An inordinate fondness for Fusarium: Phylogenetic diversity of fusaria cultivated by ambrosia beetles in the genus Euwallacea on avocado and other plant hosts

Ambrosia beetle fungiculture represents one of the most ecologically and evolutionarily successful symbioses, as evidenced by the 11 independent origins and 3500 species of ambrosia beetles. Here we document the evolution of a clade within Fusarium associated with ambrosia beetles in the genus Euwallacea (Coleoptera: Scolytinae). Ambrosia Fusarium Clade (AFC) symbionts are unusual in that some are plant pathogens that cause significant damage in naive natural and cultivated ecosystems, and currently threaten avocado production in the United States, Israel and Australia. Most AFC fusaria produce unusual clavate macroconidia that serve as a putative food source for their insect mutualists. AFC symbionts were abundant in the heads of four Euwallacea spp., which suggests that they are transported within and from the natal gallery in mandibular mycangia. In a four-locus phylogenetic analysis, the AFC was resolved in a strongly supported monophyletic group within the previously described Cade 3 of the Fusarium solani species complex (FSSC). Divergence-time estimates place the origin of the AFC in the early Miocene similar to 21.2 Mya, which coincides with the hypothesized adaptive radiation of the Xyleborini. Two strongly supported clades within the AFC (Clades A and B) were identified that include nine species lineages associated with ambrosia beetles, eight with Euwallacea spp. and one reportedly with Xyleborus ferrugineus, and two lineages with no known beetle association. More derived lineages within the AFC showed fixation of the clavate (club-shaped) macroconidial trait, while basal lineages showed a mix of clavate and more typical fusiform macroconidia. AFC lineages consisted mostly of genetically identical individuals associated with specific insect hosts in defined geographic locations, with at least three interspecific hybridization events inferred based on discordant placement in individual gene genealogies and detection of recombinant loci. Overall, these data are consistent with a strong evolutionary trend toward obligate symbiosis coupled with secondary contact and interspecific hybridization. (C) 2013 Elsevier Inc. All rights reserved.

Johnalcornia gen. et. comb. nov., and nine new combinations in Curvularia based on molecular phylogenetic analysis

An examination of ex-type and authentic cultures of 34 species of Bipolaris and Curvularia by phylogenetic analysis of four loci (EF-1α, GAPDH, ITS and LSU) resulted in nine new combinations in Curvularia, as well as new synonymies for some species of Bipolaris and Curvularia. Lectotypes are designated for Bipolaris secalis and Curvularia richardiae, and an epitype is designated for Curvularia crustacea. A new monotypic genus, Johnalcornia, is introduced to accommodate Bipolaris aberrans, which clusters sister to the newly described Porocercospora. Johnalcornia differs morphologically from this taxon by producing distinctive conidia-like chlamydospores as well as comparatively thick-walled, geniculate conidiophores, with conidiogenous cells that have conspicuous scars. Johnalcornia further differs from related genera by forming the second conidial septum in the apical cell.

Climate change impact assessment: Uncertainty modeling with imprecise probability

Hydrologic impacts of climate change are usually assessed by downscaling the General Circulation Model (GCM) output of large-scale climate variables to local-scale hydrologic variables. Such an assessment is characterized by uncertainty resulting from the ensembles of projections generated with multiple GCMs, which is known as intermodel or GCM uncertainty. Ensemble averaging with the assignment of weights to GCMs based on model evaluation is one of the methods to address such uncertainty and is used in the present study for regional-scale impact assessment. GCM outputs of large-scale climate variables are downscaled to subdivisional-scale monsoon rainfall. Weights are assigned to the GCMs on the basis of model performance and model convergence, which are evaluated with the Cumulative Distribution Functions (CDFs) generated from the downscaled GCM output (for both 20th Century [20C3M] and future scenarios) and observed data. Ensemble averaging approach, with the assignment of weights to GCMs, is characterized by the uncertainty caused by partial ignorance, which stems from nonavailability of the outputs of some of the GCMs for a few scenarios (in Intergovernmental Panel on Climate Change [IPCC] data distribution center for Assessment Report 4 [AR4]). This uncertainty is modeled with imprecise probability, i.e., the probability being represented as an interval gray number. Furthermore, the CDF generated with one GCM is entirely different from that with another and therefore the use of multiple GCMs results in a band of CDFs. Representing this band of CDFs with a single valued weighted mean CDF may be misleading. Such a band of CDFs can only be represented with an envelope that contains all the CDFs generated with a number of GCMs. Imprecise CDF represents such an envelope, which not only contains the CDFs generated with all the available GCMs but also to an extent accounts for the uncertainty resulting from the missing GCM output. This concept of imprecise probability is also validated in the present study. The imprecise CDFs of monsoon rainfall are derived for three 30-year time slices, 2020s, 2050s and 2080s, with A1B, A2 and B1 scenarios. The model is demonstrated with the prediction of monsoon rainfall in Orissa meteorological subdivision, which shows a possible decreasing trend in the future.

