A modular concept of phenotypic plasticity in plants

Based on empirical evidence from the literature we propose that, in nature, phenotypic plasticity in plants is usually expressed at a subindividual level. While reaction norms (i.e. the type and the degree of plant responses to environmental variation) are a property of genotypes, they are expressed at the level of modular subunits in most plants. We thus contend that phenotypic plasticity is not a whole-plant response, but a property of individual meristems, leaves, branches and roots, triggered by local environmental conditions. Communication and behavioural integration of interconnected modules can change the local responses in different ways: it may enhance or diminish local plastic effects, thereby increasing or decreasing the differences between integrated modules exposed to different conditions. Modular integration can also induce qualitatively different responses, which are not expressed if all modules experience the same conditions. We propose that the response of a plant to its environment is the sum of all modular responses to their local conditions plus all interaction effects that are due to integration. The local response rules to environmental variation, and the modular interaction rules may be seen as evolving traits targeted by natural selection. Following this notion, whole-plant reaction norms are an integrative by-product of modular plasticity, which has far-reaching methodological, ecological and evolutionary implications.     

A modular concept of plant foraging behaviour: the interplay between local responses and systemic control

In this paper we examined the notion that plant foraging for resources in heterogeneous environments must involve: (1) plasticity at the level of individual modules in reaction to localized environmental signals; and (2) the potential for modification of these responses either by the signals received from connected modules that may be exposed to different conditions, or by the signals reflecting the overall resource status of the plant. A conceptual model is presented to illustrate how plant foraging behaviour is achieved through these processes acting in concert, from the signal reception through signal transduction to morphological or physiological response. Evidence to support the concept is reviewed, using selective root placement under nutritionally heterogeneous conditions and elongation responses of stems and petioles to shade as examples. We discussed how the adoption of this model can promote understanding of the ecological significance of foraging behaviour. We also identified a need to widen the experimental repertoires of both molecular physiology and ecology in order to increase our insight into both the regulation and functioning of foraging responses, and their relationship with the patterns of environmental heterogeneity under which plants have evolved.     

AtGGM2014, an Arabidopsis gene co-expression network for functional studies

Gene co-expression networks provide an important tool for systems biology studies. Using microarray data from the Array Express database, we constructed an Arabidopsis gene co-expression network, termed At GGM2014, based on the graphical Gaussian model, which contains 102,644 co-expression gene pairs among 18,068 genes. The network was grouped into 622 gene co-expression modules. These modules function in diverse house-keeping, cell cycle, development, hormone response, metabolism, and stress response pathways. We developed a tool to facilitate easy visualization of the expression patterns of these modules either in a tissue context or their regulation under different treatment conditions. The results indicate that at least six modules with tissue-specific expression pattern failed to record modular regulation under various stress conditions. This discrepancy could be best explained by the fact that experiments to study plant stress responses focused mainly on leaves and less on roots, and thus failed to recover specific regulation pattern in other tissues. Overall, the modular structures revealed by our network provide extensive information to generate testable hypotheses about diverse plant signaling pathways. At GGM2014 offers a constructive tool for plant systems biology studies.     

A comparison of ecological responses among aclonal (unitary), clonal and coalescing macroalgae

Based on growth patterns, regeneration capabilities and genetic make up, benthic macroalgae include three groups of species. Similar to land plants, they include clonal and aclonal species, and, similar to colonial aquatic animals, seaweeds also include coalescing species, that have the capacity to fuse forming composite (chimeric) entities. Since the awareness of the differences between these three kinds of seaweeds is rather recent, most ecological studies have not discriminated among them. However, ecological models based on one kind of seaweeds will not necessarily apply to all kinds of seaweeds. This study reviews ecological responses of algae at the individual and community levels, and describes similarities and differences among both the three algal groups and with parallel groups in land plants and chimeric marine animals. The ecological responses reviewed are plant sizes and shapes; patterns of resource acquisition; algal life phases, reproduction and dispersal; genetic variability, intraspecific and interspecific competition and herbivory. Analysis of these responses supports the idea in distinguishing among the above three algal group, reveals the need for numerous additional ecological studies and advices on incorporating concepts from the biology of chimeric aquatic animals and from clonal theory of land plants into the study of benthic macroalgae.     

