A community-based framework for aquatic ecosystem models

Here, we communicate a point of departure in the development of aquatic ecosystem models, namely a new community-based framework, which supports an enhanced and transparent union between the collective expertise that exists in the communities of traditional ecologists and model developers. Through a literature survey, we document the growing importance of numerical aquatic ecosystem models while also noting the difficulties, up until now, of the aquatic scientific community to make significant advances in these models during the past two decades. Through a common forum for aquatic ecosystem modellers we aim to (i) advance collaboration within the aquatic ecosystem modelling community, (ii) enable increased use of models for research, policy and ecosystem-based management, (iii) facilitate a collective framework using common (standardised) code to ensure that model development is incremental, (iv) increase the transparency of model structure, assumptions and techniques, (v) achieve a greater understanding of aquatic ecosystem functioning, (vi) increase the reliability of predictions by aquatic ecosystem models, (vii) stimulate model inter-comparisons including differing model approaches, and (viii) avoid ??re-inventing the wheel??, thus accelerating improvements to aquatic ecosystem models. We intend to achieve this as a community that fosters interactions amongst ecologists and model developers. Further, we outline scientific topics recently articulated by the scientific community, which lend themselves well to being addressed by integrative modelling approaches and serve to motivate the progress and implementation of an open source model framework.     

A general eco-evolutionary framework for understanding bioinvasions

Studies of bioinvasions have revealed various strategies of invasion, depending on the ecosystem invaded and the alien species concerned. Here, we consider how migration (as a demographic factor), as well as ecological and evolutionary changes, affect invasion success. We propose three main theoretical scenarios that depend on how these factors generate the match between an invader and its new environment. Our framework highlights the features that are common to, or differ among, observed invasion cases, and clarifies some general trends that have been previously highlighted in bioinvasions. We also suggest some new directions of research, such as the assessment of the time sequence of demographic, genetic and environmental changes, using detailed temporal surveys.     

A tiered framework for assessing groundwater ecosystem health

The notion of ecosystem health has been widely adopted in environmental policy, particularly in the management of river systems. Despite this, even a notional understanding of ecosystem health and its assessment in connected aquifer ecosystems remains elusive. In this article, we propose a definition and provide a tiered framework for the assessment of ecosystem health in groundwater. From the literature we identify general attributes of a healthy groundwater ecosystem and from these develop primary (Tier 1) indicators of health. Where Tier 1 benchmarks are exceeded or more detailed assessment is required, we discuss a range of indicators (Tier 2) that may together generate a multimetric index of groundwater health. Our case study using samples from an alluvial aquifer in north-western New South Wales, Australia, demonstrates the utility of both tiers of the framework, and the ability of the approach to separate disturbed and undisturbed sites. The process of multimetric development is simple and our Tier 2 benchmarks determined from limited data. Nevertheless, our framework will be applicable and readily adaptable to site-specific contexts.     

A proposed framework for developing indicators of ecosystem health

Considerations involved in developing a suite of indicators to monitor regional environmental health, similar in conception to management use of leading economic indicators, are described. Linkages between human activities and well being and the state of the environment are considered essential to the evaluation of general environmental health. Biogeochemical and socioeconomic indicators are mutually affected by environmental degradation and examples of both categories of indicators are described. Desirable properties in indicators of environmental health vary with their specific management use. Different indicators are called for when collecting data to assess the adequacy of the environment, monitor trends over time, provide early warning of environmental degradation, or diagnose the cause of an existing problem. Tradeoffs between desirable characteristics, costs, and quality of information are inevitable when choosing indicators for management use. Decisions about what information to collect for which purpose can be made more rationally when available indicators are characterized and matched to management goals.     

A conceptual framework for ecosystem management based on tradeoff analysis

Three dimensions (natural, social and economic factors) in tradeoff analysis have not been focused in ecology. It is necessary to consider the multi-dimensions through a tradeoff analysis of disturbances to find their positive and negative effects (referred to as two-sidedness). We proposed an 11-step approach to integrate the concepts, methods and examples to understand ecological two-sidedness. We recommend that: (1) ecological complexity and large-scale systematic perspectives need to be integrated; (2) disparate disciplines should be integrated to classify the two-sidedness indicators; (3) models should be adopted to define the characteristic metrics of disturbed ecosystems; (4) researchers need to reconsider evaluation standards and for each indicator with marginal changes; and (5) initial decision-making should refer to the two-sidedness value and that final decision-making should be subject to debate. This approach has great significance for ecosystem management because decision-makers can obtain the superiority and inferiority of disturbance strategies and select optimal strategy.     

