Atsushi Ebihara

• National Museum of Nature and Science

This study revises the taxonomy of Cephalomanes javanicum (Hymenophyllaceae), a filmy fern traditionally considered widespread across the Indomalayan and Australasian regions. Through a comprehensive analysis of the literature, type specimens, and herbarium collections, we clarify the taxonomic status of three recognized varieties: typical C. javan...

Many plant species experience a prolonged subterranean phase during which they rely entirely on mycorrhizal fungi for carbon. While this mycoheterotrophic strategy spans liverworts, lycophytes, and ferns, most empirical research has centered on angiosperms. This study explores the fungal associations of Sceptridium (Ophioglossaceae), an early‐diver...

HERBARIUM PLANT SPECIMENS AND THEIR HERBARIUM HOLDINGS Natural history collections around the globe represent a dormant source of taxonomic and biogeographic information, as it is estimated that one to three billion specimens are included in such collections (Soberon 1999; Ariño 2010). In the case of botanical collections, the worldwide distributio...

The fern independent gametophytes that can maintain populations by vegetative reproduction without conspecific sporophytes have been considered an unusual phenomenon found in some epiphytic or epilithic species of Hymenophyllaceae, Pteridaceae, Lomariopsidaceae, and Polypodiaceae. By chance, the discovery of mysterious strap-like gametophytes on Iz...

A new hybrid, Dryopteris ×makabensis (Dryopteridaceae) is described from Ibaraki Prefecture, Japan. Morphological observations, ploidy analysis, as well as nuclear and plastid DNA analyses, indicate that this diploid sterile hybrid likely originated from a cross between D. caudipinna and D. tokyoensis. Its occurrence is likely infrequent because th...

Hymenophyllum pilosissimum C. Chr. (Hymenophyllaceae), recently discovered on Iriomote Island, is reported for the first time in Japan.

Previous phylogenies showed conflicting relationships among the subfamilies and genera within the fern family Ophioglossaceae. However, their classification remains unsettled where contrasting classifications recognize four to 15 genera. Since these treatments are mostly based on phylogenetic evidence using limited, plastid-only loci, a phylogenomi...

Callistopteris superba is a peculiar Asian species within the genus Callistopteris (Hymenophyllaceae). A detailed morphological study of available herbarium specimens was conducted and the species was integrated into a global molecular phylogeny of the family in order to more precisely investigate its taxonomy. Morphological analysis and dated phyl...

Hymenophyllaceae (filmy ferns), with ca. 430 species, are the most species-rich family of early diverging leptosporangiate ferns but have a poor fossil record dating back to the Late Triassic period. Traditionally, Hymenophyllaceae comprise two species-rich genera or clades: Hymenophyllum (hymenophylloids) and Trichomanes sensu lato (s.l.) (trichom...

Spicantopsis hancockii (Blechnaceae) was once thought to be endemic to Taiwan, and later known to occur in the Tokara Islands in southern Japan. Because of its high morphological similarity to S. niponica endemic to Japan, the identification of the Tokara Archipelago populations has been controversial. MIG-seq analysis using 2324 SNPs revealed that...

Haplopteris mediosora (Hayata) X. C. Zhang (Pteridaceae), a fern with linear simple fronds is widely distributed at high elevations from the Himalayas through China, the Philippines and Taiwan to Japan. In Japan, sporophytes of H. mediosora were recorded only from Azusa-shiraiwa, a mountain of Okuchichibu region, and have not been seen for over 50...

Investigation on the ploidy and morphological diversity of Plagiogyria adnata (Blume) Bedd. in Yakushima, Japan. (In Japanese)

The fern genus Didymoglossum (Hymenophyllaceae) is not so diverse in Africa with seven species at most. However, its local taxonomy is surprisingly still strongly debated, in particular within the D. erosum complex interpreted either as a single polymorphic species or as a group of at least three distinct but morphologically very close taxa (D. ero...

Lepisorus rufofuscus T. Fujiw. (Polypodiaceae, Polypodiales), a Japanese species previously treated as L. angustus Ching, is described as new based on integrated evidence from phylogenetics, cytology, and morphology. It is morphologically segregated from L. angustus by the broadly lanceolate or ovatelanceolate rhizome scales and the ovate leaf scal...