Coexistence in Mediterranean warblers: ecological differences or interspecific territoriality?

We studied the coexistence of four species of Sylvia warblers living in Mediterranean matorral in order to identify the respective role of ecological segregation and of interspecific territoriality in explaining the local distribution of these four species. Data on habitat use, foraging behaviour and interspecific spacial segregation were collected on Corsica and on Spargi (Sardinia) islands. Despite large overlap in patch selection and in foraging behaviour the four species did segregate ecologically and behaviourally while foraging (differences in the choice of plant species used for foraging, in the height of the plant selected, in the selection of the portion of the plant volume used and in the selection of the plant structure explored). Complementarity in foraging behaviour was observed in the morphologically and ecologically closest species: the Dartford ( Sylvia undata ) and the Marmora's ( Sylvia sarda ) warblers. We did not observe any evidence of direct interspecific interactions in song, alarm, or aggressive behaviour. Nor did we observe patterns of spatial distribution that would support the idea of coexistence by interspecific territorial exclusion. These results contrast with the results of Cody & Walter (1976) suggesting interspecific territoriality in Mediterranean Sylvia warblers. They are consistent with other published results emphasizing ecological differences as explanation for species coexistence.     

Characterizing the role benthos plays in large coastal seas and estuaries: A modular approach

Ecologists studying coastal and estuarine benthic communities have long taken a macroecological view, by relating benthic community patterns to environmental factors across several spatial scales. Although many general ecological patterns have been established, often a significant amount of the spatial and temporal variation in soft-sediment communities within and among systems remains unexplained. Here we propose a framework that may aid in unraveling the complex influence of environmental factors associated with the different components of coastal systems (i.e. the terrestrial and benthic landscapes, and the hydrological seascape) on benthic communities, and use this information to assess the role played by benthos in coastal ecosystems. A primary component of the approach is the recognition of system modules (e.g. marshes, dendritic systems, tidal rivers, enclosed basins, open bays, lagoons). The modules may differentially interact with key forcing functions (e.g. temperature, salinity, currents) that influence system processes and in turn benthic responses and functions. Modules may also constrain benthic characteristics and related processes within certain ecological boundaries and help explain their overall spatio-temporal variation. We present an example of how benthic community characteristics are related to the modular structure of 14 coastal seas and estuaries, and show that benthic functional group composition is significantly related to the modular structure of these systems. We also propose a framework for exploring the role of benthic communities in coastal systems using this modular approach and offer predictions of how benthic communities may vary depending on the modular composition and characteristics of a coastal system.     

Plant species richness and environmental heterogeneity in a mountain landscape: effects of variability and spatial configuration

The loss of biodiversity has become a matter of urgent concern and a better understanding of local drivers is crucial for conservation. Although environmental heterogeneity is recognized as an important determinant of biodiversity, this has rarely been tested using field data at management scale. We propose and provide evidence for the simple hypothesis that local species diversity is related to spatial environmental heterogeneity. Species partition the environment into habitats. Biodiversity is therefore expected to be influenced by two aspects of spatial heterogeneity: 1) the variability of environmental conditions, which will affect the number of types of habitat, and 2) the spatial configuration of habitats, which will affect the rates of ecological processes, such as dispersal or competition. Earlier, simulation experiments predicted that both aspects of heterogeneity will influence plant species richness at a particular site. For the first time, these predictions were tested for plant communities using field data, which we collected in a wooded pasture in the Swiss Jura mountains using a four-level hierarchical sampling design. Richness generally increased with increasing environmental variability and "roughness" (i.e. decreasing spatial aggregation). Effects occurred at all scales, but the nature of the effect changed with scale, suggesting a change in the underlying mechanisms, which will need to be taken into account if scaling up to larger landscapes. Although we found significant effects of environmental heterogeneity, other factors such as history could also be important determinants. If a relationship between environmental heterogeneity and species richness can be shown to be general, recently available high-resolution environmental data can be used to complement the assessment of patterns of local richness and improve the prediction of the effects of land use change based on mean site conditions or land use history.     

