Individual-based ecology

Recent decades have seen great advances in ecological modelling and computing power, enabling ecologists to build increasingly detailed models to more accurately represent ecological systems. To better inform environmental decision-making, it is important that the predictions of these models are expressed in simple ways that are straightforward for stakeholders to comprehend and use. One way to achieve this is to predict threshold values for environmental perturbations (e.g. climate change, habitat modification, food loss, sea level rise) associated with negative impacts on individuals, populations, communities or ecosystems. These thresholds can be used by stakeholders to inform management and policy. In this paper we demonstrate how this approach can use individual-based models of birds, their prey and habitats, to provide the evidence-base for coastal bird conservation and shellfishery management. In particular, we show how such models can be used to identify threshold values for perturbations of food abundance that can impact negatively on bird populations. We highlight how environmental thresholds could be used more widely to inform management of species and habitats under environmental change.

An ever-growing number of IBMs have been developed by modellers, who aim to aid practitioners and inform a range of issues related to conservation, natural resource management, wildlife management and human socio-economic activities. The range of practitioners using IBMs to inform their decision-making processes include statutary authorities with responsibilities in environmental and natural resource management, non-governmental organizations such as conservation charities, and those interested in the sustainable use of natural resources. Thanks to advances in computational power, data availability and ecological theory, increasingly complicated, sophisticated IBMs can be produced. Yet this does not mean that these models will be more useful in informing environmental decision-making. IBMs typically require specialist computational knowledge to build and refine the model, and analyse the model outputs, and so practitioners are unlikely to have the requisite skills to use IBMs directly. Conversely, practitioners may have greater knowledge of the system being modelled, so their input into the modelling process is highly desirable. Thus, it is important that modellers and practitioners collaborate effectively to develop models which can address the key questions that practitioners are interested in. In this paper we highlight the uses of IBMs in environmental decision-making, identify potential obstacles to their successful use, and discuss how such obstacles can be overcome. We aim to help practitioners understand the potential benefits of IBMs, and to help modellers to understand how to develop IBMs which will better aid practitioners and inform environmental management and policy. We refer to a coastal bird IBM case study, from which general lessons can be learned.

Changes in climate, food abundance and disturbance from humans threaten the ability of species to successfully use stopover sites and migrate between non-breeding and breeding areas. To devise successful conservation strategies for migratory species we need to be able to predict how such changes will affect both individuals and populations. Such predictions should ideally be process-based, focusing on the mechanisms through which changes alter individual physiological state and behavior. In this study we use a process-based model to evaluate how Black Brant (Branta bernicla nigricans) foraging on common eelgrass (Zostera marina) at a stopover site (Humboldt Bay, USA), may be affected by changes in sea level, food abundance and disturbance. The model is individual-based, with empirically based parameters, and incorporates the immigration of birds into the site, tidal changes in availability of eelgrass, seasonal and depth-related changes in eelgrass biomass, foraging behavior and energetics of the birds, and their mass-dependent decisions to emigrate. The model is validated by comparing predictions to observations across a range of system properties including the time birds spent foraging, probability of birds emigrating, mean stopover duration, peak bird numbers, rates of mass gain and distribution of birds within the site: all 11 predictions were within 35% of the observed value, and 8 within 20%. The model predicted that the eelgrass within the site could potentially support up to five times as many birds as currently use the site. Future predictions indicated that the rate of mass gain and mean stopover duration were relatively insensitive to sea level rise over the next 100 years, primarily because eelgrass habitat could redistribute shoreward into intertidal mudflats within the site to compensate for higher sea levels. In contrast, the rate of mass gain and mean stopover duration were sensitive to changes in total eelgrass biomass and the percentage of time for which birds were disturbed. We discuss the consequences of these predictions for Black Brant conservation. A wide range of migratory species responses are expected in response to environmental change. Process-based models are potential tools to predict such responses and understand the mechanisms which underpin them.

