National Museum of Natural Science

“Lingzhi” is a mushroom that has been renowned in China for more than 2,000 years because of its claimed medicinal properties plus its symbolic fortune. “Lingzhi” has high economic value mostly as a dietary supplement in the modern market especially in East Asia, and its medicinal functions have become a hot study topic. For over a century, the highly prized medicinal fungus, known as “Lingzhi” in East Asia, has been assigned to Ganoderma lucidum , a species originally described from Europe. Molecular studies in recent years have revealed that the commercially cultivated ‘ G. lucidum ’ (“Lingzhi”) in East Asia is a different species from the true G. lucidum . The present study aims to clarify the species identity of “Lingzhi” based on morphological studies and analysis of rDNA nuc-ITS sequences, and additional gene fragments of mt-SSU, RPB1, RPB2, and TEF1-α of “Lingzhi” were provided. All Ganoderma species that mostly resemble “Lingzhi” in phylogeny and /or morphology were included for analysis. We propose a new species G. lingzhi for “Lingzhi”, which has an East Asia distribution. The most striking characteristics which differentiate G. lingzhi from G. lucidum are the presence of melanoid bands in the context, a yellow pore surface and thick dissepiments (80–120 μm) at maturity. G. curtisii is most closely related to G. lingzhi in phylogeny and is from North America. Ganoderma flexipes , G. multipileum, G. sichuanense , G. tropicum and ‘ G. tsugae ’ , are also closely related with G. lingzhi and are reported from China. These species are compared and discussed. ‘ Ganoderma tsuage ’ reported from China is determined as conspecific with G. lucidum , hence the distribution of G. lucidum extends from Europe to northeastern China.

Abstract Aim We investigated the historical biogeography and diversification of Gentiana L. (Gentianaceae). Our study depicts the origin and dispersal routes of this alpine genus, and the role of the uplift of the Qinghai–Tibet Plateau ( QTP ) and past climate changes as triggers for its diversification. Location Tibeto‐Himalayan region and world‐wide mountain habitats. Methods Our sampling represents more than 50% of the extant Gentiana species, including all sections across their entire geographical ranges. We investigated the evolutionary history of Gentiana using phylogenetic reconstructions (maximum likelihood and Bayesian inference) of ITS , atp B– rbc L and trn L– trn F sequences, as well as molecular dating with beast . We tested two approaches of ancestral area reconstructions ( DEC , DIVA ) in BioGeo BEARS and investigated diversification rates using BAMM . Results The common ancestor of Gentiana and subtribe Gentianinae lived in the QTP region at around 34 (25–45) million years ago (Ma), and 40 (29–52) Ma respectively. From the surroundings of the QTP , Gentiana lineages dispersed to eastern China, Taiwan, Europe, North and South America, Australia and New Guinea, from mid‐Miocene onward ( c . 15 Ma–present), with only one older dispersal event to Europe ( c . 37–21 Ma). Diversification rates gradually increased over time, and two switches of diversification rates were identified in Gentianinae ( c . 7 Ma, simultaneously in the Pneumonanthe / Cruciata lineage and in Tripterospermum ). Main conclusions Gentiana existed in the QTP region throughout most of its uplift history following the India‐Asia collision. This region acted as the primary source area for dispersals to many areas of the world. Because steady increase in diversification rates coincides with the extension of the QTP , we argue that the museum theory rather than the explosive radiation theory prevails for gentians in this region, although rare shifts of diversification rates are associated with niche shifts across the alpine/subalpine ecotone.

