Towards a method for the economic evaluation of environmental indicators in UK Integrated Arable Farming Systems

Integrated Arable Farming Systems (IAFS), which involve a reduction in the use of off-farm inputs, are attracting considerable research interest in the UK. The objectives of these systems experiments are to compare their financial performance with that from conventional or current farming practices. To date, this comparison has taken little account of any environmental benefits (or disbenefits) of the two systems. The objective of this paper is to review the assessment methodologies available for the analysis of environmental impacts. To illustrate the results of this exercise, the methodology and environmental indicators chosen are then applied to data from one of the LINK - Integrated Farming Systems experimental sites. Data from the Pathhead site in Southern Scotland are used to evaluate the use of invertebrates and nitrate loss as environmental indicators within IAFS. The results suggest that between 1992 and 1995 the biomass of earthworms fell by 28 kg per hectare on the integrated rotation and rose by 31 kg per hectare on the conventional system. This led to environmental costs ranging between £2.24 and £13.44 per hectare for the integrated system and gains of between £2.48 and £14.88 for the conventional system. In terms of nitrate, the integrated system had an estimated loss of £72.21 per hectare in comparison to £149.40 per hectare on the conventional system. Conclusions are drawn about the advantages and disadvantages of this type of analytical framework. Keywords: Farming systems; IAFS; Environmental valuation; Economics; Earthworms; Nitrates; Soil fauna

Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity.

Background. The anaerobic spirochaete Brachyspira pilosicoli causes enteric disease in avian, porcine and human hosts, amongst others. To date, the only available genome sequence of B. pilosicoli is that of strain 95/1000, a porcine isolate. In the first intra-species genome comparison within the Brachyspira genus, we report the whole genome sequence of B. pilosicoli B2904, an avian isolate, the incomplete genome sequence of B. pilosicoli WesB, a human isolate, and the comparisons with B. pilosicoli 95/1000. We also draw on incomplete genome sequences from three other Brachyspira species. Finally we report the first application of the high-throughput Biolog phenotype screening tool on the B. pilosicoli strains for detailed comparisons between genotype and phenotype. Results. Feature and sequence genome comparisons revealed a high degree of similarity between the three B. pilosicoli strains, although the genomes of B2904 and WesB were larger than that of 95/1000 (~2,765, 2.890 and 2.596 Mb, respectively). Genome rearrangements were observed which correlated largely with the positions of mobile genetic elements. Through comparison of the B2904 and WesB genomes with the 95/1000 genome, features that we propose are non-essential due to their absence from 95/1000 include a peptidase, glycine reductase complex components and transposases. Novel bacteriophages were detected in the newly-sequenced genomes, which appeared to have involvement in intra- and inter-species horizontal gene transfer. Phenotypic differences predicted from genome analysis, such as the lack of genes for glucuronate catabolism in 95/1000, were confirmed by phenotyping. Conclusions. The availability of multiple B. pilosicoli genome sequences has allowed us to demonstrate the substantial genomic variation that exists between these strains, and provides an insight into genetic events that are shaping the species. In addition, phenotype screening allowed determination of how genotypic differences translated to phenotype. Further application of such comparisons will improve understanding of the metabolic capabilities of Brachyspira species.

Effect of cultivar type and ripening on the polyphenol content of date palm fruit

Date palm (Pheonix dactylifera) fruit contains an array of polyphenols, although how these levels alter with cultivar type and fruit ripening is unclear. Utilizing HPLC and LC-ESI-MS/MS, this study define and quantify an array of hydroxybenzoic acids, hydroxycinnamic acids, and flavonoids in three common cultivars of dates (Ajwa, Barni, and Khalas) at the main ripening stages (kimri, khalal, rutab, and tamr). Polyphenols were at highest concentration at earlier stages of ripening, with concentrations reducing with ripening. The khalal stage of the Ajwa cultivar contained significantly higher (P < 0.001) levels of polyphenols than measured in the Barni and Khalas dates at the same degree of ripening. Furthermore, the Ajwa cultivar was the only one to contain significant quantities of anthocyanidins, in particular at the khalal stage. These data suggest dates are a significant source of polyphenols, especially if the earlier edible ripening stages are consumed or utilized as food ingredients.

