g-Wei Chen

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.

Global phylogeny and biogeography of grammitid ferns (Polypodiaceae).

We examined the global historical biogeography of grammitid ferns (Polypodiaceae) within a phylogenetic context. We inferred phylogenetic relationships of 190 species representing 31 of the 33 currently recognized genera of grammitid ferns by analyzing DNA sequence variation of five plastid DNA regions. We estimated the ages of cladogenetic events on an inferred phylogeny using secondary fossil calibration points. Historical biogeographical patterns were inferred via ancestral area reconstruction. Our results supported four large-scale phylogenetic and biogeographic patterns: (1) a monophyletic grammitid clade that arose among Neotropical polypod ancestors about 31.4 Ma; (2) a paraphyletic assemblage of clades distributed in the Neotropics and the Afro-Malagasy region; (3) a large clade distributed throughout the Asia-Malesia-Pacific region that originated about 23.4 Ma; and, (4) an Australian or New Zealand origin of the circumaustral genus Notogrammitis. Most genera were supported as monophyletic except for Grammitis, Oreogrammitis, Radiogrammitis, and Zygophlebia. Grammitid ferns are a well-supported monophyletic group with two biogeographically distinct lineages: a primarily Neotropical grade exhibiting several independent successful colonizations to the Afro-Malagasy region and a primarily Paleotropical clade exhibiting multiple independent dispersals to remote Pacific islands and temperate, austral regions.

trnL-F is a powerful marker for DNA identification of field vittarioid gametophytes (Pteridaceae)

BACKGROUND AND AIMS The gametophyte phase of ferns plays an important role in habitat selection, dispersal, adaptation and evolution. However, ecological studies on fern gametophytes have been impeded due to the difficulty of species identification of free-living gametophytes. DNA barcoding provides an alternative approach to identifying fern gametophytes but is rarely applied to field studies. In this study, an example of field vittarioid gametophyte identification using DNA barcoding, which has not been done before, is given. METHODS A combination of distance-based and tree-based approaches was performed to evaluate the discriminating power of three candidate barcodes (matK, rbcL and trnL-F) on 16 vittarioid sporophytes. Sequences of the trnL-F region were generated from 15 fern gametophyte populations by tissue-direct PCR and were compared against the sporophyte dataset, using BLAST. KEY RESULTS trnL-F earns highest primer universality and discriminatory ability scores, whereas PCR success rates were very low for matK and rbcL regions (10·8 % and 41·3 %, respectively). BLAST analyses showed that all the sampled field gametophytes could be successfully identified to species level. Three gametophyte populations were also discovered to be living beyond the known occurrence of their sporophyte counterparts. CONCLUSIONS This study demonstrates that DNA barcoding (i.e. reference databasing, tissue-direct PCR and molecular analysis), especially the trnL-F region, is an efficient tool to identify field gametophytes, and has considerable potential in exploring the ecology of fern gametophytes.

A revised generic classification of vittarioid ferns (Pteridaceae) based on molecular, micromorphological, and geographic data

In ferns, as in most branches of the tree of life, phylogenetic analyses of molecular data have greatly improved our ability to identify natural groupings that are subsequently reflected in classifications grounded in the principle of monophyly (Smith & al., 2006; Rothfels & al., 2012; Christenhusz & Chase, 2014). In some cases, the results of such analyses are consistent with earlier notions of relationships inferred from morphological features (Schneider & al., 2009). However, in many other instances, lineages are revealed that are morphologically confounding and we struggle to identify synapomorphies (Sundue & Rothfels, 2014). The pursuit of such defining characteristics is especially problematic when working within a group possessing very limited morphological disparity. The well-defined vittarioid fern clade consists of 100–130 (Lindsay, 2003) highly simplified and predominantly epiphytic species (Fig. 1). These plants, characterized by the presence of silica bodies (Sundue, 2009) but a lack of sclerenchyma (Bower 1928; Ruhfel & al., 2008), were long regarded as composing a distinct family—Vittariaceae (Ching, 1940; Tryon & Tryon, 1982; Kramer, 1990). However, phylogenetic analyses have demonstrated that these ferns nest well within the Pteridaceae (Crane & al., 1995; Hasebe & al., 1995; Prado & al., 2007; Schuettpelz & al., 2007), as sister to the genus Adiantum L. (Lu & al., 2012; Rothfels & Schuettpelz, 2014; Pryer & al., 2016). The vittarioids have been variously partitioned through time (Benedict, 1911; Williams, 1927; Copeland, 1947). In the years leading up to the first molecular phylogenetic analyses of these ferns, six genera were commonly recognized based primarily on leaf division, venation, and the distribution of A revised generic classification of vittarioid ferns (Pteridaceae) based on molecular, micromorphological, and geographic data

