Application of MaxEnt modeling to evaluate the climate change effects on the geographic distribution of Lippia javanica (Burm.f.) Spreng in Africa.

Lippia javanica is a typical indigenous plant species mostly found in the higher elevation or mountainous regions in southern, central, and eastern Africa. The ongoing utilization of the species for ethnobotanical applications and traditional uses, coupled with the changing climate, increases the risk of a potential reduction in its geographic distribution range in the region. Herein, we utilized the MaxEnt species distribution modelling to build the L. javanica distribution models in tropical and subtropical African regions for current and future climates. The MaxEnt models were calibrated and fitted using 286 occurrence records and six environmental variables. Temperatures, including temperature seasonality [Bio 4] and the maximum temperature of the warmest month [Bio 5], were observed to be the most significant determinants of L. javanica's distribution. The current projected range for L. javanica was estimated to be 2,118,457 km2. Future model predictions indicated that L. javanica may increase its geographic distribution in western areas of the continent and regions around the equator; however, much of the geographic range in southern Africa may shift southwards, causing the species to lose portions of the northern limits of the habitat range. These current findings can help increase the conservation of L. javanica and other species and combat localized species loss induced by climate change and human pressure. We also emphasize the importance of more investigations and enhanced surveillance of traditionally used plant species in regions that are acutely susceptible to climate change.

Evolution of phenotypic disparity in the plant kingdom.

The plant kingdom exhibits diverse bodyplans, from single-celled algae to complex multicellular land plants, but it is unclear how this phenotypic disparity was achieved. Here we show that the living divisions comprise discrete clusters within morphospace, separated largely by reproductive innovations, the extinction of evolutionary intermediates and lineage-specific evolution. Phenotypic complexity correlates not with disparity but with ploidy history, reflecting the role of genome duplication in plant macroevolution. Overall, the plant kingdom exhibits a pattern of episodically increasing disparity throughout its evolutionary history that mirrors the evolutionary floras and reflects ecological expansion facilitated by reproductive innovations. This pattern also parallels that seen in the animal and fungal kingdoms, suggesting a general pattern for the evolution of multicellular bodyplans.

Characterization of the complete chloroplast genome of Dalbergia congesta (Fabaceae), an endangered legume endemic to the Nilgiri Hills of Tamil Nadu, India.

Reference-guided de novo assembly of the Dalbergia congesta chloroplast genome was carried out using whole-genome sequencing data. The newly generated chloroplast genome size had a total length of 156,048 bp and a GC content of 36.1%. The plastome showed the classical quadripartite structure with two inverted repeats regions (IRs; each 25,715 bp) separating the large single-copy region (LSC; 85,456 bp) from the small single-copy region (SSC; 19,162 bp). The plastid genome contained 111 unique genes, including 77 protein-coding genes (CDS), 30 tRNAs, and 4 rRNAs. The phylogenomic analyses based on whole chloroplast genome sequences recovered Dalbergia as a distinct clade of the Papilionoideae, with Dalbergia congesta having a sister relationship to a clade comprising D. fusca and D. cultrata. The newly available plastome sequence will facilitate future genetic and conservational research aiming to protect this economically important but highly threatened legume species.

Begoniafimbristipulasubsp.siamensis (sect. Diploclinium, Begoniaceae), a new taxon of the megadiverse genus endemic to Thailand.

The genus Begonia has not only been recognised to be one of the mega-diverse plant genera but also as one found to comprise many undiscovered species. In particular, the increase of extensive field surveys in tropical regions of Southeast Asia has added to the discovery of many new species that are often found only in a few localities. In this study, the new taxon Begoniafimbristipulasubsp.siamensissubsp. nov. from Thailand is described. The Thailand accessions are highly similar in their morphology to accessions of B.fimbristipula from southern China but differ in their tuber shape, peduncle trichomes, petiole trichomes and number of female tepals. The new taxon has been found only in the northern parts of Thailand occurring at elevations above 1,300 meters. The new findings not only contribute to our knowledge of the plant diversity of Thailand but provide also critical information contributing to the protection of this species. In China, this species is endangered which is of special concern given its utilisation as a medical herb in traditional Chinese medicine. Considering IUCN Red List Categories, the new subspecies is considered to be Vulnerable. The disjunct distribution of the two subspecies of B.fimbristipula encourages urgently needed comparative taxonomic studies across the Indo-Burma biodiversity hotspot.