Background: Polypodiales suborder Dennstaedtiineae contain a single family Dennstaedtiaceae, eleven genera, and about 270 species, and include some groups that were previously placed in Dennstaedtiaceae, Hypolepidaceae, Monachosoraceae, and Pteridaceae. The classification and phylogenetic relationships among these eleven genera have been poorly und...

The taxonomy of the filmy fern Hymenophyllum polyanthos species complex has been unclear for a long time. A recent study clarified the phylogenetic and morphological relationships among Taiwanese plants of the complex. This raised questions about which lineages occurred in the surrounding geographic regions. Hence, we investigated whether the Taiwa...

Whole genome duplication has been recognized as a major process in speciation of land plants, especially in ferns. Whereas genome downsizing contributes greatly to the post-genome shock responses of polyploid flowering plants, diploidization of polyploid ferns diverges by maintaining most of the duplicated DNA and is thus expected to be dominated b...

Premise of the study: The successful establishment of polyploid species is hypothesized to be promoted by niche differentiation from the parental species, or by range shifts during climate oscillations. However, few studies have considered both causes simultaneously. Here we resolve the origin of a tetraploid fern, Lepisorus yamaokae, and explore...

The Pteris fauriei group (Pteridaceae) has a wide distribution in Eastern Asia and includes 18 species with similar but varied morphology. We collected more than 300 specimens of the P. fauriei group and determined ploidy by flow cytometry and inferred phylogenies by molecular analyses of chloroplast and nuclear DNA markers. Our results reveal a co...

We provide an annotated checklist of all known lycophytes and ferns in the Solomon Islands following an updated classification. It comprises two classes, 12 orders, 3 families, 122 genera, 449 species, and six infraspecific taxa, including 1 new species described here and 18 species newly recorded for the country. In addition, we make six new nomen...

Vandenboschia radicans (supposedly Neotropical and African), V. speciosa (supposedly European and Macaronesian) and V. gigantea (supposedly from western Indian Ocean) are morphologically close species and often confused in collections and in floras. Moreover, the status of African populations is still strongly debated. We undertook to combine morph...

Premise: Biodiversity is often only measured with species richness. However, this ignores evolutionary history and is not sufficient for making conservation decisions. Here, we characterize multiple facets and drivers of biodiversity to understand how these relate to bioregions and conservation status in the ferns of Japan. Methods: We compiled...

Two East Asian Lomariopsis (Lomariopsidaceae, Polypodiales) species, Lomariopsis moorei and Lomariopsis longini, which were previously misidentified as L. spectabilis, are here described as new species based on evidence from morphological characters and a molecular phylogeny. The two species differ from the three other described species in East Asi...

Premise: The great variation of genome size (C-value) across land plants is linked to various adaptative features. Flow cytometry (FCM), the standard approach to estimating C-values, relies mostly on fresh materials, performing poorly when used with herbarium materials. No fern C-value reports have been derived from herbarium specimens; however, t...

The Adiantum pedatum complex is disjunctly distributed in North America and eastern Asia. In this study, we carried out a detailed morphological study based on 137 specimens representing the biogeographic diversity of this complex. The sequences of eight chloroplast markers of 35 samples were analyzed with maximum likelihood and Bayesian inference....

Phegopteris decursivepinnata harbors diploid and tetraploid strains, forming a polyploid species complex together with P. koreana. Hybridization and polyploidization in the complex blur species boundaries, making it challenging to apply the proper taxonomic treatment. Ploidy determinations, phylogenetic analyses, and morphological investigations to...

The history of the study on pterido-flora in Vietnam is reviewed. Two new records, Adiantum capillus-junonis and Actinostachys wagneri are reported for Vietnam based on our new collections. A new species, Hymenophyllum bryoides , is described to accommodate its morphological and genetic distinctiveness from other congeneric species. Photographs of...

The Eurasian and Mediterranean Selaginella helvetica group is one of the taxonomically challenging groups in the cosmopolitan lycophyte genus Selaginella. Species of the S. helvetica group are all small plants with lax strobili composed of more or less isomorphic sporophylls (isosporophylls) that are basically non-resupinate. Owing to the similar a...

Premise Biodiversity is often only measured with species richness. However, this ignores evolutionary history and is not sufficient for making conservation decisions. Here, we characterize multiple facets and drivers of biodiversity to understand how these relate to bioregions and conservation status in the ferns of Japan. Methods We compiled a co...

The filmy fern genus Trichomanes mainly comprises Neotropical species and a few taxa in Africa and the western Indian Ocean. The aim of this study is to infer the phylogenetic placement of all five Afro-Malagasy taxa in the genus and to investigate their history via an expanded and dated phylogenetic analysis including 39 species representing over...

