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.

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.

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.

Allopolyploid Speciation Accompanied by Gene Flow in a Tree Fern.

Hybridization in plants may result in hybrid speciation or introgression and, thus, is now widely understood to be an important mechanism of species diversity on an evolutionary timescale. Hybridization is particularly common in ferns, as is polyploidy, which often results from hybrid crosses. Nevertheless, hybrid speciation as an evolutionary process in fern lineages remains poorly understood. Here, we employ flow cytometry, phylogeny, genomewide single nucleotide polymorphism data sets, and admixture and coalescent modeling to show that the scaly tree fern, Gymnosphaera metteniana is a naturally occurring allotetraploid species derived from hybridization between the diploids, G. denticulata and G. gigantea. Moreover, we detected ongoing gene flow between the hybrid species and its progenitors, and we found that G. gigantea and G. metteniana inhabit distinct niches, whereas climatic niches of G. denticulata and G. metteniana largely overlap. Taken together, these results suggest that either some degree of intrinsic genetic isolation between the hybrid species and its parental progenitors or ecological isolation over short distances may be playing an important role in the evolution of reproductive barriers. Historical climate change may have facilitated the origin of G. metteniana, with the timing of hybridization coinciding with a period of intensification of the East Asian monsoon during the Pliocene and Pleistocene periods in southern China. Our study of allotetraploid G. metteniana represents the first genomic-level documentation of hybrid speciation in scaly tree ferns and, thus, provides a new perspective on evolution in the lineage.

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.

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.

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.

The timescale of early land plant evolution.

Establishing the timescale of early land plant evolution is essential for testing hypotheses on the coevolution of land plants and Earth's System. The sparseness of early land plant megafossils and stratigraphic controls on their distribution make the fossil record an unreliable guide, leaving only the molecular clock. However, the application of molecular clock methodology is challenged by the current impasse in attempts to resolve the evolutionary relationships among the living bryophytes and tracheophytes. Here, we establish a timescale for early land plant evolution that integrates over topological uncertainty by exploring the impact of competing hypotheses on bryophyte-tracheophyte relationships, among other variables, on divergence time estimation. We codify 37 fossil calibrations for Viridiplantae following best practice. We apply these calibrations in a Bayesian relaxed molecular clock analysis of a phylogenomic dataset encompassing the diversity of Embryophyta and their relatives within Viridiplantae. Topology and dataset sizes have little impact on age estimates, with greater differences among alternative clock models and calibration strategies. For all analyses, a Cambrian origin of Embryophyta is recovered with highest probability. The estimated ages for crown tracheophytes range from Late Ordovician to late Silurian. This timescale implies an early establishment of terrestrial ecosystems by land plants that is in close accord with recent estimates for the origin of terrestrial animal lineages. Biogeochemical models that are constrained by the fossil record of early land plants, or attempt to explain their impact, must consider the implications of a much earlier, middle Cambrian-Early Ordovician, origin.

Nonlinear Charge Transport in InGaAs Nanowires at Terahertz Frequencies.

We probe the electron transport properties in the shell of GaAs/In0.2Ga0.8As core/shell nanowires at high electric fields using optical pump/THz probe spectroscopy with broadband THz pulses and peak electric fields up to 0.6 MV/cm. The plasmon resonance of the photoexcited charge carriers exhibits a systematic redshift and a suppression of its spectral weight for THz driving fields exceeding 0.4 MV/cm. This behavior is attributed to the intervalley electron scattering that results in the doubling of the average electron effective mass. Correspondingly, the electron mobility at the highest fields drops to about half of the original value. We demonstrate that the increase of the effective mass is nonuniform along the nanowires and takes place mainly in their middle part, leading to a spatially inhomogeneous carrier response. Our results quantify the nonlinear transport regime in GaAs-based nanowires and show their high potential for development of nanodevices operating at THz frequencies.

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.

A study of male fertility control in Medicago truncatula uncovers an evolutionarily conserved recruitment of two tapetal bHLH subfamilies in plant sexual reproduction.