Evolution of genome space occupation in ferns: linking genome diversity and species richness.

BACKGROUND AND AIMS: The dynamics of genome evolution caused by whole genome duplications and other processes are hypothesized to shape the diversification of plants and thus contribute to the astonishing variation in species richness among the main lineages of land plants. Ferns, the second most species-rich lineage of land plants, are highly suitable to test this hypothesis because of several unique features that distinguish fern genomes from those of seed plants. In this study, we tested the hypothesis that genome diversity and disparity shape fern species diversity by recording several parameters related to genome size and chromosome number. METHODS: We conducted de novo measurement of DNA C-values across the fern phylogeny to reconstruct the phylogenetic history of the genome space occupation in ferns by integrating genomic parameters such as genome size, chromosome number and average DNA amount per chromosome into a time-scaled phylogenetic framework. Using phylogenetic generalized least square methods, we determined correlations between chromosome number and genome size, species diversity and evolutionary rates of their transformation. KEY RESULTS: The measurements of DNA C-values for 233 species more than doubled the taxon coverage from ~2.2 % in previous studies to 5.3 % of extant diversity. The dataset not only documented substantial differences in the accumulation of genomic diversity and disparity among the major lineages of ferns but also supported the predicted correlation between species diversity and the dynamics of genome evolution. CONCLUSIONS: Our results demonstrated substantial genome disparity among different groups of ferns and supported the prediction that alterations of reproductive modes alter trends of genome evolution. Finally, we recovered evidence for a close link between the dynamics of genome evolution and species diversity in ferns for the first time.

Genomic insights into genetic diploidization in the homosporous fern Adiantum nelumboides.

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 by genic processes. As a consequence, fern genomes provide excellent opportunities to study ecological speciation enforced by expansion of protein families via polyploidy. To test the key predictions of this hypothesis, we reported the de novo genome sequence of Adiantum nelumboides, a tetraploid homosporous fern. The obtained draft genome had a size of 6.27 Gb assembled into 11,767 scaffolds with the contig N50 of 1.37 Mb. Repetitive DNA sequences contributed with about 81.7%, a remarkably high proportion of the genome. With 69,568 the number of predicted protein-coding genes exceeded those reported in most other land plant genomes. Intragenomic synteny analyses recovered 443 blocks with the average block size of 1.29 Mb and the average gene content of 16 genes. The results are consistent with the hypothesis of high ancestral chromosome number, lack of substantial genome downsizing, and dominance of genic diploidization. As expected in the calciphilous plants, a notable number of detected genes were involved in calcium uptake and transport. In summary, the genome sequence of a tetraploid homosporous fern not only provides access to a genomic resource of a derived fern, but also supports the hypothesis of maintenance of high chromosome numbers and duplicated DNA in young polyploid ferns.

Bacterial Microbiome in the Phyllo-Endosphere of Highly Specialized Rock Spleenwort.

Bacteria communities associated with plants have been given increasing consideration because they are arguably beneficial to their host plants. To understand the ecological and evolutionary impact of these mutualistic associations, it is important to explore the vast unknown territory of bacterial genomic diversity and their functional contributions associated with the major branches of the tree-of-life. Arguably, this aim can be achieved by profiling bacterial communities by applying high throughput sequencing approaches, besides establishing model plant organisms to test key predictions. This study utilized the Illumina Miseq reads of bacterial 16S rRNA sequences to determine the bacterial diversity associated with the endosphere of the leaves of the highly specialized rock spleenwort Asplenium delavayi (Aspleniaceae). By documenting the bacterial communities associated with ferns collected in natural occurrence and cultivation, this study discovered the most species-rich bacterial communities associated with terrestrial ferns reported until now. Despite the substantial variations of species diversity and composition among accessions, a set of 28 bacterial OTUs was found to be shared among all accessions. Functional analyses recovered evidence to support the predictions that changes in bacterial community compositions correspond to functional differentiation. Given the ease of cultivating this species, Asplenium delavayi is introduced here as a model organism to explore the ecological and evolutionary benefits created by mutualistic associations between bacteria and ferns.

Fire-prone Rhamnaceae with South African affinities in Cretaceous Myanmar amber.