The Pteris fauriei group (Pteridaceae) includes Pteris with bipinnatisect laminae and entire pinnules. The taxonomic debate is led by morphological similarity and aggravated by the wide geographic distribution and a large number of involved taxa. We collected more than 500 plants and examined related herbarium specimens. Based on the evidence of mo...

Diploid chromosome number 2n = 62 observed in the Taiwanese populations of Coryphopteris castanea supported the distinctness of this species from tetraploid Thelypteris (Coryphopteris) japonica. Although much variation in frond size was observed across its populations of Taiwan and Iriomote Island in southern Ryukyu of Japan, their alleles of nucle...

Evolution of mating systems has become one of the most important research areas in evolutionary biology. Cyrtomium falcatum is a homosporous fern species native to eastern Asia. Two subspecies belonging to a sexual diploid race of C. falcatum are recognized: subsp. littorale and subsp. australe . Subspecies littorale shows intermediate selfing rate...

A broad-leaved form of Thelypteris nipponica, usually called “var. borealis”, was identified as an allotetraploid originated from hybridization between two diploid species T. nipponica and T. musashiensis based on chromosome number, plastid rbcL sequence and nuclear gapCp “short” sequence. We found that the original material of Thelypteris nipponic...

Floristic surveys are crucial to the conservation of biodiversity, but the vast majority of such surveys are limited to listing species names, and few take into account the evolutionary history of species. Here, we combine classical taxonomic and molecular phylogenetic (DNA barcoding) approaches to catalog the biodiversity of pteridophytes (ferns a...

New Guinea is the world’s largest tropical island and has fascinated naturalists for centuries. Home to some of the best-preserved ecosystems on the planet and to intact ecological gradients—from mangroves to tropical alpine grasslands—that are unmatched in the Asia-Pacific region, it is a globally recognized centre of biological and cultural diver...

The thelypteroid fern genus Stegnogramma s.l. contains around 18–35 species and has a global, cross‐continental distribution ranging from tropical to temperate regions. Several genera and infrageneric sections have been recognized previously in Stegnogramma s.l., but their phylogenetic relationships are still unclear. In this study, we present a gl...

Hymenophyllum subg. Mecodium (Hymenophyllaceae) is represented by ca. 35 epiphytic species. Past reports suggest that Hymenophyllum polyanthos (Sw.) Sw., a pantropical species, does not represent a monophyletic grouping as it is recognized today. This research focuses on the H. polyanthos species complex, while comparing it to other species of subg...

In the original publication of this article, the affiliation of one of the authors was listed incorrectly as "Smithsonian Institute".

The past quarter-century has witnessed a revolution in our understanding of the phylogenetics, systematics, and ecology of pteridophytes (ferns and lycophytes), particularly due to the rapid accumulation of plastid sequence data and a renewed interest in the ecology of the sexual phase of the life cycle. We here compile 19 papers recently published...

The fern and lycophyte flora of Japan comprising 721 native taxa (including subspecies and varieties) plus 371 interspecific hybrids was reassessed using a nearly comprehensively sampled distribution map at 10 km resolution vouchered by 216,687 specimens, up-to-date cytotaxonomic information covering 74% of the taxa, and an rbcL sequence dataset co...

Mycorrhizal symbiosis between plants and fungi is ubiquitous, and has been played key roles in plant terrestrialization and diversification. Although arbuscular mycorrhizal (AM) symbioses with Glomeromycotina fungi have long been recognized as both ancient and widespread symbionts, recent studies showed that Mucoromycotina fungi were also ancestral...

We analyzed molecular phylogenetically using two low-copy nuclear markers (AK1 and Esterase) and plastid ndhF DNA sequence in the Dryopteris atrata complex. According to nuclear allele constitution and plastid ndhF sequence, apogamous species of the D. atrata complex seemed to be of hybrid origin. The genome constitution of the D. atrata complex sh...

Following the advice of Carl Linnaean, his apostle Carl Peter Thunberg first explored Japan, a forbidden country for Europeans at that time. Thunberg collected several plants from Japan and described them in detail in his Flora Japonica. He also introduced some new species, the names of which are still accepted today, but as he published them later...