Phylogenetic analysis of human Chlamydia pneumoniae strains reveals a distinct Australian indigenous clade that predates European exploration of the continent

Background The obligate intracellular bacterium Chlamydia pneumoniae is a common respiratory pathogen, which has been found in a range of hosts including humans, marsupials and amphibians. Whole genome comparisons of human C. pneumoniae have previously highlighted a highly conserved nucleotide sequence, with minor but key polymorphisms and additional coding capacity when human and animal strains are compared. Results In this study, we sequenced three Australian human C. pneumoniae strains, two of which were isolated from patients in remote indigenous communities, and compared them to all available C. pneumoniae genomes. Our study demonstrated a phylogenetically distinct human C. pneumoniae clade containing the two indigenous Australian strains, with estimates that the most recent common ancestor of these strains predates the arrival of European settlers to Australia. We describe several polymorphisms characteristic to these strains, some of which are similar in sequence to animal C. pneumoniae strains, as well as evidence to suggest that several recombination events have shaped these distinct strains. Conclusions Our study reveals a greater sequence diversity amongst both human and animal C. pneumoniae strains, and suggests that a wider range of strains may be circulating in the human population than current sampling indicates.

Assessing uncertainty in pollutant build-up and wash-off processes

Assessing build-up and wash-off process uncertainty is important for accurate interpretation of model outcomes to facilitate informed decision making for developing effective stormwater pollution mitigation strategies. Uncertainty inherent to pollutant build-up and wash-off processes influences the variations in pollutant loads entrained in stormwater runoff from urban catchments. However, build-up and wash-off predictions from stormwater quality models do not adequately represent such variations due to poor characterisation of the variability of these processes in mathematical models. The changes to the mathematical form of current models with the incorporation of process variability, facilitates accounting for process uncertainty without significantly affecting the model prediction performance. Moreover, the investigation of uncertainty propagation from build-up to wash-off confirmed that uncertainty in build-up process significantly influences wash-off process uncertainty. Specifically, the behaviour of particles <150µm during build-up primarily influences uncertainty propagation, resulting in appreciable variations in the pollutant load and composition during a wash-off event.

Influence of uncertainty inherent to heavy metal build-up and wash-off on stormwater quality

Uncertainty inherent to heavy metal build-up and wash-off stems from process variability. This results in inaccurate interpretation of stormwater quality model predictions. The research study has characterised the variability in heavy metal build-up and wash-off processes based on the temporal variations in particle-bound heavy metals commonly found on urban roads. The study outcomes found that the distribution of Al, Cr, Mn, Fe, Ni, Cu, Zn, Cd and Pb were consistent over particle size fractions <150µm and >150µm, with most metals concentrated in the particle size fraction <150µm. When build-up and wash-off are considered as independent processes, the temporal variations in these processes in relation to the heavy metals load are consistent with variations in the particulate load. However, the temporal variations in the load in build-up and wash-off of heavy metals and particulates are not consistent for consecutive build-up and wash-off events that occur on a continuous timeline. These inconsistencies are attributed to interactions between heavy metals and particulates <150µm and >150µm, which are influenced by particle characteristics such as organic matter content. The behavioural variability of particles determines the variations in the heavy metals load entrained in stormwater runoff. Accordingly, the variability in build-up and wash-off of particle-bound pollutants needs to be characterised in the description of pollutant attachment to particulates in stormwater quality modelling. This will ensure the accounting of process uncertainty, and thereby enhancing the interpretation of the outcomes derived from modelling studies.

