生物分子网络弹性研究进展

弹性是生物分子网络重要且基础的属性之一,一方面弹性赋予生物分子网络抵抗内部噪声与环境干扰并维持其自身基本功能的能力,另一方面,弹性为网络状态的恢复制造了阻力。生物分子网络弹性研究试图回答如下3个问题：a. 生物分子网络弹性的产生机理是什么？b. 弹性影响下生物分子网络的状态如何发生转移？c. 如何预测生物网络状态转换临界点,以防止系统向不理想的状态演化？因此,研究生物分子网络弹性有助于理解生物系统内部运作机理,同时对诸如疾病发生临界点预测、生物系统状态逆转等临床应用具有重要的指导意义。鉴于此,本文主要针对以上生物分子网络弹性领域的3个热点研究问题,在研究方法和生物学应用上进行了系统地综述,并对未来生物分子网络弹性的研究方向进行了展望。     

A Systems Model Approach to Determining Resilience Surrogates for Case Studies

Resilience theory offers a framework for understanding the dynamics of complex systems. However, operationalizing resilience theory to develop and test empirical hypotheses can be difficult. We present a method in which simple systems models are used as a framework to identify resilience surrogates for case studies. The process of constructing a systems model for a particular case offers a path for identifying important variables related to system resilience, including the slowly-changing variables and thresholds that often are keys to understanding the resilience of a system. We develop a four-step process for identifying resilience surrogates through development of systems models. Because systems model development is often a difficult step, we summarize four basic existing systems models and give examples of how each may be used to identify resilience surrogates. The construction and analysis of simple systems models provides a useful basis for guiding and directing the selection of surrogate variables that will offer appropriate empirical measures of resilience.     

Embracing a world of subtlety and nuance on coral reefs

Climate change will homogenise the environment and generate a preponderance of mediocre reefs. Managing seascapes of mediocrity will be challenging because our science is ill prepared to deal with the ‘shades of grey’ of reef health; we tend to study natural processes in the healthiest reefs available. Yet much can be gained by examining the drivers and implications of even subtle changes in reef state. Where strong ecological interactions are discovered, even small changes in abundance can have profound impacts on coral resilience. Indeed, if we are to develop effective early warnings of critical losses of resilience, then monitoring must place greater emphasis on measuring and interpreting changes in reef recovery rates. In terms of mechanism, a more nuanced approach is needed to explore the generality of what might be considered ‘dogma’. A more nuanced approach to science will serve managers needs well and help minimise the rise of mediocrity in coral reef ecosystems.

     

Beyond the fragmentation threshold hypothesis: regime shifts in biodiversity across fragmented landscapes

Ecological systems are vulnerable to irreversible change when key system properties are pushed over thresholds, resulting in the loss of resilience and the precipitation of a regime shift. Perhaps the most important of such properties in human-modified landscapes is the total amount of remnant native vegetation. In a seminal study Andrén proposed the existence of a fragmentation threshold in the total amount of remnant vegetation, below which landscape-scale connectivity is eroded and local species richness and abundance become dependent on patch size. Despite the fact that species patch-area effects have been a mainstay of conservation science there has yet to be a robust empirical evaluation of this hypothesis. Here we present and test a new conceptual model describing the mechanisms and consequences of biodiversity change in fragmented landscapes, identifying the fragmentation threshold as a first step in a positive feedback mechanism that has the capacity to impair ecological resilience, and drive a regime shift in biodiversity. The model considers that local extinction risk is defined by patch size, and immigration rates by landscape vegetation cover, and that the recovery from local species losses depends upon the landscape species pool. Using a unique dataset on the distribution of non-volant small mammals across replicate landscapes in the Atlantic forest of Brazil, we found strong evidence for our model predictions--that patch-area effects are evident only at intermediate levels of total forest cover, where landscape diversity is still high and opportunities for enhancing biodiversity through local management are greatest. Furthermore, high levels of forest loss can push native biota through an extinction filter, and result in the abrupt, landscape-wide loss of forest-specialist taxa, ecological resilience and management effectiveness. The proposed model links hitherto distinct theoretical approaches within a single framework, providing a powerful tool for analysing the potential effectiveness of management interventions.     

