Vertical distribution and radiative effects of mineral dust and biomass burning aerosol over West Africa during DABEX

This paper presents measurements of the vertical distribution of aerosol extinction coefficient over West Africa during the Dust and Biomass-burning Aerosol Experiment (DABEX)/African Monsoon Multidisciplinary Analysis dry season Special Observing Period Zero (AMMA-SOP0). In situ aircraft measurements from the UK FAAM aircraft have been compared with two ground-based lidars (POLIS and ARM MPL) and an airborne lidar on an ultralight aircraft. In general, mineral dust was observed at low altitudes (up to 2 km), and a mixture of biomass burning aerosol and dust was observed at altitudes of 2–5 km. The study exposes difficulties associated with spatial and temporal variability when intercomparing aircraft and ground measurements. Averaging over many profiles provided a better means of assessing consistent errors and biases associated with in situ sampling instruments and retrievals of lidar ratios. Shortwave radiative transfer calculations and a 3-year simulation with the HadGEM2-A climate model show that the radiative effect of biomass burning aerosol was somewhat sensitive to the vertical distribution of aerosol. In particular, when the observed low-level dust layer was included in the model, the absorption of solar radiation by the biomass burning aerosols increased by 10%. We conclude that this absorption enhancement was caused by the dust reflecting solar radiation up into the biomass burning aerosol layer. This result illustrates that the radiative forcing of anthropogenic absorbing aerosol can be sensitive to the presence of natural aerosol species.

Palaeovegetation in China during the late Quaternary: Biome reconstructions based on a global scheme of plant functional types

Two previous reconstructions of palaeovegetation across the whole of China were performed using a simple classification of plant functional types (PFTs). Now a more explicit, global PFT classification scheme has been developed, and a substantial number of additional pollen records have become available. Here we apply the global scheme of PFTs to a comprehensive set of pollen records available from China to test the applicability of the global scheme of PFTs in China, and to obtain a well-founded reconstruction of changing palaeovegetation patterns. A total of 806 pollen surface samples, 188 mid-Holocene (MH, 6000 14C yr BP) and 50 last glacial maximum (LGM, 18,000 14C yr BP) pollen records were used to reconstruct vegetation patterns in China, based on a new global classification system of PFTs and a standard numerical technique for biome assignment (biomization). The biome reconstruction based on pollen surface samples showed convincing agreement with present potential natural vegetation. Coherent patterns of change in biome distribution between MH, LGM and present are observed. In the MH, cold and cool-temperate evergreen needleleaf forests and mixed forests, temperate deciduous broadleaf forest, and warm-temperate evergreen broadleaf and mixed forest in eastern China were shifted northward by 200–500 km. Cold-deciduous forest in northeastern China was replaced by cold evergreen needleleaf forest while in central northern China, cold-deciduous forest was present at some sites now occupied by temperate grassland and desert. The forest–grassland boundary was 200–300 km west of its present position. Temperate xerophytic shrubland, temperate grassland and desert covered a large area on the Tibetan Plateau, but the area of tundra was reduced. Treeline was 300–500 m higher than present in Tibet. These changes imply generally warmer winters, longer growing seasons and more precipitation during the MH. Westward shifts of the forest–shrubland–grassland and grassland–desert boundaries imply greater moisture availability in the MH, consistent with a stronger summer monsoon. During the LGM, in contrast, cold-deciduous forest, cool-temperate evergreen needleleaf forest, cool mixed forests, warm-temperate evergreen broadleaf and mixed forest in eastern China were displaced to the south by 300–1000 km, while temperate deciduous broadleaf forest, pure warm-temperate evergreen forest, tropical semi-evergreen and evergreen broadleaf forests were restricted or absent from the mainland of southern China, implying colder winters than present. Strong shifts of temperate xerophytic shrubland, temperate grassland and desert to the south and east in northern and western China and on the Tibetan Plateau imply drier conditions than present.