Uncertainty based online planning for UAV target finding in cluttered and GPS-denied environments

There are some scenarios in which Unmmaned Aerial Vehicle (UAV) navigation becomes a challenge due to the occlusion of GPS systems signal, the presence of obstacles and constraints in the space in which a UAV operates. An additional challenge is presented when a target whose location is unknown must be found within a confined space. In this paper we present a UAV navigation and target finding mission, modelled as a Partially Observable Markov Decision Process (POMDP) using a state-of-the-art online solver in a real scenario using a low cost commercial multi rotor UAV and a modular system architecture running under the Robotic Operative System (ROS). Using POMDP has several advantages to conventional approaches as they take into account uncertainties in sensor information. We present a framework for testing the mission with simulation tests and real flight tests in which we model the system dynamics and motion and perception uncertainties. The system uses a quad-copter aircraft with an board downwards looking camera without the need of GPS systems while avoiding obstacles within a confined area. Results indicate that the system has 100% success rate in simulation and 80% rate during flight test for finding targets located at different locations.

Phylogenetic studies of cyanobacterial lichens

Phylogenetic studies of cyanobacterial lichens Lichens are symbiotic assemblages between fungi (mycobiont) and green algae (phycobiont) or/and cyanobacteria (cyanobiont). Fossil records show that lichen-like symbioses occurred already 600 million years ago. Lichen symbiosis has since then become an important life strategy for the Fungi, particularly for species in the phylum Ascomycota as approximately 98% of the lichenized fungal species are ascomycetes. The taxonomy of lichen associations is based on the mycobiont. We reconstructed, using DNA sequence data, hypotheses of phylogenetic relationships of lichen-forming fungi that include species associated with cyanobacteria. These hypotheses of phylogeny should form the basis for the taxonomy. They also allowed studies of the origin and the evolution of specific symbioses. Genetic diversity and phylogenetic relationships of symbiotic cyanobionts were also studied in order to examine selectivity of cyanobionts and mycobionts as well as possible co-evolution between partners involved in lichen associations. The suggested circumscription of the family Stereocaulaceae to include Stereocaulon and Lepraria is supported. The recently described crustose Stereocaulon species seem to be correctly placed in the genus, although Stereocaulon traditionally included only fruticose species. The monospecific crustose genus Muhria is also shown to be best placed in Stereocaulon. Family Lobariaceae as currently delimited is monophyletic. Within Lobariaceae genus Sticta including Dendriscocaulon dendroides form a monophyletic group while the genera Lobaria and Pseudocyphellaria are non-monophyletic. A new classification of Lobariaceae is obviously needed. Further studies are however required before a final proposal for a new classification can be made. Our results show that the cyanobacterial symbiotic state has been gained repeatedly in the Ascomycota while losses of symbiotic cyanobacteria appear to be rare. The symbiosis with green algae is confirmed to have been gained repeatedly in Ascomycota but also repeatedly lost. Cyanobacterial symbioses therefore seem to be more stable than green algal associations. Cyanobacteria are perhaps more beneficial for the lichen fungi and therefore maintained. The results indicate a dynamic association of the lichen symbiosis. This evolutionary instability will perhaps be important for the lichen fungi as the utilization of options will perhaps enable lichens to colonize new substrates and survive environmental changes. Some cyanobacterial lichen genera seem to be highly selective towards the cyanobiont while others form symbioses with a broad spectrum of cyanobacteria. No evidence of co-evolution between fungi and cyanobacteria in cyanolichens could be demonstrated.

A comparative structural bioinformatics analysis of the insulin receptor family ectodomain based on phylogenetic information

The insulin receptor (IR), the insulin-like growth factor 1 receptor (IGF1R) and the insulin receptor-related receptor (IRR) are covalently-linked homodimers made up of several structural domains. The molecular mechanism of ligand binding to the ectodomain of these receptors and the resulting activation of their tyrosine kinase domain is still not well understood. We have carried out an amino acid residue conservation analysis in order to reconstruct the phylogeny of the IR Family. We have confirmed the location of ligand binding site 1 of the IGF1R and IR. Importantly, we have also predicted the likely location of the insulin binding site 2 on the surface of the fibronectin type III domains of the IR. An evolutionary conserved surface on the second leucine-rich domain that may interact with the ligand could not be detected. We suggest a possible mechanical trigger of the activation of the IR that involves a slight ‘twist’ rotation of the last two fibronectin type III domains in order to face the likely location of insulin. Finally, a strong selective pressure was found amongst the IRR orthologous sequences, suggesting that this orphan receptor has a yet unknown physiological role which may be conserved from amphibians to mammals.