The exposure,sensitivity and vulnerability of natural vegetation in China to climate thermal variability (1901–2013): An indicator-based approach

Vulnerability assessments can be helpful in assessing the impact of climate change on natural ecosystems and are expected to support adaptation and/or mitigation strategies in the 21st century. A challenge when conducting such assessments is the integration of the multi-level properties and processes of ecosystems into an assessment framework. Focusing on the primary stresses of climate thermal variability (at both upper and lower extremes), this study proposes a quantitative indicator system—following the IPCC framework of vulnerability assessment—that assesses the impact of historical climate change, during 1901–2013, on the natural terrestrial vegetation types in China. The final output of the vulnerability assessment was expressed as a composite index, composed of ecosystem exposure, sensitivity and resilience to climate thermal change, and including biological, ecological and spatial traits of vegetation types in the assessment. The exposure to temperature variability was generally higher in January than in July, and higher in non-arborous vegetation types than forests. In contrast, sensitivity was higher for forests, wetlands and alpine tundra regions, especially for small areas and areas with scattered patterns. Original forests—especially those distributed in the north—had lower resilience than other vegetation types. The vulnerability of natural vegetation types in China to the temperature variability of the past century was very low to moderate, with a few exceptions, including tropical mangroves and the semi-arid to arid vegetation types in northwestern China, which had high vulnerability. Vulnerability was stronger in winter than in summer. Our results are generally in accord with the scenario-based projections on the geographical pattern of vegetation vulnerability to climate change, and revealed the difference caused by not considering moisture. The risks for these fragmented and narrow-range ecosystems are highlighted, and the importance of natural resilience is stressed for the assessment of vegetation vulnerability to climate change. Given the inadequate coverage of the natural reserve network in China (after the large investment in recent decades) found in the high-vulnerability vegetation types (with a few exceptions), the assessment of natural resilience of ecosystems could be critical for the optimal design of socio-economic strategies in response to the impacts of future climate change.     

Global patterns of resilience decline in vertebrate populations

Maintaining the resilience of natural populations, their ability to resist and recover from disturbance, is crucial to prevent biodiversity loss. However, the lack of appropriate data and quantitative tools has hampered our understanding of the factors determining resilience on a global scale. Here, we quantified the temporal trends of two key components of resilience—resistance and recovery—in >2000 population time-series of >1000 vertebrate species globally. We show that the number of threats to which a population is exposed is the main driver of resilience decline in vertebrate populations. Such declines are driven by a non-uniform loss of different components of resilience (i.e. resistance and recovery). Increased anthropogenic threats accelerating resilience loss through a decline in the recovery ability—but not resistance—of vertebrate populations. These findings suggest we may be underestimating the impacts of global change, highlighting the need to account for the multiple components of resilience in global biodiversity assessments.     

Building resilience into practical conservation: identifying local management responses to global climate change in the southern Great Barrier Reef

Climate change is now considered the greatest long-term threat to coral reefs, with some future change inevitable despite mitigation efforts. Managers must therefore focus on supporting the natural resilience of reefs, requiring that resilient reefs and reef regions be identified. We develop a framework for assessing resilience and trial it by applying the framework to target management responses to climate change on the southern Great Barrier Reef. The framework generates a resilience score for a site based on the evaluation of 19 differentially weighted indicators known or thought to confer resilience to coral reefs. Scores are summed, and sites within a region are ranked in terms of (1) their resilience relative to the other sites being assessed, and (2) the extent to which managers can influence their resilience. The framework was applied to 31 sites in Keppel Bay of the southern Great Barrier Reef, which has a long history of disturbance and recovery. Resilience and ‘management influence potential’ were both found to vary widely in Keppel Bay, informing site selection for the staged implementation of resilience-based management strategies. The assessment framework represents a step towards making the concept of resilience operational to reef managers and conservationists. Also, it is customisable, easy to teach and implement and effective in building support among local communities and stakeholders for management responses to climate change.     