Effective wildlife management is needed for conservation, economic and human well-being objectives. However, traditional
population control methods are frequently ineffective, unpopular with stakeholders, may affect non-target species, and can
be both expensive and impractical to implement. New methods which address these issues and offer effective wildlife
management are required. We used an individual-based model to predict the efficacy of a sacrificial feeding area in
preventing grazing damage by mute swans (Cygnus olor) to adjacent river vegetation of high conservation and economic
value. The accuracy of model predictions was assessed by a comparison with observed field data, whilst prediction
robustness was evaluated using a sensitivity analysis. We used repeated simulations to evaluate how the efficacy of the
sacrificial feeding area was regulated by (i) food quantity, (ii) food quality, and (iii) the functional response of the forager.
Our model gave accurate predictions of aquatic plant biomass, carrying capacity, swan mortality, swan foraging effort, and
river use. Our model predicted that increased sacrificial feeding area food quantity and quality would prevent the depletion
of aquatic plant biomass by swans. When the functional response for vegetation in the sacrificial feeding area was
increased, the food quantity and quality in the sacrificial feeding area required to protect adjacent aquatic plants were
reduced. Our study demonstrates how the insights of behavioural ecology can be used to inform wildlife management. The
principles that underpin our model predictions are likely to be valid across a range of different resource-consumer
interactions, emphasising the generality of our approach to the evaluation of strategies for resolving wildlife management
problems.

The purpose of this project was to assess the mussel (Mytilus edulis) food requirements of oystercatcher (Haematopus ostralegus) in the Exe Estuary, which has been designated a Special Protection Area for overwintering waterbirds, including oystercatcher. The overwintering oystercatcher population of the Exe Estuary has been well-studied, and the birds are known to feed predominantly upon mussels in intertidal areas. There have been recent declines in the population size of oystercatcher in the Exe Estuary, mirroring wider declines throughout Europe, the reasons for which are unknown.

The study comprised:
• The collection of new data on the area of mussel beds, the density and size distribution of mussels on these beds, and the numbers and behaviour of oystercatcher on these beds;
• The collation of existing data on the food supply of oystercatchers in the Exe Estuary;
• The development of models to predict the food requirements of oystercatcher;
• Running simulations of the models to predict whether there is / could be any effect on oystercatcher survival of the current / potential future ways of managing the mussel fishery on the Exe Estuary.

The current mussel fishery on the Exe provides a feeding resource for oystercatcher on intertidal lays that are exposed on spring tides. Two potential management options that could be effective at improving the feeding conditions of oystercatcher would be to increase the number and area of intertidal mussel lays, and / or to place mussel discards at a relatively high shore level close to the oystercatcher roost.

This project documented a number of changes that have occurred to the Exe Estuary mussel and oystercatcher populations including:
• The number and size of mussel beds have decreased since traditional methods of maintaining mussel beds in the estuary have ceased.
• The density of mussels within the size range consumed by the birds has generally decreased, but the density of the larger mussels within this size range, which are more profitable to oystercatcher, has generally increased.
• Oystercatcher lose a higher proportion of mussels to attacks by carrion crows and herring gulls than they have in the past.
• The number of oystercatcher wintering in the estuary has declined, but the number of birds feeding on the mussel beds has been relatively stable.

The models developed in the project predict that the present day mussel population is sufficient to support the number of oystercatcher that were observed to feed on mussels.

The presence of mussel lays provides extra food for oystercatcher when these lays are exposed on spring tides. The present area, or increases in the area of mussel lays could increase the survival rate of oystercatcher if the number of birds feeding on mussels was over 2000. Below this threshold, starvation was predicted to affect 0 % of the population and so additional food resources cannot further reduce the starvation. The effect over 2000 birds is relatively small because the lays are only exposed for a short time, and so oystercatcher will obtain the majority of their food from mussel beds that are higher on the shore, and hence exposed for longer. Simulations were not run in which lays were positioned higher on the shore because this would not be commercially viable from a fishery perspective; the growth rate of mussels declines as they are positioned further up the shore because they are inundated with water for less time and so have less time to feed.

