Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: High rates of intra-species recombination – a driving force in the emergence of new strains

In Sudan Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is an important pathogen of pulses that are grown both for local consumption, and for export. Although a few studies have characterised CpCDV genomes from countries in the Middle East, Africa and the Indian subcontinent, little is known about CpCDV diversity in any of the major chickpea production areas in these regions. Here we analyse the diversity of 146 CpCDV isolates characterised from pulses collected across the chickpea growing regions of Sudan. Although we find that seven of the twelve known CpCDV strains are present within the country, strain CpCDV-H alone accounted for ∼73% of the infections analysed. Additionally we identified four new strains (CpCDV-M, -N, -O and -P) and show that recombination has played a significant role in the diversification of CpCDV, at least in this region. Accounting for observed recombination events, we use the large amounts of data generated here to compare patterns of natural selection within protein coding regions of CpCDV and other dicot-infecting mastrevirus species.

Spectroscopy and photochemistry of hydrogen peroxide and its complexes in solid rare gases

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Intermolecular Interactions of Noble-Gas-Containing Species

The importance of intermolecular interactions to chemistry, physics, and biology is difficult to overestimate. Without intermolecular forces, condensed phase matter could not form. The simplest way to categorize different types of intermolecular interactions is to describe them using van der Waals and hydrogen bonded (H-bonded) interactions. In the H-bond, the intermolecular interaction appears between a positively charged hydrogen atom and electronegative fragments and it originates from strong electrostatic interactions. H-bonding is important when considering the properties of condensed phase water and in many biological systems including the structure of DNA and proteins. Vibrational spectroscopy is a useful tool for studying complexes and the solvation of molecules. Vibrational frequency shift has been used to characterize complex formation. In an H-bonded system A∙∙∙H-X (A and X are acceptor and donor species, respectively), the vibrational frequency of the H-X stretching vibration usually decreases from its value in free H-X (red-shift). This frequency shift has been used as evidence for H-bond formation and the magnitude of the shift has been used as an indicator of the H-bonding strength. In contrast to this normal behavior are the blue-shifting H-bonds, in which the H-X vibrational frequency increases upon complex formation. In the last decade, there has been active discussion regarding these blue-shifting H-bonds. Noble-gases have been considered inert due to their limited reactivity with other elements. In the early 1930 s, Pauling predicted the stable noble-gas compounds XeF6 and KrF6. It was not until three decades later Neil Bartlett synthesized the first noble-gas compound, XePtF6, in 1962. A renaissance of noble-gas chemistry began in 1995 with the discovery of noble-gas hydride molecules at the University of Helsinki. The first hydrides were HXeCl, HXeBr, HXeI, HKrCl, and HXeH. These molecules have the general formula of HNgY, where H is a hydrogen atom, Ng is a noble-gas atom (Ar, Kr, or Xe), and Y is an electronegative fragment. At present, this class of molecules comprises 23 members including both inorganic and organic compounds. The first and only argon-containing neutral chemical compound HArF was synthesized in 2000 and its properties have since been investigated in a number of studies. A helium-containing chemical compound, HHeF, was predicted computationally, but its lifetime has been predicted to be severely limited by hydrogen tunneling. Helium and neon are the only elements in the periodic table that do not form neutral, ground state molecules. A noble-gas matrix is a useful medium in which to study unstable and reactive species including ions. A solvated proton forms a centrosymmetric NgHNg+ (Ng = Ar, Kr, and Xe) structure in a noble-gas matrix and this is probably the simplest example of a solvated proton. Interestingly, the hypothetical NeHNe+ cation is isoelectronic with the water-solvated proton H5O2+ (Zundel-ion). In addition to the NgHNg+ cations, the isoelectronic YHY- (Y = halogen atom or pseudohalogen fragment) anions have been studied with the matrix-isolation technique. These species have been known to exist in alkali metal salts (YHY)-M+ (M = alkali metal e.g. K or Na) for more than 80 years. Hydrated HF forms the FHF- structure in aqueous solutions, and these ions participate in several important chemical processes. In this thesis, studies of the intermolecular interactions of HNgY molecules and centrosymmetric ions with various species are presented. The HNgY complexes show unusual spectral features, e.g. large blue-shifts of the H-Ng stretching vibration upon complexation. It is suggested that the blue-shift is a normal effect for these molecules, and that originates from the enhanced (HNg)+Y- ion-pair character upon complexation. It is also found that the HNgY molecules are energetically stabilized in the complexed form, and this effect is computationally demonstrated for the HHeF molecule. The NgHNg+ and YHY- ions also show blue-shifts in their asymmetric stretching vibration upon complexation with nitrogen. Additionally, the matrix site structure and hindered rotation (libration) of the HNgY molecules were studied. The librational motion is a much-discussed solid state phenomenon, and the HNgY molecules embedded in noble-gas matrices are good model systems to study this effect. The formation mechanisms of the HNgY molecules and the decay mechanism of NgHNg+ cations are discussed. A new electron tunneling model for the decay of NgHNg+ absorptions in noble-gas matrices is proposed. Studies of the NgHNg+∙∙∙N2 complexes support this electron tunneling mechanism.