An Extended N-Player Network Game and Simulation of Four Investment Strategies on a Complex Innovation Network

As computer science and complex network theory develop, non-cooperative games and their formation and application on complex networks have been important research topics. In the inter-firm innovation network, it is a typical game behavior for firms to invest in their alliance partners. Accounting for the possibility that firms can be resource constrained, this paper analyzes a coordination game using the Nash bargaining solution as allocation rules between firms in an inter-firm innovation network. We build an extended inter-firm n-player game based on nonidealized conditions, describe four investment strategies and simulate the strategies on an inter-firm innovation network in order to compare their performance. By analyzing the results of our experiments, we find that our proposed greedy strategy is the best-performing in most situations. We hope this study provides a theoretical insight into how firms make investment decisions.     

Improving Environmental Sanitation, Health, and Well-Being: A Conceptual Framework for Integral Interventions

We introduce a conceptual framework for improving health and environmental sanitation in urban and peri-urban areas using an approach combining health, ecological, and socioeconomic and cultural assessments. The framework takes into account the three main components: i) health status, ii) physical environment, and iii) socioeconomic and cultural environment. Information on each of these three components can be obtained by using standard disciplinary methods and an innovative combination of these methods. In this way, analyses lead to extended characterization of health, ecological, and social risks while allowing the comprehensive identification of critical control points (CCPs) in relation to biomedical, epidemiological, ecological, and socioeconomic and cultural factors. The proposed concept complements the conventional CCP approach by including an actor perspective that considers vulnerability to risk and patterns of resilience. Interventions deriving from the comprehensive analysis consider biomedical, engineering, and social science perspectives, or a combination of them. By this way, the proposed framework jointly addresses health and environmental sanitation improvements, and recovery and reuse of natural resources. Moreover, interventions encompass not only technical solutions but also behavioral, social, and institutional changes which are derived from the identified resilience patterns. The interventions are assessed with regards to their potential to eliminate or reduce specific risk factors and vulnerability, enhance health status, and assure equity. The framework is conceptualized and validated for the context of urban and peri-urban settings in developing countries focusing on waste, such as excreta, wastewater, and solid waste, their influence on food quality, and their related pathogens, nutrients, and chemical pollutants.     

Resilience and tipping points of an exploited fish population over six decades

Complex natural systems with eroded resilience, such as populations, ecosystems and socio‐ecological systems, respond to small perturbations with abrupt, discontinuous state shifts, or critical transitions. Theory of critical transitions suggests that such systems exhibit fold bifurcations featuring folded response curves, tipping points and alternate attractors. However, there is little empirical evidence of fold bifurcations occurring in actual complex natural systems impacted by multiple stressors. Moreover, resilience of complex systems to change currently lacks clear operational measures with generic application. Here, we provide empirical evidence for the occurrence of a fold bifurcation in an exploited fish population and introduce a generic measure of ecological resilience based on the observed fold bifurcation attributes. We analyse the multivariate development of Barents Sea cod (Gadus morhua), which is currently the world's largest cod stock, over six decades (1949–2009), and identify a population state shift in 1981. By plotting a multivariate population index against a multivariate stressor index, the shift mechanism was revealed suggesting that the observed population shift was a nonlinear response to the combined effects of overfishing and climate change. Annual resilience values were estimated based on the position of each year in relation to the fitted attractors and assumed tipping points of the fold bifurcation. By interpolating the annual resilience values, a folded stability landscape was fit, which was shaped as predicted by theory. The resilience assessment suggested that the population may be close to another tipping point. This study illustrates how a multivariate analysis, supported by theory of critical transitions and accompanied by a quantitative resilience assessment, can clarify shift mechanisms in data‐rich complex natural systems.     