Environmental factors and uncertainty in fisheries management in the northern Baltic Sea

The Baltic Sea is a geologically young, large brackish water basin, and few of the species living there have fully adapted to its special conditions. Many of the species live on the edge of their distribution range in terms of one or more environmental variables such as salinity or temperature. Environmental fluctuations are know to cause fluctuations in populations abundance, and this effect is especially strong near the edges of the distribution range, where even small changes in an environmental variable can be critical to the success of a species. This thesis examines which environmental factors are the most important in relation to the success of various commercially exploited fish species in the northern Baltic Sea. It also examines the uncertainties related to fish stocks current and potential status as well as to their relationship with their environment. The aim is to quantify the uncertainties related to fisheries and environmental management, to find potential management strategies that can be used to reduce uncertainty in management results and to develop methodology related to uncertainty estimation in natural resources management. Bayesian statistical methods are utilized due to their ability to treat uncertainty explicitly in all parts of the statistical model. The results show that uncertainty about important parameters of even the most intensively studied fish species such as salmon (Salmo salar L.) and Baltic herring (Clupea harengus membras L.) is large. On the other hand, management approaches that reduce uncertainty can be found. These include utilising information about ecological similarity of fish stocks and species, and using management variables that are directly related to stock parameters that can be measured easily and without extrapolations or assumptions.

Phylogenetics, taxon delimitation and phylogenetic diversity

Throughout the history of Linnean taxonomy, species have been described with varying degrees of justification. Many descriptions have been based on only a few ambiguous morphological characters. Moreover, species have been considered natural, well-defined units whereas higher taxa have been treated as disparate, non-existent creations. In the present thesis a few such cases were studied in detail. Often the species-level descriptions were based on only a few specimens and the variation previously thought to be interspecific was found to be intraspecific. In some cases morphological characters were sufficient to resolve the evolutionary relationships between the taxa, but generally more resolution was gained by the addition of molecular evidence. However, both morphological and molecular data were found to be deceptive in some cases. The DNA sequences of morphologically similar specimens were found to differ distinctly in some cases, whereas in other closely related species the morphology of specimens with identical DNA sequences differed substantially. This study counsels caution when evolutionary relationships are being studied utilizing only one source of evidence or a very limited number of characters (e.g. barcoding). Moreover, it emphasizes the importance of high quality data as well as the utilization of proper methods when making scientific inferences. Properly conducted analyses produce robust results that can be utilized in numerous interesting ways. The present thesis considered two such extensions of systematics. A novel hypothesis on the origin of bioluminescence in Elateriformia beetles is presented, tying it to the development of the clicking mechanism in the ancestors of these animals. An entirely different type of extension of systematics is the proposed high value of the white sand forests in maintaining the diversity of beetles in the Peruvian Amazon. White sand forests are under growing pressure from human activities that lead to deforestation. They were found to harbor an extremely diverse beetle fauna and many taxa were specialists living only in this unique habitat. In comparison to the predominant clay soil forests, considerably more elateroid beetles belonging to all studied taxonomic levels (species, genus, tribus, and subfamily) were collected in white sand forests. This evolutionary diversity is hypothesized to be due to a combination of factors: (1) the forest structure, which favors the fungus-plant interactions important for the elateroid beetles, (2) the old age of the forest type favoring survival of many evolutionary lineages and (3) the widespread distribution and fragmentation of the forests in the Miocene, favoring speciation.