Linguistic evidence supports date for Homeric epics

The Homeric epics are among the greatest masterpieces of literature, but when they were produced is not known with certainty. Here we apply evolutionary-linguistic phylogenetic statistical methods to differences in Homeric, Modern Greek and ancient Hittite vocabulary items to estimate a date of approximately 710–760 BCE for these great works. Our analysis compared a common set of vocabulary items among the three pairs of languages, recording for each item whether the words in the two languages were cognate – derived from a shared ancestral word – or not. We then used a likelihood-based Markov chain Monte Carlo procedure to estimate the most probable times in years separating these languages given the percentage of words they shared, combined with knowledge of the rates at which different words change. Our date for the epics is in close agreement with historians' and classicists' beliefs derived from historical and archaeological sources.

Development of convection along the SPCZ within a Madden-Julian oscillation

A subtropical Rossby-wave propagation mechanism is proposed to account for the poleward and eastward progression of intraseasonal convective anomalies along the South Pacific convergence zone (SPCZ) that is observed in a significant proportion of Madden–Julian oscillations (MJOs). Large-scale convection, associated with an MJO, is assumed to be already established over the Indonesian region. The latent heating associated with this convection forces an equatorial Rossby-wave response with an upper-tropospheric anticyclone centred over, or slightly to the west of, the convection. Large potential-vorticity (PV) gradients, associated with the subtropical jet and the tropopause, lie just poleward of the anticyclone, and large magnitude PV air is advected equatorwards on the eastern side of the anticyclone. This ‘high’ PV air, or upper-tropospheric trough, is far enough off the equator that it has associated strong horizontal temperature gradients, and it induces deep ascent on its eastern side, at a latitude of about 15–30°. If this deep ascent is over a region susceptible to deep convection, such as the SPCZ, then convection may be forced or triggered. Hence convection develops along the SPCZ as a forced response to convection over Indonesia. The response mechanism is essentially one of subtropical Rossby-wave propagation. This hypothesis is based on a case study of a particularly strong MJO in early 1988, and is tested by idealized modelling studies. The mechanism may also be relevant to the existence of the mean SPCZ, as a forced response to mean Indonesian convection.

Using a case-study approach to improve the Madden-Julian oscillation in the Hadley Centre model

In its default configuration, the Hadley Centre climate model (GA2.0) simulates roughly one-half the observed level of Madden–Julian oscillation activity, with MJO events often lasting fewer than seven days. We use initialised, climate-resolution hindcasts to examine the sensitivity of the GA2.0 MJO to a range of changes in sub-grid parameterisations and model configurations. All 22 changes are tested for two cases during the Years of Tropical Convection. Improved skill comes only from (a) disabling vertical momentum transport by convection and (b) increasing mixing entrainment and detrainment for deep and mid-level convection. These changes are subsequently tested in a further 14 hindcast cases; only (b) consistently improves MJO skill, from 12 to 22 days. In a 20-year integration, (b) produces near-observed levels of MJO activity, but propagation through the Maritime Continent remains weak. With default settings, GA2.0 produces precipitation too readily, even in anomalously dry columns. Implementing (b) decreases the efficiency of convection, permitting instability to build during the suppressed MJO phase and producing a more favourable environment for the active phase. The distribution of daily rain rates is more consistent with satellite data; default entrainment produces 6–12 mm/day too frequently. These results are consistent with recent studies showing that greater sensitivity of convection to moisture improves the representation of the MJO.

Propagation of the Madden-Julian Oscillation through the Maritime Continent and scale interaction with the diurnal cycle of precipitation

The convectively active part of the Madden-Julian Oscillation (MJO) propagates eastward through the warm pool, from the Indian Ocean through the Maritime Continent (the Indonesian archipelago) to the western Pacific. The Maritime Continent's complex topography means the exact nature of the MJO propagation through this region is unclear. Model simulations of the MJO are often poor over the region, leading to local errors in latent heat release and global errors in medium-range weather prediction and climate simulation. Using 14 northern winters of TRMM satellite data it is shown that, where the mean diurnal cycle of precipitation is strong, 80% of the MJO precipitation signal in the Maritime Continent is accounted for by changes in the amplitude of the diurnal cycle. Additionally, the relationship between outgoing long-wave radiation (OLR) and precipitation is weakened here, such that OLR is no longer a reliable proxy for precipitation. The canonical view of the MJO as the smooth eastward propagation of a large-scale precipitation envelope also breaks down over the islands of the Maritime Continent. Instead, a vanguard of precipitation (anomalies of 2.5 mm day^-1 over 10^6 km^2) jumps ahead of the main body by approximately 6 days or 2000 km. Hence, there can be enhanced precipitation over Sumatra, Borneo or New Guinea when the large-scale MJO envelope over the surrounding ocean is one of suppressed precipitation. This behaviour can be accommodated into existing MJO theories. Frictional and topographic moisture convergence and relatively clear skies ahead of the main convective envelope combine with the low thermal inertia of the islands, to allow a rapid response in the diurnal cycle which rectifies onto the lower-frequency MJO. Hence, accurate representations of the diurnal cycle and its scale interaction appear to be necessary for models to simulate the MJO successfully.