To assess the role of human disturbances in species' extinction requires an understanding of the species population history before human impact. The passenger pigeon was once the most abundant bird in the world, with a population size estimated at 3-5 billion in the 1800s; its abrupt extinction in 1914 raises the question of how such an abundant bird could have been driven to extinction in mere decades. Although human exploitation is often blamed, the role of natural population dynamics in the passenger pigeon's extinction remains unexplored. Applying high-throughput sequencing technologies to obtain sequences from most of the genome, we calculated that the passenger pigeon's effective population size throughout the last million years was persistently about 1/10,000 of the 1800's estimated number of individuals, a ratio 1,000-times lower than typically found. This result suggests that the passenger pigeon was not always super abundant but experienced dramatic population fluctuations, resembling those of an "outbreak" species. Ecological niche models supported inference of drastic changes in the extent of its breeding range over the last glacial-interglacial cycle. An estimate of acorn-based carrying capacity during the past 21,000 y showed great year-to-year variations. Based on our results, we hypothesize that ecological conditions that dramatically reduced population size under natural conditions could have interacted with human exploitation in causing the passenger pigeon's rapid demise. Our study illustrates that even species as abundant as the passenger pigeon can be vulnerable to human threats if they are subject to dramatic population fluctuations, and provides a new perspective on the greatest human-caused extinction in recorded history.

True frogs of the genus Rana are widely used as model organisms in studies of development, genetics, physiology, ecology, behavior, and evolution. Comparative studies among the more than 100 species of Rana rely on an understanding of the evolutionary history and patterns of diversification of the group. We estimate a well-resolved, time-calibrated phylogeny from sequences of six nuclear and three mitochondrial loci sampled from most species of Rana, and use that phylogeny to clarify the group's diversification and global biogeography. Our analyses consistently support an "Out of Asia" pattern with two independent dispersals of Rana from East Asia to North America via Beringian land bridges. The more species-rich lineage of New World Rana appears to have experienced a rapid radiation following its colonization of the New World, especially with its expansion into montane and tropical areas of Mexico, Central America, and South America. In contrast, Old World Rana exhibit different trajectories of diversification; diversification in the Old World began very slowly and later underwent a distinct increase in speciation rate around 29-18 Ma. Net diversification is associated with environmental changes and especially intensive tectonic movements along the Asian margin from the Oligocene to early Miocene. Our phylogeny further suggests that previous classifications were misled by morphological homoplasy and plesiomorphic color patterns, as well as a reliance primarily on mitochondrial genes. We provide a phylogenetic taxonomy based on analyses of multiple nuclear and mitochondrial gene loci. [Amphibians; biogeography; diversification rate; Holarctic; transcontinental dispersal.

An oviraptosaurian specimen (Dinosauria, Theropoda) from an Upper Cretaceous formation in China retains a pair of shelled eggs in the pelvis, providing direct evidence that oviraptorosaurian dinosaurs laid paired elongatoolithid eggs. The presence of the paired eggs suggests that theropod dinosaurs had two functional oviducts (like crocodiles) but that each oviduct produced only one egg at a time and that an entire egg clutch was laid through multiple ovipositions (like birds). The orientations of the eggs inside the skeleton and in clutches indicate that the mother came to the center of the nest to lay eggs.

Although Inonotus linteus complex is placed in the genus Inonotus , its perennial basidiocarps with a dimitic hyphal system, at least in the trama, distinguish the complex from other species in the genus, which have an annual habit and a monomitic hyphal system. The species number of Inonotus linteus complex has been increased in China and tropical America in recent publications. However, whether species in this complex belong to Inonotus has not specifically been addressed. To explore the phylogenetic placement of species of Inonotus linteus complex, we performed a comprehensive study using morphological and phylogenetic data based on global samples. nLSU (53 with 13 new) and ITS (70 with 18 new) datasets were used to produce the phylogenetic results. Taking into consideration the phylogenies inferred from the nLSU and ITS datasets, Inonotus is a polyphyletic genus comprising at least three clades. Clade A, the core Inonotus clade, contains the generic type, Inonotus hispidus , while Clades B and C comprise species from the Inonotus linteus complex. Morphological and phylogenetic evidence indicates that Clades B and C are new genera, and Sanghuangporus and Tropicoporus are introduced in this study. Ten species are transferred to Sanghuangporus and seven to Tropicoporus. Tropicoporus excentrodendri and T. guanacastensis spp. nov. are described, and their distinctive characters are discussed. Keys to the two new genera and the Inonotus sensu stricto , and to species of each new genus are provided.

