Representing the acquisition and use of energy by individuals in agent-based models of animal populations

Summary 1. Agent-based models (ABMs) are widely used to predict how populations respond to changing environments. As the availability of food varies in space and time, individuals should have their own energy budgets, but there is no consensus as to how these should be modelled. Here, we use knowledge of physiological ecology to identify major issues confronting the modeller and to make recommendations about how energy budgets for use in ABMs should be constructed. 2. Our proposal is that modelled animals forage as necessary to supply their energy needs for maintenance, growth and reproduction. If there is sufficient energy intake, an animal allocates the energy obtained in the order: maintenance, growth, reproduction, energy storage, until its energy stores reach an optimal level. If there is a shortfall, the priorities for maintenance and growth/reproduction remain the same until reserves fall to a critical threshold below which all are allocated to maintenance. Rates of ingestion and allocation depend on body mass and temperature. We make suggestions for how each of these processes should be modelled mathematically. 3. Mortality rates vary with body mass and temperature according to known relationships, and these can be used to obtain estimates of background mortality rate. 4. If parameter values cannot be obtained directly, then values may provisionally be obtained by parameter borrowing, pattern-oriented modelling, artificial evolution or from allometric equations. 5. The development of ABMs incorporating individual energy budgets is essential for realistic modelling of populations affected by food availability. Such ABMs are already being used to guide conservation planning of nature reserves and shell fisheries, to assess environmental impacts of building proposals including wind farms and highways and to assess the effects on nontarget organisms of chemicals for the control of agricultural pests. Keywords: bioenergetics; energy budget; individual-based models; population dynamics.

Mid-Holocene and glacial-maximum vegetation geography of the northern continents and Africa.

BIOME 6000 is an international project to map vegetation globally at mid-Holocene (6000 14C yr bp) and last glacial maximum (LGM, 18,000 14C yr bp), with a view to evaluating coupled climate-biosphere model results. Primary palaeoecological data are assigned to biomes using an explicit algorithm based on plant functional types. This paper introduces the second Special Feature on BIOME 6000. Site-based global biome maps are shown with data from North America, Eurasia (except South and Southeast Asia) and Africa at both time periods. A map based on surface samples shows the method’s skill in reconstructing present-day biomes. Cold and dry conditions at LGM favoured extensive tundra and steppe. These biomes intergraded in northern Eurasia. Northern hemisphere forest biomes were displaced southward. Boreal evergreen forests (taiga) and temperate deciduous forests were fragmented, while European and East Asian steppes were greatly extended. Tropical moist forests (i.e. tropical rain forest and tropical seasonal forest) in Africa were reduced. In south-western North America, desert and steppe were replaced by open conifer woodland, opposite to the general arid trend but consistent with modelled southward displacement of the jet stream. The Arctic forest limit was shifted slighly north at 6000 14C yr bp in some sectors, but not in all. Northern temperate forest zones were generally shifted greater distances north. Warmer winters as well as summers in several regions are required to explain these shifts. Temperate deciduous forests in Europe were greatly extended, into the Mediterranean region as well as to the north. Steppe encroached on forest biomes in interior North America, but not in central Asia. Enhanced monsoons extended forest biomes in China inland and Sahelian vegetation into the Sahara while the African tropical rain forest was also reduced, consistent with a modelled northward shift of the ITCZ and a more seasonal climate in the equatorial zone. Palaeobiome maps show the outcome of separate, independent migrations of plant taxa in response to climate change. The average composition of biomes at LGM was often markedly different from today. Refugia for the temperate deciduous and tropical rain forest biomes may have existed offshore at LGM, but their characteristic taxa also persisted as components of other biomes. Examples include temperate deciduous trees that survived in cool mixed forest in eastern Europe, and tropical evergreen trees that survived in tropical seasonal forest in Africa. The sequence of biome shifts during a glacial-interglacial cycle may help account for some disjunct distributions of plant taxa. For example, the now-arid Saharan mountains may have linked Mediterranean and African tropical montane floras during enhanced monsoon regimes. Major changes in physical land-surface conditions, shown by the palaeobiome data, have implications for the global climate. The data can be used directly to evaluate the output of coupled atmosphere-biosphere models. The data could also be objectively generalized to yield realistic gridded land-surface maps, for use in sensitivity experiments with atmospheric models. Recent analyses of vegetation-climate feedbacks have focused on the hypothesized positive feedback effects of climate-induced vegetation changes in the Sahara/Sahel region and the Arctic during the mid-Holocene. However, a far wider spectrum of interactions potentially exists and could be investigated, using these data, both for 6000 14C yr bp and for the LGM.