A New Vittarioid Fern Species, Haplopteris heterophylla (Pteridaceae)

Abstract A vittarioid fern (Pteridaceae) distributed in Eastern Asia is described here as a new species, Haplopteris heterophylla, which has long been included in H. hainanensis. A description, illustration, distribution, ecology, and a key to congeneric relatives of the new species are provided. Obovoid-shaped paraphyses and frond dimorphism are the diagnostic characteristics of H. heterophylla. In a trnL-F + matK + ndhF phylogeny of 14 Asian Haplopteris species, including H. hainanensis, both morphological observations and the cpDNA phylogeny support the systematic uniqueness of H. heterophylla.

New insights on the phylogeny of Tectaria (Tectariaceae), with special reference to Polydictyum as a distinct lineage

The fern genus Tectaria (Tectariaceae) Cav. is morphologically diverse and difficult in terms of recognizing species and species groups. To infer the systematic positions of some species and identity‐unknown collections with special morphological characters, we undertook phylogenetic analyses based on sequences of five plastid regions (atpB, ndhF + ndhF‐trnL, rbcL, rps16‐matK + matK, and trnL‐F). Three analysis methods (maximum parsimony, maximum likelihood, and Bayesian inference) were used to reconstruct the phylogeny of Tectaria. The most surprising result is that T. menyanthidis (C. Presl) Copel., T. ternata (Baker) Copel., and T. variabilis Tardieu & Ching are revealed to represent a distinct lineage from Tectaria, which should be called Polydictyum C. Presl, and is supported as sister to Pteridrys C. Chr. & Ching. Other accessions of Tectaria are well resolved into four major clades, which is consistent with the results of previous studies. Of the four clades, Clade II (T. subtriphylla (Hook. & Arn.) Copel. group) is unpredictable, with morphologically very diverse species clustered there, and is supposed to be a minor evolutionary line within Tectaria in the Old World. In addition, the position of the climbing genus Arthropteris J. Sm. and the utility of molecular data in recognizing species of Tectaria are briefly discussed. As a conclusion, we formally reinstate the genus Polydictyum by providing diagnostic characters, key to species, nomenclature, and information of detailed distribution and habitat for the currently known three species.

Phylogenetic analyses place the monotypic Dryopolystichum within Lomariopsidaceae

Abstract The monotypic fern genus Dryopolystichum Copel. combines a unique assortment of characters that obscures its relationship to other ferns. Its thin-walled sporangium with a vertical and interrupted annulus, round sorus with peltate indusium, and petiole with several vascular bundles place it in suborder Polypodiineae, but more precise placement has eluded previous authors. Here we investigate its phylogenetic position using three plastid DNA markers, rbcL, rps4-trnS, and trnL-F, and a broad sampling of Polypodiineae. We also provide new data on Dryopolystichum including spore number counts, reproductive mode, spore SEM images, and chromosome counts. Our maximum-likelihood and Bayesian-inference phylogenetic analyses unambiguously place Dryopolystichum within Lomariopsidaceae, a position not previously suggested. Dryopolystichum was resolved as sister to a clade comprising Dracoglossum and Lomariopsis, with Cyclopeltis as sister to these, but clade support is not robust. All examined sporangia of Dryopolystichum produced 32 spores, and the chromosome number of sporophyte somatic cells is ca. 164. Flow cytometric results indicated that the genome size in the spore nuclei is approximately half the size of those from sporophyte leaf tissues, suggesting that Dryopolystichum reproduces sexually. Our findings render Lomariopsidaceae as one of the most morphologically heterogeneous fern families. A recircumscription is provided for both Lomariopsidaceae and Dryopolystichum, and selected characters are briefly discussed considering the newly generated data.

