Inference on microsatellite mutation processes in the invasive mite, Varroa destructor, using reversible jump Markov chain Monte Carlo

Varroa destructor is a parasitic mite of the Eastern honeybee Apis cerana. Fifty years ago, two distinct evolutionary lineages (Korean and Japanese) invaded the Western honeybee Apis mellifera. This haplo-diploid parasite species reproduces mainly through brother sister matings, a system which largely favors the fixation of new mutations. In a worldwide sample of 225 individuals from 21 locations collected on Western honeybees and analyzed at 19 microsatellite loci, a series of de novo mutations was observed. Using historical data concerning the invasion, this original biological system has been exploited to compare three mutation models with allele size constraints for microsatellite markers: stepwise (SMM) and generalized (GSM) mutation models, and a model with mutation rate increasing exponentially with microsatellite length (ESM). Posterior probabilities of the three models have been estimated for each locus individually using reversible jump Markov Chain Monte Carlo. The relative support of each model varies widely among loci, but the GSM is the only model that always receives at least 9% support, whatever the locus. The analysis also provides robust estimates of mutation parameters for each locus and of the divergence time of the two invasive lineages (67,000 generations with a 90% credibility interval of 35,000-174,000). With an average of 10 generations per year, this divergence time fits with the last post-glacial Korea Japan land separation. (c) 2005 Elsevier Inc. All rights reserved.

Extinction processes in hot spots of avian biodiversity and the targeting of pre-emptive conservation action

Hot spots of endemism are regarded as important global sites for conservation as they are rich in threatened endemic species and currently experiencing extensive habitat loss. Targeting pre-emptive conservation action to sites that are currently relatively intact but which would be vulnerable to particular human activities if they occurred in the future is, however, also valuable but has received less attention. Here, we address this issue by using data on Endemic Bird Areas (EBAs). First, we identify the ecological factors that affect extinction risk in the face of particular human activities, and then use these insights to identify EBAs that should be priorities for pre-emptive conservation action. Threatened endemic species in EBAs are significantly more likely to be habitat specialists or relatively large-bodied than non-threatened species, when compared across avian families. Increasing habitat loss causes a significant increase in extinction risk among habitat specialists, but we found no evidence to suggest that the presence of alien species/human exploitation causes a significant increase in extinction risk among large-bodied species. This suggests that these particular human activities are contributing to high extinction risk among habitat specialists, but not among large-bodied species. Based on these analyses, we identify 39 EBAs containing 570 species (24% of the total in EBAs) that are not currently threatened with severe habitat loss, but would be ecologically vulnerable to future habitat loss should it occur. We show that these sites tend to be poorly represented in existing priority setting exercises involving hot spots, suggesting that vulnerability must be explicitly included within these exercises if such sites are to be adequately protected.

Development and application of diazirines in biological and synthetic macromolecular systems

Many different reagents and methodologies have been utilised for the modification of synthetic and biological macromolecular systems. In addition, an area of intense research at present is the construction of hybrid biosynthetic polymers, comprised of biologically active species immobilised or complexed with synthetic polymers. One of the most useful and widely applicable techniques available for functionalisation of macromolecular systems involves indiscriminate carbene insertion processes. The highly reactive and non-specific nature of carbenes has enabled a multitude of macromolecular structures to be functionalised without the need for specialised reagents or additives. The use of diazirines as stable carbene precursors has increased dramatically over the past twenty years and these reagents are fast becoming the most popular photophors for photoaffinity labelling and biological applications in which covalent modification of macromolecular structures is the basis to understanding structure-activity relationships. This review reports the synthesis and application of a diverse range of diazirines in macromolecular systems.