Ecophysiological and bioclimatic foundations for a global plant functional classification

Question: What plant properties might define plant functional types (PFTs) for the analysis of global vegetation responses to climate change, and what aspects of the physical environment might be expected to predict the distributions of PFTs? Methods: We review principles to explain the distribution of key plant traits as a function of bioclimatic variables. We focus on those whole-plant and leaf traits that are commonly used to define biomes and PFTs in global maps and models. Results: Raunkiær's plant life forms (underlying most later classifications) describe different adaptive strategies for surviving low temperature or drought, while satisfying requirements for reproduction and growth. Simple conceptual models and published observations are used to quantify the adaptive significance of leaf size for temperature regulation, leaf consistency for maintaining transpiration under drought, and phenology for the optimization of annual carbon balance. A new compilation of experimental data supports the functional definition of tropical, warm-temperate, temperate and boreal phanerophytes based on mechanisms for withstanding low temperature extremes. Chilling requirements are less well quantified, but are a necessary adjunct to cold tolerance. Functional traits generally confer both advantages and restrictions; the existence of trade-offs contributes to the diversity of plants along bioclimatic gradients. Conclusions: Quantitative analysis of plant trait distributions against bioclimatic variables is becoming possible; this opens up new opportunities for PFT classification. A PFT classification based on bioclimatic responses will need to be enhanced by information on traits related to competition, successional dynamics and disturbance.

Climate-driven spatial mismatches between British orchards and their pollinators: increased risks of pollination deficits

Understanding how climate change can affect crop-pollinator systems helps predict potential geographical mismatches between a crop and its pollinators, and therefore identify areas vulnerable to loss of pollination services. We examined the distribution of orchard species (apples, pears, plums and other top fruits) and their pollinators in Great Britain, for present and future climatic conditions projected for 2050 under the SRES A1B Emissions Scenario. We used a relative index of pollinator availability as a proxy for pollination service. At present there is a large spatial overlap between orchards and their pollinators, but predictions for 2050 revealed that the most suitable areas for orchards corresponded to low pollinator availability. However, we found that pollinator availability may persist in areas currently used for fruit production, but which are predicted to provide sub-optimal environmental suitability for orchard species in the future. Our results may be used to identify mitigation options to safeguard orchard production against the risk of pollination failure in Great Britain over the next 50 years; for instance choosing fruit tree varieties that are adapted to future climatic conditions, or boosting wild pollinators through improving landscape resources. Our approach can be readily applied to other regions and crop systems, and expanded to include different climatic scenarios.

The population dynamics of disease on short and long time-scales

Observational evidence is scarce concerning the distribution of plant pathogen population sizes or densities as a function of time-scale or spatial scale. For wild pathosystems we can only get indirect evidence from evolutionary patterns and the consequences of biological invasions.We have little or no evidence bearing on extermination of hosts by pathogens, or successful escape of a host from a pathogen. Evidence over the last couple of centuries from crops suggest that the abundance of particular pathogens in the spectrum affecting a given host can vary hugely on decadal timescales. However, this may be an artefact of domestication and intensive cultivation. Host-pathogen dynamics can be formulated mathematically fairly easily–for example as SIR-type differential equation or difference equation models, and this has been the (successful) focus of recent work in crops. “Long-term” is then discussed in terms of the time taken to relax from a perturbation to the asymptotic state. However, both host and pathogen dynamics are driven by environmental factors as well as their mutual interactions, and both host and pathogen co-evolve, and evolve in response to external factors. We have virtually no information about the importance and natural role of higher trophic levels (hyperpathogens) and competitors, but they could also induce long-scale fluctuations in the abundance of pathogens on particular hosts. In wild pathosystems the host distribution cannot be modelled as either a uniform density or even a uniform distribution of fields (which could then be treated as individuals). Patterns of short term density-dependence and the detail of host distribution are therefore critical to long-term dynamics. Host density distributions are not usually scale-free, but are rarely uniform or clearly structured on a single scale. In a (multiply structured) metapopulation with coevolution and external disturbances it could well be the case that the time required to attain equilibrium (if it exists) based on conditions stable over a specified time-scale is longer than that time-scale. Alternatively, local equilibria may be reached fairly rapidly following perturbations but the meta-population equilibrium be attained very slowly. In either case, meta-stability on various time-scales is a more relevant than equilibrium concepts in explaining observed patterns.

