Ran Wei

A community-derived classification for extant lycophytes and ferns

Phylogeny has long informed pteridophyte classification. As our ability to infer evolutionary trees has improved, classifications aimed at recognizing natural groups have become increasingly predictive and stable. Here, we provide a modern, comprehensive classification for lycophytes and ferns, down to the genus level, utilizing a community‐based approach. We use monophyly as the primary criterion for the recognition of taxa, but also aim to preserve existing taxa and circumscriptions that are both widely accepted and consistent with our understanding of pteridophyte phylogeny. In total, this classification treats an estimated 11 916 species in 337 genera, 51 families, 14 orders, and two classes. This classification is not intended as the final word on lycophyte and fern taxonomy, but rather a summary statement of current hypotheses, derived from the best available data and shaped by those most familiar with the plants in question. We hope that it will serve as a resource for those wanting references to the recent literature on pteridophyte phylogeny and classification, a framework for guiding future investigations, and a stimulus to further discourse.

Toward a new circumscription of the twinsorus-fern genus Diplazium (Athyriaceae): A molecular phylogeny with morphological implications and infrageneric taxonomy

Diplazium and allied segregates (Allantodia, Callipteris, Monomelangium) represent highly diverse genera belong- ing to the lady-fern family Athyriaceae. Because of the morphological diversity and lack of molecular phylogenetic analyses of this group of ferns, generic circumscription and infrageneric relationships within it are poorly understood. In the present study, the phylogenetic relationships of these genera were investigated using a comprehensive taxonomic sampling including 89 species representing all formerly accepted segregates. For each species, we sampled over 6000 DNA nucleotides of up to seven plastid genomic regions: atpA, atpB, matK, rbcL, rps4, rps4-trnS IGS, and trnL intron plus trnL-trnF IGS. Phylogenetic analyses including maximum parsimony, maximum likelihood and Bayesian methods congruently resolved Allantodia, Cal - lipteris and Monomelangium nested within Diplazium; therefore a large genus concept of Diplazium is accepted to keep this group of ferns monophyletic and to avoid paraphyletic or polyphyletic taxa. Four well-supported clades and eight robust sub- clades were found in the phylogenetic topology. Reconstruction of the evolutionary pattern of morphological characters, such as dissections of leaves, petiole/rachis scales, and shapes of sori, recovered some character combinations of systematic value for infrageneric classification. In light of morphological characters and our molecular phylogeny, a re-defined Diplazium and an infrageneric classification are proposed.

Plastid Phylogenomics Resolve Deep Relationships among Eupolypod II Ferns with Rapid Radiation and Rate Heterogeneity

Abstract The eupolypods II ferns represent a classic case of evolutionary radiation and, simultaneously, exhibit high substitution rate heterogeneity. These factors have been proposed to contribute to the contentious resolutions among clades within this fern group in multilocus phylogenetic studies. We investigated the deep phylogenetic relationships of eupolypod II ferns by sampling all major families and using 40 plastid genomes, or plastomes, of which 33 were newly sequenced with next-generation sequencing technology. We performed model-based analyses to evaluate the diversity of molecular evolutionary rates for these ferns. Our plastome data, with more than 26,000 informative characters, yielded good resolution for deep relationships within eupolypods II and unambiguously clarified the position of Rhachidosoraceae and the monophyly of Athyriaceae. Results of rate heterogeneity analysis revealed approximately 33 significant rate shifts in eupolypod II ferns, with the most heterogeneous rates (both accelerations and decelerations) occurring in two phylogenetically difficult lineages, that is, the Rhachidosoraceae–Aspleniaceae and Athyriaceae clades. These observations support the hypothesis that rate heterogeneity has previously constrained the deep phylogenetic resolution in eupolypods II. According to the plastome data, we propose that 14 chloroplast markers are particularly phylogenetically informative for eupolypods II both at the familial and generic levels. Our study demonstrates the power of a character-rich plastome data set and high-throughput sequencing for resolving the recalcitrant lineages, which have undergone rapid evolutionary radiation and dramatic changes in substitution rates.