Sensitivity of a hydraulic model to changes in channel erosion during extreme flooding

Recent research into flood modelling has primarily concentrated on the simulation of inundation flow without considering the influences of channel morphology. River channels are often represented by a simplified geometry that is implicitly assumed to remain unchanged during flood simulations. However, field evidence demonstrates that significant morphological changes can occur during floods to mobilise the boundary sediments. Despite this, the effect of channel morphology on model results has been largely unexplored. To address this issue, the impact of channel cross-section geometry and channel long-profile variability on flood dynamics is examined using an ensemble of a 1D-2D hydraulic model (LISFLOOD-FP) of the 1:2102 year recurrence interval floods in Cockermouth, UK, within an uncertainty framework. A series of hypothetical scenarios of channel morphology were constructed based on a simple velocity based model of critical entrainment. A Monte-Carlo simulation framework was used to quantify the effects of channel morphology together with variations in the channel and floodplain roughness coefficients, grain size characteristics, and critical shear stress on measures of flood inundation. The results showed that the bed elevation modifications generated by the simplistic equations reflected a good approximation of the observed patterns of spatial erosion despite its overestimation of erosion depths. The effect of uncertainty on channel long-profile variability only affected the local flood dynamics and did not significantly affect the friction sensitivity and flood inundation mapping. The results imply that hydraulic models generally do not need to account for within event morphodynamic changes of the type and magnitude modelled, as these have a negligible impact that is smaller than other uncertainties, e.g. boundary conditions. Instead morphodynamic change needs to happen over a series of events to become large enough to change the hydrodynamics of floods in supply limited gravel-bed rivers like the one used in this research.

Effects of agricultural management practices on earthworm populations and crop yield: validation and application of a mechanistic modelling approach

There is little consensus on how agriculture will meet future food demands sustainably. Soils and their biota play a crucial role by mediating ecosystem services that support agricultural productivity. However, a multitude of site-specific environmental factors and management practices interact to affect the ability of soil biota to perform vital functions, confounding the interpretation of results from experimental approaches. Insights can be gained through models, which integrate the physiological, biological and ecological mechanisms underpinning soil functions. We present a powerful modelling approach for predicting how agricultural management practices (pesticide applications and tillage) affect soil functioning through earthworm populations. By combining energy budgets and individual-based simulation models, and integrating key behavioural and ecological drivers, we accurately predict population responses to pesticide applications in different climatic conditions. We use the model to analyse the ecological consequences of different weed management practices. Our results demonstrate that an important link between agricultural management (herbicide applications and zero, reduced and conventional tillage) and earthworms is the maintenance of soil organic matter (SOM). We show how zero and reduced tillage practices can increase crop yields while preserving natural ecosystem functions. This demonstrates how management practices which aim to sustain agricultural productivity should account for their effects on earthworm populations, as their proliferation stimulates agricultural productivity. Synthesis and applications. Our results indicate that conventional tillage practices have longer term effects on soil biota than pesticide control, if the pesticide has a short dissipation time. The risk of earthworm populations becoming exposed to toxic pesticides will be reduced under dry soil conditions. Similarly, an increase in soil organic matter could increase the recovery rate of earthworm populations. However, effects are not necessarily additive and the impact of different management practices on earthworms depends on their timing and the prevailing environmental conditions. Our model can be used to determine which combinations of crop management practices and climatic conditions pose least overall risk to earthworm populations. Linking our model mechanistically to crop yield models would aid the optimization of crop management systems by exploring the trade-off between different ecosystem services.

Is behavioral ecology important for understanding and predicting population dynamics?

