Proposal for a unified nomenclature for target site mutations associated with resistance to fungicides

Evolved resistance to fungicides is a major problem limiting our ability to control agricultural, medical and veterinary pathogens and is frequently associated with substitutions in the amino acid sequence of the target protein. The convention for describing amino-acid substitutions is to cite the wild type amino acid, the codon number and the new amino acid, using the one letter amino acid code. It has frequently been observed that orthologous amino acid mutations have been selected in different species by fungicides from the same mode of action class, but the amino acids have different numbers. These differences in numbering arise from the different lengths of the proteins in each species. The purpose of the current paper is to propose a system for unifying the labelling of amino acids in fungicide target proteins. To do this we have produced alignments between fungicide target proteins of relevant species fitted to a well-studied “archetype” species. Orthologous amino acids in all species are then assigned numerical “labels” based on the position of the amino acid in the archetype protein.

Land use for England and Wales: evaluation of management options to support 'good ecological status' in surface freshwaters

This paper analyses historic records of agricultural land use and management for England and Wales from 1931 and 1991 and uses export coefficient modelling to hindcast the impact of these practices on the rates of diffuse nitrogen (N) and phosphorus (P) export to water bodies for each of the major geo-climatic regions of England and Wales. Key trends indicate the importance of animal agriculture as a contributor to the total diffuse agricultural nutrient loading on waters, and the need to bring these sources under control if conditions suitable for sustaining 'Good Ecological Status' under the Water Framework Directive are to be generated. The analysis highlights the importance of measuring changes in nutrient loading in relation to the catchment-specific baseline state for different water bodies. The approach is also used to forecast the likely impact of broad regional scale scenarios on nutrient export to waters and highlights the need to take sensitive land out of production, introduce ceilings on fertilizer use and stocking densities, and controls on agricultural practice in higher risk areas where intensive agriculture is combined with a low intrinsic nutrient retention capacity, although the uncertainties associated with the modelling applied at this scale should be taken into account in the interpretation of model output. The paper advocates the need for a two-tiered approach to nutrient management, combining broad regional policies with targeted management in high risk areas at the catchment and farm scale.

Managing maize under pest species competition: is Bt (Bacillus thuringiensis) maize the solution?

Transgenic crops that contain Cry genes from Bacillus thuringiensis (Bt) have been adopted by farmers over the last 17 years. Unlike traditional broad spectrum chemical insecticides, Bt's toxicity spectrum is relatively narrow and selective, which may indirectly benefit secondary insects that may become important pests. The economic damage caused by the rise of secondary pests could offset some or all of the benefits associated with the use of Bt varieties. We develop a bioeconomic model to analyze the interactions between primary and secondary insect populations and the impact of different management options on insecticide use and economic impact over time. Results indicate that some of the benefits associated with the adoption of genetically engineered insect resistant crops may be eroded when taking into account ecological dynamics. It is suggested that secondary pests could easily become key insect pests requiring additional measures - such as insecticide applications or stacked traits – to keep their populations under the economic threshold.

The Soil: Nature, Sustainable Use, Management, and Protection - An Overview

Soil forms the outer skin of the earth's land surface. Often less than a metre in depth, it is essential to sustain natural terrestrial ecosystems and human life. Soils result from the interactions over time between climate, parent material, topography, vegetation, and biota. They vary from place to place. Mineral soils are composed of mineral matter, organic matter, and gas- or liquid-filled pores in varying proportions. Soils perform a wide range of functions and provide many ecosystem or environmental services; with the climate problem, the soil is increasingly being recognised as a potential sink for carbon from the atmosphere. In part because of humankind's (over)use of soils and in part because of natural and human-induced environmental change, there is a widespread decline in soil quality and an increasing number of threats to soil, which jeopardise both the soil's natural functions and its use by humans. As a limited resource, soils must be used sustainably. Soil protection strategies have been indirectly embodied in a number of United Nations conventions, and there are now national and supranational developments towards specific regulations and legislation to protect soils and their functions.