Acystopteris taiwaniana, formerly known only from Taiwan, is newly recorded in Japan (northern and central Honshu and Shikoku). Chromosome counts and DNA sequences (plastid rbcL and nuclear PgiC) suggested that it is an allotetraploid species originating from hybridization between diploid A. japonica and an unknown diploid species. Acystopteris tai...

We report new records of pteridophytes in Myanmar: Abrodictyum idoneum (C. V. Morton) Ebihara & K. Iwats. (Hymenophyllaceae) and Thelypteris calcarata (Blume) Ching (Thelypteridaceae) in Kachin State; and Pteris henryi Christ (Pteridaceae) in Mandalay Division.

Many apogamous fern species show morphological and genetic variation because of hybridization between sexual species. In this study, we determined the relationships among species comprising the Dryopteris erythrosora complex (Dryopteridaceae) in Japan and adjacent areas using two plastid DNA markers, rbcL and ndhF, and two nuclear DNA markers, G6PD...

Many apogamous fern species show morphological and genetic variation because of hybridization with sexual species. In this study, we determined the relationships among species comprising the Dryopteris erythrosora complex (Dryopteridaceae) in Japan and adjacent areas using two plastid DNA markers, rbcL and ndhF, and two nuclear DNA markers, G6PD an...

Arachniodes (Dryopteridaceae) is one of the most confusing and controversial fern genera in terms of its circumscription, nomenclature, and taxonomy. Estimates of species number range from 40 to 200. Previous molecular works included only 2–17 accessions representing 2–12 species of Arachniodes and allied genera, leaving most of the Asian species r...

Current molecular phylogenetic analyses support the monophyly and circumscription of the athyrioid fern genus Deparia (Athyr-iaceae), which includes previously recognized genera including Athyriopsis, 3Depazium, Dictyodroma, Dryoathyrium (5 Parathyrium), Lunathyrium, and Neotriblemma (5 Triblemma Ching), and 3Neotribleparia. This broad generic conc...

The Dryopteris varia complex (subg. Erythrovariae sect. Variae Fraser-Jenk.) is an apogamous fern complex. Most species of the complex are triploid apogamous, show morphological and genetic variation, and present difficulties in their identification. Recent molecular research suggested that the reason that each apogamous species in the complex is s...

Recent studies on both genera Abrodictyum and Trichomanes (Hymenophyllaceae) in western Indian Ocean (Madagascar and neighbouring islands) resolved many taxonomic problems and led to the identification of new species. We propose here to finalize the taxonomic revision of both genera for the region, by completing and combining an expanded rbcL molec...

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 morphol...

Based on a worldwide dataset of molecular sequence data from three plastid DNA markers (rbcL, rbcL-accD-accD, rps4-trnS) obtained from 109 species of Hymenophyllum (Hymenophyllaceae), we investigated the systematics and bioge- ographic origins of the New Caledonian (NC) members of this fern genus, which were thought to include 16 species with 10 en...

Pyrrosia Mirb. (Polypodiaceae) comprises about 59 species, most of which occur in Southeast Asia, but some taxa are also in Africa and Oceania. Although several authors have investigated the species diver- sity of the genus, a phylogenetic study focusing on the relationship between species has not been avail- able. We used sequences of three plasti...

An Asia-Pacific fern species Pteris terminalis, formerly known as ‘Pteris excelsa’ is variable in terms of frond morphology as well as cytological characters. In particular, the results of previous cytological studies raised question on naturalness of currently accepted infraspecific taxa—‘P. excelsa var. simplicior’ (not yet combined with P. termi...

Polyploidy is widely considered as a major process in the evolution of plants but the accumulation of polyploid species diversity is still controversial. Some recent studies proposed increased extinction risk in neopolyploids compared with their diploid ancestors. The high proportion of polyploid ferns is expected to be formed mainly by neopolyploi...

The fern genera Crepidomanes and Polyphlebium are clearly distinct, yet often confused in the wild and in collections. Morphological and molecular investigations were performed to find taxonomic characters for discriminating species occurring in southeastern South America (southern Brazil and northeastern Argentina). Our results show that the genus...

Reflecting the results of recent studies on Japanese ferns, some new taxonomic treatments are proposed including the transfer of two varieties of Athyrium to the forma rank (Athyrium otophorum f. okanum and A. wardii f. inadae) and recognition of two new subspecies of Cyrtomium falcatum (subsp. littorale and subsp. australe).