Exploring resilience with agent-based models: State of the art,knowledge gaps and recommendations for coping with multidimensionality

Anthropogenic pressures increasingly alter natural systems. Therefore, understanding the resilience of agent-based complex systems such as ecosystems, i.e. their ability to absorb these pressures and sustain their functioning and services, is a major challenge. However, the mechanisms underlying resilience are still poorly understood. A main reason for this is the multidimensionality of both resilience, embracing the three fundamental stability properties recovery, resistance and persistence, and of the specific situations for which stability properties can be assessed. Agent-based models (ABM) complement empirical research which is, for logistic reasons, limited in coping with these multiple dimensions. Besides their ability to integrate multidimensionality through extensive manipulation in a fully controlled system, ABMs can capture the emergence of system resilience from individual interactions and feedbacks across different levels of organization. To assess the extent to which this potential of ABMs has already been exploited, we reviewed the state of the art in exploring resilience and its multidimensionality in ecological and socio-ecological systems with ABMs. We found that the potential of ABMs is not utilized in most models, as they typically focus on a single dimension of resilience by using variability as a proxy for persistence, and are limited to one reference state, disturbance type and scale. Moreover, only few studies explicitly test the ability of different mechanisms to support resilience. To overcome these limitations, we recommend to simultaneously assess multiple stability properties for different situations and under consideration of the mechanisms that are hypothesised to render a system resilient. This will help us to better exploit the potential of ABMs to understand and quantify resilience mechanisms, and hence support solving real-world problems related to the resilience of agent-based complex systems.     

危机干扰下旅游共生网络韧性变化及机制——以武陵山片区为例

旅游共生网络韧性是提升旅游业抗风险能力的关键。结合共生理论与韧性理论,建立"干扰-响应-状态"旅游共生网络韧性研究框架,引入共生力度指标优化生长性、层级性、匹配性、连通性和传输性等网络韧性指标的测度方法,基于此分析了危机干扰下武陵山片区旅游共生网络韧性变化及机制。结果表明:(1)旅游共生网络韧性表现出复杂的时空变化特征,节点的共生力度呈差异性增强变化,生长性呈波动增强变化,层级性和匹配性呈摆动变化,连通性和传输性呈非线性非同步增强变化;(2)旅游共生网络对干扰具有不同响应特征,表现为不同时期节点共生力度和节点失效对连通性和传输性的差异影响,以及网络抗干扰能力不同程度的恢复变化;(3)危机干扰下旅游共生网络韧性表现出波动变化特征,结构与要素间呈复杂交互作用机制。要素的协调作用和有序发展,是提升旅游共生网络韧性的重要途径。研究对促进区域旅游业韧性发展具有重要意义。     

Generalist Species Have a Central Role In a Highly Diverse Plant–Frugivore Network

Analysis of plant–frugivore interactions provides a quantitative framework for integrating community structure and ecosystem function in terms of how the roles and attributes of individual species contribute to network structure and resilience. In this study, we used centrality metrics to rank and detect the most important species in a mutualistic network of fruit‐eating birds and plants in a cloud forest in the Colombian Andes. We identified a central core of ten bird and seven plant species in a network of 135 species that perform dual roles as local hubs and connectors. The birds were mostly large forest frugivores, such as cracids, cotingas, and toucans, which consume fruits of all sizes. The plants were species of intermediate successional stages with small‐ to medium‐sized seeds that persist in mature forest or forest borders (e.g., Miconia, Cecropia, Ficus). We found the resilience of our network depends on super‐generalist species, because their elimination makes the network more prone to disassemble than random extinctions, potentially disrupting seed‐dispersal processes. At our study site, extirpation of large frugivores has already been documented, and if this continues, the network might collapse despite its high diversity. Our results suggest that generalist species play critical roles in ecosystem function and should be incorporated into conservation and monitoring programs.     