Managing invasive alien species with professional and hobby farmers: insights from ecological-economic modelling

Biosecurity is a great challenge to policy-makers globally. Biosecurity policies aim to either prevent invasions before they occur or to eradicate and/or effectively manage the invasive species and diseases once an invasion has occurred. Such policies have traditionally been directed towards professional producers in natural resource based sectors, including agriculture. Given the wide scope of issues threatened by invasive species and diseases, it is important to account for several types of stakeholders that are involved. We investigate the problem of an invasive insect pest feeding on an agricultural crop with heterogeneous producers: profit-oriented professional farmers and utility-oriented hobby farmers. We start from an ecological-economic model conceptually similar to the one developed by Eiswerth and Johnson [Eiswerth, M.E. and Johnson, W.S., 2002. Managing nonindigenous invasive species: insights from dynamic analysis. Environmental and Resource Economics 23, 319-342.] and extend it in three ways. First, we make explicit the relationship between the invaded state carrying capacity and farmers' planting decisions. Second, we add another producer type into the framework and hence account for the existence of both professional and hobby fanners. Third, we provide a theoretical contribution by discussing two alternative types of equilibria. We also apply the model to an empirical case to extract a number of stylised facts and in particular to assess: a) under which circumstances the invasion is likely to be not controllable; and b) how extending control policies to hobby farmers could affect both types of producers. (C) 2008 Elsevier B.V. All rights reserved.

Managing threatened species – the ecological toolbox, evolutionary theory and the declining-population paradigm

1. The management of threatened species is an important practical way in which conservationists can intervene in the extinction process and reduce the loss of biodiversity. Understanding the causes of population declines (past, present and future) is pivotal to designing effective practical management. This is the declining-population paradigm identified by Caughley. 2. There are three broad classes of ecological tool used by conservationists to guide management decisions for threatened species: statistical models of habitat use, demographic models and behaviour-based models. Each of these is described here, illustrated with a case study and evaluated critically in terms of its practical application. 3. These tools are fundamentally different. Statistical models of habitat use and demographic models both use descriptions of patterns in abundance and demography, in relation to a range of factors, to inform management decisions. In contrast, behaviourbased models describe the evolutionary processes underlying these patterns, and derive such patterns from the strategies employed by individuals when competing for resources under a specific set of environmental conditions. 4. Statistical models of habitat use and demographic models have been used successfully to make management recommendations for declining populations. To do this, assumptions are made about population growth or vital rates that will apply when environmental conditions are restored, based on either past data collected under favourable environmental conditions or estimates of these parameters when the agent of decline is removed. As a result, they can only be used to make reliable quantitative predictions about future environments when a comparable environment has been experienced by the population of interest in the past. 5. Many future changes in the environment driven by management will not have been experienced by a population in the past. Under these circumstances, vital rates and their relationship with population density will change in the future in a way that is not predictable from past patterns. Reliable quantitative predictions about population-level responses then need to be based on an explicit consideration of the evolutionary processes operating at the individual level. 6. Synthesis and applications. It is argued that evolutionary theory underpins Caughley’s declining-population paradigm, and that it needs to become much more widely used within mainstream conservation biology. This will help conservationists examine critically the reliability of the tools they have traditionally used to aid management decision-making. It will also give them access to alternative tools, particularly when predictions are required for changes in the environment that have not been experienced by a population in the past.

Influence of management type on Diptera communities of coniferous plantations and deciduous woodlands

The contribution of four types of secondary woodlands to Scottish invertebrate biodiversity was investigated for coniferous plantation forestry, riparian ash-alder woodlands, early successional deciduous woodlands and climax deciduous woodlands. Considerable variation in the type and intensity of management within these four woodland types existed. Adult Diptera from 21 families, representing diverse trophic and ecological guilds, were sampled from 31 woodlands in the Aberdeenshire region of northeast Scotland, between June and August 2001. Environmental differences between woodlands were recorded at each site using environmental parameters such as pH and organic matter content, vegetation characteristics, including percentage canopy cover and dominant field layer plant species. Multivariate ordination techniques detected significant responses in the Dipteran communities to soil type, organic matter content, soil pH, field layer plant species richness, dominant field layer plant species and percentage cover of Pteridium aquilinum. Responses in terms of Dipteran abundance, species richness, diversity and evenness were observed to soil type and dominant species of the field layer vegetation. The role of woodland type and management in diversifying Diptera communities is discussed with a view to maintain and possibly enhance Dipteran and other invertebrate communities in Scottish secondary woodlands. (C) 2002 Elsevier Science B.V. All rights reserved.