Veneer Grade Analysis of Early to Mid-rotation Plantation Eucalyptus Species in Australia

Processing Australian hardwood plantations into rotary veneer can produce more acceptable marketable product recoveries compared to traditional processing techniques (e.g. sawmilling). Veneers resulting from processing trials from six commercially important Australian hardwood species were dominated by D-grade veneer. Defects such as encased knots, gum pockets, gum veins, surface roughness, splits, bark pockets, and decay impacted the final assigned grade. Four grading scenarios were adopted. The first included a change to the grade limitations for gum pockets and gum veins, while the second investigated the potential impact of effective pruning on grade recovery. Although both scenarios individually had a positive impact on achieving higher face grade veneer qualities, the third and fourth scenarios, which combined both, had a substantial impact, with relative veneer values increasing up to 18.2% using conservative calculations (scenario three) or up to 22.6% (scenario four) where some of the upgraded veneers were further upgraded to A-grade, which attracts superior value. The total change in veneer value was found to depend on the average billet diameter unless defects other than those relating to the scenarios (gum or knots) restricted the benefit of pruning and gum upgrading. This was the case for species prone to high levels of growth stress and related defects.

Historical demography of Lantana camara L. reveals clues about the influence of land use and weather in the management of this widespread invasive species

Weather is a general stochastic influence on the life history of weeds. In contrast, anthropogenic disturbance (e.g. land use) is an important deterministic influence on weed demography. Our aim with this study was to investigate the relative contributions of land use and weather on the demography of Lantana camara (lantana), a weed of agricultural and natural habitats, based on the intensive monitoring of lantana populations under three land uses (viz. farm[pasture], and burnt and grazed forests) in subtropical Australia. Lantana populations were growing vigorously across all land uses (asymptotic population growth rate, lambda > 3). Examination of historical demography using retrospective perturbation analyses showed that weather was a strong influence on lantana demography with the transition from an El Nino (2008-09) to a La Nina (2009-10) year having a strong positive effect on population growth rate. This effect was most marked at the grazed site, and to a lesser extent at the burnt site, with seedling-to-juvenile and juvenile-to-adult transitions contributing most to these effects. This is likely the result of burning and grazing having eliminated/reduced interspecific competition at these sites. Prospective perturbation analyses revealed that lambda was most sensitive to proportionate changes in growth transitions, followed by fecundity and survival transitions. Examination of context-specific patterns in elasticity revealed that growth and fecundity transitions are likely to be the more critical vital rates to reduce lambda in wet years at the burnt and grazed forest sites, compared to the farm/pasture site. Management of lantana may need to limit the transition of juveniles into the adult stages, especially in sites where lantana is free from competition (e.g. in the presence of fire or grazing), and this particularly needs to be achieved in wet years. Collectively, these results shed light on aspects of spatial and temporal variation in the demography of lantana, and offer insights on its context-specific management.

Generic relationships of two obscure Australian Thysanoptera species described by A.A. Girault

Two previously unrecognisable species of Australian thrips described by A.A. Girault are placed generically. Giraultithrips gen. n. is described to include G. nigricoxa (Girault), comb, n., originally placed in Bagnalliella Karny and currently included in Haplothrips Amyot & Serville, while Azaleothrips perniger (Girault), comb. n. is transferred from Glyptothrips Hood.

Rare earth transition metal sulfides, LnMS3

Ternary rare earth transition metal sulfides LnMS3 with Ln = La, Nd, and Gd, and M = V and Cr; as well as Ln = La and M = Mn, Fe, Co, and Ni have been prepared and characterized. The vanadium and chromium sulfides crystallize in a monoclinic layer structure isotypic with LaCrS3, while the other LnMS3 sulfides crystallize in a hexagonal structure. Chemical shifts of the metal K-absorption edge and XPS binding energies of core levels indicate that the transition metal is trivalent in the V and Cr sulfides, while it is divalent in the Mn, Fe, Co, and Ni sulfides. Electrical and magnetic properties of the sulfides are discussed in terms of their structures and the electronic configurations of the transition metal ions.

Three new species of Tilletia on Eriachne from north-western Australia

Three new species of Tilletia are described from species of Eriachne (Poaceae) in the arid tropics of north-western Australia. In Western Australia, T. mactaggartii sp. nov. infects E. burkittii, and T. geeringii sp. nov. infects E. festucacea. Tilletia marjaniae sp. nov. infects E. pulchella subsp. dominii in Western Australia and the Northern Territory. These species are the first records of Tilletia on Eriachne. Phylogenetic relationships of these species were inferred from internal transcribed spacer of ribosomal RNA region and large subunit ribosomal RNA gene sequences.

