Genomic evidence for the parallel evolution of coastal forms in the Senecio lautus complex

Instances of parallel ecotypic divergence where adaptation to similar conditions repeatedly cause similar phenotypic changes in closely related organisms are useful for studying the role of ecological selection in speciation. Here we used a combination of traditional and next generation genotyping techniques to test for the parallel divergence of plants from the Senecio lautus complex, a phenotypically variable groundsel that has adapted to disparate environments in the South Pacific. Phylogenetic analysis of a broad selection of Senecio species showed that members of the S. lautus complex form a distinct lineage that has diversified recently in Australasia. An inspection of thousands of polymorphisms in the genome of 27 natural populations from the S. lautus complex in Australia revealed a signal of strong genetic structure independent of habitat and phenotype. Additionally, genetic differentiation between populations was correlated with the geographical distance separating them, and the genetic diversity of populations strongly depended on geographical location. Importantly, coastal forms appeared in several independent phylogenetic clades, a pattern that is consistent with the parallel evolution of these forms. Analyses of the patterns of genomic differentiation between populations further revealed that adjacent populations displayed greater genomic heterogeneity than allopatric populations and are differentiated according to variation in soil composition. These results are consistent with a process of parallel ecotypic divergence in face of gene flow.

The evolution and biogeography of the austral horse fly tribe Scionini (Diptera: Tabanidae: Pangoniinae) inferred from multiple mitochondrial and nuclear genes

Phylogenetic relationships within the Tabanidae are largely unknown, despite their considerable medical and ecological importance. The first robust phylogenetic hypothesis for the horse fly tribe Scionini is provided, completing the systematic placement of all tribes in the subfamily Pangoniinae. The Scionini consists of seven mostly southern hemisphere genera distributed in Australia, New Guinea, New Zealand and South America. A 5757. bp alignment of 6 genes, including mitochondrial (COI and COII), ribosomal (28S) and nuclear (AATS and CAD regions 1, 3 and 4) genes, was analysed for 176 taxa using both Bayesian and maximum likelihood approaches. Results indicate the Scionini are strongly monophyletic, with the exclusion of the only northern hemisphere genus Goniops. The South American genera Fidena, Pityocera and Scione were strongly monophyletic, corresponding to current morphology-based classification schemes. The most widespread genus Scaptia was paraphyletic and formed nine strongly supported monophyletic clades, each corresponding to either the current subgenera or several previously synonymised genera that should be formally resurrected. Molecular results also reveal a newly recognised genus endemic to New Zealand, formerly placed within Scaptia. Divergence time estimation was employed to assess the global biogeographical patterns in the Pangoniinae. These analyses demonstrated that the Scionini are a typical Gondwanan group whose diversification was influenced by the fragmentation of that ancient land mass. Furthermore, results indicate that the Scionini most likely originated in Australia and subsequently radiated to New Zealand and South American by both long distance dispersal and vicariance. The phylogenetic framework of the Scionini provided herein will be valuable for taxonomic revisions of the Tabanidae.

Evolution of epitaxial graphene layers on 3C SiC/Si (111) as a function of annealing temperature in UHV

The growth of graphene on SiC/Si substrates is an appealing alternative to the growth on bulk SiC for cost reduction and to better integrate the material with Si based electronic devices. In this paper, we present a complete in-situ study of the growth of epitaxial graphene on 3C SiC (111)/Si (111) substrates via high temperature annealing (ranging from 1125˚C to 1375˚C) in ultra high vacuum (UHV). The quality and number of graphene layers have been thoroughly investigated by using x-ray photoelectron spectroscopy (XPS), while the surface characterization have been studied by scanning tunnelling microscopy (STM). Ex-situ Raman spectroscopy measurements confirm our findings, which demonstrate the exponential dependence of the number of graphene layer from the annealing temperature.

Hydrogen evolution by a metal-free electrocatalyst

Electrocatalytic reduction of water to molecular hydrogen via the hydrogen evolution reaction may provide a sustainable energy supply for the future, but its commercial application is hampered by the use of precious platinum catalysts. All alternatives to platinum thus far are based on nonprecious metals, and, to our knowledge, there is no report about a catalyst for electrocatalytic hydrogen evolution beyond metals. Here we couple graphitic-carbon nitride with nitrogen-doped graphene to produce a metal-free hybrid catalyst, which shows an unexpected hydrogen evolution reaction activity with comparable overpotential and Tafel slope to some of well-developed metallic catalysts. Experimental observations in combination with density functional theory calculations reveal that its unusual electrocatalytic properties originate from an intrinsic chemical and electronic coupling that synergistically promotes the proton adsorption and reduction kinetics.