Male sterility is an important tool for plant breeding and hybrid seed production. Male-sterile mutants are largely due to an abnormal development of either the sporophytic or gametophytic anther tissues. Tapetum, a key sporophytic tissue, provides nutrients for pollen development, and its delayed degeneration induces pollen abortion. Numerous bHLH proteins have been documented to participate in the degeneration of the tapetum in angiosperms, but relatively little attention has been given to the evolution of the involved developmental pathways across the phylogeny of land plants. A combination of cellular, molecular, biochemical and evolutionary analyses was used to investigate the male fertility control in Medicago truncatula. We characterized the male-sterile mutant empty anther1 (ean1) and identified EAN1 as a tapetum-specific bHLH transcription factor necessary for tapetum degeneration. Our study uncovered an evolutionarily conserved recruitment of bHLH subfamily II and III(a + c)1 in the regulation of tapetum degeneration. EAN1 belongs to the subfamily II and specifically forms heterodimers with the subfamily III(a + c)1 members, which suggests a heterodimerization mechanism conserved in angiosperms. Our work suggested that the pathway of two tapetal-bHLH subfamilies is conserved in all land plants, and likely was established before the divergence of the spore-producing land plants.

Exploring phylogeny of the microsoroid ferns (Polypodiaceae) based on six plastid DNA markers.

The microsoroid ferns are one of the largest subfamilies of the Polypodiaceae with over 180 species mainly found in the humid forests of tropical Australasia. The phylogenetic relationships are still unclear, especially the delimitation of the genus Microsorum which has been recognized to be non-monophyletic. We analysed the microsoroid ferns using six chloroplast DNA regions (rbcL, rps4+rps4-trnS, trnL+trnL-trnF, atpA, atpB and matK) in order to present a robust hypothesis of their phylogeny. Our results suggest that they comprise up to 17 genera; of them, 12 agree with a previously accepted generic classification. Five tribes are proposed based on the phylogenetic relationships. Most of the species traditionally included in the genus Microsorum are found in six genera belonging to two tribes. In addition to the commonly used DNA markers, the additional atpA and matK are helpful to provide information about the phylogenetic relationships of the microsoroid ferns.

All-THz pump-probe spectroscopy of the intersubband AC-Stark effect in a wide GaAs quantum well.

We report the observation of the intersubband AC-Stark effect in a single wide GaAs/AlGaAs quantum well. In a three-level configuration, the n = 2 to n = 3 intersubband transition is resonantly pumped at 3.5 THz using a free-electron laser. The induced spectral changes are probed using THz time-domain spectroscopy with a broadband pulse extending up to 4 THz. We observe an Autler-Townes splitting at the 1 - 2 intersubband transition as well as an indication of a Mollow triplet at the 2 - 3 transition, both evidencing the dressed states. For longer delay times, a relaxation of the hot-electron system with a time constant of around 420 ps is measured.

Non-plasmonic improvement in photoconductive THz emitters using nano- and micro-structured electrodes.

We investigate here terahertz enhancement effects arising from micrometer and nanometer structured electrode features of photoconductive terahertz emitters. Nanostructured electrode based emitters utilizing the palsmonic effect are currently one of the hottest topics in the research field. We demonstrate here that even in the absence of any plasmonic resonance with the pump pulse, such structures can improve the antenna effect by enhancing the local d.c. electric field near the structure edges. Utilizing this effect in Hilbert-fractal and grating-like designs, enhancement of the THz field of up to a factor of ∼ 2 is observed. We conclude that the cause of this THz emission enhancement in our emitters is different from the earlier reported plasmonic-electrode effect in a similar grating-like structure. In our structure, the proximity of photoexcited carriers to the electrodes and local bias field enhancement close to the metallization cause the enhanced efficiency. Due to the nature of this effect, the THz emission efficiency is almost independent of the pump laser polarization. Compared to the plasmonic effect, these effects work under relaxed device fabrication and operating conditions.

Chloroplast phylogenomics of liverworts: a reappraisal of the backbone phylogeny of liverworts with emphasis on Ptilidiales.