Floristic composition and pasture condition of Aristida/Bothriochloa pastures in central Queensland. I. Pasture floristics

A survey was conducted in central inland Queensland, Australia of 108 sites that were deemed to contain Aristida/Bothriochloa native pastures to quantitatively describe the pastures and attempt to delineate possible sub-types. The pastures were described in terms of their floristic composition, plant density and crown cover. There were generally ~20 (range 5–33) main pasture species at a site. A single dominant perennial grass was rare with three to six prominent species the norm. Chrysopogon fallax (golden-beard grass) was the perennial grass most consistently found in all pastures whereas Aristida calycina (dark wiregrass), Enneapogon spp. (bottlewasher grasses), Brunoniella australis (blue trumpet) and Panicum effusum (hairy panic) were all regularly present. The pastures did not readily separate into broad floristic sub-groups, but three groups that landholders could recognise from a combination of the dominant tree and soil type were identified. The three groups were Eucalyptus crebra (narrow-leaved ironbark), E. melanophloia (silver-leaved ironbark) and E. populnea (poplar box). The pastures of the three main sub-groups were then characterised by the prominent presence, singly or in combination, of Bothriochloa ewartiana (desert bluegrass), Eremochloa bimaculata (poverty grass), Bothriochloa decipiens (pitted bluegrass) or Heteropogon contortus (black speargrass). The poplar box group had the greatest diversity of prominent grasses whereas the narrow-leaved ironbark group had the least. Non-native Cenchrus ciliaris (buffel grass) and Melinis repens (red Natal grass) were generally present at low densities. Describing pastures in terms of frequency of a few species or species groups sometimes failed to capture the true nature of the pasture but plant abundance for most species, as density, herbage mass of dry matter or plant crown cover, was correlated with its recorded frequency. A quantitative description of an average pasture in fair condition is provided but it was not possible to explain why some species often occur together or fail to co-exist in Aristida/Bothriochloa pastures, for example C. ciliaris and E. bimaculata rarely co-exist whereas Tragus australianus (small burrgrass) and Enneapogon spp. are frequently recorded together. Most crown cover was provided by perennial grasses but many of these are Aristida spp. (wiregrasses) and not regarded as useful forage for livestock. No new or improved categorisation of the great variation evident in the Aristida/Bothriochloa native pasture type can be given despite the much improved detail provided of the floristic composition by this survey.

Extremely Low Microsatellite Diversity but Distinct Population Structure in a Long-Lived Threatened Species, the Australian Lungfish Neoceratodus forsteri (Dipnoi)

The Australian lungfish is a unique living representative of an ancient dipnoan lineage, listed as ‘vulnerable’ to extinction under Australia’s Environment Protection and Biodiversity Conservation Act 1999. Historical accounts indicate this species occurred naturally in two adjacent river systems in Australia, the Burnett and Mary. Current day populations in other rivers are thought to have arisen by translocation from these source populations. Early genetic work detected very little variation and so had limited power to answer questions relevant for management including how genetic variation is partitioned within and among sub-populations. In this study, we use newly developed microsatellite markers to examine samples from the Burnett and Mary Rivers, as well as from two populations thought to be of translocated origin, Brisbane and North Pine. We test whether there is significant genetic structure among and within river drainages; assign putatively translocated populations to potential source populations; and estimate effective population sizes. Eleven polymorphic microsatellite loci genotyped in 218 individuals gave an average within-population heterozygosity of 0.39 which is low relative to other threatened taxa and for freshwater fishes in general. Based on F_ST values (average over loci = 0.11) and STRUCTURE analyses, we identify three distinct populations in the natural range, one in the Burnett and two distinct populations in the Mary. These analyses also support the hypothesis that the Mary River is the likely source of translocated populations in the Brisbane and North Pine rivers, which agrees with historical published records of a translocation event giving rise to these populations. We were unable to obtain bounded estimates of effective population size, as we have too few genotype combinations, although point estimates were low, ranging from 29 - 129. We recommend that, in order to preserve any local adaptation in the three distinct populations that they be managed separately.

Novel species of Cercospora and Pseudocercospora (Capnodiales, Mycosphaerellaceae) from Australia

Novel species of Cercospora and Pseudocercospora are described from Australian native plant species. These taxa are Cercospora ischaemi sp. nov. on Ischaemum australe (Poaceae); Pseudocercospora airliensis sp. nov. on Polyalthia nitidissima (Annonaceae); Pseudocercospora proiphydis sp. nov. on Proiphys amboinensis (Amaryllidaceae); and Pseudocercospora jagerae sp. nov. on Jagera pseudorhus var. pseudorhus (Sapindaceae). These species were characterised by morphology and an analysis of partial nucleotide sequence data for the three gene loci, ITS, LSU and EF-1α. Recent divergence of closely related Australian species of Pseudocercospora on native plants is proposed.