Molecular Phylogeny of the Cliff Ferns (Woodsiaceae: Polypodiales) with a Proposed Infrageneric Classification

The cliff fern family Woodsiaceae has experienced frequent taxonomic changes at the familial and generic ranks since its establishment. The bulk of its species were placed in Woodsia, while Cheilanthopsis, Hymenocystis, Physematium, and Protowoodsia are segregates recognized by some authors. Phylogenetic relationships among the genera of Woodsiaceae remain unclear because of the extreme morphological diversity and inadequate taxon sampling in phylogenetic studies to date. In this study, we carry out comprehensive phylogenetic analyses of Woodsiaceae using molecular evidence from four chloroplast DNA markers (atpA, matK, rbcL and trnL–F) and covering over half the currently recognized species. Our results show three main clades in Woodsiaceae corresponding to Physematium (clade I), Cheilanthopsis–Protowoodsia (clade II) and Woodsia s.s. (clade III). In the interest of preserving monophyly and taxonomic stability, a broadly defined Woodsia including the other segregates is proposed, which is characterized by the distinctive indument and inferior indusia. Therefore, we present a new subgeneric classification of the redefined Woodsia based on phylogenetic and ancestral state reconstructions to better reflect the morphological variation, geographic distribution pattern, and evolutionary history of the genus. Our analyses of the cytological character evolution support multiple aneuploidy events that have resulted in the reduction of chromosome base number from 41 to 33, 37, 38, 39 and 40 during the evolutionary history of the cliff ferns.

Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns

Abstract 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.

A total-evidence phylogeny of the lady fern genus Athyrium Roth (Athyriaceae) with a new infrageneric classification

The lady fern genus Athyrium represents one of the most diversified lineages in Athyriaceae with about 160-220 known species, and is notorious for its taxonomic difficulty. Despite progress in recent phylogenetic studies involving this genus, it still lacks a modern systematic and taxonomic update using integrative analyses of molecular and morphological evidence based on a broad species sampling. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the genus to date based on a total-evidence approach, covering all formerly accepted segregates within the athyrioid ferns. We sampled up to eight plastid markers and 20 morphological characters for each species. Our analyses, including maximum parsimony, maximum likelihood and Bayesian inference, yield a robust phylogenetic framework. We find that Athyrium is not monophyletic by recovering Athyrium skinneri and A. alpestre nested with Anisocampium and Cornopteris respectively while Pseudocystopteris is included in Athyrium. Furthermore, eight well-resolved clades and two isolated species within Athyrium are found in the phylogenetic topology, which can be also characterized by morphological synapomorphies from traits of petioles, leaves, sori and spores. In the interest of recognizing monophyletic taxa with morphological synapomorphies, we agree with the inclusion of Pseudocystopteris in Athyrium as proposed in previous studies, but treat Anisocampium and Cornopteris as separate genera. We further propose to resurrect a monotypic Pseudathyrium to accommodate A. alpestre. Based on morphological characters and molecular phylogeny, a new infrageneric classification system of Athyrium is proposed which subdivided it into ten sections, and one New-World species A. skinneri is transferred into Anisocampium.

New infrageneric classification of Abies in light of molecular phylogeny and high diversity in western North America: New infrageneric classification of Abies

Abies Mill. represents one of the most diverse lineages in Pinaceae with ca. 50 species. Recent phylogenetic studies of Abies using regions of the nuclear and plastid genomes generally support recent classifications. However, we have previously shown that in several cases sectional memberships should be revised, and more species are needed to generate a robust infrageneric classification. Therefore, we present a revision of Abies taxonomy based on phylogeny using the most comprehensive taxon sampling (52 taxa worldwide) to date and five chloroplast gene regions and one single‐copy nuclear gene (LFY). Our phylogenetic analyses, including maximum parsimony, maximum likelihood, and Bayesian inference, yield seven well‐supported lineages that are consistent with previous studies. Our taxonomic revision integrates the phylogenies presented here as well as those from other studies. We merged sect. Pseudopicea with sect. Momi, recognized the merger of sect. Abies with sect. Piceaster, and sect. Grandis with sect. Oiamel. We recognized sect. Balsamea by excluding A. kawakamii (Hayata) T. Itô and we suspect that ancient hybridization was involved in its origin. A short morphological description is provided for each section, as well as its geographic distribution and list of accepted names of species. Five of the seven sections consist primarily of species in western North America, especially within the California Floristic Province. Phylogenetic results show that western North America is home to an exceptionally high diversity of fir lineages, which is further corroborated by the cuticle morphology and internal transcribed spacer genotypes based on the length differences.

