Rapid assessment of historic, current and future habitat quality for biodiversity around UK Natura 2000 sites

Changes in landscape composition and structure may impact the conservation and management of protected areas. Species that depend on specific habitats are at risk of extinction when these habitats are degraded or lost. Designing robust methods to evaluate landscape composition will assist decision- and policy-making in emerging landscapes. This paper describes a rapid assessment methodology aimed at evaluating landcover quality for birds, plants, butterflies and bees around seven UK Natura 2000 sites. An expert panel assigned quality values to standard Coordination of Information on the Environment (CORINE) landcover classes for each taxonomic group. Quality was assessed based on historical (1950, 1990), current (2000) and future (2030) land-cover data, the last projected using three alternative scenarios: a growth applied strategy (GRAS), a business-as-might-beusual (BAMBU) scenario, and sustainable European development goal (SEDG) scenario. A quantitative quality index weighted the area of each land-cover parcel with a taxa-specific quality measure. Land parcels with high quality for all taxonomic groups were evaluated for temporal changes in area, size and adjacency. For all sites and taxonomic groups, the rate of deterioration of land-cover quality was greater between 1950 and 1990 than current rates or as modelled using the alternative future scenarios (2000– 2030). Model predictions indicated land-cover quality stabilized over time under the GRAS scenario, and was close to stable for the BAMBU scenario. The SEDG scenario suggested an ongoing loss of quality, though this was lower than the historical rate of c. 1% loss per decade. None of the future scenarios showed accelerated fragmentation, but rather increases in the area, adjacency and diversity of high quality land parcels in the landscape.

First contribution of mites (Acari) to the forensic analysis of hanged corpses: a case study from Spain

This case study from North Spain, highlights the importance of the collection of mites in addition to insects, from crime scenes or corpses subjected to environmental constraints that reduce or minimise insect activity, such as hanged corpses. In addition, this analysis highlights the relevance of arthropods’ collection in the field, even after the corpse has been moved away for autopsy. Four species of mites, phoretic on carrion (Silphidae) and rove (Staphylinidae) beetles, complemented and reinforced the autopsy analysis as well as the scarce information provided by insect activity. Poecilochirus carabi Canestrini & Canestrini, 1882 and Poecilochirus (Physoparasitus) davydovae Hyatt, 1980 (Mesostigmata: Parasitidae) were found in association with two Silphidae, Nicrophorus Fabricius, 1775 and Necrodes Leach, 1815, only when sampled in the autopsy room; this is suggestive of host-switching of mites and was likely due to the lack of availability of specific carriers in the field. The interpretation of the activity of Parasitidae mites both in the field and the autopsy room allows a better understanding of the timing and circumstances of decomposition. Phoretic deutonymphs of Pelzneria Scheucher 1957 (Astigmata: Histiostomatidae) were highly abundant, mostly P. crenulata Oudemans, 1909 and are reported for the first time on a Staphylinidae rove beetle, Creophilus maxillosus (L., 1758). Surprisingly, in this case study no Pelzneria were associated with the Silphidae found, which are their most common hosts, such as Necrodes littoralis (L., 1758) and Nicrophorus interruptus (Stephens, 1830). All histiostomatids were removed from the staphylinid (rove beetle) collected from the soil, at the scene of death, suggesting a recent arrival of the beetle. The occurrence of Staphylinidae beetles and their associated mites, such as Parasitidae and Pelzneria, and the information they provided would have been easily overlooked or lost if only the autopsy sampling would have been considered in the analysis of the case. The four mite species are reported for the first time for the Iberian Peninsula.

Multi‐method global sensitivity analysis (MMGSA) for modelling floodplain hydrological processes

When studying hydrological processes with a numerical model, global sensitivity analysis (GSA) is essential if one is to understand the impact of model parameters and model formulation on results. However, different definitions of sensitivity can lead to a difference in the ranking of importance of the different model factors. Here we combine a fuzzy performance function with different methods of calculating global sensitivity to perform a multi-method global sensitivity analysis (MMGSA). We use an application of a finite element subsurface flow model (ESTEL-2D) on a flood inundation event on a floodplain of the River Severn to illustrate this new methodology. We demonstrate the utility of the method for model understanding and show how the prediction of state variables, such as Darcian velocity vectors, can be affected by such a MMGSA. This paper is a first attempt to use GSA with a numerically intensive hydrological model.