End of an enigma: Aenigmopteris belongs in Tectaria (Tectariaceae: Polypodiopsida)

The phylogenetic affinities of the fern genus Aenigmopteris have been the subject of considerable disagreement, but until now, no molecular data were available from the genus. Based on the analysis of three chloroplast DNA regions (rbcL, rps16-matK, and trnL-F) we demonstrate that Aenigmopteris dubia (the type species of the genus) and A. elegans are closely related and deeply imbedded in Tectaria. The other three species of genus are morphologically very similar; we therefore transfer all five known species into Tectaria. Detailed morphological comparison further shows that previously proposed diagnostic characters of Aenigmopteris fall within the range of variation of a broadly circumscribed Tectaria.

Pteris borneensis (Pteridaceae), a New Species from Borneo, with Re-Circumscription of Pteris decrescens and Pteris Parviloba

Abstract A new species was collected during a fern expedition in the Nuluhon Trusmadi Forest Reserve, Sabah, Borneo. Morphologically, it is similar to both Pteris decrescens Christ and P. parviloba Christ but can be distinguished by frond characters. Specifically, the new species differs from the other two species by having basiscopic secondary pinnae (vs. without basiscopic secondary pinnae), petiolulate pinnae (vs. sessile pinnae), without bristles on the stipes (vs. with bristles on the stipes), a crenate margin of the pinna-segment apex (vs. a serrate apex), and entire pseudoindusia (vs. ciliate pseudoindusia). Furthermore, P. decrescens and P. parviloba differ in the number of lateral pinnae (5 or 6 vs. 8–16 pairs) and the length of the basal pinna-segments being shortest or longest of all lateral pinnae. Two plastid genes, rbcL and matK, were used to decipher their phylogenetic relationships. The new species was resolved in different clades from P. decrescens and P. parviloba, providing further support of its uniqueness. The morphology, illustrations, ecology, and distribution of the new species are provided. We also found that the type materials of P. decrescens included two different species, P. decrescens and P. parviloba.A lectotype of P. decrescens was therefore designated. Based on the results of this study, P. decrescens and P. parviloba are re-circumscribed, and the new species is described as P. borneensis sp. nov.

Not only in the temperate zone: independent gametophytes of two vittarioid ferns (Pteridaceae, Polypodiales) in East Asian subtropics

Independent gametophyte ferns are unique among vascular plants because they are sporophyteless and reproduce asexually to maintain their populations in the gametophyte generation. Such ferns had been primarily discovered in temperate zone, and usually hypothesized with (sub)tropical origins and subsequent extinction of sporophyte due to climate change during glaciations. Presumably, independent fern gametophytes are unlikely to be distributed in tropics and subtropics because of relatively stable climates which are less affected by glaciations. Nonetheless, the current study presents cases of two independent gametophyte fern species in subtropic East Asia. In this study, we applied plastid DNA sequences (trnL-L-F and matK + ndhF + chlL datasets) and comprehensive sampling (~80%) of congeneric species for molecular identification and divergence time estimation of these independent fern gametophytes. The two independent gametophyte ferns were found belonging to genus Haplopteris (vittarioids, Pteridaceae) and no genetic identical sporophyte species in East Asia. For one species, divergence times between its populations imply recent oversea dispersal(s) by spores occurred during Pleistocene. By examining their ex situ and in situ fertility, prezygotic sterility was found in these two Haplopteris, in which gametangia were not or very seldom observed, and this prezygotic sterility might attribute to their lacks of functional sporophytes. Our field observation and survey on their habitats suggest microhabitat conditions might attribute to this prezygotic sterility. These findings point to consideration of whether recent climate change during the Pleistocene glaciation resulted in ecophysiological maladaptation of non-temperate independent gametophyte ferns. In addition, we provided a new definition to classify fern gametophyte independences at the population level. We expect that continued investigations into tropical and subtropical fern gametophyte floras will further illustrate the biogeographic significance of non-temperate fern gametophyte independence.