Not drowning, (hand)waving? Molecular phylogenetics, biogeography and evolutionary tempo of the ‘Gondwanan’ midge Stictocladius Edwards (Diptera: Chironomidae)

Many insect clades, especially within the Diptera (true flies), have been considered classically ‘Gondwanan’, with an inference that distributions derive from vicariance of the southern continents. Assessing the role that vicariance has played in the evolution of austral taxa requires testing the location and tempo of diversification and speciation against the well-established predictions of fragmentation of the ancient super-continent. Several early (anecdotal) hypotheses that current austral distributions originate from the breakup of Gondwana derive from studies of taxa within the family Chironomidae (non-biting midges). With the advent of molecular phylogenetics and biogeographic analytical software, these studies have been revisited and expanded to test such conclusions better. Here we studied the midge genus Stictocladius Edwards, from the subfamily Orthocladiinae, which contains austral-distributed clades that match vicariance-based expectations. We resolve several issues of systematic relationships among morphological species and reveal cryptic diversity within many taxa. Time-calibrated phylogenetic relationships among taxa accorded partially with the predicted tempo from geology. For these apparently vagile insects, vicariance-dated patterns persist for South America and Australia. However, as often found, divergence time estimates for New Zealand at c. 50 mya post-date separation of Zealandia from Antarctica and the remainder of Gondwana, but predate the proposed Oligocene ‘drowning’ of these islands. We detail other such ‘anomalous’ dates and suggest a single common explanation rather than stochastic processes. This could involve synchronous establishment following recovery from ‘drowning’ and/or deleteriously warming associated with the mid-Eocene climatic optimum (hence ‘waving’, which refers to cycles of drowning events) plus new availability of topography providing of cool running waters, or all these factors in combination. Alternatively a vicariance explanation remains available, given the uncertain duration of connectivity of Zealandia to Australia–Antarctic–South America via the Lord Howe and Norfolk ridges into the Eocene.

Structure evolution characterization of Anyang anthracites via H2O2 oxidization and HF acidification

The structural characteristics of the raw coal (AY), the H2O2 oxidized coals (AY–H2O2) and the HF acidized AY–H2O2 (AY–H2O2–HF) were investigated by SEM, X-ray diffraction, Raman and FTIR spectroscopy. The results indicate that the derivative coals show an obvious increase in the aromaticity, crystalline carbon content and hydroxyl content, especially the AY–H2O2–HF. The stacking layer number of crystalline carbon decreases and the aspect ratio (La/Lc) remarkably increases for AY–H2O2 and AY–H2O2–HF. The crystalline layers become much thinner. The particle size of AY–H2O2–HF in width significantly decreases from 1 μm to less than 100 nm. The combination of H2O2 oxidization and HF acidification is effective to reduce the size of the aromatic layers and to increase the reactivity of derivative coals. The process can help us obtain the superfine crystalline carbon materials like graphite structure.

Molecular analysis of asymptomatic bacteriuria escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition

Urinary tract infections (UTIs) are among the most common infectious diseases of humans, with Escherichia coli responsible for >80% of all cases. One extreme of UTI is asymptomatic bacteriuria (ABU), which occurs as an asymptomatic carrier state that resembles commensalism. To understand the evolution and molecular mechanisms that underpin ABU, the genome of the ABU E. coli strain VR50 was sequenced. Analysis of the complete genome indicated that it most resembles E. coli K-12, with the addition of a 94-kb genomic island (GI-VR50-pheV), eight prophages, and multiple plasmids. GI-VR50-pheV has a mosaic structure and contains genes encoding a number of UTI-associated virulence factors, namely, Afa (afimbrial adhesin), two autotransporter proteins (Ag43 and Sat), and aerobactin. We demonstrated that the presence of this island in VR50 confers its ability to colonize the murine bladder, as a VR50 mutant with GI-VR50-pheV deleted was attenuated in a mouse model of UTI in vivo. We established that Afa is the island-encoded factor responsible for this phenotype using two independent deletion (Afa operon and AfaE adhesin) mutants. E. coli VR50afa and VR50afaE displayed significantly decreased ability to adhere to human bladder epithelial cells. In the mouse model of UTI, VR50afa and VR50afaE displayed reduced bladder colonization compared to wild-type VR50, similar to the colonization level of the GI-VR50-pheV mutant. Our study suggests that E. coli VR50 is a commensal-like strain that has acquired fitness factors that facilitate colonization of the human bladder.