A framework for assessing ecological quality based on ecosystem services

Existing environmental legislation and ecological quality definitions such as ecosystem integrity tend to rely on measures that, either implicitly or explicitly, utilize naturalness as a key criterion. There are marked practical difficulties with employing the concept of naturalness in human dominated landscapes, and the management of such ecosystems is inevitably going to need to take account of human needs and expectations. We propose that ecological quality could be assessed by its ecosystem service profile (ESP): the overlap between societal expectations for, and the sustainable provision of, suites of ecosystem services. The status for each individual ecosystem service is defined by the ratio of its sustained provision to the expected level of provision for the service. The ESP measure is a multi-criterion, context-specific assessment of the match between expectation for and sustainable supply of ecosystem services. It provides a flexible measure of quality which takes into account that the “ideal” ecosystem state is largely dependent on the specific management context. The implementation of ESPs challenges us to develop indicators for the sustained provision of individual ecosystem services, much better understanding of the trade-offs among services, and practical tools for gauging societal demands. All of which are challenging problems. The proposed framework can help to strategically address research needs and monitoring requirements and foster a more integrative approach to ecosystem assessment and management in the future. The need for this follows from the fact that the undisturbed reference state represents only one aspect of an ecosystem and that ecological quality in human dominated landscapes will, ultimately, be determined by the value society places on the sustainable provision of multiple ecosystem services.     

A structural framework for understanding the multifunctional character of lactoferrin

Lactoferrin (Lf) is widely distributed, in mammalian milks, other secretory fluids and white blood cells, and its biology is complex. The three-dimensional structure of this important protein was determined in 1987, giving the first atomic view of any member of the transferrin family. This review examines how structural knowledge has contributed to our understanding of Lf function, and what we have yet to understand. The internal structure of Lf is highly conserved, and is dedicated to binding iron, which is sequestered in two almost identical sites, one in each lobe of the molecule. The processes of iron binding and release, and the accompanying conformational changes, are well understood. Some functional properties of Lf derive from this property, both through iron scavenging, and because the structure and dynamics of Lf are altered by its iron status. On the other hand, the external structure (its molecular surface) is much more variable between different Lfs, making it more difficult to identify functionally important sites. One key feature is clear - the cationic N-terminus and associated lactoferricin domain on the N-lobe of Lf. Recent work shows that this region, in addition to its role in antibacterial activity and probable role in DNA binding, is also involved in complex formation with other proteins. Other parts of the surface are more variable and may result in functional differences between the Lfs of different species. Finally, it may be time to re-examine the importance of glycosylation, given the growing evidence that many pathogens depend on binding to glycans for pathogenesis.     

A conceptual framework for understanding arthropod predator and parasitoid invasions

Arthropods make up the largest group of invasive alien species (IAS) worldwide. Although invasion research has been biased towards alien plants and vertebrates, it has suggested potential mechanisms for the success of IAS and provided a theoretical framework for further investigation. Here we address key concepts from invasion biology that are essential to our understanding of the success of invasive alien arthropod predators and parasitoids including human intervention, environmental characteristics, propagule pressure, biological traits, and biological interactions. To gain a greater understanding of the factors most likely to influence the different stages of invasion (arrival, establishment, and spread) for alien arthropod predators and parasitoids, we use a comparative approach to compare and contrast the differential success of invasions by alien phytophagous and carnivorous arthropods. Insights gained from this comparison suggest that future research will require a multitrophic approach in order to enhance our understanding of invasions at higher trophic levels.     

生态系统管理学的概念框架及其生态学基础

系统地要领了生态系统管理学产生的历史背景和发展进程,讨论了生态系统管理的一些基本概念,生态学基础,管理目标及管理体制与实施方式,详细地论述了生态系统的生态学完整性与边界和时空尺度,生态系统的结构,功能与生态系统整体性,生态系统演替与系统动力学特性,生态系统的干扰与系统稳定性,生态系统的复杂性与不确定性,生态系统多样性与可持续生态系统,生态模型与数据收集和监测,人类活动对环境影响的双重性等生态学基础问题,阐述了在维持生态系统产品和服务功能的可持续性总体目标下,各类生态系统管理的具体目标。     

Ecospace: A unified framework for understanding variation in terrestrial biodiversity