Incorporating toxicokinetics into an individual-based model for more realistic pesticide exposure estimates: A case study of the wood mouse

The potential risk of agricultural pesticides to mammals typically depends on internal concentrations within individuals, and these are determined by the amount ingested and by absorption, distribution, metabolism, and excretion (ADME). Pesticide residues ingested depend, amongst other things, on individual spatial choices which determine how much and when feeding sites and areas of pesticide application overlap, and can be calculated using individual-based models (IBMs). Internal concentrations can be calculated using toxicokinetic (TK) models, which are quantitative representations of ADME processes. Here we provide a population model for the wood mouse (Apodemus sylvaticus) in which TK submodels were incorporated into an IBM representation of individuals making choices about where to feed. This allows us to estimate the contribution of individual spatial choice and TK processes to risk. We compared the risk predicted by four IBMs: (i) “AllExposed-NonTK”: assuming no spatial choice so all mice have 100% exposure, no TK, (ii) “AllExposed-TK”: identical to (i) except that the TK processes are included where individuals vary because they have different temporal patterns of ingestion in the IBM, (iii) “Spatial-NonTK”: individual spatial choice, no TK, and (iv) “Spatial-TK”: individual spatial choice and with TK. The TK parameters for hypothetical pesticides used in this study were selected such that a conventional risk assessment would fail. Exposures were standardised using risk quotients (RQ; exposure divided by LD50 or LC50). We found that for the exposed sub-population including either spatial choice or TK reduced the RQ by 37–85%, and for the total population the reduction was 37–94%. However spatial choice and TK together had little further effect in reducing RQ. The reasons for this are that when the proportion of time spent in treated crop (PT) approaches 1, TK processes dominate and spatial choice has very little effect, and conversely if PT is small spatial choice dominates and TK makes little contribution to exposure reduction. The latter situation means that a short time spent in the pesticide-treated field mimics exposure from a small gavage dose, but TK only makes a substantial difference when the dose was consumed over a longer period. We concluded that a combined TK-IBM is most likely to bring added value to the risk assessment process when the temporal pattern of feeding, time spent in exposed area and TK parameters are at an intermediate level; for instance wood mice in foliar spray scenarios spending more time in crop fields because of better plant cover.

Cognitive and environmental factors influencing the process of spatial knowledge acquisition within virtual reality environments

As the fidelity of virtual environments (VE) continues to increase, the possibility of using them as training platforms is becoming increasingly realistic for a variety of application domains, including military and emergency personnel training. In the past, there was much debate on whether the acquisition and subsequent transfer of spatial knowledge from VEs to the real world is possible, or whether the differences in medium during training would essentially be an obstacle to truly learning geometric space. In this paper, the authors present various cognitive and environmental factors that not only contribute to this process, but also interact with each other to a certain degree, leading to a variable exposure time requirement in order for the process of spatial knowledge acquisition (SKA) to occur. The cognitive factors that the authors discuss include a variety of individual user differences such as: knowledge and experience; cognitive gender differences; aptitude and spatial orientation skill; and finally, cognitive styles. Environmental factors discussed include: Size, Spatial layout complexity and landmark distribution. It may seem obvious that since every individual's brain is unique - not only through experience, but also through genetic predisposition that a one size fits all approach to training would be illogical. Furthermore, considering that various cognitive differences may further emerge when a certain stimulus is present (e.g. complex environmental space), it would make even more sense to understand how these factors can impact spatial memory, and to try to adapt the training session by providing visual/auditory cues as well as by changing the exposure time requirements for each individual. The impact of this research domain is important to VE training in general, however within service and military domains, guaranteeing appropriate spatial training is critical in order to ensure that disorientation does not occur in a life or death scenario.