A method for evaluating alternative landscape management scenarios in relation to the biodiversity conservation of habitats

A perennial issue for land use policy is the evaluation of landscape biodiversity and the associated cost effectiveness of any biodiversity conservation policy actions. Based on the CUA methodology as applied to species conservation, this paper develops a methodology for evaluating the impact on habitats of alternative landscape management scenarios. The method incorporates three dimensions of habitats, quantity change, quality change and relative scarcity, and is illustrated in relation to the alternative landscape management scenarios for the Scottish Highlands (Cairngorms) study area of the BioScene project. The results demonstrate the value of the method for evaluating biodiversity conservation policies through their impact on habitats.

Making ecological science policy relevant: issues of scale and disciplinary integration

In this paper, we ask why so much ecological scientific research does not have a greater policy impact in the UK. We argue that there are two potentially important and related reasons for this failing. First, much current ecological science is not being conducted at a scale that is readily meaningful to policy-makers. Second, to make much of this research policy-relevant requires collaborative interdisciplinary research between ecologists and social scientists. However, the challenge of undertaking useful interdisciplinary research only re-emphasises the problems of scale: ecologists and social scientists traditionally frame their research questions at different scales and consider different facets of natural resource management, setting different objectives and using different language. We argue that if applied ecological research is to have greater impact in informing environmental policy, much greater attention needs to be given to the scale of the research efforts as well as to the interaction with social scientists. Such an approach requires an adjustment in existing research and funding infrastructures.

Managing threatened species: the ecological toolbox, evolutionary theory and declining-population paradigm

1. The management of threatened species is an important practical way in which conservationists can intervene in the extinction process and reduce the loss of biodiversity. Understanding the causes of population declines (past, present and future) is pivotal to designing effective practical management. This is the declining-population paradigm identified by Caughley. 2. There are three broad classes of ecological tool used by conservationists to guide management decisions for threatened species: statistical models of habitat use, demographic models and behaviour-based models. Each of these is described here, illustrated with a case study and evaluated critically in terms of its practical application. 3. These tools are fundamentally different. Statistical models of habitat use and demographic models both use descriptions of patterns in abundance and demography, in relation to a range of factors, to inform management decisions. In contrast, behaviour-based models describe the evolutionary processes underlying these patterns, and derive such patterns from the strategies employed by individuals when competing for resources under a specific set of environmental conditions. 4. Statistical models of habitat use and demographic models have been used successfully to make management recommendations for declining populations. To do this, assumptions are made about population growth or vital rates that will apply when environmental conditions are restored, based on either past data collected under favourable environmental conditions or estimates of these parameters when the agent of decline is removed. As a result, they can only be used to make reliable quantitative predictions about future environments when a comparable environment has been experienced by the population of interest in the past. 5. Many future changes in the environment driven by management will not have been experienced by a population in the past. Under these circumstances, vital rates and their relationship with population density will change in the future in a way that is not predictable from past patterns. Reliable quantitative predictions about population-level responses then need to be based on an explicit consideration of the evolutionary processes operating at the individual level. 6. Synthesis and applications. It is argued that evolutionary theory underpins Caughley's declining-population paradigm, and that it needs to become much more widely used within mainstream conservation biology. This will help conservationists examine critically the reliability of the tools they have traditionally used to aid management decision-making. It will also give them access to alternative tools, particularly when predictions are required for changes in the environment that have not been experienced by a population in the past.

Demographic models and the management of endangered species: a case study of the critically endangered Seychelles magpie robin