Understanding patterns in biodiversity is a core ambition in ecological research. Existing ecological theories focusing on individual species, populations, communities, or niches aid in understanding the determinants of biodiversity patterns, yet very few general models for biodiversity have emerged from simplistic approaches. We propose that a systematic, low-dimensional representation of environmental space with building blocks adopted from gradient, niche, metapopulation and assembly theory may unite old and new aspects of biodiversity theory and improve our understanding of variation in terrestrial biodiversity.We propose the term ecospace to cover the local conditions and resources underlying diversity. Our definition of ecospace encompasses abiotic position, biotic expansion and spatiotemporal continuity, which all affect the biodiversity of a biotope (α-diversity). Position refers to placement along abiotic gradients such as temperature, soil pH and fertility, leading to environmental filtering known from classical community theory. Expansion represents the build-up and diversification of organic matter that are not strictly given by position. Continuity refers to the spatiotemporal extension of position and expansion.Biodiversity is scale dependent. The contribution of one biotope to large scale diversity must be estimated by considering its unique contribution to the species richness of the surrounding landscape or region or to the biodiversity of the entire planet. In addition to the relationship between ecospace and biotope richness (α-diversity), we also propose a relation between the uniqueness of the biotope ecospace and the unique contribution of species to the surrounding larger-scale richness.Whereas the impacts of ecospace position and continuity on biodiversity have been studied in isolation, studies comparing or combining them are rare. Furthermore, biotic expansion has never been fully developed as a determinant of biodiversity, ignoring the megadiverse carbon-depending groups of insects and fungi. Precursors of the ecospace concept have been presented over the last 70 years, but they were never fully developed conceptually for terrestrial biodiversity or applied to prediction of biodiversity.Ecospace unites classical and – at times – contradicting theories such as niche theory, island biogeography theory and a suite of community assembly theories into one framework for further development of a general theory of terrestrial biodiversity.     

A cognitive neuroscience framework for understanding causal reasoning and the law

Over the past couple of decades, there have been great developments in the fields of psychology and cognitive neuroscience that have allowed the advancement of our understanding of how people make judgements about causality in several domains. We provide a review of some of the contemporary psychological models of causal thinking that are directly relevant to legal reasoning. In addition, we cover some exciting new research using advanced neuroimaging techniques that have helped to uncover the underlying neural signatures of complex causal reasoning. Through the use of functional imaging, we provide a first-hand look at how the brain responds to evidence that is either consistent or inconsistent with one's beliefs and expectations. Based on the data covered in this review, we propose some ideas for how the effectiveness of causal reasoning, especially as it pertains to legal decision-making, may be facilitated.     

A conceptual framework for ecosystem stoichiometry: balancing resource supply and demand

The development of ecological stoichiometry has centered on organisms and their interactions, with less emphasis on the meaning or value of a comprehensive ecosystem stoichiometry at larger scales. Here we develop a conceptual framework that relates internal processes and exogenous factors in spatially- and temporally-linked ecosystems. This framework emerges from a functional view of ecosystem stoichiometry rooted in understanding the causes and consequences of relative stoichiometric balance, defined as the balance between ratios of resource supply and demand. We begin by modifying a graphical model based on resource ratio competition theory that relates resource supply and demand to ecosystem processes. This approach identified mechanisms, or stoichiometric schemes, through which ecosystems respond to variable resource supply. We expand this view by considering the effects of exogenous factors other then resource supply that comprise a stoichiometric template that influences stoichiometric balance within ecosystems. We then describe a number of examples of patterns in organismal stoichiometry in several types of ecosystems that illustrate stoichiometric schemes and factors that impinge directly on stoichiometric patterns. Next, we conduct an initial analysis of the stoichiometric effects of spatial linkages between ecosystems, and how those relate to boundary dynamics and hot spot development. We conclude by outlining research directions that will significantly advance our understanding of stoichiometric constraints on ecosystem structure and function.     

A framework for community and ecosystem genetics: from genes to ecosystems

Can heritable traits in a single species affect an entire ecosystem? Recent studies show that such traits in a common tree have predictable effects on community structure and ecosystem processes. Because these 'community and ecosystem phenotypes' have a genetic basis and are heritable, we can begin to apply the principles of population and quantitative genetics to place the study of complex communities and ecosystems within an evolutionary framework. This framework could allow us to understand, for the first time, the genetic basis of ecosystem processes, and the effect of such phenomena as climate change and introduced transgenic organisms on entire communities.     