A spatial view of ensemble spread in convection permitting ensembles

With movement toward kilometer-scale ensembles, new techniques are needed for their characterization. A new methodology is presented for detailed spatial ensemble characterization using the fractions skill score (FSS). To evaluate spatial forecast differences, the average and standard deviation are taken of the FSS calculated over all ensemble member–member pairs at different scales and lead times. These methods were found to give important information about the ensemble behavior allowing the identification of useful spatial scales, spinup times for the model, and upscale growth of errors and forecast differences. The ensemble spread was found to be highly dependent on the spatial scales considered and the threshold applied to the field. High thresholds picked out localized and intense values that gave large temporal variability in ensemble spread: local processes and undersampling dominate for these thresholds. For lower thresholds the ensemble spread increases with time as differences between the ensemble members upscale. Two convective cases were investigated based on the Met Office United Model run at 2.2-km resolution. Different ensemble types were considered: ensembles produced using the Met Office Global and Regional Ensemble Prediction System (MOGREPS) and an ensemble produced using different model physics configurations. Comparison of the MOGREPS and multiphysics ensembles demonstrated the utility of spatial ensemble evaluation techniques for assessing the impact of different perturbation strategies and the need for assessing spread at different, believable, spatial scales.

Biomineralisation by earthworms: an investigation into the stability and distribution of amorphous calcium carbonate

Background Many biominerals form from amorphous calcium carbonate (ACC), but this phase is highly unstable when synthesised in its pure form inorganically. Several species of earthworm secrete calcium carbonate granules which contain highly stable ACC. We analysed the milky fluid from which granules form and solid granules for amino acid (by liquid chromatography) and functional group (by Fourier transform infrared (FTIR) spectroscopy) compositions. Granule elemental composition was determined using inductively coupled plasma-optical emission spectroscopy (ICP-OES) and electron microprobe analysis (EMPA). Mass of ACC present in solid granules was quantified using FTIR and compared to granule elemental and amino acid compositions. Bulk analysis of granules was of powdered bulk material. Spatially resolved analysis was of thin sections of granules using synchrotron-based μ-FTIR and EMPA electron microprobe analysis. Results The milky fluid from which granules form is amino acid-rich (≤ 136 ± 3 nmol mg−1 (n = 3; ± std dev) per individual amino acid); the CaCO3 phase present is ACC. Even four years after production, granules contain ACC. No correlation exists between mass of ACC present and granule elemental composition. Granule amino acid concentrations correlate well with ACC content (r ≥ 0.7, p ≤ 0.05) consistent with a role for amino acids (or the proteins they make up) in ACC stabilisation. Intra-granule variation in ACC (RSD = 16%) and amino acid concentration (RSD = 22–35%) was high for granules produced by the same earthworm. Maps of ACC distribution produced using synchrotron-based μ-FTIR mapping of granule thin sections and the relative intensity of the ν2: ν4 peak ratio, cluster analysis and component regression using ACC and calcite standards showed similar spatial distributions of likely ACC-rich and calcite-rich areas. We could not identify organic peaks in the μ-FTIR spectra and thus could not determine whether ACC-rich domains also had relatively high amino acid concentrations. No correlation exists between ACC distribution and elemental concentrations determined by EMPA. Conclusions ACC present in earthworm CaCO3 granules is highly stable. Our results suggest a role for amino acids (or proteins) in this stability. We see no evidence for stabilisation of ACC by incorporation of inorganic components.