Magnetoreception by honeybees (Apis mellifera) is demonstrated by such activities as comb building and homing orientation, which are affected by the geomagnetic field. In other magnetoreceptive species, iron oxide crystals in the form of magnetite have been shown to be necessary for primary detection of magnetic fields. Here it is shown that trophocytes, which are apparently the only iron granule-containing cells in honeybees, contain super-paramagnetic magnetite. These cells are innervated by the nervous system, which suggests that trophocytes might be primarily responsible for magnetoreception. Electron microscopy also shows cytoskeletal attachments to the iron granule membrane.

Variation partitioning of species composition into components explained by environmental and spatial variables is often used to identify a signature of niche- and dispersal-based processes in community assembly. Such interpretation, however, strongly depends on the quality of the environmental data available. In recent studies conducted in forest dynamics plots, the environment was represented only by readily available topographical variables. Using data from a subtropical broad-leaved dynamics plot in Taiwan, we focus on the question of how would the conclusion about importance of niche- and dispersal-based processes change if soil variables are also included in the analysis. To gain further insight, we introduced multiscale decomposition of a pure spatial component [c] in variation partitioning. Our results indicate that, if only topography is included, dispersal-based processes prevail, while including soil variables reverses this conclusion in favor of niche-based processes. Multiscale decomposition of [c] shows that if only topography was included, broad-scaled spatial variation prevails in [c], indicating that other as yet unmeasured environmental variables can be important. However, after also including soil variables this pattern disappears, increasing importance of meso- and fine-scaled spatial patterns indicative of dispersal processes.

In this study, ionospheric solar flare effects on the total electron content (TEC) and associated time rate of change (rTEC) derived from ground‐based global positioning system (GPS) receivers in the midday region are examined. The occurrence times and locations of 11 solar flares are isolated from the 1–8 Å X‐ray radiations of the geosynchronous operational environmental satellite (GOES) and the SOHO Extreme Ultraviolet Imaging Telescope (EIT) images, respectively, while the TEC and rTEC are obtained from the international GPS services (IGS). Results show that the maximum value of the TEC increase solely depends on the flare class, while the maximum value of the rTEC increase is related to not only the flare class but also the time rate of change in flare radiations. A statistical analysis further demonstrates that the two maximum values are inversely proportional to the cosine of the great circle angle between the center and flare locations on the solar disc.

PREMISE OF THE STUDY: Protocorm-like bodies (PLBs) of orchids are important in orchid micropropagation and outwardly resemble somatic embryos in form and development. To determine whether PLBs are truly embryogenetic, we compared PLBs with somatic embryos and zygotic embryos to determine whether they had similar surface molecules and whether hydroxyproline-rich glycoprotein (HRGP) inhibitors similarly alter their growth. METHODS: Embryogenic calluses (ECs), zygotic embryos, and protocorms were collected for histological and histochemical studies with light microscopy. The presence of JIM11 and JIM20 epitopes was determined using immunodot blots and immunolocalization procedures. The importance of wall proteins in the formation of PLBs was investigated using 3,4-dehydro-l-proline (3,4-DHP), an inhibitor of HRGP biosynthesis. KEY RESULTS: At the early stages of PLB formation, the cytoplasm of the globular cell clusters and meristemoids took on a vacuolated appearance. Starch granules and protein bodies appeared, albeit transitory in nature. Positive localizations of JIM11 and JIM20 were noted in the embryogenic culture and developing PLBs similar to zygotic embryos. The inclusion of an inhibitor to HRGPs inhibited PLB formation. CONCLUSIONS: This study demonstrates that during the early stages of PLB formation, the cells show cytological characteristics and cell wall markers similar to zygotic embryo development, justifying the statement that PLBs are indeed somatic embryos of orchids. Thus, these results suggest that PLBs could be used as an experimental embryological system for physiological or molecular characterization.