1. Demographic models are assuming an important role in management decisions for endangered species. Elasticity analysis and scope for management analysis are two such applications. Elasticity analysis determines the vital rates that have the greatest impact on population growth. Scope for management analysis examines the effects that feasible management might have on vital rates and population growth. Both methods target management in an attempt to maximize population growth. 2. The Seychelles magpie robin Copsychus sechellarum is a critically endangered island endemic, the population of which underwent significant growth in the early 1990s following the implementation of a recovery programme. We examined how the formal use of elasticity and scope for management analyses might have shaped management in the recovery programme, and assessed their effectiveness by comparison with the actual population growth achieved. 3. The magpie robin population doubled from about 25 birds in 1990 to more than 50 by 1995. A simple two-stage demographic model showed that this growth was driven primarily by a significant increase in the annual survival probability of first-year birds and an increase in the birth rate. Neither the annual survival probability of adults nor the probability of a female breeding at age 1 changed significantly over time. 4. Elasticity analysis showed that the annual survival probability of adults had the greatest impact on population growth. There was some scope to use management to increase survival, but because survival rates were already high (> 0.9) this had a negligible effect on population growth. Scope for management analysis showed that significant population growth could have been achieved by targeting management measures at the birth rate and survival probability of first-year birds, although predicted growth rates were lower than those achieved by the recovery programme when all management measures were in place (i.e. 1992-95). 5. Synthesis and applications. We argue that scope for management analysis can provide a useful basis for management but will inevitably be limited to some extent by a lack of data, as our study shows. This means that identifying perceived ecological problems and designing management to alleviate them must be an important component of endangered species management. The corollary of this is that it will not be possible or wise to consider only management options for which there is a demonstrable ecological benefit. Given these constraints, we see little role for elasticity analysis because, when data are available, a scope for management analysis will always be of greater practical value and, when data are lacking, precautionary management demands that as many perceived ecological problems as possible are tackled.

Knowledge, attitudes and practices of farmers on rodent pests and their management in the lowlands of the Sierra Madre Biodiversity Corridor, Philippines

A survey of the knowledge, attitudes and practices (KAP) of 100 rice farmers and 50 coconut farmers was conducted in the coastal lowland agro-ecosystems of the Sierra Madre Biodiversity Corridor, Luzon, Philippines to identify current rodent management practices and to understand the extent of rat damage and the attitudes of farmers to community actions for rodent management. Pests were most commonly listed as one of the three most important rice and coconut production constraints. Other major crop production constraints were typhoons and insufficient water. Farmers consider rats to be the major pest of coconut and of rice during the wet season rice crop, with average yield losses of 3.0% and 13.2%, respectively. Rice and coconut farmers practised a wide range of rodent management techniques. These included scrub clearance, hunting and trapping. Of the 42 rice farmers and 3 coconut farmers that applied rodenticides to control rodents, all used the acute rodenticide, zinc phosphide. However, only ten rice farmers (23.8%) applied rodenticides prior to the booting stage and only seven farmers (15.6%) conducted pre-baiting before applying zinc phosphide. The majority of farmers belonged to farmer organisations and believed that rat control can only be done by farmers working together. However, during the last cropping season, less than a third of rice farmers (31.2%) applied rodent management as a group. In order to reduce the impact of rodents on the farmers of the coastal lowlands of the Sierra Madre Biodiversity Corridor, integrated management strategies need to be developed that specifically target the pest rodents in a sustainable manner, and community actions for rodent management should be promoted.

Local management and landscape drivers of pollination and biological control services in a Kenyan agro-ecosystem

Arthropods that have a direct impact on crop production (i.e. pests, natural enemies and pollinators) can be influenced by both local farm management and the context within which the fields occur in the wider landscape. However, the contributions and spatial scales at which these drivers operate and interact are not fully understood, particularly in the developing world. The impact of both local management and landscape context on insect pollinators and natural enemy communities and on their capacity to deliver related ecosystem services to an economically important tropical crop, pigeonpea was investigated. The study was conducted in nine paired farms across a gradient of increasing distance to semi-native vegetation in Kibwezi, Kenya. Results show that proximity of fields to semi-native habitats negatively affected pollinator and chewing insect abundance. Within fields, pesticide use was a key negative predictor of pollinator, pest and foliar active predator abundance. On the contrary, fertilizer application significantly enhanced pollinator and both chewing and sucking insect pest abundance. At a 1 km spatial scale of fields, there were significant negative effects of the number of semi-native habitat patches within fields dominated by mass flowering pigeonpea on pollinators abundance. For service provision, a significant decline in fruit set when insects were excluded from flowers was recorded. This study reveals the interconnections of pollinators, predators and pests with pigeonpea crop. For sustainable yields and to conserve high densities of both pollinators and predators of pests within pigeonpea landscapes, it is crucial to target the adoption of less disruptive farm management practices such as reducing pesticide and fertilizer inputs.