The rapid Cretaceous diversification of flowering plants remains Darwin's 'abominable mystery' despite numerous fossil flowers discovered in recent years. Wildfires were frequent in the Cretaceous and many such early flower fossils are represented by charcoalified fragments, lacking complete delicate structures and surface textures, making their similarity to living forms difficult to discern. Furthermore, scarcity of information about the ecology of early angiosperms makes it difficult to test hypotheses about the drivers of their diversification, including the role of fire in shaping flowering plant evolution. We report the discovery of two exquisitely preserved fossil flower species, one identical to the inflorescences of the extant crown-eudicot genus Phylica and the other recovered as a sister group to Phylica, both preserved as inclusions together with burned plant remains in Cretaceous amber from northern Myanmar (~99 million years ago). These specialized flower species, named Phylica piloburmensis sp. nov. and Eophylica priscastellata gen. et sp. nov., exhibit traits identical to those of modern taxa in fire-prone ecosystems such as the fynbos of South Africa, and provide evidence of fire adaptation in angiosperms.

Thylacopterisminuta (Polypodiaceae), a new fern species from Myanmar.

The genus Thylacopteris is a small, phylogenetically isolated genus belonging to the fern family Polypodiaceae. This study describes a new species, Thylacopterisminuta, based on collections obtained during field surveys of Shan State, Myanmar. This new species is distinct from other species of Thylacopteris in its small size and presence of sclerenchyma strands in the rhizome. This species is also distinct from the only other species of Thylacopteris with molecular data available, T.papillosa, in a plastid rbcL phylogeny of Polypodiaceae. This new discovery of Thylacopteris from Myanmar suggests that this genus is still overlooked in Southeast Asia.

Lepisorusmedioximus (Polypodiales, Polypodiaceae), a new species from Shan State of Myanmar.

A new species of the species-rich fern genus Lepisorus (Polypodiales, Polypodiaceae) has been found to occur in Shan state, Myanmar. Lepisorusmedioximus is described based on morphological characters and phylogenetic evidence. Phylogenetic analyses showed that the specimens of L.medioximus formed a distinct clade nested in the Pseudovittaria clade. The morphological comparison demonstrated that the species is distinct from phylogenetically related species, namely L.elegans, L.contortus, and L.tosaensis, in the morphology of the rhizome scales, size, and shape of the lamina, position of sori, and paraphyses.

High electron mobility in strained GaAs nanowires.

Transistor concepts based on semiconductor nanowires promise high performance, lower energy consumption and better integrability in various platforms in nanoscale dimensions. Concerning the intrinsic transport properties of electrons in nanowires, relatively high mobility values that approach those in bulk crystals have been obtained only in core/shell heterostructures, where electrons are spatially confined inside the core. Here, it is demonstrated that the strain in lattice-mismatched core/shell nanowires can affect the effective mass of electrons in a way that boosts their mobility to distinct levels. Specifically, electrons inside the hydrostatically tensile-strained gallium arsenide core of nanowires with a thick indium aluminium arsenide shell exhibit mobility values 30-50 % higher than in equivalent unstrained nanowires or bulk crystals, as measured at room temperature. With such an enhancement of electron mobility, strained gallium arsenide nanowires emerge as a unique means for the advancement of transistor technology.

The evolutionary emergence of land plants.

There can be no doubt that early land plant evolution transformed the planet but, until recently, how and when this was achieved was unclear. Coincidence in the first appearance of land plant fossils and formative shifts in atmospheric oxygen and CO2 are an artefact of the paucity of earlier terrestrial rocks. Disentangling the timing of land plant bodyplan assembly and its impact on global biogeochemical cycles has been precluded by uncertainty concerning the relationships of bryophytes to one another and to the tracheophytes, as well as the timescale over which these events unfolded. New genome and transcriptome sequencing projects, combined with the application of sophisticated phylogenomic modelling methods, have yielded increasing support for the Setaphyta clade of liverworts and mosses, within monophyletic bryophytes. We consider the evolution of anatomy, genes, genomes and of development within this phylogenetic context, concluding that many vascular plant (tracheophytes) novelties were already present in a comparatively complex last common ancestor of living land plants (embryophytes). Molecular clock analyses indicate that embryophytes emerged in a mid-Cambrian to early Ordovician interval, compatible with hypotheses on their role as geoengineers, precipitating early Palaeozoic glaciations.

Simultaneous diversification of Polypodiales and angiosperms in the Mesozoic.

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.

Limitation of THz conversion efficiency in DSTMS pumped by intense femtosecond pulses.