Deparia, including the previously recognized genera Lunathyrium, Dryoathyrium (=Parathyrium), Athyriopsis, Triblemma, and Dictyodroma, is a fern genus comprising about 70 species in Athyriaceae. In this study, we inferred a robust Deparia phylogeny based on a comprehensive taxon sampling (~81% of species) that captures the morphological diversity d...

A systematic study of the vittarioid ferns of East Asia including China, Japan, Korea and Taiwan is presented based on an integrated analysis of morphology and molecular phylogeny. Several new taxonomic insights are derived from well-resolved phylogenetic trees and detailed morphological comparison. The morphological variation and molecular phyloge...

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 primar- ily discovered in temperate zone, and usually hypothesized with (sub)tropical origins and subsequent extinction of sporophyte due to climate c...

The taxonomy of the genus Abrodictyum is complex, with many species showing similar gross morphology, especially those supposedly related to A. rigidum. Morphological and morphometric comparisons were performed on Neotropical A. rigidum specimens, African specimens first attributed to A. rigidum and two supposedly new distinct Abrodictyum species f...

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 a...

The impact of variation in mating system on genetic diversity is a well-debated topic in evolutionary biology. The diploid sexual race of Cyrtomium falcatum (Japanese holly fern) shows mating system variation, i.e., it displays two different types of sexual expression (gametangia formation) in gametophytes: mixed (M) type and separate (S) type. We...

Prior and posterior distributions for each parameter obtained by DIYABC analysis for each population. X axis indicates values for the parameter described in the title of each graph; pmic: the parameter of the geometric distribution to generate multiple stepwise mutations; smic: Mean mutation rate of single nucleotide indel; μmic: mean mutation rate...

Genetic diversity indices and inbreeding coefficient values for seven populations of diploid Cyrtomium falcatum. (DOCX)

Null allele frequencies at each locus estimated by INEST2. (DOC)

Genotype list of all samples. (XLSX)

Inbreeding coefficient (FIS) values estimated by INEST2 for seven populations of the northern type of diploid Cyrtomium falcatum. (DOCX)

Demographic parameters of scenario 1 obtained by DIYABC. (XLSX)

Posterior probability of each scenario by DIYABC. (XLSX)

Demographic models used in DIYABC for each population of C. falcatum. Scenario 1. Bottleneck model: the ancestral effective population size (Na) was changed at t1 to the modern effective population size (N1) and N1 was set to be smaller than Na Scenario 2. Constant model: the ancestral effective population size (Nb) and the modern one (N1) were set...

The values of posterior probability of the data (Ln P(D)) from 10 runs for each value of K (1–15; A) and ΔK (right B). (EPS)

Principal Component Analysis (PCA) score plot obtained from DIYABC analysis for each population. PCA plots of prior, posterior and observed data set for summary statistics. (PPTX)

Primer sequences, repeat motifs, and accession numbers of source sequences for eight microsatellite markers developed in this study. (DOCX)

An accurate recognition and delimitation of species of the family Hymenophyllaceae is especially complicated, due to the simplicity of form of these plants, which usually bear one-cell thick leaves and have only a few centimeters of size. Hymenophyllum polyanthos, which has a broad pantropical distribution, occurring in elevated areas of the South...

Monachosorum arakii Tagawa is a plant species endemic to the western part of the main island of Japan. It is characterized by large bulbils on the rachises and is a close relative of M. henryi Christ, which can be found in the Sino-Himalayan region and is not present in Japan. Although M. arakii was reported to be a hexaploid, we determined that it...

A global plastid phylogeny of the brake fern genus Pteris (Pteridaceae) and related genera in the Pteridoideae Abstract The brake fern genus Pteris belongs to the Pteridaceae subfamily Pteridoideae. It contains 200–250 species distributed on all continents except Antarctica, with its highest species diversity in tropical and subtropical regions. Th...

To determine the mycorrhizal status of pteridophyte gametophytes in diverse taxa, the mycorrhizal colonization of wild gametophytes was investigated in terrestrial cordate gametophytes of pre-polypod leptosporangiate ferns, i.e., one species of Osmundaceae (Osmunda banksiifolia), two species of Gleicheniaceae (Diplopterygium glaucum, Dicranopteris...

The filmy fern Abrodictyum cupressoides, initially reported from Madagascar and the Seychelles (locus classicus), is often confused in the field and in collections with similar local species, especially the pantropical A. rigidum. A comparative morphological investigation of Malagasy and Seychellois specimens finds strong differences between A. cup...