Building Resilience in Lagoon Social–Ecological Systems: A Local-level Perspective

Building resilience in integrated human and nature systems or social–ecological systems (SES) is key for sustainability. Therefore, developing ways of assessing resilience is of practical as well as theoretical significance. We approached the issue by focusing on the local level and using five lagoon systems from various parts of the world for illustration. We used a framework based on four categories of factors for building resilience: (1) learning to live with change and uncertainty; (2) nurturing diversity for reorganization and renewal; (3) combining different kinds of knowledge; and (4) creating opportunity for self-organization. Under each category, the cases generated a number of items for building resilience, and potential surrogates of resilience, that is, variables through which the persistence of SES emerging through change can be assessed. The following factors were robust across all five lagoon SES cases: learning from crisis, responding to change, nurturing ecological memory, monitoring the environment, and building capacity for self-organization and conflict management.     

Extending the viability theory framework of resilience to uncertain dynamics,and application to lake eutrophication

Resilience, the capacity for a system to recover from a perturbation so as to keep its properties and functions, is of growing concern to a wide range of environmental systems. The challenge is often to render this concept operational without betraying it, nor diluting its content. The focus here is on building on the viability theory framework of resilience to extend it to discrete-time stochastic dynamical systems. The viability framework describes properties of the system as a subset of its state space. This property is resilient to a perturbation if it can be recovered and kept by the system after a perturbation: its trajectory can come back and stay in the subset. This is shown to reflect a general definition of resilience. With stochastic dynamics, the stochastic viability kernel describes the robust states, in which the system has a high probability of staying in the subset for a long time. Then, probability of resilience is defined as the maximal probability that the system reaches a robust state within a time horizon. Management strategies that maximize the probability of resilience can be found through dynamic programming. It is then possible to compute a range of statistics on the time for restoring the property. The approach is illustrated on the example of lake eutrophication and shown to foster the use of different indicators that are adapted to distinct situations. Its relevance for the management of ecological systems is also discussed.     

Using a network framework to quantitatively select ecological indicators

Ecological indicators are often constructed as an integrated set to represent key information and characteristics of the ecosystem which are tightly linked to management objectives. As an effective tool, ecological indicators play an increasingly important role in ecosystem monitoring, assessment and management. Reasonable selection of an indicator is a prerequisite for effectively using it. A defined protocol with scientific rigor to select ecological indicators is imperative to solve the challenges in ecological indicator selection. This paper compares the Causal Network (CN) with the Ecological Hierarchy Network (EHN) as a framework to select ecological indicators. These frameworks are not exclusive but interdependent in constructing a network framework. Based on the network framework, a quantitative ecological indicator selection method is demonstrated through a theoretical example. In the selection process, the criteria and requirements considering the balance of science and utility are proposed and translated into quantitative constraints of a selection model. By resolving the model under a mathematical operation, the human arbitrary disturbance will be reduced and random selection minimized.     

Plant biomes demonstrate that landscape resilience today is the lowest it has been since end‐Pleistocene megafaunal extinctions

Resilient landscapes have helped maintain terrestrial biodiversity during periods of climatic and environmental change. Identifying the tempo and mode of landscape transitions and the drivers of landscape resilience is critical to maintaining natural systems and preserving biodiversity given today's rapid climate and land use changes. However, resilient landscapes are difficult to recognize on short time scales, as perturbations are challenging to quantify and ecosystem transitions are rare. Here we analyze two components of North American landscape resilience over 20,000 years: residence time and recovery time. To evaluate landscape dynamics, we use plant biomes, preserved in the fossil pollen record, to examine how long a biome type persists at a given site (residence time) and how long it takes for the biome at that site to reestablish following a transition (recovery time). Biomes have a median residence time of only 230–460 years. Only 64% of biomes recover their original biome type, but recovery time is 140–290 years. Temperatures changing faster than 0.5°C per 500 years result in much reduced residence times. Following a transition, biodiverse biomes reestablish more quickly. Landscape resilience varies through time. Notably, short residence times and long recovery times directly preceded the end‐Pleistocene megafauna extinction, resulting in regional destabilization, and combining with more proximal human impacts to deliver a one‐two punch to megafauna species. Our work indicates that landscapes today are once again exhibiting low resilience, foreboding potential extinctions to come. Conservation strategies focused on improving both landscape and ecosystem resilience by increasing local connectivity and targeting regions with high richness and diverse landforms can mitigate these extinction risks.     