Molecular data extend Australian Cricotopus midge (Chironomidae) species diversity, and provide a phylogenetic hypothesis for biogeography and freshwater monitoring

Resolving species relationships and confirming diagnostic morphological characters for insect clades that are highly plastic, and/or include morphologically cryptic species, is crucial for both academic and applied reasons. Within the true fly (Diptera) family Chironomidae, a most ubiquitous freshwater insect group, the genera CricotopusWulp, 1874 and ParatrichocladiusSantos-Abreu, 1918 have long been taxonomically confusing. Indeed, until recently the Australian fauna had been examined in just two unpublished theses: most species were known by informal manuscript names only, with no concept of relationships. Understanding species limits, and the associated ecology and evolution, is essential to address taxonomic sufficiency in biomonitoring surveys. Immature stages are collected routinely, but tolerance is generalized at the genus level, despite marked variation among species. Here, we explored this issue using a multilocus molecular phylogenetic approach, including the standard mitochondrial barcode region, and tested explicitly for phylogenetic signal in ecological tolerance of species. Additionally, we addressed biogeographical patterns by conducting Bayesian divergence time estimation. We sampled all but one of the now recognized Australian Cricotopus species and tested monophyly using representatives from other austral and Asian locations. Cricotopus is revealed as paraphyletic by the inclusion of a nested monophyletic Paratrichocladius, with in-group diversification beginning in the Eocene. Previous morphological species concepts are largely corroborated, but some additional cryptic diversity is revealed. No significant relationship was observed between the phylogenetic position of a species and its ecology, implying either that tolerance to deleterious environmental impacts is a convergent trait among many Cricotopus species or that sensitive and restricted taxa have diversified into more narrow niches from a widely tolerant ancestor.

Nonlinear Enzyme Kinetics Can Lead to High Metabolic Flux Control Coefficients: Implications for the Evolution of Dominance

In a classic study, Kacser & Burns (1981, Genetics 97, 639-666) demonstrated that given certain plausible assumptions, the flux in a metabolic pathway was more or less indifferent to the activity of any of the enzymes in the pathway taken singly. It was inferred from this that the observed dominance of most wild-type alleles with respect to loss-of-function mutations did not require an adaptive, meaning selectionist, explanation. Cornish-Bowden (1987, J. theor. Biol. 125, 333-338) showed that the Kacser-Burns inference was not valid when substrate concentrations were large relative to the relevant Michaelis constants. We find that in a randomly constructed functional pathway, even when substrate levels are small, one can expect high values of control coefficients for metabolic flux in the presence of significant nonlinearities as exemplified by enzymes with Hill coefficients ranging from two to six, or by the existence of oscillatory loops. Under these conditions the flux can be quite sensitive to changes in enzyme activity as might be caused by inactivating one of the two alleles in a diploid. Therefore, the phenomenon of dominance cannot be a trivial ''default'' consequence of physiology but must be intimately linked to the manner in which metabolic networks have been moulded by natural selection.

Crystal engineering in two dimensions: An approach to molecular nanopatterning

We describe a surprising cooperative adsorption process observed by scanning tunneling microscopy (STM) at the liquid−solid interface. The process involves the association of a threefold hydrogen-bonding unit, trimesic acid (TMA), with straight-chain aliphatic alcohols of varying length (from C7 to C30), which coadsorb on highly oriented pyrolytic graphite (HOPG) to form linear patterns. In certain cases, the known TMA “flower pattern” can coexist temporarily with the linear TMA−alcohol patterns, but it eventually disappears. Time-lapsed STM imaging shows that the evolution of the flower pattern is a classical ripening phenomenon. The periodicity of the linear TMA−alcohol patterns can be modulated by choosing alcohols with appropriate chain lengths, and the precise structure of the patterns depends on the parity of the carbon count in the alkyl chain. Interactions that lead to this odd−even effect are analyzed in detail. The molecular components of the patterns are achiral, yet their association by hydrogen bonding leads to the formation of enantiomeric domains on the surface. The interrelation of these domains and the observation of superperiodic structures (moiré patterns) are rationalized by considering interactions with the underlying graphite surface and within the two-dimensional crystal of the adsorbed molecules. Comparison of the observed two-dimensional structures with the three-dimensional crystal structures of TMA−alcohol complexes determined by X-ray crystallography helps reveal the mechanism of molecular association in these two-component systems.