Factors that would affect the beneficial effect of discards include the size of the discards, the size of the discard bed and the date from which discards are replenished. Our simulations predicted that larger discards spread at lower density over a larger bed increased oystercatcher survival by the greatest amount. This happened because interference competition excluded some birds from smaller patches, and oystercatcher can maintain high intake rate down to low mussel densities. It is unlikely that the size of discards could be increased, but the simulations suggest that the greatest benefit to oystercatchers could be achieved by spreading discards over a larger area. Our simulations predicted that making discards available from January increased oystercatcher survival by the same amount as making them available from September. This was because the feeding conditions of birds deteriorate through winter as, for example, the ash-free dry mass of prey declines, interference competition intensifies and day length shortens. The intake rate of birds feeding on discards was not measured during the study, but we recommend that this is done to between understand the potential benefit of discards. We recommend that the best place for the discard bed would be along the top of the shore on an area of gravel (and hence of relatively low food value to the birds), to the south of Cockwood. This is south of an area where discards have been laid and exploited by oystercatcher in the past, but would experience lower levels of disturbance from human activity.

Long-term studies are those studies with a longer duration than usual in its topic. They have been essential in ecology to understand the ecological processes that happen in long temporal scales, to determine how general is a pattern emerging from a punctual finding, and to connect cause and effect in biological processes happening with some time lag. Most of ecologists agree about the scientific relevance of long-term studies, but they seldom carry out them (0.3% of published studies). The main handicap is to keep continuous funding during a long time because funding and evaluation system of science is based on short periods. However, there are opportunities to develop long-term studies with available data yet, such as monitoring programs of protected areas or threatened species, museum collections, hunting bags, fisheries or citizen sciences projects; although we will need to keep in mind that those data were not gathered with a long-term aim and this fact may constrain soundness of our conclusions. In spite of the fact that behavioral ecology is a young discipline in Spain, there are already some notable examples of long-term studies. For instance, it has been demonstrated that birds and insects are changing their life cycles in response to climate change and these changes can be leading to phenological mismatchings with the trophic levels in which they rely on. Marking and monitoring of the same individuals along years in the host-parasite system of magpies and cuckoos demonstrated that magpies learn to protect themselves against parasites, while have an inflexible reproductive phenology unable to adapt to environmental variation. Individual-based monitoring of black kites showed the effect of senescence and learning in migratory behavior, breeding territory acquisition, and fitness changes along the life of these birds. Similar results were found for other long-lived birds such as white storks, gulls or storm petrels. Individual marking has allowed building complete pedigrees in bird populations using nest boxes for breeding. Such pedigrees have been essential to understand heritability of several coloration traits of plumage directly linked to the phenotypic individual quality.

Keywords: animal models; individual-based monitoring; microevolution; phenotypic plasticity; replication; temporal trends.

We present a model describing the fluxes of matter and energy through a detritus-based aquatic community. The model is based on the investigation of the decomposition of Phragmites australis in a Southern Italian coastal lagoon (Lake Alimini Grande). It reproduces the behaviour of the detritus-based system by simulating processes of microbial growth and macroinvertebrate colonization in a specific patch of detritus. Specifically, the macroinvertebrate colonization is seen as a dynamic process in which individuals move towards the patch according to resource availability. The good agreement between simulated and experimental data suggests that the behaviourally-based mechanism of invertebrate col-onization characterising our model provides an effective description of the decomposition patterns observed in nature.

The intertidal areas of UK coasts are important habitats for shellfish species, such as cockles Cerastoderma edule and mussels Mytilus edulis. Commercial harvesting of shellfish is worth an annual £250 million to the UK economy, providing both food and employment (DEFRA, 2013). These shellfish are also the principal food resource for overwintering shorebirds such as oystercatchers Haematopus ostralegus and knots Calidris canutus. Shorebirds are key components of UK coastal biodiversity and are protected under the European Union Wild Birds Directive (2009/147/EEC), which legally obligates the UK government to maintain healthy shorebird populations.