Athyrium sessilipinnum : A new lady fern (Athyriaceae) from southern China

A new species of Athyrium from southern China is described and illustrated as Athyrium sessilipinnum. Morphological comparisons among this new species and similar ones (e.g., A. arisanense, A. gedeanum, A. epirachis, and A. otophorum) are provided. Molecular evidence reveals a sister relationship between the new species and A. arisanense. The most distinctive characters of A. sessilipinnum are the sessile, non-pinnatifid and non-shortened pinnae.

Hiya: A new genus segregated from Hypolepis in the fern family Dennstaedtiaceae, based on phylogenetic evidence and character evolution

The relationship of Hypolepis brooksiae, H. nigrescens, and H. scabristipes to the remainder of Hypolepis (Dennstaedtiaceae) has been questioned by previous authors based on their unique combination of morphological characters and different base chromosome number. Using four chloroplast genes including rbcL, atpA, rpL6, and rps4-trnS intergenic spacer (IGS) from 32 samples, representing 24 species of Dennstaedtiaceae, we recovered a clade comprising H. brooksiae and H. nigrescens, distinct from the remaining species of Hypolepis. This clade is resolved as sister to the clade comprising Blotiella, Paesia and Histiopteris. We reconstructed ancestral states of 16 morphological characters and found that this clade is distinguished by indeterminate, scandent leaves exhibiting rhythmic growth, provided with recurved black-tipped prickles, and stipule-like pinnules that protect the emerging crosier and pinnae departures, rachis-costa architecture where the adaxial sulcus is confluent with the next lower order, and a base chromosome number of x = 29. In light of this molecular and morphological evidence, we describe a new genus, Hiya, and provide nomenclatural combinations to accommodate the three known species segregated from Hypolepis: Hiya brooksiae, Hiya nigrescens, and Hiya scabristipes.

Phylogeny, historical biogeography and characters evolution of the drought resistant fern Pyrrosia Mirbel (Polypodiaceae) inferred from plastid and nuclear markers

Pyrrosia s.l. comprises ca. 60 species with a disjunct Africa/Asia and Australia distribution. The infrageneric classification of Pyrrosia s.l. is controversial based on the phylogenetic analyses of chloroplast markers and morphology. Based on the expanded taxon sampling of Pyrrosia s.l. (51 species), we investigated its phylogeny, biogeography, character evolution and environmental adaptation by employing five chloroplastid markers (rbcL, matK, psbA-trnH, and rps4 + rps4-trnS) and one single (low)-copy nuclear gene, LEAFY. Pyrrosia s.l. was divided into six major clades and eight subclades. Reticulate evolution was revealed both among clades and among species in Pyrrosia s.l. Ancestral character state optimization revealed high levels of homoplastic evolution of the diagnostic characters in Pyrrosia s.l., while the crassulacean acid metabolism pathway seems to have an independent origin. Molecular dating and biogeographic diversification analyses suggested that Pyrrosia s.l. originated no later than the Oligocene and the main clades diversified during the Oligocene and Miocene, with southern Asia, the Indo-China Peninsula and southwestern and southern China as the most likely ancestral areas. Transoceanic long-distance dispersal, rather than vicariance, contributed to the intercontinental disjunction. Diversification scenarios of Pyrrosia s.l. under geological movements and climate fluctuation are also discussed.