Recent studies of an increasing number of hominin fossils highlight regional and chronological diversities of archaic Homo in the Pleistocene of eastern Asia. However, such a realization is still based on limited geographical occurrences mainly from Indonesia, China and Russian Altai. Here we describe a newly discovered archaic Homo mandible from Taiwan (Penghu 1), which further increases the diversity of Pleistocene Asian hominins. Penghu 1 revealed an unexpectedly late survival (younger than 450 but most likely 190–10 thousand years ago) of robust, apparently primitive dentognathic morphology in the periphery of the continent, which is unknown among the penecontemporaneous fossil records from other regions of Asia except for the mid-Middle Pleistocene Homo from Hexian, Eastern China. Such patterns of geographic trait distribution cannot be simply explained by clinal geographic variation of Homo erectus between northern China and Java, and suggests survival of multiple evolutionary lineages among archaic hominins before the arrival of modern humans in the region. Growing evidence reveals great diversity of archaic Asian hominins. Here, Chang and colleagues describe a newly discovered archaic Homomandible from Taiwan, which suggests the survival of multiple evolutionary lineages among archaic hominins before the arrival of modern humans to eastern Asia.

Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of phylogenetic diversity in the mega-phylogeny were more consistent, thereby removing a potential source of bias at the plot-level, and demonstrating the value of assessing phylogenetic relationships simultaneously within a mega-phylogeny. An unexpected result of the comparisons among plots based on the mega-phylogeny was that the communities in the ForestGEO plots in general appear to be assemblages of more closely related species than expected by chance, and that differentiation among communities is very low, suggesting deep floristic connections among communities and new avenues for future analyses in community ecology.

In this study of Arabidopsis (Arabidopsis thaliana), we investigated the relationship between FOREVER YOUNG FLOWER (FYF) and Ethylene Response DNA-binding Factors (EDFs) and functionally analyzed a key FYF target, an Ethylene-Responsive Factor (ERF), that controls flower senescence/abscission. Ectopic expression of EDF1/2/3/4 caused promotion of flower senescence/abscission and the activation of the senescence-associated genes. The presence of a repressor domain in EDFs and the enhancement of the promotion of senescence/abscission in EDF1/2/3/4+SRDX (converting EDFs to strong repressors by fusion with the ERF-associated amphiphilic repression motif repression domain SRDX) transgenic plants suggested that EDFs act as repressors. The significant reduction of β-glucuronidase (GUS) expression by 35S:FYF in EDF1/2/3/4:GUS plants indicates that EDF1/2/3/4 functions downstream of FYF in regulating flower senescence/abscission. In this study, we also characterized an ERF gene, FOREVER YOUNG FLOWER UP-REGULATING FACTOR1 (FUF1), which is up-regulated by FYF during flower development. Ectopic expression of FUF1 caused similar delayed flower senescence/abscission as seen in 35S:FYF plants. This phenotype was correlated with deficient abscission zone formation, ethylene insensitivity, and down-regulation of EDF1/2/3/4 and abscission-associated genes in 35S:FUF1 flowers. In contrast, significant promotion of flower senescence/abscission and up-regulation of EDF1/2/3/4 were observed in 35S:FUF1+SRDX transgenic dominant-negative plants, in which FUF1 is converted to a potent repressor by fusion to an SRDX-suppressing motif. Thus, FUF1 acts as an activator in suppressing EDF1/2/3/4 function and senescence/abscission of the flowers. Our results reveal that FYF regulates flower senescence/abscission by negatively regulating EDF1/2/3/4, which is the downstream gene in the ethylene response, by activating FUF1 in Arabidopsis.

