Hedyotiskonhanungensis (Rubiaceae): A new species from the central highlands of Vietnam.

A new species of Hedyotis L. (Rubiaceae), Hedyotiskonhanungensis B.H. Quang, T.A. Le, K.S. Nguyen & Neupane, is described and illustrated from the central highlands of Vietnam based on morphological and phylogenetic evidence. The new species belongs to the morphologically diverse tribe Spermacoceae (ca. 1000 species) of the family Rubiaceae, which is represented by 70-80 species in Vietnam. The phylogenetic analysis, based on four DNA regions (ITS, ETS, petD, rps 16), confirms the new species' placement within the genus Hedyotis - one of the largest genera in the tribe, comprising ca. 180 species across Asia and the Pacific. Hedyotiskonhanungensis is morphologically distinct from all southeastern Asian Hedyotis L. in its set of traits such as leaf type (shape and thickness), growth habit, and floral parts (color of inflorescence axis and the shape of calyx lobes). The new species shows similarities with Hedyotisshenzhenensis, H.shiuyingiae, and H.yangchunensis from China in its herbaceous habit, fleshy ovate leaf blades, and dark purple floral parts, but it is phylogenetically distinct and can be distinguished from them by the following combination of morphological traits: habit with slightly smaller stature (<25 cm), broadly ovate or deltoid stipules with cuspidate apex and entire margin, and ovate or nearly ovate calyx lobes.

Order, please! Uncertainty in the ordinal-level classification of Chlorophyceae.

BACKGROUND: Chlorophyceae is one of three most species-rich green algal classes and also the only class in core Chlorophyta whose monophyly remains uncontested as gene and taxon sampling improves. However, some key relationships within Chlorophyceae are less clear-cut and warrant further investigation. The present study combined genome-scale chloroplast data and rich sampling in an attempt to resolve the ordinal classification in Chlorophyceae. The traditional division into Sphaeropleales and Volvocales (SV), and a clade containing Oedogoniales, Chaetopeltidales, and Chaetophorales (OCC) was of particular interest with the addition of deeply branching members of these groups, as well as the placement of several incertae sedis taxa. METHODS: We sequenced 18 chloroplast genomes across Chlorophyceae to compile a data set of 58 protein-coding genes of a total of 68 chlorophycean taxa. We analyzed the concatenated nucleotide and amino acid datasets in the Bayesian and Maximum Likelihood frameworks, supplemented by analyses to examine potential discordant signal among genes. We also examined gene presence and absence data across Chlorophyceae. RESULTS: Concatenated analyses yielded at least two well-supported phylogenies: nucleotide data supported the traditional classification with the inclusion of the enigmatic Treubarinia into Sphaeropleales sensu lato. However, amino acid data yielded equally strong support for Sphaeropleaceae as sister to Volvocales, with the rest of the taxa traditionally classified in Sphaeropleales in a separate clade, and Treubarinia as sister to all of the above. Single-gene and other supplementary analyses indicated that the data have low phylogenetic signal at these critical nodes. Major clades were supported by genomic structural features such as gene losses and trans-spliced intron insertions in the plastome. DISCUSSION: While the sequence and gene order data support the deep split between the SV and OCC lineages, multiple phylogenetic hypotheses are possible for Sphaeropleales s.l. Given this uncertainty as well as the higher-taxonomic disorder seen in other algal groups, dwelling on well-defined, strongly supported Linnaean orders is not currently practical in Chlorophyceae and a less formal clade system may be more useful in the foreseeable future. For example, we identify two strongly and unequivocally supported clades: Treubarinia and Scenedesminia, as well as other smaller groups that could serve a practical purpose as named clades. This system does not preclude future establishment of new orders, or emendment of the current ordinal classification if new data support such conclusions.

Assessing Combinability of Phylogenomic Data Using Bayes Factors.

With the rapid reduction in sequencing costs of high-throughput genomic data, it has become commonplace to use hundreds of genes to infer phylogeny of any study system. While sampling a large number of genes has given us a tremendous opportunity to uncover previously unknown relationships and improve phylogenetic resolution, it also presents us with new challenges when the phylogenetic signal is confused by differences in the evolutionary histories of sampled genes. Given the incorporation of accurate marginal likelihood estimation methods into popular Bayesian software programs, it is natural to consider using the Bayes Factor (BF) to compare different partition models in which genes within any given partition subset share both tree topology and edge lengths. We explore using marginal likelihood to assess data subset combinability when data subsets have varying levels of phylogenetic discordance due to deep coalescence events among genes (simulated within a species tree), and compare the results with our recently described phylogenetic informational dissonance index (D) estimated for each data set. BF effectively detects phylogenetic incongruence and provides a way to assess the statistical significance of D values. We use BFs to assess data combinability using an empirical data set comprising 56 plastid genes from the green algal order Volvocales. We also discuss the potential need for calibrating BFs and demonstrate that BFs used in this study are correctly calibrated.