Nitrogen processes in aquatic ecosystems

Executive summary Nature of the problem (science/management/policy) • Freshwater ecosystems play a key role in the European nitrogen (N) cycle, both as a reactive agent that transfers, stores and processes N loadings from the atmosphere and terrestrial ecosystems, and as a natural environment severely impacted by the increase of these loadings. Approaches • This chapter is a review of major processes and factors controlling N transport and transformations for running waters, standing waters, groundwaters and riparian wetlands. Key findings/state of knowledge • The major factor controlling N processes in freshwater ecosystems is the residence time of water, which varies widely both in space and in time, and which is sensitive to changes in climate, land use and management. • The effects of increased N loadings to European freshwaters include acidification in semi-natural environments, and eutrophication in more disturbed ecosystems, with associated loss of biodiversity in both cases. • An important part of the nitrogen transferred by surface waters is in the form of organic N, as dissolved organic N (DON) and particulate organic N (PON). This part is dominant in semi-natural catchments throughout Europe and remains a significant component of the total N load even in nitrate enriched rivers. • In eutrophicated standing freshwaters N can be a factor limiting or co-limiting biological production, and control of both N and phosphorus (P) loading is oft en needed in impacted areas, if ecological quality is to be restored. Major uncertainties/challenges • The importance of storage and denitrifi cation in aquifers is a major uncertainty in the global N cycle, and controls in part the response of catchments to land use or management changes. In some aquifers, the increase of N concentrations will continue for decades even if efficient mitigation measures are implemented now. • Nitrate retention by riparian wetlands has oft en been highlighted. However, their use for mitigation must be treated with caution, since their effectiveness is difficult to predict, and side effects include increased DON emissions to adjacent open waters, N2O emissions to the atmosphere, and loss of biodiversity. • In fact, the character and specific spatial origins of DON are not fully understood, and similarly the quantitative importance of indirect N2O emissions from freshwater ecosystems as a result of N leaching losses from agricultural soils is still poorly known at the regional scale. • These major uncertainties remain due to the lack of adequate monitoring (all forms of N at a relevant frequency), especially – but not only – in the southern and eastern EU countries. Recommendations (research/policy) • The great variability of transfer pathways, buffering capacity and sensitivity of the catchments and of the freshwater ecosystems calls for site specific mitigation measures rather than standard ones applied at regional to national scale. • The spatial and temporal variations of the N forms, the processes controlling the transport and transformation of N within freshwaters, require further investigation if the role of N in influencing freshwater ecosystem health is to be better understood, underpinning the implementation of the EU Water Framework Directive for European freshwaters.

Using learning networks to understand complex systems: a case study of biological, geophysical and social research in the Amazon

Developing high-quality scientific research will be most effective if research communities with diverse skills and interests are able to share information and knowledge, are aware of the major challenges across disciplines, and can exploit economies of scale to provide robust answers and better inform policy. We evaluate opportunities and challenges facing the development of a more interactive research environment by developing an interdisciplinary synthesis of research on a single geographic region. We focus on the Amazon as it is of enormous regional and global environmental importance and faces a highly uncertain future. To take stock of existing knowledge and provide a framework for analysis we present a set of mini-reviews from fourteen different areas of research, encompassing taxonomy, biodiversity, biogeography, vegetation dynamics, landscape ecology, earth-atmosphere interactions, ecosystem processes, fire, deforestation dynamics, hydrology, hunting, conservation planning, livelihoods, and payments for ecosystem services. Each review highlights the current state of knowledge and identifies research priorities, including major challenges and opportunities. We show that while substantial progress is being made across many areas of scientific research, our understanding of specific issues is often dependent on knowledge from other disciplines. Accelerating the acquisition of reliable and contextualized knowledge about the fate of complex pristine and modified ecosystems is partly dependent on our ability to exploit economies of scale in shared resources and technical expertise, recognise and make explicit interconnections and feedbacks among sub-disciplines, increase the temporal and spatial scale of existing studies, and improve the dissemination of scientific findings to policy makers and society at large. Enhancing interaction among research efforts is vital if we are to make the most of limited funds and overcome the challenges posed by addressing large-scale interdisciplinary questions. Bringing together a diverse scientific community with a single geographic focus can help increase awareness of research questions both within and among disciplines, and reveal the opportunities that may exist for advancing acquisition of reliable knowledge. This approach could be useful for a variety of globally important scientific questions.

A metabolic system-wide characterisation of the pig: a model for human physiology

The pig is a single-stomached omnivorous mammal and is an important model of human disease and nutrition. As such, it is necessary to establish a metabolic framework from which pathology-based variation can be compared. Here, a combination of one and two-dimensional (1)H and (13)C nuclear magnetic resonance spectroscopy (NMR) and high-resolution magic angle spinning (HR-MAS) NMR was used to provide a systems overview of porcine metabolism via characterisation of the urine, serum, liver and kidney metabolomes. The metabolites observed in each of these biological compartments were found to be qualitatively comparable to the metabolic signature of the same biological matrices in humans and rodents. The data were modelled using a combination of principal components analysis and Venn diagram mapping. Urine represented the most metabolically distinct biological compartment studied, with a relatively greater number of NMR detectable metabolites present, many of which are implicated in gut-microbial co-metabolic processes. The major inter-species differences observed were in the phase II conjugation of extra-genomic metabolites; the pig was observed to conjugate p-cresol, a gut microbial metabolite of tyrosine, with glucuronide rather than sulfate as seen in man. These observations are important to note when considering the translatability of experimental data derived from porcine models.