Terahertz (THz) generation via optical rectification (OR) of near-infrared femtosecond pulses in DSTMS is systematically studied using a quasi-3D theoretical model, which takes into account cascaded OR, three-photon absorption (3PA) of the near-infrared radiation, and material dispersion/absorption properties. The simulation results and the comparison with experimental data for pump pulses with the center wavelength of 1.4 µm indicate that the 3PA process is one of the main limiting factors for THz generation in DSTMS at high pump fluences. The THz conversion efficiency is reduced further by the enhanced group velocity dispersion effect caused by the spectral broadening due to the cascaded OR. We predict that for broadband pump pulses with a duration of 30 fs, the THz conversion efficiency can be enhanced by a factor of 1.5 by using a positive pre-chirping that partially suppresses the cascaded OR and the 3PA effects.

High-field THz pulses from a GaAs photoconductive emitter for non-linear THz studies.

We report the emission of high-field terahertz pulses from a GaAs large-area photoconductive emitter pumped with a Ti:Sapphire amplifier laser system at 800 nm wavelength and 1 kHz repetition rate. The maximum estimated terahertz electric field at the focus is ≳ 230 kV/cm. We also demonstrate the capability of the terahertz field to cause a non-linear effect, which usually requires high-field terahertz pulses generated through optical rectification or an air plasma. A significant drop in the optical conductivity of optically pumped GaAs due to Γ-L inter-valley scattering of free electrons caused by the strong THz field is found.

Construction of DNA Tools for Hyperexpression in Marchantia Chloroplasts.

Chloroplasts are attractive platforms for synthetic biology applications since they are capable of driving very high levels of transgene expression, if mRNA production and stability are properly regulated. However, plastid transformation is a slow process and currently limited to a few plant species. The liverwort Marchantia polymorpha is a simple model plant that allows rapid transformation studies; however, its potential for protein hyperexpression has not been fully exploited. This is partially due to the fact that chloroplast post-transcriptional regulation is poorly characterized in this plant. We have mapped patterns of transcription in Marchantia chloroplasts. Furthermore, we have obtained and compared sequences from 51 bryophyte species and identified putative sites for pentatricopeptide repeat protein binding that are thought to play important roles in mRNA stabilization. Candidate binding sites were tested for their ability to confer high levels of reporter gene expression in Marchantia chloroplasts, and levels of protein production and effects on growth were measured in homoplastic transformed plants. We have produced novel DNA tools for protein hyperexpression in this facile plant system that is a test-bed for chloroplast engineering.

A Two-Dimensional Polyimide-Graphene Heterostructure with Ultra-fast Interlayer Charge Transfer.

Two-dimensional polymers (2DPs) are a class of atomically/molecularly thin crystalline organic 2D materials. They are intriguing candidates for the development of unprecedented organic-inorganic 2D van der Waals heterostructures (vdWHs) with exotic physicochemical properties. In this work, we demonstrate the on-water surface synthesis of large-area (cm2 ), monolayer 2D polyimide (2DPI) with 3.1-nm lattice. Such 2DPI comprises metal-free porphyrin and perylene units linked by imide bonds. We further achieve a scalable synthesis of 2DPI-graphene (2DPI-G) vdWHs via a face-to-face co-assembly of graphene and 2DPI on the water surface. Remarkably, femtosecond transient absorption spectroscopy reveals an ultra-fast interlayer charge transfer (ca. 60 fs) in the resultant 2DPI-G vdWH upon protonation by acid, which is equivalent to that of the fastest reports among inorganic 2D vdWHs. Such large interlayer electronic coupling is ascribed to the interlayer cation-π interaction between 2DP and graphene.

On the spore ornamentation of the microsoroid ferns (microsoroideae, polypodiaceae).

Microsoroideae is the third largest of the six subfamilies of Polypodiaceae, containing over 180 species. These ferns are widely distributed in the tropical and subtropical regions of the Old World and Oceania. We documented the spore ornamentation and integrated these data into the latest phylogenetic hypotheses, including a sampling of 100 taxa representing each of 17 major lineages of microsoroid ferns. This enabled us to reconstruct the ancestral states of the spore morphology. The results show verrucate ornamentation as an ancestral state for Goniophlebieae and Lecanoptereae, globular for Microsoreae, and rugulate surface for Lepisoreae. In addition, spore ornamentation can be used to distinguish certain clades of the microsoroid ferns. Among all five tribes, Lecanoptereae show most diversity in spore surface ornamentation.