Population ecology is a discipline that studies changes in the number and composition (age, sex) of the individuals that form a population. Many of the mechanisms that generate these changes are associated with individual behavior, for example how individuals defend their territories, find mates or disperse. Therefore, it is important to model population dynamics considering the potential influence of behavior on the modeled dynamics. This study illustrates the diversity of behaviors that influence population dynamics describing several methods that allow integrating behavior into population models and range from simpler models that only consider the number of individuals to complex individual-based models that capture great levels of detail. A series of examples shows the importance of explicitly considering behavior in population modeling to avoid reaching erroneous conclusions. This integration is particularly relevant for conservation, as incorrect predictions regarding the dynamics of populations of conservation interest can lead to inadequate assessment and management. Improved predictions can favor effective protection of species and better use of the limited financial and human conservation resources.

Strategic management of non-point source pollution from sewage sludge

In the UK, the recycling of sewage sludge to land is expected to double by 2006 but the security of this route is threatened by environmental concerns and health scares. Strategic investment is needed to ensure sustainable and secure sludge recycling outlets. At present, the security of this landbank for sludge recycling is determined by legislation relating to nutrient rather than potentially toxic elements (PTEs) applications to land - especially the environmental risk linked to soil phosphorus (P) saturation. We believe that not all land has an equal risk of contributing nutrients derived from applications to land to receiving waters. We are currently investigating whether it is possible to minimise nutrient loss by applying sludge to land outside Critical Source Areas (CSAs) regardless of soil P Index status. Research is underway to develop a predictive and spatially-sensitive, semi-distributed model of critical thresholds for sludge application that goes beyond traditional 'end-of-pipe" or "edge-of-field" modelling, to include hydrological flow paths and delivery mechanisms to receiving waters from non-point sources at the catchment scale.

Modeling the mechanisms that control in-stream dissolved organic carbon dynamics in upland and forested catchments

[1] We present a new, process-based model of soil and stream water dissolved organic carbon (DOC): the Integrated Catchments Model for Carbon (INCA-C). INCA-C is the first model of DOC cycling to explicitly include effects of different land cover types, hydrological flow paths, in-soil carbon biogeochemistry, and surface water processes on in-stream DOC concentrations. It can be calibrated using only routinely available monitoring data. INCA-C simulates daily DOC concentrations over a period of years to decades. Sources, sinks, and transformation of solid and dissolved organic carbon in peat and forest soils, wetlands, and streams as well as organic carbon mineralization in stream waters are modeled. INCA-C is designed to be applied to natural and seminatural forested and peat-dominated catchments in boreal and temperate regions. Simulations at two forested catchments showed that seasonal and interannual patterns of DOC concentration could be modeled using climate-related parameters alone. A sensitivity analysis showed that model predictions were dependent on the mass of organic carbon in the soil and that in-soil process rates were dependent on soil moisture status. Sensitive rate coefficients in the model included those for organic carbon sorption and desorption and DOC mineralization in the soil. The model was also sensitive to the amount of litter fall. Our results show the importance of climate variability in controlling surface water DOC concentrations and suggest the need for further research on the mechanisms controlling production and consumption of DOC in soils.

Modelling stream and soil water nitrate dynamics during experimentally increased nitrogen deposition in a coniferous forest catchment at Gardsjon, Sweden

Increased atmospheric deposition of inorganic nitrogen (N) may lead to increased leaching of nitrate (NO3-) to surface waters. The mechanisms responsible for, and controls on, this leaching are matters of debate. An experimental N addition has been conducted at Gardsjon, Sweden to determine the magnitude and identify the mechanisms of N leaching from forested catchments within the EU funded project NITREX. The ability of INCA-N, a simple process-based model of catchment N dynamics, to simulate catchment-scale inorganic N dynamics in soil and stream water during the course of the experimental addition is evaluated. Simulations were performed for 1990-2002. Experimental N addition began in 1991. INCA-N was able to successfully reproduce stream and soil water dynamics before and during the experiment. While INCA-N did not correctly simulate the lag between the start of N addition and NO 2 3 breakthrough, the model was able to simulate the state change resulting from increased N deposition. Sensitivity analysis showed that model behaviour was controlled primarily by parameters related to hydrology and vegetation dynamics and secondarily by in-soil processes.