Rice blast disease resistance to the fungal pathogen Magnaporthe grisea is triggered by a physical interaction between the protein products of the host R (resistance) gene, Pi-ta, and the pathogen Avr (avirulence) gene, AVR-pita. The genotype variation and resistant/susceptible phenotype at the Pi-ta locus of wild rice (Oryza rufipogon), the ancestor of cultivated rice (O. sativa), was surveyed in 36 locations worldwide to study the molecular evolution and functional adaptation of the Pi-ta gene. The low nucleotide polymorphism of the Pi-ta gene of O. rufipogon was similar to that of O. sativa, but greatly differed from what has been reported for other O. rufipogon genes. The haplotypes can be subdivided into two divergent haplogroups named H1 and H2. H1 is derived from H2, with nearly no variation and at a low frequency. H2 is common and is the ancestral form. The leucine-rich repeat (LRR) domain has a high pi(non)/pi(syn) ratio, and the low polymorphism of the Pi-ta gene might have primarily been caused by recurrent selective sweep and constraint by other putative physiological functions. Meanwhile, we provide data to show that the amino acid Ala-918 of H1 in the LRR domain has a close relationship with the resistant phenotype. H1 might have recently arisen during rice domestication and may be associated with the scenario of a blast pathogen-host shift from Italian millet to rice.

The temporal control mechanisms that precisely control animal development remain largely elusive. The timing of major developmental transitions in insects, including molting and metamorphosis, is coordinated by the steroid hormone 20-hydroxyecdysone (20E). 20E involves feedback loops to maintain pulses of ecdysteroid biosynthesis leading to its upsurge, whereas the underpinning molecular mechanisms are not well understood. Using the silkworm Bombyx mori as a model, we demonstrated that E75, the 20E primary response gene, mediates a regulatory loop between ecdysteroid biosynthesis and 20E signaling. E75 isoforms A and C directly bind to retinoic acid receptor-related response elements in Halloween gene promoter regions to induce gene expression thus promoting ecdysteroid biosynthesis and developmental transition, whereas isoform B antagonizes the transcriptional activity of isoform A/C through physical interaction. As the expression of E75 isoforms is differentially induced by 20E, the E75-mediated regulatory loop represents a fine autoregulation of steroidogenesis, which contributes to the precise control of developmental timing.

Gynostemium and ovule development in orchid are unique developmental processes in the plant kingdom. Characterization of C- and D-class MADS-box genes could help reveal the molecular mechanisms underlying gynostemium and ovule development in orchids. In this study, we isolated and characterized a C- and a D-class gene, PeMADS1 and PeMADS7, respectively, from Phalaenopsis equestris. These two genes showed parallel spatial and temporal expression profiles, which suggests their cooperation in gynostemium and ovule development. Furthermore, only PeMADS1 was ectopically expressed in the petals of the gylp (gynostemium-like petal) mutant, whose petals were transformed into gynostemium-like structures. Protein-protein interaction analyses revealed that neither PeMADS1 and PeMADS7 could form a homodimer or a heterodimer. An E-class protein was needed to bridge the interaction between these two proteins. A complementation test revealed that PeMADS1 could rescue the phenotype of the AG mutant. Overexpression of PeMADS7 in Arabidopsis caused typical phenotypes of the D-class gene family. Together, these results indicated that both C-class PeMADS1 and D-class PeMADS7 play important roles in orchid gynostemium and ovule development.

This study was aimed to determine the patterns as well as the effects of biological, anthropogenic, and climatic factors on plant invasions in China. About 270 volumes of national and regional floras were employed to compile a naturalized flora of China. Habit, life form, origin, distribution, and uses of naturalized plants were also analyzed to determine patterns on invasion. Correlations between biological, anthropogenic and climatic parameters were estimated at province and regional scales. Naturalized species represent 1% of the flora of China. Asteraceae, Fabaceae, and Poaceae are the dominant families, but Euphorbiaceae and Cactaceae have the largest ratios of naturalized species to their global numbers. Oenothera , Euphorbia , and Crotalaria were the dominant genera. Around 50% of exotic species were introduced intentionally for medicinal purposes. Most of the naturalized species originated in tropical America, followed by Asia and Europe. Number of naturalized species was significantly correlated to the number of native species/log area. The intensity of plant invasion showed a pattern along climate zones from mesic to xeric, declining with decreasing temperature and precipitation across the nation. Anthropogenic factor, such as distance of transportation, was significantly correlated to plant invasions at a regional scale. Although anthropogenic factors were largely responsible for creating opportunities for exotic species to spread and establish, the local biodiversity and climate factors were the major factors shaping the pattern of plant invasions in China. The warm regions, which are the hot spots of local biodiversity, and relatively developed areas of China, furthermore, require immediate attentions.