Spatial structuring of arbuscular mycorrhizal communities in benchmark and modified temperate eucalypt woodlands

Arbuscular mycorrhizal fungi (AMF) are crucial to the functioning of the plant–soil system, but little is known about the spatial structuring of AMF communities across landscapes modified by agriculture. AMF community composition was characterized across four sites in the highly cleared south-western Australian wheatbelt that were originally dominated by forb-rich eucalypt woodlands. Environmentally induced spatial structuring in AMF composition was examined at four scales: the regional scale associated with location, the site scale associated with past management (benchmark woodlands with no agricultural management history, livestock grazing, recent revegetation), the patch scale associated with trees and canopy gaps, and the fine scale associated with the herbaceous plant species beneath which soils were sourced. Field-collected soils were cultured in trap pots; then, AMF composition was determined by identifying spores and through ITS1 sequencing. Structuring was strongest at site scales, where composition was strongly related to prior management and associated changes in soil phosphorus. The two fields were dominated by the genera Funneliformis and Paraglomus, with little convergence back to woodland composition after revegetation. The two benchmark woodlands were characterized by Ambispora gerdemannii and taxa from Gigasporaceae. Their AMF communities were strongly structured at patch scales associated with trees and gaps, in turn most strongly related to soil N. By contrast, there were few patterns at fine scales related to different herbaceous plant species, or at regional scales associated with the 175 km distance between benchmark woodlands. Important areas for future investigation are to identify the circumstances in which recolonization by woodland AMF may be limited by fungal propagule availability, reduced plant diversity and/or altered chemistry in agricultural soils.

Designing a sampling scheme to reveal correlations between weeds and soil properties at multiple spatial scales

Weeds tend to aggregate in patches within fields and there is evidence that this is partly owing to variation in soil properties. Because the processes driving soil heterogeneity operate at different scales, the strength of the relationships between soil properties and weed density would also be expected to be scale-dependent. Quantifying these effects of scale on weed patch dynamics is essential to guide the design of discrete sampling protocols for mapping weed distribution. We have developed a general method that uses novel within-field nested sampling and residual maximum likelihood (REML) estimation to explore scale-dependent relationships between weeds and soil properties. We have validated the method using a case study of Alopecurus myosuroides in winter wheat. Using REML, we partitioned the variance and covariance into scale-specific components and estimated the correlations between the weed counts and soil properties at each scale. We used variograms to quantify the spatial structure in the data and to map variables by kriging. Our methodology successfully captured the effect of scale on a number of edaphic drivers of weed patchiness. The overall Pearson correlations between A. myosuroides and soil organic matter and clay content were weak and masked the stronger correlations at >50 m. Knowing how the variance was partitioned across the spatial scales we optimized the sampling design to focus sampling effort at those scales that contributed most to the total variance. The methods have the potential to guide patch spraying of weeds by identifying areas of the field that are vulnerable to weed establishment.

Distribution of lipids in the grain of wheat (cv Hereward) determined by lipidomic analysis of milling and pearling fractions

Lipidomic analyses of milling and pearling fractions from wheat grain were carried out to determine differences in composition which could relate to the spatial distribution of lipids in the grain. Free fatty acids and triacylglycerols were major components in all fractions, but the relative contents of polar lipids varied, particularly lysophosphatidyl choline and digalactosyldiglyceride, which were enriched in flour fractions. By contrast, minor phospholipids were enriched in bran and offal fractions. The most abundant fatty acids in the analysed acyl lipids were C16:0 and C18:2 and their combinations, including C36:4 and C34:2. Phospholipids and galactolipids have been reported to have beneficial properties for bread making, while free fatty acids and triacylglycerols are considered detrimental. The subtle differences in the compositions of fractions determined in the present study could therefore underpin the production of flour fractions with optimised compositions for different end uses.