Sources, sinks, and transatlantic transport of North African dust aerosol: a multimodel analysis and comparison with remote sensing data

This study evaluates model-simulated dust aerosols over North Africa and the North Atlantic from five global models that participated in the Aerosol Comparison between Observations and Models phase II model experiments. The model results are compared with satellite aerosol optical depth (AOD) data from Moderate Resolution Imaging Spectroradiometer (MODIS), Multiangle Imaging Spectroradiometer (MISR), and Sea-viewing Wide Field-of-view Sensor, dust optical depth (DOD) derived from MODIS and MISR, AOD and coarse-mode AOD (as a proxy of DOD) from ground-based Aerosol Robotic Network Sun photometer measurements, and dust vertical distributions/centroid height from Cloud Aerosol Lidar with Orthogonal Polarization and Atmospheric Infrared Sounder satellite AOD retrievals. We examine the following quantities of AOD and DOD: (1) the magnitudes over land and over ocean in our study domain, (2) the longitudinal gradient from the dust source region over North Africa to the western North Atlantic, (3) seasonal variations at different locations, and (4) the dust vertical profile shape and the AOD centroid height (altitude above or below which half of the AOD is located). The different satellite data show consistent features in most of these aspects; however, the models display large diversity in all of them, with significant differences among the models and between models and observations. By examining dust emission, removal, and mass extinction efficiency in the five models, we also find remarkable differences among the models that all contribute to the discrepancies of model-simulated dust amount and distribution. This study highlights the challenges in simulating the dust physical and optical processes, even in the best known dust environment, and stresses the need for observable quantities to constrain the model processes.

Coordinated ground-based, low altitude satellite and Cluster observations on global and local scales during a transient post-noon sector excursion of the magnetospheric cusp

On 14 January 2001, the four Cluster spacecraft passed through the northern magnetospheric mantle in close conjunction to the EISCAT Svalbard Radar (ESR) and approached the post-noon dayside magnetopause over Greenland between 13:00 and 14:00 UT During that interval, a sudden reorganisation of the high-latitude dayside convection pattern accurred after 13:20 UT most likely caused by a direction change of the Solar wind magnetic field. The result was an eastward and poleward directed flow-channel, as monitored by the SuperDARN radar network and also by arrays of ground-based magnetometers in Canada, Greenland and Scandinavia. After an initial eastward and later poleward expansion of the flow-channel between 13:20 and 13:40 UT, the four Cluster spacecraft, and the field line footprints covered by the eastward looking scan cycle of the Sondre Stromfjord incoherent scatter radar were engulfed by cusp-like precipitation with transient magnetic and electric field signatures. In addition, the EISCAT Svalbard Radar detected strong transient effects of the convection reorganisation, a poleward moving precipitation, and a fast ion flow-channel in association with the auroral structures that suddenly formed to the west and north of the radar. From a detailed analysis of the coordinated Cluster and ground-based data, it was found that this extraordinary transient convection pattern, indeed, had moved the cusp precipitation from its former pre-noon position into the late post-noon sector, allowing for the first and quite unexpected encounter of the cusp by the Cluster spacecraft. Our findings illustrate the large amplitude of cusp dynamics even in response to moderate solar wind forcing. The global ground-based data proves to be an invaluable tool to monitor the dynamics and width of the affected magnetospheric regions.

Location and characteristics of the reconnection X line deduced from low-altitude satellite and ground-based observations: 2. Defense Meteorological Satellite Program and European Incoherent Scatter data

We present an analysis of a cusp ion step, observed by the Defense Meteorological Satellite Program (DMSP) F10 spacecraft, between two poleward moving events of enhanced ionospheric electron temperature, observed by the European Incoherent Scatter (EISCAT) radar. From the ions detected by the satellite, the variation of the reconnection rate is computed for assumed distances along the open-closed field line separatrix from the satellite to the X line, do. Comparison with the onset times of the associated ionospheric events allows this distance to be estimated, but with an uncertainty due to the determination of the low-energy cutoff of the ion velocity distribution function, ƒ(ν). Nevertheless, the reconnection site is shown to be on the dayside magnetopause, consistent with the reconnection model of the cusp during southward interplanetary magnetic field (IMF). Analysis of the time series of distribution function at constant energies, ƒ(ts), shows that the best estimate of the distance do is 14.5±2 RE. This is consistent with various magnetopause observations of the signatures of reconnection for southward IMF. The ion precipitation is used to reconstruct the field-parallel part of the Cowley D ion distribution function injected into the open low-latitude boundary layer in the vicinity of the X line. From this reconstruction, the field-aligned component of the magnetosheath flow is found to be only −55±65 km s−1 near the X line, which means either that the reconnection X line is near the stagnation region at the nose of the magnetosphere, or that it is closely aligned with the magnetosheath flow streamline which is orthogonal to the magnetosheath field, or both. In addition, the sheath Alfvén speed at the X line is found to be 220±45 km s−1, and the speed with which newly opened field lines are ejected from the X line is 165±30 km s−1. We show that the inferred magnetic field, plasma density, and temperature of the sheath near the X line are consistent with a near-subsolar reconnection site and confirm that the magnetosheath field makes a large angle (>58°) with the X line.