The effect of the Madden-Julian Oscillation on station rainfall and river level in the Fly River system, Papua New Guinea

The Madden-Julian oscillation (MJO) is the dominant mode of intraseasonal variability in tropical rainfall on the large scale, but its signal is often obscured in individual station data, where effects are most directly felt at the local level. The Fly River system, Papua New Guinea, is one of the wettest regions on Earth and is at the heart of the MJO envelope. A 16 year time series of daily precipitation at 15 stations along the river system exhibits strong MJO modulation in rainfall. At each station, the difference in rainfall rate between active and suppressed MJO conditions is typically 40% of the station mean. The spread of rainfall between individual MJO events was small enough such that the rainfall distributions between wet and dry phases of the MJO were clearly separated at the catchment level. This implies that successful prediction of the large-scale MJO envelope will have a practical use for forecasting local rainfall. In the steep topography of the New Guinea Highlands, the mean and MJO signal in station precipitation is twice that in the satellite Tropical Rainfall Measuring Mission 3B42HQ product, emphasizing the need for ground-truthing satellite-based precipitation measurements. A clear MJO signal is also present in the river level, which peaks simultaneously with MJO precipitation input in its upper reaches but lags the precipitation by approximately 18 days on the flood plains.

The Madden-Julian Oscillation and the diurnal cycle over the Maritime Continent: scale interactions and modelling

The Maritime Continent archipelago, situated on the equator at 95-165E, has the strongest land-based precipitation on Earth. The latent heat release associated with the rainfall affects the atmospheric circulation throughout the tropics and into the extra-tropics. The greatest source of variability in precipitation is the diurnal cycle. The archipelago is within the convective region of the Madden-Julian Oscillation (MJO), which provides the greatest variability on intra-seasonal time scales: large-scale (∼10^7 km^2) active and suppressed convective envelopes propagate slowly (∼5 m s^-1) eastwards between the Indian and Pacific Oceans. High-resolution satellite data show that a strong diurnal cycle is triggered to the east of the advancing MJO envelope, leading the active MJO by one-eighth of an MJO cycle (∼6 days). Where the diurnal cycle is strong its modulation accounts for 81% of the variability in MJO precipitation. Over land this determines the structure of the diagnosed MJO. This is consistent with the equatorial wave dynamics in existing theories of MJO propagation. The MJO also affects the speed of gravity waves propagating offshore from the Maritime Continent islands. This is largely consistent with changes in static stability during the MJO cycle. The MJO and its interaction with the diurnal cycle are investigated in HiGEM, a high-resolution coupled model. Unlike many models, HiGEM represents the MJO well with eastward-propagating variability on intra-seasonal time scales at the correct zonal wavenumber, although the inter-tropical convergence zone's precipitation peaks strongly at the wrong time, interrupting the MJO's spatial structure. However, the modelled diurnal cycle is too weak and its phase is too early over land. The modulation of the diurnal amplitude by the MJO is also too weak and accounts for only 51% of the variability in MJO precipitation. Implications for forecasting and possible causes of the model errors are discussed, and further modelling studies are proposed.

Coupled versus uncoupled hindcast simulations of the Madden-Julian oscillation in the Year of Tropical Convection

This study investigates the impact of a full interactive ocean on daily initialised 15 day hindcasts of the Madden-Julian oscillation (MJO), measured against a Met Office Unified Model (MetUM) atmosphere control simulation (AGCM) during a 3 month period of the Year of Tropical Convection (YOTC). Results indicated that the coupled configuration (CGCM) extends MJO predictability over that of the AGCM, by up to 3-5 days. Propagation is improved in the CGCM, which we partly attribute to a more realistic phase relationship between sea surface temperature (SST) and convection. In addition, the CGCM demonstrates skill in representing downwelling oceanic Kelvin and Rossby waves which warm SSTs along their trajectory, with the potential to feed back on the atmosphere. These results imply that an ocean model capable of simulating internal ocean waves may be required to capture the full effect of air-sea coupling for the MJO.