pointRes 2.0: New functions to describe tree resilience

After being proposed by Lloret et al. in 2011, the resilience components resistance, recovery, resilience and relative resilience became highly popular for studying tree growth responses to disturbances and extreme weather events. As the ‘Lloret indices’, however, have conceptual limitations, various additional indices to characterize tree resilience have been discussed since then, namely: recovery period, total growth reduction, average recovery rate, and average growth reduction. In pointRes 2.0, a major update of the R-package pointRes, these new indices have now been implemented. Besides convenient functions for calculating and plotting resilience indices, two new functions for calculating pointer years using (i) the interval trend method, and (ii) a 'z-transformation of site chronology'-approach have been included as well. This technical note illustrates pointRes' new functionalities.     

Role of capitals and capabilities in ensuring economic resilience of land conservation efforts: A case study of the grain for green project in China’s Loess Hills

The article describes how economic resilience of farming households can be measured using a composite indicator of revealed adaptive actions, and investigates how capabilities of farm households to recombine human, financial, natural and physical capitals are linked to observed economic resilience to land set-aside interventions. The land set-aside intervention known as the Grain for Green Project (GGP), which has been altering livelihoods of farming households in China’s Loess Hills since 1999, is taken as a case study. Household surveys were conducted in three V-shaped valleys and three riparian areas in Yanhe Township in northwestern China in an effort to measure household resilience and explore its’ relationship to forms of capital. A composite index of adaptive strategies that can reorganize livelihood activities under land set-aside intervention into a new economic equilibrium is crafted using an objective weighting scheme based on principal component analysis. Subsequently, a multiple regression model was utilized to examine the relationship between the composite resilience index and various indicators related to human, social, financial, natural and physical capitals. The results reveal the latent structure and internal correlations of adaptive strategies, and present quantitative evidence about the relationship between livelihood capitals and household economic resilience. The analysis shows that household resilience deteriorates when the ratio of GGP land to cultivated farmland goes above a threshold level, and revealed that interventions targeting various forms of capitals can enhance the economic resilience for households to conservation efforts.     

Wildfires affect tree growth and resilience in Northeastern China natural Dahurian larch forests: A dendrochronological perspective

Wildfires are natural and ubiquitous disturbances in boreal forests. Assessing their impacts on tree growth and resilience are particularly important to recognize the adaptation strategies of fire-tolerant species and forest succession in fire conditions. To date, the growth resilience of fire-tolerant species in boreal forests remains largely unquantified, and the drivers of resilience are poorly understood. Here, we measured the tree-ring widths of 99 fire-scarred trees from three sites in natural Dahurian larch (Larix gmelinii) forests. Three moderate-severity fire events in years 1987, 1990, and 2000 occurring at three sites were detected from the records of local forestry bureau. Based on tree-ring width data, we calculated resilience components (i.e., resistance, recovery, resilience and relative resilience) to quantify the responses of growth resilience in the larch trees to fires and analyzed their drivers at three sites. Results indicated that fires significantly reduced the tree growth. With the increasing tree age, these reductions were more pronounced. As for resilience components, our study showed a limited resistance but high recovery of tree growth against fires, and resistance tended to increase northwards but recovery showed the opposite, suggesting a growth-survival tradeoff was exhibited in Dahurian larch trees. With an increasing tree age, regional resistance and resilience showed a decreasing trend, whereas recovery and relative resilience showed an increasing trend. Resilience components were mainly affected by the climatic factors in spring. An increase in moisture availability enhanced resistance, a reduction in diurnal temperature range enhanced recovery, and an increase in mean temperature enhanced resilience and relative resilience. This study reveals that Dahurian larch could be even less favorable when faced with moderate or severe fire events, but a high capacity of recovery enables this species to adapt to the fire-prone condition. Moreover, this work highlights that the resilience of tree growth should be considered to understand tree behaviors and survival strategies of boreal forests following fires across fire-prone regions under future climate warming.