Biogas innovation processes and innovation system: lessons from Davao del Sur, Philippines

This paper examines biogas innovation system and processes in two farming communities in Davao del Sur, Philippines. Innovation histories were traced through workshops, semi-structured interviews, observations and document analysis. The paper shows that there were diverse innovation actors both from public and private sectors. Restrictive attitudes and practices resulted in weak and limited interactions among actors. Multi-actor interaction was weak, signifying a lack of innovation actors that focus on creating, developing and strengthening linkages, networks and partnerships. The lack of support in the socio-organisational institutions that constitute the enabling environment within which innovation actors operate may lead to systemic failure.

Terahertz spectroscopy and imaging at the nanoscale for biological and security applications

The chemical specificity of terahertz spectroscopy, when combined with techniques for sub-wavelength sensing, is giving new understanding of processes occurring at the nanometre scale in biological systems and offers the potential for single molecule detection of chemical and biological agents and explosives. In addition, terahertz techniques are enabling the exploration of the fundamental behaviour of light when it interacts with nanoscale optical structures, and are being used to measure ultrafast carrier dynamics, transport and localisation in nanostructures. This chapter will explain how terahertz scale modelling can be used to explore the fundamental physics of nano-optics, it will discuss the terahertz spectroscopy of nanomaterials, terahertz near-field microscopy and other sub-wavelength techniques, and summarise recent developments in the terahertz spectroscopy and imaging of biological systems at the nanoscale. The potential of using these techniques for security applications will be considered.

Impact of oceanic processes on the carbon cycle during the last termination

During the last termination (from ~18 000 years ago to ~9000 years ago), the climate significantly warmed and the ice sheets melted. Simultaneously, atmospheric CO2 increased from ~190 ppm to ~260 ppm. Although this CO2 rise plays an important role in the deglacial warming, the reasons for its evolution are difficult to explain. Only box models have been used to run transient simulations of this carbon cycle transition, but by forcing the model with data constrained scenarios of the evolution of temperature, sea level, sea ice, NADW formation, Southern Ocean vertical mixing and biological carbon pump. More complex models (including GCMs) have investigated some of these mechanisms but they have only been used to try and explain LGM versus present day steady-state climates. In this study we use a coupled climate-carbon model of intermediate complexity to explore the role of three oceanic processes in transient simulations: the sinking of brines, stratification-dependent diffusion and iron fertilization. Carbonate compensation is accounted for in these simulations. We show that neither iron fertilization nor the sinking of brines alone can account for the evolution of CO2, and that only the combination of the sinking of brines and interactive diffusion can simultaneously simulate the increase in deep Southern Ocean δ13C. The scenario that agrees best with the data takes into account all mechanisms and favours a rapid cessation of the sinking of brines around 18 000 years ago, when the Antarctic ice sheet extent was at its maximum. In this scenario, we make the hypothesis that sea ice formation was then shifted to the open ocean where the salty water is quickly mixed with fresher water, which prevents deep sinking of salty water and therefore breaks down the deep stratification and releases carbon from the abyss. Based on this scenario, it is possible to simulate both the amplitude and timing of the long-term CO2 increase during the last termination in agreement with ice core data. The atmospheric δ13C appears to be highly sensitive to changes in the terrestrial biosphere, underlining the need to better constrain the vegetation evolution during the termination.

A metabolic system-wide characterisation of the pig: a model for human physiology

The pig is a single-stomached omnivorous mammal and is an important model of human disease and nutrition. As such, it is necessary to establish a metabolic framework from which pathology-based variation can be compared. Here, a combination of one and two-dimensional 1H and 13C nuclear magnetic resonance spectroscopy (NMR) and high-resolution magic angle spinning (HR-MAS) NMR was used to provide a systems overview of porcine metabolism via characterisation of the urine, serum, liver and kidney metabolomes. The metabolites observed in each of these biological compartments were found to be qualitatively comparable to the metabolic signature of the same biological matrices in humans and rodents. The data were modelled using a combination of principal components analysis and Venn diagram mapping. Urine represented the most metabolically distinct biological compartment studied, with a relatively greater number of NMR detectable metabolites present, many of which are implicated in gut-microbial co-metabolic processes. The major interspecies differences observed were in the phase II conjugation of extra-genomic metabolites; the pig was observed to conjugate p-cresol, a gut microbial metabolite of tyrosine, with glucuronide rather than sulfate as seen in man. These observations are important to note when considering the translatability of experimental data derived from porcine models.