Evolution of woody life form on tropical mountains in the tribe Spermacoceae (Rubiaceae).

PREMISE OF THE STUDY: Spermacoceae are mainly an herbaceous group in the Rubiaceae. However, a few lineages are woody and are found in a diverse range of habitat types. Three of the largest woody lineages (Arcytophyllum, Hedyotis, and Kadua) are characterized by their distribution in the moist tropical mountains and have disjunct distribution patterns with respect to their closest relatives. In this study, we explore the cases of derived woodiness in these three lineages and their diversification dynamics in the tropical mountains of Asia, the Pacific, and the Americas. METHODS: By combining phylogenetic results with wood anatomical studies, we estimated timing of origin of the three woody groups, inferred their ancestral traits and ancestral distribution ranges, analyzed their associations with the tropical upland habitat, and elucidated their diversification across tropical mountains. KEY RESULTS: The three woody clades originated and diversified from herbaceous ancestors in close association with the tropical upland habitat during the Miocene. The ancestral range for Asian-Pacific Hedyotis is Africa/Madagascar and continental Asia for Pacific Kadua. The complex geological history of tropical Asia allowed Hedyotis to diversify faster and create narrow endemics near oceans in the highlands of the Western Ghats in India, Sri Lanka, Southeast Asia including southeastern China, and New Guinea. CONCLUSIONS: The three major woody clades in Spermacoceae have gained their woodiness independently from one another, subsequent to colonization by their ancestors from a different geographic environment. The evolution and diversification along the tropical mountain orogeny is strongly linked with the formation of woody habit and many narrow endemic species.

Estimating Bayesian Phylogenetic Information Content.

Measuring the phylogenetic information content of data has a long history in systematics. Here we explore a Bayesian approach to information content estimation. The entropy of the posterior distribution compared with the entropy of the prior distribution provides a natural way to measure information content. If the data have no information relevant to ranking tree topologies beyond the information supplied by the prior, the posterior and prior will be identical. Information in data discourages consideration of some hypotheses allowed by the prior, resulting in a posterior distribution that is more concentrated (has lower entropy) than the prior. We focus on measuring information about tree topology using marginal posterior distributions of tree topologies. We show that both the accuracy and the computational efficiency of topological information content estimation improve with use of the conditional clade distribution, which also allows topological information content to be partitioned by clade. We explore two important applications of our method: providing a compelling definition of saturation and detecting conflict among data partitions that can negatively affect analyses of concatenated data. [Bayesian; concatenation; conditional clade distribution; entropy; information; phylogenetics; saturation.].

Enhanced Magnetic Properties of Graphene Coated with Fe2O3 Nanoparticles.

Graphene, with its unique 2D nanostructure and excellent electrical, thermal, and mechanical properties, is considered an alternative to carbon nanotubes in nanocomposites. In this study, we present a one step approach for the deposition of iron oxide (Fe2O3) nanoparticles onto graphene sheets through solution mixture. The morphology, crystallinity, and magnetic properties of as-synthesized composites were investigated. It was shown that highly crystalline Fe2O3 nanoparticles were densely and uniformly coated on graphene surface. Magnetic measurements reveal that, as compared to weak diamagnetism of pristine graphene, graphene-Fe2O3 nanocomposites display ferromagnetic behavior with coercivity of 101 Oe, saturation magnetization of 12.6 emu g(-1), and remanent magnetization of 3.13 emu g(-1) at room temperature. The enhanced magnetic performance was attributed to the homogeneous dispersion of Fe2O3 nanoparticles in graphene matrix and such nanocomposites are promising materials for applications in magnetic media and energy storage.

Evolution of endemism on a young tropical mountain.

Tropical mountains are hot spots of biodiversity and endemism, but the evolutionary origins of their unique biotas are poorly understood. In varying degrees, local and regional extinction, long-distance colonization, and local recruitment may all contribute to the exceptional character of these communities. Also, it is debated whether mountain endemics mostly originate from local lowland taxa, or from lineages that reach the mountain by long-range dispersal from cool localities elsewhere. Here we investigate the evolutionary routes to endemism by sampling an entire tropical mountain biota on the 4,095-metre-high Mount Kinabalu in Sabah, East Malaysia. We discover that most of its unique biodiversity is younger than the mountain itself (6 million years), and comprises a mix of immigrant pre-adapted lineages and descendants from local lowland ancestors, although substantial shifts from lower to higher vegetation zones in this latter group were rare. These insights could improve forecasts of the likelihood of extinction and 'evolutionary rescue' in montane biodiversity hot spots under climate change scenarios.