Abstract The chemical composition of the Gaoping River in Taiwan reflects the weathering of both silicate and carbonate rocks found in its metasedimentary catchment. Major dissolved ion chemistry and radiocarbon signatures of dissolved inorganic carbon (DIC) reveal the importance of pyrite-derived sulphuric acid weathering on silicates and carbonates. Two-thirds of the dissolved load of the Gaoping River derives from sulphuric acid-mediated weathering of rocks within its catchment. This is reflected in the lowest reported signatures DI 14 C for a small mountainous river (43 to 71 percent modern carbon), with rock-derived carbonate constituting a 14 C-free DIC source. Using an inverse modelling approach integrating riverine major dissolved ion chemistry and DI 14 C, we provide quantitative constraints of mineral weathering pathways and calculate atmospheric CO 2 fluxes resulting from the erosion of the Taiwan orogeny over geological timescales. The results reveal that weathering on Taiwan releases 0.31 ± 0.12 MtC/yr, which is offset by burial of terrestrial biospheric organic carbon in offshore sediments. The latter tips the balance with respect to the total CO 2 budget of Taiwan such that the overall system acts as a net sink, with 0.24 ± 0.13 MtC/yr of atmospheric CO 2 consumed over geological timescales.

Ganoderma leucocontextum was described from Tibet Autonomous Region and Sichuan Province of China. The new species was characterized by red brown to purplish or blackish red brown pileus, white to cream pore surface, white context, thickset stipe, broadly ellipsoid basidiospores (9.5–12.5 × 7–9 μm) with coarse echinulae, and the mostly regular cuticle hyphae. Ganoderma leucocontextum was known only grow on deciduous wood and closely related to the G. lucidum complex.

The genus Phanerochaete (Polyporales, Basidiomycota) has traditionally been delimited based on the gross morphology of the fruiting body and on the nature of the hyphal structure, cystidia, and spores. However, several recent studies based on molecular data indicate that the genus is polyphyletic as presently circumscribed, although most of its species are found in the phlebioid clade of the Polyporales . To further our understanding of the genus, 54 new sequences from the large subunit of the nuclear ribosomal DNA of 45 previously unsequenced Phanerochaete species were obtained and analyzed jointly with a large selection of taxa in the phlebioid clade. The results show that there is a well-supported Phanerochaete core group that includes the type species Phanerochaete velutina (the currently accepted name of the generic type, Thelephora alnea ). Representatives of a few satellite genera, including Hjortstamia , Phlebiopsis , and Rhizochaete , are found in the immediate topological vicinity of Phanerochaete . Outside the core group but still within the phlebioid clade are several taxa that have been referred to as members of Phanerochaete by some authors but that are here assigned to at least five different monophyletic clades. Phanerochaete viticola is found in the Hymenochaetales and is shown to have phylogenetic affinities to the partially symbiotic Rickenellaceae . A new genus, Ginnsia , is erected for this species, and the new combinations Ginnsia viticola , Hjortstamia brunneocystidiata , H. laxa , and Phlebiopsis lamprocystidiata are proposed. A denser taxon and gene sampling in the phleboid clade will be needed to settle the precise taxonomic affiliation of many of the species presently referred to as Phanerochaete , and numerous nomenclatural changes are doubtlessly looming on the horizon.