As one of the four main lineages diverging from the early diversification of land plants, the phylogeny of liverworts holds the information about nearly 500 Myr of independent adaptation to changing environments. Thus, resolving the phylogenetic history of liverworts will provide unique insights into the successful diversification of early land plants in terrestrial ecosystems. However, the deep diverging events of this group remain incompletely resolved, such as the definite position of Ptilidiales. Here, we aimed to reconstruct the backbone relationships of liverworts using 84 protein-coding chloroplast genes, a dataset comprising 35 representatives from all major lineages of liverworts, and three phylogenetic analyses, namely maximum parsimony, maximum likelihood and Bayesian inference. To test the impact of composition biases, the phylogenetic analyses were carried out using three alignments representing the same dataset either as: (i) nucleotides, (ii) amino acids, or (iii) recoded nucleotides applying ambiguity base code. Chloroplast genome data consistently supported the monophyletic origin of three major lineages in liverworts, as well as the majority of backbone relationships. Ptilidiales were found to be sister to Jungermanniales. The rapid accumulation of G/C tracks as a consequence of increased GC content is an important cause for the long branches inferred in this group. Our study not only provides empirical evidence to support the significance of plastid genome sequencing to reconstruct the phylogeny of this important plant lineage, but also suggests that the GC content has played a critical role in the evolutionary dynamics of plastid genomes in land plants.

Association of dietary intake of milk and dairy products with blood concentrations of insulin-like growth factor 1 (IGF-1) in Bavarian adults.

PURPOSE: Circulating IGF-1 concentrations have been associated with higher cancer risk, particularly prostate, breast and colorectal cancer. There is evidence from observational and intervention studies that milk and dairy products intake is associated with higher IGF-1 concentrations, but results were not always consistent. The purpose of this study was to examine the relationship between dairy intake and circulating IGF-1 concentrations in participants of the Second Bavarian Food Consumption Survey, thereby providing data for a German population for the first time. METHODS: In this cross-sectional study of 526 men and women aged 18-80 years, in contrast to most previous investigations, dietary intake was assessed with a more detailed instrument than food frequency questionnaires (FFQs), i.e., by three 24-h dietary recalls conducted on random days close in time to the blood collection. Circulating IGF-1 concentrations were measured in blood samples. Multivariable linear regression models were used to examine the association of dairy intake with IGF-1 concentrations. RESULTS: Each 400 g increment in daily dairy intake was associated with 16.8 µg/L (95% CI 6.9, 26.7) higher IGF-1 concentrations. Each 200 g increment in milk per day was associated with 10.0 µg/L (95% CI 4.2, 15.8) higher IGF-1. In contrast, we observed no association between cheese or yogurt intake and IGF-1 concentrations. CONCLUSIONS: Our findings are in line with most previous investigations and support the hypothesis that dairy and milk intake are associated with higher IGF-1 concentrations.

Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.).

Unraveling the phylogenetic relationships between the four major lineages of terrestrial plants (mosses, liverworts, hornworts, and vascular plants) is essential for an understanding of the evolution of traits specific to land plants, such as their complex life cycles, and the evolutionary development of stomata and vascular tissue. Well supported phylogenetic hypotheses resulting from different data and methods are often incongruent due to processes of nucleotide evolution that are difficult to model, for example substitutional saturation and composition heterogeneity. We reanalysed a large published dataset of nuclear data and modelled these processes using degenerate-codon recoding and tree-heterogeneous composition substitution models. Our analyses resolved bryophytes as a monophyletic group and showed that the nonnonmonophyly of the clade that is supported by the analysis of nuclear nucleotide data is due solely to fast-evolving synonymous substitutions. The current congruence among phylogenies of both nuclear and chloroplast analyses lent considerable support to the conclusion that the bryophytes are a monophyletic group. An initial split between bryophytes and vascular plants implies that the bryophyte life cycle (with a dominant gametophyte nurturing an unbranched sporophyte) may not be ancestral to all land plants and that stomata are likely to be a symplesiomorphy among embryophytes.