Vertical structure and physical processes of the Madden-Julian oscillation: Linking hindcast fidelity to simulated diabatic heating and moistening

Many theories for the Madden-Julian oscillation (MJO) focus on diabatic processes, particularly the evolution of vertical heating and moistening. Poor MJO performance in weather and climate models is often blamed on biases in these processes and their interactions with the large-scale circulation. We introduce one of three components of a model-evaluation project, which aims to connect MJO fidelity in models to their representations of several physical processes, focusing on diabatic heating and moistening. This component consists of 20-day hindcasts, initialised daily during two MJO events in winter 2009-10. The 13 models exhibit a range of skill: several have accurate forecasts to 20 days' lead, while others perform similarly to statistical models (8-11 days). Models that maintain the observed MJO amplitude accurately predict propagation, but not vice versa. We find no link between hindcast fidelity and the precipitation-moisture relationship, in contrast to other recent studies. There is also no relationship between models' performance and the evolution of their diabatic-heating profiles with rain rate. A more robust association emerges between models' fidelity and net moistening: the highest-skill models show a clear transition from low-level moistening for light rainfall to mid-level moistening at moderate rainfall and upper-level moistening for heavy rainfall. The mid-level moistening, arising from both dynamics and physics, may be most important. Accurately representing many processes may be necessary, but not sufficient for capturing the MJO, which suggests that models fail to predict the MJO for a broad range of reasons and limits the possibility of finding a panacea.

Vertical structure and physical processes of the Madden-Julian oscillation: synthesis and summary

The "Vertical structure and physical processes of the Madden-Julian oscillation (MJO)" project comprises three experiments, designed to evaluate comprehensively the heating, moistening and momentum associated with tropical convection in general circulation models (GCMs). We consider here only those GCMs that performed all experiments. Some models display relatively higher or lower MJO fidelity in both initialized hindcasts and climate simulations, while others show considerable variations in fidelity between experiments. Fidelity in hindcasts and climate simulations are not meaningfully correlated. The analysis of each experiment led to the development of process-oriented diagnostics, some of which distinguished between GCMs with higher or lower fidelity in that experiment. We select the most discriminating diagnostics and apply them to data from all experiments, where possible, to determine if correlations with MJO fidelity hold across scales and GCM states. While normalized gross moist stability had a small but statistically significant correlation with MJO fidelity in climate simulations, we find no link with fidelity in medium-range hindcasts. Similarly, there is no association between timestep-to-timestep rainfall variability, identified from short hindcasts, and fidelity in medium-range hindcasts or climate simulations. Two metrics that relate precipitation to free-tropospheric moisture--the relative humidity for extreme daily precipitation, and variations in the height and amplitude of moistening with rain rate--successfully distinguish between higher- and lower-fidelity GCMs in hindcasts and climate simulations. To improve the MJO, developers should focus on relationships between convection and both total moisture and its rate of change. We conclude by offering recommendations for further experiments.

Vertical structure and physical processes of the Madden-Julian oscillation: exploring key model physics in climate simulations

Aimed at reducing deficiencies in representing the Madden-Julian oscillation (MJO) in general circulation models (GCMs), a global model evaluation project on vertical structure and physical processes of the MJO was coordinated. In this paper, results from the climate simulation component of this project are reported. It is shown that the MJO remains a great challenge in these latest generation GCMs. The systematic eastward propagation of the MJO is only well simulated in about one-fourth of the total participating models. The observed vertical westward tilt with altitude of the MJO is well simulated in good MJO models, but not in the poor ones. Damped Kelvin wave responses to the east of convection in the lower troposphere could be responsible for the missing MJO preconditioning process in these poor MJO models. Several process-oriented diagnostics were conducted to discriminate key processes for realistic MJO simulations. While large-scale rainfall partition and low-level mean zonal winds over the Indo-Pacific in a model are not found to be closely associated with its MJO skill, two metrics, including the low-level relative humidity difference between high and low rain events and seasonal mean gross moist stability, exhibit statistically significant correlations with the MJO performance. It is further indicated that increased cloud-radiative feedback tends to be associated with reduced amplitude of intraseasonal variability, which is incompatible with the radiative instability theory previously proposed for the MJO. Results in this study confirm that inclusion of air-sea interaction can lead to significant improvement in simulating the MJO.