polyploidization was common in the genus, more extensively in Northern America. Based on our results and the previously reported data, the basic chromosome numbers and poly- ploidization are discussed. Combined with gross morphology and geographical distribution of Parnassia, the phylo- genetic implications of the cytological data are also discussed. It is suggested that eastern Asia and western N America are probably the modern divergent centers of the genus.

Swertia mussotii is an important species in Tibetan folk medicine. However, it is quite expensive and frequently adulterated, so reliable methods for authentication of putative specimens and preparations of the species are needed to protect consumers and to support conservation measures. We show here that the chloroplast (cp) DNA rpl16 intron has limited utility for differentiating S. mussotii from closely related species, since the cpDNA rpl16 sequences are identical in S. mussotii and two other species of Swertia. However, the rDNA internal transcribed spacer (ITS) sequences differ significantly between S. mussotii and all of 13 tested potential adulterants. Thus, the ITS region provides a robust molecular marker for differentiating the medicinal S. mussotii from related adulterants. Therefore, a pair of allele-specific diagnostic primers based on the divergent ITS region was designed to distinguish S. mussotii from the other species. Authentication by allele-specific diagnostic PCR using these primers is convenient, effective and both simpler and less time-consuming than sequencing the ITS region.

Cyrtomium is an Asiatic genus characterized by anastomosing veins with included veinlets, and comprises about 40 species. We sequenced rbcL and trnL-F sequences of 19 species of Cyrtomium and eight species from related genera in order to elucidate a molecular phylogeny of the genus using maximum-parsimony methods. The phylogenetic trees did not agree with traditional classifications. Cyrtomium was resolved as paraphyletic, and a clade including subseries Balansana of Cyrtomium, Cyrtogonellum, Polystichum subacutidens and Cyrtomidictyum (the BCPC clade) and a second one containing Cyrtomium sensu stricto were monophyletic. The results also implied that: (1) C. uniseriale was synonymous with C. balansae; (2) C. falcatum was likely the female parent of C. devexiscapulae; and (3) based on the rbcL and trnL-F sequence data, C. nephrolepioides and C. grossum were the female parents of C. shingianum and C. chingianum, respectively, although other evidence is needed for the confirmation of this hypothesis.

Cyrtomium C. Presl is mostly distributed in China and Japan, and exhibits five different distribution patterns, viz., Sino-Himalayan, Sino-Japanese, South Indian-East African, East Himalayan-Taiwan disjunction, and Endemic; the endemics are restricted to Southwest China. Cyrtomium has two reproductive types, sexual and apogamous. The species having both reproductive types are mostly distributed in Southwest China. The reproductive types are correlated to altitude of habitat, ploidy level, distribution and morphology. Southwest China is the epicenter of evolution and diversification of Cyrtomium.