Towards more precise sugar beet management based on geostatistical analysis of spatial variability within fields

Within-field variation in sugar beet yield and quality was investigated in three commercial sugar beet fields in the east of England to identify the main associated variables and to examine the possibility of predicting yield early in the season with a view to spatially variable management of sugar beet crops. Irregular grid sampling with some purposively-located nested samples was applied. It revealed the spatial variability in each sugar beet field efficiently. In geostatistical analyses, most variograms were isotropic with moderate to strong spatial dependency indicating a significant spatial variation in sugar beet yield and associated growth and environmental variables in all directions within each field. The Kriged maps showed spatial patterns of yield variability within each field and visual association with the maps of other variables. This was confirmed by redundancy analyses and Pearson correlation coefficients. The main variables associated with yield variability were soil type, organic matter, soil moisture, weed density and canopy temperature. Kriged maps of final yield variability were strongly related to that in crop canopy cover, LAI and intercepted solar radiation early in the growing season, and the yield maps of previous crops. Therefore, yield maps of previous crops together with early assessment of sugar beet growth may make an early prediction of within-field variability in sugar beet yield possible. The Broom’s Barn sugar beet model failed to account for the spatial variability in sugar yield, but the simulation was greatly improved when corrected for early canopy development cover and when the simulated yield was adjusted for weeds and plant population. Further research to optimize inputs to maximise sugar yield should target the irrigation and fertilizing of areas within fields with low canopy cover early in the season.

'The debatable territory where geology and archaeology meet': reassessing the early archaeobotanical work of Clement Reid and Arthur Lyell at Roman Silchester

The first large-scale archaeobotanical study in Britain, conducted from 1899 to 1909 by Clement Reid and Arthur Lyell at Silchester, provided the first evidence for the introduction of Roman plant foods to Britain, yet the findings have thus far remained unverified. This paper presents a reassessment of these archaeobotanical remains, now stored as part of the Silchester Collection in Reading Museum. The documentary evidence for the Silchester study is summarised, before the results are presented for over a 1000 plant remains including an assessment of preservation, identification and modern contamination. The dataset includes both evidence for the presence of nationally rare plant foods, such as medlar, and several archaeophytes. The methodologies and original interpretations of Reid and Lyell’s study are reassessed in light of current archaeobotanical knowledge. Spatial and contextual patterns in the distribution of plant foods and ornamental taxa are also explored. Finally, the legacy of the study for the development of archaeobotany in the 20th century is evaluated.

Environmental controls on the distribution and diversity of lentic Chironomidae (Insecta: Diptera) across an altitudinal gradient in tropical South America

To predict the response of aquatic ecosystems to future global climate change, data on the ecology and distribution of keystone groups in freshwater ecosystems are needed. In contrast to mid- and high-latitude zones, such data are scarce across tropical South America (Neotropics). We present the distribution and diversity of chironomid species using surface sediments of 59 lakes from the Andes to the Amazon (0.1–17°S and 64–78°W) within the Neotropics. We assess the spatial variation in community assemblages and identify the key variables influencing the distributional patterns. The relationships between environmental variables (pH, conductivity, depth, and sediment organic content), climatic data, and chironomid assemblages were assessed using multivariate statistics (detrended correspondence analysis and canonical correspondence analysis). Climatic parameters (temperature and precipitation) were most significant in describing the variance in chironomid assemblages. Temperature and precipitation are both predicted to change under future climate change scenarios in the tropical Andes. Our findings suggest taxa of Orthocladiinae, which show a preference to cold high-elevation oligotrophic lakes, will likely see range contraction under future anthropogenic-induced climate change. Taxa abundant in areas of high precipitation, such as Micropsectra and Phaenopsectra, will likely become restricted to the inner tropical Andes, as the outer tropical Andes become drier. The sensitivity of chironomids to climate parameters makes them important bio-indicators of regional climate change in the Neotropics. Furthermore, the distribution of chironomid taxa presented here is a vital first step toward providing urgently needed autecological data for interpreting fossil chironomid records of past ecological and climate change from the tropical Andes.