Species diversity and dominance-richness relationships for ground and arboreal ant (Hymenoptera: Formicidae) assemblages in Namibian desert, saltpan, and savannah

Namibia has high levels of invertebrate endemism, but biodiversity research has been geographically and taxonomically limited. In South African savannah, species richness of ground-foraging ant assemblages is regulated by dominant ant species, but this pattern has not been tested in other arid environments. In this study, we provide a description of ant diversity at baits in three different Namibian habitats (savannah, saltpan and desert), and we test the relationship between ant dominance and richness for ground-foraging and arboreal species. Forty-two ant species were collected in this study, with species richness being highest in the saltpan, followed by savannah and then desert. Ant assemblages were most similar between the savannah and desert, due to shared arboreal species. Similarity between savannah and saltpan ant assemblages was due to an overlap in ground-foraging species. Ground ants were more diverse than arboreal ants, and several species were observed at baits for both strata, although the degree of overlap varied with habitat type. The dominance-richness relationship varied depending on habitat and sampling strata. We found a unimodal relationship in the saltpan, but not in the savannah. For ground ants the relationship was logarithmic, with increasing abundance of dominants leading to decreasing overall species richness. However, no trend was observed for the arboreal ant assemblage. In the desert, low ant abundance meant that we were unable to assign species dominance, possibly due to reduced foraging activity caused by high temperatures. The lack of a consistent dominance-richness trend across assemblages may be the result of varying degrees of environmental stress or competition. Our study is a preliminary description of diversity and dominance in Namibia, and we hope it stimulates further research on ant assemblages in arid regions of Africa.

Multi-method global sensitivity analysis (MMGSA) for modelling floodplain hydrological processes

When studying hydrological processes with a numerical model, global sensitivity analysis (GSA) is essential if one is to understand the impact of model parameters and model formulation on results. However, different definitions of sensitivity can lead to a difference in the ranking of importance of the different model factors. Here we combine a fuzzy performance function with different methods of calculating global sensitivity to perform a multi-method global sensitivity analysis (MMGSA). We use an application of a finite element subsurface flow model (ESTEL-2D) on a flood inundation event on a floodplain of the River Severn to illustrate this new methodology. We demonstrate the utility of the method for model understanding and show how the prediction of state variables, such as Darcian velocity vectors, can be affected by such a MMGSA. This paper is a first attempt to use GSA with a numerically intensive hydrological model

A model analysis of climate and CO2 controls on tree growth in a semi-arid woodland

We used a light-use efficiency model of photosynthesis coupled with a dynamic carbon allocation and tree-growth model to simulate annual growth of the gymnosperm Callitris columellaris in the semi-arid Great Western Woodlands, Western Australia, over the past 100 years. Parameter values were derived from independent observations except for sapwood specific respiration rate, fine-root turnover time, fine-root specific respiration rate and the ratio of fine-root mass to foliage area, which were estimated by Bayesian optimization. The model reproduced the general pattern of interannual variability in radial growth (tree-ring width), including the response to the shift in precipitation regimes that occurred in the 1960s. Simulated and observed responses to climate were consistent. Both showed a significant positive response of tree-ring width to total photosynthetically active radiation received and to the ratio of modeled actual to equilibrium evapotranspiration, and a significant negative response to vapour pressure deficit. However, the simulations showed an enhancement of radial growth in response to increasing atmospheric CO2 concentration (ppm) ([CO2]) during recent decades that is not present in the observations. The discrepancy disappeared when the model was recalibrated on successive 30-year windows. Then the ratio of fine-root mass to foliage area increases by 14% (from 0.127 to 0.144 kg C m-2) as [CO2] increased while the other three estimated parameters remained constant. The absence of a signal of increasing [CO2] has been noted in many tree-ring records, despite the enhancement of photosynthetic rates and water-use efficiency resulting from increasing [CO2]. Our simulations suggest that this behaviour could be explained as a consequence of a shift towards below-ground carbon allocation.