National and sub-national assessments of soil organic carbon stocks and changes: The GEFSOC modelling system

Soil organic carbon (SOC) plays a vital role in ecosystem function, determining soil fertility, water holding capacity and susceptibility to land degradation. In addition, SOC is related to atmospheric CO, levels with soils having the potential for C release or sequestration, depending on land use, land management and climate. The United Nations Convention on Climate Change and its Kyoto Protocol, and other United Nations Conventions to Combat Desertification and on Biodiversity all recognize the importance of SOC and point to the need for quantification of SOC stocks and changes. An understanding of SOC stocks and changes at the national and regional scale is necessary to further our understanding of the global C cycle, to assess the responses of terrestrial ecosystems to climate change and to aid policy makers in making land use/management decisions. Several studies have considered SOC stocks at the plot scale, but these are site specific and of limited value in making inferences about larger areas. Some studies have used empirical methods to estimate SOC stocks and changes at the regional scale, but such studies are limited in their ability to project future changes, and most have been carried out using temperate data sets. The computational method outlined by the Intergovernmental Panel on Climate Change (IPCC) has been used to estimate SOC stock changes at the regional scale in several studies, including a recent study considering five contrasting eco regions. This 'one step' approach fails to account for the dynamic manner in which SOC changes are likely to occur following changes in land use and land management. A dynamic modelling approach allows estimates to be made in a manner that accounts for the underlying processes leading to SOC change. Ecosystem models, designed for site scale applications can be linked to spatial databases, giving spatially explicit results that allow geographic areas of change in SOC stocks to be identified. Some studies have used variations on this approach to estimate SOC stock changes at the sub-national and national scale for areas of the USA and Europe and at the watershed scale for areas of Mexico and Cuba. However, a need remained for a national and regional scale, spatially explicit system that is generically applicable and can be applied to as wide a range of soil types, climates and land uses as possible. The Global Environment Facility Soil Organic Carbon (GEFSOC) Modelling System was developed in response to this need. The GEFSOC system allows estimates of SOC stocks and changes to be made for diverse conditions, providing essential information for countries wishing to take part in an emerging C market, and bringing us closer to an understanding of the future role of soils in the global C cycle. (C) 2007 Elsevier B.V. All rights reserved.

Predictive vegetation mapping in the Mediterranean context: Considerations and methodological issues

The need to map vegetation communities over large areas for nature conservation and to predict the impact of environmental change on vegetation distributions, has stimulated the development of techniques for predictive vegetation mapping. Predictive vegetation studies start with the development of a model relating vegetation units and mapped physical data, followed by the application of that model to a geographic database and over a wide range of spatial scales. This field is particularly important for identifying sites for rare and endangered species and locations of high biodiversity such as many areas of the Mediterranean Basin. The potential of the approach is illustrated with a mapping exercise in the alti-meditterranean zone of Lefka Ori in Crete. The study established the nature of the relationship between vegetation communities and physical data including altitude, slope and geomorphology. In this way the knowledge of community distribution was improved enabling a GIS-based model capable of predicting community distribution to be constructed. The paper describes the development of the spatial model and the methodological problems of predictive mapping for monitoring Mediterranean ecosystems. The paper concludes with a discussion of the role of predictive vegetation mapping and other spatial techniques, such as fuzzy mapping and geostatistics, for improving our understanding of the dynamics of Mediterranean ecosystems and for practical management in a region that is under increasing pressure from human impact.

Influences of space, soil, nematodes and plants on microbial community composition of chalk grassland soils

Microbial communities respond to a variety of environmental factors related to resources (e.g. plant and soil organic matter), habitat (e.g. soil characteristics) and predation (e.g. nematodes, protozoa and viruses). However, the relative contribution of these factors on microbial community composition is poorly understood. Here, we sampled soils from 30 chalk grassland fields located in three different chalk hill ridges of Southern England, using a spatially explicit sampling scheme. We assessed microbial communities via phospholipid fatty acid (PLFA) analyses and PCR-denaturing gradient gel electrophoresis (DGGE) and measured soil characteristics, as well as nematode and plant community composition. The relative influences of space, soil, vegetation and nematodes on soil microorganisms were contrasted using variation partitioning and path analysis. Results indicate that soil characteristics and plant community composition, representing habitat and resources, shape soil microbial community composition, whereas the influence of nematodes, a potential predation factor, appears to be relatively small. Spatial variation in microbial community structure was detected at broad (between fields) and fine (within fields) scales, suggesting that microbial communities exhibit biogeographic patterns at different scales. Although our analysis included several relevant explanatory data sets, a large part of the variation in microbial communities remained unexplained (up to 92% in some analyses). However, in several analyses, significant parts of the variation in microbial community structure could be explained. The results of this study contribute to our understanding of the relative importance of different environmental and spatial factors in driving the composition of soil-borne microbial communities.