In situ transmission electron microscopy observation of electrochemical sodiation of individual Co9S8-filled carbon nanotubes.

The comprehension of fundamental electrochemical behavior and sodiation mechanism is critical for the design of high-performance electrode materials for sodium-ion (Na-ion) batteries. In this paper, the electrochemical sodiation process and microstructure evolution of individual Co9S8-filled carbon nanotubes (CNTs) have been directly visualized and studied using in situ transmission electron microscopy. Upon the first sodiation, a reaction front propagates progressively along the filling nanowire, causing the filled CNT to inflate. The filled CNTs behave differently depending on their structures and the magnitude of the sodiation voltage. For a Co9S8-filled CNT with an open end, the sodiated Co9S8 filler shows a substantial axial elongation of 120.8% and a small radial swelling due to the extrusion of CNT walls. In contrast, the closed CNT shows a major radial expansion of 40.6% and a small axial elongation because of the mechanical confinement of the carbon shells. After sodiation, the spacing between the carbon shells increases from 3.4 to 3.8 Å due to the Na(+)-ion insertion and the single-crystalline Co9S8 filler converts to numerous Co nanograins dispersed in a Na2S matrix. Compared with the gentle microstructure evolution of the CNT under small charging voltage, a strong electrochemical reaction accompanying drastic swelling and fracturing of CNT shells is observed for the CNT electrode under large charging voltage. Our observations provide direct evidence and important insights for the electrochemical process of CNT-based composite materials in Na-ion batteries.

In situ transmission electron microscopy investigation of the electrochemical lithiation-delithiation of individual Co9S8/Co-filled carbon nanotubes.

Carbon nanotube (CNT)-encapsulated metal sulfides/oxides are promising candidates for application as anode materials in lithium ion battery (LIB), while their electrochemical behavior and mechanism still remain unclear. A comprehensive understanding of the lithiation mechanism at nanoscale of this type of composites will benefit the design and development of high-performance LIB materials. Here, we use Co9S8/Co nanowire-filled CNTs as a model material to investigate the lithium storage mechanism by in situ transmission electron microscopy. For a Co9S8/Co nanowire-filled closed CNT, the reaction front propagates progressively during lithiation, causing an axial elongation of 4.5% and a radial expansion of 32.4%, while the lithiated nanowire core is still confined inside the CNT. Contrastingly, for an open CNT, the lithiated Co9S8 nanowire shows an axial elongation of 94.2% and is extruded out from the open CNT. In particular, a thin graphite shell is drawn out from the CNT wall by the extruded lithiated Co9S8. The thin graphite shell confines the extruded filler and protects the filler from pulverization in the following lithiation-delithiation cycles. During multiple cycles, the Co segment remains intact while the Co9S8 exhibits a reversible transformation between Co9S8 and Co nanograins. Our observations provide direct electrochemical behavior and mechanism that govern the CNT-based anode performance in LIBs.

Multiple step growth of single crystalline rutile nanorods with the assistance of self-assembled monolayer for dye sensitized solar cells.

A novel multiple step growth (MSG) process has been developed to synthesize rutile nanorods (NRs) on fluorine-doped tin oxide (FTO) glass with the assistance of a self-assembled monolayer (SAM) aiming to increase the internal surface area of the 1D materials for dye sensitized solar cell (DSSC) applications. The experimental result reveals that the SAM layer can be selectively decomposed at the tip of the nanorod, namely the rutile (001) surface, due to the anisotropic photocatalytic property of the rutile. The remaining SAM layer on the side-wall of the NRs remains intact and serves as water repellent which prevents the radial growth of the NRs during the next step hydrothermal synthesis; therefore, the spacing between the NRs and the porosity of the NR array can be retained after additional growth cycles. On the other hand, introduction of a middle layer formed via TiCl4 solution treatment before the next growth cycle is found to be an effective way to control the diameters of the newly grown NRs. The performance of DSSC made from the rutile NRs grown using the MSG technique has been examined, and it is significantly affected by the internal surfaces of the NRs. Furthermore, the MSG combined with NR etching treatment by acid at low temperature (150 °C) leads to a significant enhancement in the solar cell performance. The gigantic wettability difference of the NRs before and after the SAM treatment as well as the MSG method could be adapted to prepare superhydrophobic and superhydrophilic nanostructured patterns for other applications.