The effect of model configuration on modelled hillslope–riparian interactions

The transfer of hillslope water to and through the riparian zone forms a research area of importance in hydrological investigations. Numerical modelling schemes offer a way to visualise and quantify first-order controls on catchment runoff response and mixing. We use a two-dimensional Finite Element model to assess the link between model setup decisions (e.g. zero-flux boundary definitions, soil algorithm choice) and the consequential hydrological process behaviour. A detailed understanding of the consequences of model configuration is required in order to produce reliable estimates of state variables. We demonstrate that model configuration decisions can determine effectively the presence or absence of particular hillslope flow processes and, the magnitude and direction of flux at the hillslope–riparian interface. If these consequences are not fully explored for any given scheme and application, the resulting process inference may well be misleading.

New opportunities for secure communication networks using shaped femtosecond laser pulses inducing filamentation processes in the atmosphere

The current study discusses new opportunities for secure ground to satellite communications using shaped femtosecond pulses that induce spatial hole burning in the atmosphere for efficient communications with data encoded within super-continua generated by femtosecond pulses. Refractive index variation across the different layers in the atmosphere may be modelled using assumptions that the upper strata of the atmosphere and troposphere behaving as layered composite amorphous dielectric networks composed of resistors and capacitors with different time constants across each layer. Input-output expressions of the dynamics of the networks in the frequency domain provide the transmission characteristics of the propagation medium. Femtosecond pulse shaping may be used to optimize the pulse phase-front and spectral composition across the different layers in the atmosphere. A generic procedure based on evolutionary algorithms to perform the pulse shaping is proposed. In contrast to alternative procedures that would require ab initio modelling and calculations of the propagation constant for the pulse through the atmosphere, the proposed approach is adaptive, compensating for refractive index variations along the column of air between the transmitter and receiver.

Patterns of maximum body size evolution in Cenozoic land mammals: eco-evolutionary processes and abiotic forcing

There is accumulating evidence that macroevolutionary patterns of mammal evolution during the Cenozoic follow similar trajectories on different continents. This would suggest that such patterns are strongly determined by global abiotic factors, such as climate, or by basic eco-evolutionary processes such as filling of niches by specialization. The similarity of pattern would be expected to extend to the history of individual clades. Here, we investigate the temporal distribution of maximum size observed within individual orders globally and on separate continents. While the maximum size of individual orders of large land mammals show differences and comprise several families, the times at which orders reach their maximum size over time show strong congruence, peaking in the Middle Eocene, the Oligocene and the Plio-Pleistocene. The Eocene peak occurs when global temperature and land mammal diversity are high and is best explained as a result of niche expansion rather than abiotic forcing. Since the Eocene, there is a significant correlation between maximum size frequency and global temperature proxy. The Oligocene peak is not statistically significant and may in part be due to sampling issues. The peak in the Plio-Pleistocene occurs when global temperature and land mammal diversity are low, it is statistically the most robust one and it is best explained by global cooling. We conclude that the macroevolutionary patterns observed are a result of the interplay between eco-evolutionary processes and abiotic forcing

Geotechnical systems that evolve with ecological processes

Geotechnical systems, such as landfills, mine tailings storage facilities (TSFs), slopes, and levees, are required to perform safely throughout their service life, which can span from decades for levees to “in perpetuity” for TSFs. The conventional design practice by geotechnical engineers for these systems utilizes the as-built material properties to predict its performance throughout the required service life. The implicit assumption in this design methodology is that the soil properties are stable through time. This is counter to long-term field observations of these systems, particularly where ecological processes such as plant, animal, biological, and geochemical activity are present. Plant roots can densify soil and/or increase hydraulic conductivity, burrowing animals can increase seepage, biological activity can strengthen soil, geochemical processes can increase stiffness, etc. The engineering soil properties naturally change as a stable ecological system is gradually established following initial construction, and these changes alter system performance. This paper presents an integrated perspective and new approach to this issue, considering ecological, geotechnical, and mining demands and constraints. A series of data sets and case histories are utilized to examine these issues and to propose a more integrated design approach, and consideration is given to future opportunities to manage engineered landscapes as ecological systems. We conclude that soil scientists and restoration ecologists must be engaged in initial project design and geotechnical engineers must be active in long-term management during the facility’s service life. For near-surface geotechnical structures in particular, this requires an interdisciplinary perspective and the embracing of soil as a living ecological system rather than an inert construction material.