Polyphasic characterization of four new plant pathogenic Phyllosticta species from China, Japan, and the United States

The black rot disease of Vitis species and other host genera of Vitacease is caused by Phyllosticta ampelicida and allied taxa which is considered to be a species complex. In this paper, we introduce four new species of Phyllosticta, including two from the P. ampelicida complex, based on a polyphasic characterization including disease symptoms and host association, morphology, and molecular phylogeny. The phylogenetic analysis was conducted based on the ribosomal internal transcribed spacer (ITS) region and a combined multi-locus alignment of the ITS, actin (ACT), partial translation elongation factor 1-alpha (TEF-1), and glyceraldehydes 3-phosphate dehydrogenase (GPDH) gene regions. Our study confirms the phylogenetic distinctions of the four new species, as well as their phenotypic differences with known species in the genus.

Historical demography of Lantana camara L. reveals clues about the influence of land use and weather in the management of this widespread invasive species

Weather is a general stochastic influence on the life history of weeds. In contrast, anthropogenic disturbance (e.g. land use) is an important deterministic influence on weed demography. Our aim with this study was to investigate the relative contributions of land use and weather on the demography of Lantana camara (lantana), a weed of agricultural and natural habitats, based on the intensive monitoring of lantana populations under three land uses (viz. farm[pasture], and burnt and grazed forests) in subtropical Australia. Lantana populations were growing vigorously across all land uses (asymptotic population growth rate, λ > 3). Examination of historical demography using retrospective perturbation analyses showed that weather was a strong influence on lantana demography with the transition from an El Niño (2008–09) to a La Niña (2009–10) year having a strong positive effect on population growth rate. This effect was most marked at the grazed site, and to a lesser extent at the burnt site, with seedling-to-juvenile and juvenile-to-adult transitions contributing most to these effects. This is likely the result of burning and grazing having eliminated/reduced interspecific competition at these sites. Prospective perturbation analyses revealed that λ was most sensitive to proportionate changes in growth transitions, followed by fecundity and survival transitions. Examination of context-specific patterns in elasticity revealed that growth and fecundity transitions are likely to be the more critical vital rates to reduce λ in wet years at the burnt and grazed forest sites, compared to the farm/pasture site. Management of lantana may need to limit the transition of juveniles into the adult stages, especially in sites where lantana is free from competition (e.g. in the presence of fire or grazing), and this particularly needs to be achieved in wet years. Collectively, these results shed light on aspects of spatial and temporal variation in the demography of lantana, and offer insights on its context-specific management.

Assessment of functional forms of crop yield loss models of invasive plant species applied in decision support tools and bioeconomic modelling

AbstractObjectives Decision support tools (DSTs) for invasive species management have had limited success in producing convincing results and meeting users' expectations. The problems could be linked to the functional form of model which represents the dynamic relationship between the invasive species and crop yield loss in the DSTs. The objectives of this study were: a) to compile and review the models tested on field experiments and applied to DSTs; and b) to do an empirical evaluation of some popular models and alternatives. Design and methods This study surveyed the literature and documented strengths and weaknesses of the functional forms of yield loss models. Some widely used models (linear, relative yield and hyperbolic models) and two potentially useful models (the double-scaled and density-scaled models) were evaluated for a wide range of weed densities, maximum potential yield loss and maximum yield loss per weed. Results Popular functional forms include hyperbolic, sigmoid, linear, quadratic and inverse models. Many basic models were modified to account for the effect of important factors (weather, tillage and growth stage of crop at weed emergence) influencing weed–crop interaction and to improve prediction accuracy. This limited their applicability for use in DSTs as they became less generalized in nature and often were applicable to a much narrower range of conditions than would be encountered in the use of DSTs. These factors' effects could be better accounted by using other techniques. Among the model empirically assessed, the linear model is a very simple model which appears to work well at sparse weed densities, but it produces unrealistic behaviour at high densities. The relative-yield model exhibits expected behaviour at high densities and high levels of maximum yield loss per weed but probably underestimates yield loss at low to intermediate densities. The hyperbolic model demonstrated reasonable behaviour at lower weed densities, but produced biologically unreasonable behaviour at low rates of loss per weed and high yield loss at the maximum weed density. The density-scaled model is not sensitive to the yield loss at maximum weed density in terms of the number of weeds that will produce a certain proportion of that maximum yield loss. The double-scaled model appeared to produce more robust estimates of the impact of weeds under a wide range of conditions. Conclusions Previously tested functional forms exhibit problems for use in DSTs for crop yield loss modelling. Of the models evaluated, the double-scaled model exhibits desirable qualitative behaviour under most circumstances.