A cell based modelling framework for skeletal tissue engineering applications

In this study, a cell based lattice free modelling framework is proposed to study cell aggregate behaviour in bone tissue engineering applications. The model encompasses cell-to-cell and cell–environment interactions such as adhesion, repulsion and drag forces. Oxygen, nutrients, waste products, growth factors and inhibitors are explicitly represented in the model influencing cellular behaviour. Furthermore, a model for cell metabolism is incorporated representing the basic enzymic reactions of glycolysis and the Krebs cycle. Various types of cell death such as necrosis, apoptosis and anoikis are implemented. Finally, an explicit model of the cell cycle controls the proliferation process, taking into account the presence or absence of various metabolites, sufficient space and mechanical stress. Several examples are presented demonstrating the potential of the modelling framework. The behaviour of a synchronised cell aggregate under ideal circumstances is simulated, clearly showing the different stages of the cell cycle and the resulting growth of the aggregate. Also the difference in aggregate development under ideal (normoxic) and hypoxic conditions is simulated, showing hypoxia induced necrosis mainly in the centre of the aggregate grown under hypoxic conditions. The next step in this research will be the application of this modelling framework to specific experimental set-ups for bone tissue engineering applications.     

Post-mortem ecosystem engineering by oysters creates habitat for a rare marsh plant

Oysters are ecosystem engineers in marine ecosystems, but the functions of oyster shell deposits in intertidal salt marshes are not well understood. The annual plant Suaeda linearis is associated with oyster shell deposits in Georgia salt marshes. We hypothesized that oyster shell deposits promoted the distribution of Suaeda linearis by engineering soil conditions unfavorable to dominant salt marsh plants of the region (the shrub Borrichia frutescens, the rush Juncus roemerianus, and the grass Spartina alterniflora). We tested this hypothesis using common garden pot experiments and field transplant experiments. Suaeda linearis thrived in Borrichia frutescens stands in the absence of neighbors, but was suppressed by Borrichia frutescens in the with-neighbor treatment, suggesting that Suaeda linearis was excluded from Borrichia frutescens stands by interspecific competition. Suaeda linearis plants all died in Juncus roemerianus and Spartina alterniflora stands, regardless of neighbor treatments, indicating that Suaeda linearis is excluded from these habitats by physical stress (likely water-logging). In contrast, Borrichia frutescens, Juncus roemerianus, and Spartina alterniflora all performed poorly in Suaeda linearis stands regardless of neighbor treatments, probably due to physical stresses such as low soil water content and low organic matter content. Thus, oyster shell deposits play an important ecosystem engineering role in influencing salt marsh plant communities by providing a unique niche for Suaeda linearis, which otherwise would be rare or absent in salt marshes in the southeastern US. Since the success of Suaeda linearis is linked to the success of oysters, efforts to protect and restore oyster reefs may also benefit salt marsh plant communities.     

A general multi-trait-based framework for studying the effects of biodiversity on ecosystem functioning

Environmental change is as multifaceted as are the species and communities that respond to these changes. Current theoretical approaches to modeling ecosystem response to environmental change often deal only with single environmental drivers or single species traits, simple ecological interactions, and/or steady states, leading to concern about how accurately these approaches will capture future responses to environmental change in real biological systems. To begin addressing this issue, we generalize a previous trait-based framework to incorporate aspects of frequency dependence, functional complementarity, and the dynamics of systems composed of species that are defined by multiple traits that are tied to multiple environmental drivers. The framework is particularly well suited for analyzing the role of temporal environmental fluctuations in maintaining trait variability and the resultant effects on community response to environmental change. Using this framework, we construct simple models to investigate two ecological problems. First, we show how complementary resource use can significantly enhance the nutrient uptake of plant communities through two different mechanisms related to increased productivity (over-yielding) and larger trait variability. Over-yielding is a hallmark of complementarity and increases the total biomass of the community and, thus, the total rate at which nutrients are consumed. Trait variability also increases due to the lower levels of competition associated with complementarity, thus speeding up the rate at which more efficient species emerge as conditions change. Second, we study systems in which multiple environmental drivers act on species defined by multiple, correlated traits. We show that correlations in these systems can increase trait variability within the community and again lead to faster responses to environmental change. The methodological advances provided here will apply to almost any function that relates species traits and environmental drivers to growth, and should prove useful for studying the effects of climate change on the dynamics of biota.