New strings for old : the role of similarity processing in an incidental learning task

This paper reports three experiments that examine the role of similarity processing in McGeorge and Burton's (1990) incidental learning task. In the experiments subjects performed a distractor task involving four-digit number strings, all of which conformed to a simple hidden rule. They were then given a forced-choice memory test in which they were presented with pairs of strings and were led to believe that one string of each pair had appeared in the prior learning phase. Although this was not the case, one string of each pair did conform to the hidden rule. Experiment 1 showed that, as in the McGeorge and Burton study, subjects were significantly more likely to select test strings that conformed to the hidden rule. However, additional analyses suggested that rather than having implicitly abstracted the rule, subjects may have been selecting strings that were in some way similar to those seen during the learning phase. Experiments 2 and 3 were designed to try to separate out effects due to similarity from those due to implicit rule abstraction. It was found that the results were more consistent with a similarity-based model than implicit rule abstraction per se.

Personal status laws in Morocco and Tunisia: A comparative exploration of the possibilities for equality-enhancing reform in Bangladesh

This paper focuses on successful reform strategies invoked in parts of the Muslim world to address issues of gender inequality in the context of Islamic personal law. It traces the development of personal status laws in Tunisia and Morocco, exploring the models they offer in initiating equality-enhancing reforms in Bangladesh, where a secular and equality-based reform approach conflicts with Islamic-based conservatism. Recent landmark family law reforms in Morocco show the possibility of achieving ‘women-friendly’ reforms within an Islamic legal framework. Moreover, the Tunisian Personal Status Code, with its successive reforms, shows that a gender equality-based model of personal law can be successfully integrated into the Muslim way of life. This study examines the response of Muslim societies to equality-based reforms and differences in approach in initiating them. The paper maps these sometimes competing approaches, locating them within contemporary feminist debates related to gender equality in the East and West.

Emergence of Chenopodium album and Stellaria media of different origins under different climatic conditions

The emergence behaviour of weed species in relation to cultural and meteorological events was studied. Dissimilarities between populations in dormancy and germination ecology, between-year maturation conditions and seed quality and burial site climate all contribute to potentially unpredictable variability. Therefore, a weed emergence data set was produced for weed seeds of Stellaria media and Chenopodium album matured and collected from three populations (Italy, Sweden and UK). The seeds were collected in two consecutive seasons (1999 and 2000) and subsequently buried in the autumn of the same year of maturation in eight contrasting climatic locations throughout Europe and the USA. The experiment sought to explore and explain differences between the three populations in their emergence behaviour. Evidence was demonstrated of synchrony in the timing of the emergence of different populations of a species at a given burial site. The relative magnitudes of emergence from the three populations at a given burial site in a given year were generally similar across all the burial sites in the study. The resulting data set was also used to construct a simple weed emergence model, which was tested for its application to the range of different burial environments and populations. The study demonstrated the possibility of using a simple thermal time-based model to describe part of the emergence behaviour across different burial sites, seed populations and seasons, and a simple winter chilling relationship to adjust for the magnitude of the flush of emergence at a given burial site. This study demonstrates the possibility of developing robust generic models for simple predictions of emergence timing across populations.

Senescence rates are determined by ranking on the fast-slow life-history continuum

Comparative analyses of survival senescence by using life tables have identified generalizations including the observation that mammals senesce faster than similar-sized birds. These generalizations have been challenged because of limitations of life-table approaches and the growing appreciation that senescence is more than an increasing probability of death. Without using life tables, we examine senescence rates in annual individual fitness using 20 individual-based data sets of terrestrial vertebrates with contrasting life histories and body size. We find that senescence is widespread in the wild and equally likely to occur in survival and reproduction. Additionally, mammals senesce faster than birds because they have a faster life history for a given body size. By allowing us to disentangle the effects of two major fitness components our methods allow an assessment of the robustness of the prevalent life-table approach. Focusing on one aspect of life history - survival or recruitment - can provide reliable information on overall senescence.