Structure and Rheology of Cationic Molecular Hydrogels of Quinuclidine Grafted Bile Salts. Influence of the Ionic Strength and Counter-Ion type

Quinuclidine grafted cationic bile salts are forming salted hydrogels. An extensive investigation of the effect of the electrolyte and counterions on the gelation has been envisaged. The special interest of the quinuclidine grafted bile salt is due to its broader experimental range of gelation to study the effect of electrolyte. Rheological features of the hydrogels are typical of enthalpic networks exhibiting a scaling law of the elastic shear modulus with the concentration (scaling exponent 2.2) modeling cellular solids in which the bending modulus is the dominant parameter. The addition of monovalent salt (NaCl) favors the formation of gels in a first range (0.00117 g cm-3 (0.02 M) < TNaCl < 0.04675 g cm-3 (0.8 M)). At larger salt concentrations, the gels become more heterogeneous with nodal zones in the micron scale. Small-angle neutron scattering experiments have been used to characterize the rigid fibers ( ≈ 68 Å) and the nodal zones. Stress sweep and creeprecovery measurements are used to relate the lack of linear viscoelastic domain to a mechanism of disentanglement of the fibers from their associations into fagots. The electrostatic interactions can be screened by addition of salt to induce a progressive evolution toward flocculation. SEM, UV absorbance, and SAXS study of the Bragg peak at large Q-values complete the investigation.

DNA structural variability as a factor in gene expression and evolution

Redundant DNA can buffer sequence dependent structural deviations from an ideal double helix. Buffering serves a mechanistic function by reducing extraneous conformational effects which could interfere with readout or which would impose energetic constraints on evolution. It also serves an evolutionary function by allowing for gradual variations in conformation-dependent regulation of gene expression. Such gradualism is critical for the rate of evolution. The buffer structure concept provides a new interpretation for repetitive DNA and for exons and introns.

Molecular dynamics simulations of sliding in an Fe-Cu tribopair system

Experimental evidence suggests that high strain rates, stresses, strains and temperatures are experienced near sliding interfaces. The associated microstructural changes are due to several dynamic an interacting phenomena. 3D non-equilibrium molecular dynamics (MD) simulations of sliding were conducted with the aim of understanding the dynamic processes taking place in crystalline tribopairs, with a focus on plastic deformation and microstructural evolution. Embedded atom potentials were employed for simulating sliding of an Fe-Cu tribopair. Sliding velocity, crystal orientation and presence of lattice defects were some of the variables in these simulations. Extensive plastic deformation involving dislocation and twin activity, dynamic recrystallization, amorphization and/or nanocrystallization, mechanical mixing and material transfer were observed. Mechanical mixing in the vicinity of the sliding interface was observed even in the Fe-Cu system, which would cluster under equilibrium conditions, hinting at the ballistic nature of the process. Flow localization was observed at high velocities implying the possible role of adiabatic heating. The presence of preexisting defects (such as dislocations and interfaces) played a pivotal role in determining friction and microstructural evolution. The study also shed light on the relationship between adhesion and plastic deformation, and friction. Comparisons with experiments suggest that such simulations can indeed provide valuable insights that are difficult to obtain from experiments.

Molecular characterisation of dicot-infecting mastreviruses from Australia

Monocotyledonous and dicotyledonous plant infecting mastreviruses threaten various agricultural systems throughout Africa, Eurasia and Australasia. In Australia three distinct mastrevirus species are known to infect dicotyledonous hosts such as chickpea, bean and tobacco. Amongst 34 new "dicot-infecting" mastrevirus full genome sequences obtained from these hosts we discovered one new species, four new strains, and various variants of previously described mastrevirus species. Besides providing additional support for the hypothesis that evolutionary processes operating during dicot-infecting mastrevirus evolution (such as patterns of pervasive homologous and non-homologous recombination, and strong purifying selection acting on all genes) have mostly mirrored those found in their monocot-infecting counterparts, we find that the Australian dicot-infecting viruses display patterns of phylogeographic clustering reminiscent of those displayed by monocot infecting mastrevirus species such as Panicum streak virus and Maize streak virus.