Landscape connectivity: a key to effective habitat restoration in lowland agricultural landscapes

Landscape scale habitat restoration has the potential to reconnect habitats in fragmented landscapes. This study investigates landscape connectivity as a key to effective habitat restoration in lowland agricultural landscapes and applies these findings to transferable management recommendations. The study area is the Stonehenge World Heritage Site, UK, where landscape scale chalk grassland restoration has been implemented. Here, the ecological benefits of landscape restoration and the species, habitat and landscape characteristics that facilitate or impede the enhancement of biodiversity and landscape connectivity were investigated. Lepidoptera were used as indictors of restoration success and results showed restoration grasslands approaching the ecological conditions of the target chalk grassland habitat and increasing in biodiversity values within a decade. Restoration success is apparent for four species with a broad range of grass larval host plants (e.g. Melanargia galathea, Maniola jurtina) or with intermediate mobility (Polyommatus icarus). However, two species with specialist larval host plants and low mobility (Lysandra bellargus), are restricted to chalk grassland fragments. Studies of restoration grassland of different ages show that recent grassland restoration (1 or 2 years old) may reduce the functional isolation of chalk grassland fragments. A management experiment showed that mowing increases boundary following behaviour in two species of grassland Lepidoptera; Maniola jurtina and Zygaena filipendulae. Analysis of the landscape scale implications of the grassland restoration illustrates an increase in grassland habitat network size and in landscape connectivity, which is likely to benefit the majority of grassland associated Lepidoptera. Landscape and habitat variables can be managed to increase the success of restoration projects including the spatial targeting of receptor sites, vegetation structure and selection of seed source and management recommendations are provided that are transferrable to other species-rich grassland landscape scale restoration projects. Overall results show restoration success for some habitats and species within a decade. However, additional management is required to assist the re-colonisation of specialist species. Despite this, habitat restoration at the landscape scale can be an effective, long term approach to enhance butterfly biodiversity and landscape connectivity.

Efficient incorporation of channel cross-section geometry uncertainty into regional and global scale flood inundation models

This paper investigates the challenge of representing structural differences in river channel cross-section geometry for regional to global scale river hydraulic models and the effect this can have on simulations of wave dynamics. Classically, channel geometry is defined using data, yet at larger scales the necessary information and model structures do not exist to take this approach. We therefore propose a fundamentally different approach where the structural uncertainty in channel geometry is represented using a simple parameterization, which could then be estimated through calibration or data assimilation. This paper first outlines the development of a computationally efficient numerical scheme to represent generalised channel shapes using a single parameter, which is then validated using a simple straight channel test case and shown to predict wetted perimeter to within 2% for the channels tested. An application to the River Severn, UK is also presented, along with an analysis of model sensitivity to channel shape, depth and friction. The channel shape parameter was shown to improve model simulations of river level, particularly for more physically plausible channel roughness and depth parameter ranges. Calibrating channel Manning’s coefficient in a rectangular channel provided similar water level simulation accuracy in terms of Nash-Sutcliffe efficiency to a model where friction and shape or depth were calibrated. However, the calibrated Manning coefficient in the rectangular channel model was ~2/3 greater than the likely physically realistic value for this reach and this erroneously slowed wave propagation times through the reach by several hours. Therefore, for large scale models applied in data sparse areas, calibrating channel depth and/or shape may be preferable to assuming a rectangular geometry and calibrating friction alone.

Comparative analysis of performance and stability among composite cross populations, variety mixtures and pure lines of winter wheat in organic and conventional cropping systems