Managing uncertainty to improve the cost performance of complex infrastructure projects

There has been a recent spate of high profile infrastructure cost overruns in Australia and internationally. This is just the tip of a longer-term and more deeply-seated problem with initial budget estimating practice, well recognised in both academic research and industry reviews: the problem of uncertainty. A case study of the Sydney Opera House is used to identify and illustrate the key causal factors and system dynamics of cost overruns. It is conventionally the role of risk management to deal with such uncertainty, but the type and extent of the uncertainty involved in complex projects is shown to render established risk management techniques ineffective. This paper considers a radical advance on current budget estimating practice which involves a particular approach to statistical modelling complemented by explicit training in estimating practice. The statistical modelling approach combines the probability management techniques of Savage, which operate on actual distributions of values rather than flawed representations of distributions, and the data pooling technique of Skitmore, where the size of the reference set is optimised. Estimating training employs particular calibration development methods pioneered by Hubbard, which reduce the bias of experts caused by over-confidence and improve the consistency of subjective decision-making. A new framework for initial budget estimating practice is developed based on the combined statistical and training methods, with each technique being explained and discussed.

Reservoir performance under uncertainty in hydrologic impacts of climate change

Relatively few studies have addressed water management and adaptation measures in the face of changing water balances due to climate change. The current work studies climate change impact on a multipurpose reservoir performance and derives adaptive policies for possible futurescenarios. The method developed in this work is illustrated with a case study of Hirakud reservoir on the Mahanadi river in Orissa, India,which is a multipurpose reservoir serving flood control, irrigation and power generation. Climate change effects on annual hydropower generation and four performance indices (reliability with respect to three reservoir functions, viz. hydropower, irrigation and flood control, resiliency, vulnerability and deficit ratio with respect to hydropower) are studied. Outputs from three general circulation models (GCMs) for three scenarios each are downscaled to monsoon streamflow in the Mahanadi river for two future time slices, 2045-65 and 2075-95. Increased irrigation demands, rule curves dictated by increased need for flood storage and downscaled projections of streamflow from the ensemble of GCMs and scenarios are used for projecting future hydrologic scenarios. It is seen that hydropower generation and reliability with respect to hydropower and irrigation are likely to show a decrease in future in most scenarios, whereas the deficit ratio and vulnerability are likely to increase as a result of climate change if the standard operating policy (SOP) using current rule curves for flood protection is employed. An optimal monthly operating policy is then derived using stochastic dynamic programming (SDP) as an adaptive policy for mitigating impacts of climate change on reservoir operation. The objective of this policy is to maximize reliabilities with respect to multiple reservoir functions of hydropower, irrigation and flood control. In variations to this adaptive policy, increasingly more weightage is given to the purpose of maximizing reliability with respect to hydropower for two extreme scenarios. It is seen that by marginally sacrificing reliability with respect to irrigation and flood control, hydropower reliability and generation can be increased for future scenarios. This suggests that reservoir rules for flood control may have to be revised in basins where climate change projects an increasing probability of droughts. However, it is also seen that power generation is unable to be restored to current levels, due in part to the large projected increases in irrigation demand. This suggests that future water balance deficits may limit the success of adaptive policy options. (C) 2010 Elsevier Ltd. All rights reserved.

Revisiting Coptotermes (Isoptera: Rhinotermitidae): a global taxonomic road map for species validity and distribution of an economically important subterranean termite genus

Coptotermes Wasmann (Isoptera: Rhinotermitidae) is one of the most economically important subterranean termite genera and some species are successful invaders. However, despite its important pest status, the taxonomic validity of many named Coptotermes species remains unclear. In this study, we reviewed all named species within the genus and investigated evidence supporting the validity of each named species. Species were systematically scrutinized according to the region of their original description: Southeast Asia, India, China, Africa, the Neotropics, and Australia. We estimate that of the currently 69 named species described by accepted nomenclatural rules, only 21 taxa have solid evidence for validity, 44 names have uncertain status, and the remaining species names should be synonymized or were made unavailable. Species with high degrees of invasiveness may be known under additional junior synonyms due to independent parochial descriptions. Molecular data for a vast majority of species are scarce and significant effort is needed to complete the taxonomic and phylogenetic revision of the genus. Because of the wide distribution of Coptotermes, we advocate for an integrative taxonomic effort to establish the distribution of each putative species, provide specimens and corresponding molecular data, check original descriptions and type specimens (if available), and provide evidence for a more robust phylogenetic position of each species. This study embodies both consensus and contention of those studying Coptotermes and thus pinpoints the current uncertainty of many species. This project is intended to be a roadmap for identifying those Coptotermes species names that need to be more thoroughly investigated, as an incentive to complete a necessary revision process.