This study investigated the effects of increased genetic diversity in winter wheat (Triticum aestivum L.), either from hybridization across genotypes or from physical mixing of lines, on grain yield, grain quality, and yield stability in different cropping environments. Sets of pure lines (no diversity), chosen for high yielding ability or high quality, were compared with line mixtures (intermediate level of diversity), and lines crossed with each other in composite cross populations (CCPn, high diversity). Additional populations containing male sterility genes (CCPms) to increase outcrossing rates were also tested. Grain yield, grain protein content, and protein yield were measured at four sites (two organically-managed and two conventionally-managed) over three years, using seed harvested locally in each preceding year. CCPn and mixtures out-yielded the mean of the parents by 2.4% and 3.6%, respectively. These yield differences were consistent across genetic backgrounds but partly inconsistent across cropping environments and years. Yield stability measured by environmental variance was higher in CCPn and CCPms than the mean of the parents. An index of yield reliability tended to be higher in CCPn, CCPms and mixtures than the mean of the parents. Lin and Binns’ superiority values of yield and protein yield were consistently and significantly lower (i.e. better) in the CCPs than in the mean of the parents, but not different between CCPs and mixtures. However, CCPs showed greater early ground cover and plant height than mixtures. When compared with the (locally non-predictable) best-yielding pure line, CCPs and mixtures exhibited lower mean yield and somewhat lower yield reliability but comparable superiority values. Thus, establishing CCPs from smaller sets of high-performing parent lines might optimize their yielding ability. On the whole, the results demonstrate that using increased within-crop genetic diversity can produce wheat crops with improved yield stability and good yield reliability across variable and unpredictable cropping environments.

Transcriptomic analysis of Enterohaemorrhagic Escherichia coli O157:H7 in response to plant extracts

Enterohaemorrhagic Escherichia coli (EHEC) are a group of food and contact-borne pathogens responsible for haemorrhagic colitis. The bacteria can be transmitted by contaminated meat, but importantly, also by plants. The bacteria can use plants as an alternative host, where they associate with both the leaves and the roots. Colonisation in the rhizosphere of plants is thought to be the main habitat for colonisation. Four different plant species, commonly associated with EHEC outbreaks, were infected with EHEC O157:H7 isolates Sakai and TUV 93-0 over ten days to assess the colonisation potential of the bacteria in both the phyllosphere and rhizosphere of plants. The rhizosphere was found to sustain a higher population level of bacteria over time in comparison to the phyllosphere, yet both strains were unable to utilize root exudates for growth. Global gene expression changes of EHEC O157:H7 strain Sakai were measured in response to plant extracts such as leaf lysates, root exudates and leaf cell wall polysaccharides from spinach cultivar Amazon and lettuce cultivar Salinas. Microarrays analysis showed a significant change in expression of 17 % of genes on exposure to leaf lysates of spinach. A more specific response was seen to spinach leaf cell wall polysaccharides with only a 1.5 % change. In contrast, when exposed to lettuce leaf cell wall polysaccharides a higher change of 4.8 % was seen. Genes that were differentially expressed belonged to multiple functional groups, including metabolism, indicating the utilization of plant-specific polysaccharides. Several areas of further investigation have been determined from this project, including the importance of culturing bacterial strains at a relevant temperature, the proposed lack of the type III secretion system in plant colonization by EHEC O157:H7 and the utilization of plant components for growth and persistence in the plant environment.

Using Distributed Temperature Sensing to monitor field scale dynamics of ground surface temperature and related substrate heat flux

We present one of the first studies of the use of Distributed Temperature Sensing (DTS) along fibre-optic cables to purposely monitor spatial and temporal variations in ground surface temperature (GST) and soil temperature, and provide an estimate of the heat flux at the base of the canopy layer and in the soil. Our field site was at a groundwater-fed wet meadow in the Netherlands covered by a canopy layer (between 0-0.5 m thickness) consisting of grass and sedges. At this site, we ran a single cable across the surface in parallel 40 m sections spaced by 2 m, to create a 40×40 m monitoring field for GST. We also buried a short length (≈10 m) of cable to depth of 0.1±0.02 m to measure soil temperature. We monitored the temperature along the entire cable continuously over a two-day period and captured the diurnal course of GST, and how it was affected by rainfall and canopy structure. The diurnal GST range, as observed by the DTS system, varied between 20.94 and 35.08◦C; precipitation events acted to suppress the range of GST. The spatial distribution of GST correlated with canopy vegetation height during both day and night. Using estimates of thermal inertia, combined with a harmonic analysis of GST and soil temperature, substrate and soil-heat fluxes were determined. Our observations demonstrate how the use of DTS shows great promise in better characterising area-average substrate/soil heat flux, their spatiotemporal variability, and how this variability is affected by canopy structure. The DTS system is able to provide a much richer data set than could be obtained from point temperature sensors. Furthermore, substrate heat fluxes derived from GST measurements may be able to provide improved closure of the land surface energy balance in micrometeorological field studies. This will enhance our understanding of how hydrometeorological processes interact with near-surface heat fluxes.