Responses of seagrass to anthropogenic and natural disturbances do not equally translate to its consumers

Coastal communities are under threat from many and often co‐occurring local (e.g., pollution, eutrophication) and global stressors (e.g., climate change), yet understanding the interactive and cumulative impacts of multiple stressors in ecosystem function is far from being accomplished. Ecological redundancy may be key for ecosystem resilience, but there are still many gaps in our understanding of interspecific differences within a functional group, particularly regarding response diversity, that is, whether members of a functional group respond equally or differently to anthropogenic stressors. Herbivores are critical in determining plant community structure and the transfer of energy up the food web. Human disturbances may alter the ecological role of herbivory by modifying the defense strategies of plants and thus the feeding patterns and performance of herbivores. We conducted a suite of experiments to examine the independent and interactive effects of anthropogenic (nutrient and CO₂ additions) and natural (simulated herbivory) disturbances on a seagrass and its interaction with two common generalist consumers to understand how multiple disturbances can impact both a foundation species and a key ecological function (herbivory) and to assess the potential existence of response diversity to anthropogenic and natural changes in these systems. While all three disturbances modified seagrass defense traits, there were contrasting responses of herbivores to such plant changes. Both CO₂ and nutrient additions influenced herbivore feeding behavior, yet while sea urchins preferred nutrient‐enriched seagrass tissue (regardless of other experimental treatments), isopods were deterred by these same plant tissues. In contrast, carbon enrichment deterred sea urchins and attracted isopods, while simulated herbivory only influenced isopod feeding choice. These contrasting responses of herbivores to disturbance‐induced changes in seagrass help to better understand the ecological functioning of seagrass ecosystems in the face of human disturbances and may have important implications regarding the resilience and conservation of these threatened ecosystems.     

Selection on phenotypic plasticity of morphological traits in response to flooding and competition in the clonal shore plant Ranunculus reptans

Adaptive evolution of phenotypic plasticity requires that plastic genotypes have the highest global fitness. We studied selection by spatial heterogeneity of interspecific competition and flooding, and by temporal heterogeneity of flooding on morphological plasticity of 52 genotypes of the clonal shore plant Ranunculus reptans. Competition reduced clone size, rosette size, leaf length and stolon internode thickness. Flooding had similar effects and reduced competition. Differences in selection between environments imply potential for either local adaptation or for indirect evolution of phenotypic plasticity. We also detected direct selection for plastic reductions in internode length in response to flooding and for a plastic increase in internode length in response to competition. Plastic responses of some morphological traits to flooding were in line with selection thereon, suggesting that they indeed are adaptive and might have evolved in response to direct selection on plasticity.     

Metabolic scaling in modular animals

Metabolic scaling is the relationship between organismal metabolic rate and body mass. Understanding the patterns and causes of metabolic scaling provides a powerful foundation for predicting biological processes at the level of individuals, populations, communities, and ecosystems. Despite intense interest in, and debate on, the mechanistic basis of metabolic scaling, relatively little attention has been paid to metabolic scaling in clonal animals with modular construction, such as colonial cnidarians, bryozoans, and colonial ascidians. Unlike unitary animals, modular animals are structural individuals subdivided into repeated morphological units, or modules, each able to acquire, process, and share resources. A modular design allows flexibility in organism size and shape with consequences for metabolic scaling. Furthermore, with careful consideration of the biology of modular animals, the size and shape of individual colonies can be experimentally manipulated to test competing theories pertaining to metabolic scaling. Here, we review metabolic scaling in modular animals and find that a wide range of scaling exponents, rather than a single value, has been reported for a variety of modular animals. We identify factors influencing variation in intraspecific scaling in this group that relate to the general observation that not all modules within a colony are identical. We highlight current gaps in our understanding of metabolic scaling in modular animals, and suggest future research directions, such as manipulating metabolic states and comparisons among species that differ in extent of module integration.     

A framework for integrating thermal biology into fragmentation research

Habitat fragmentation changes thermal conditions in remnant patches, and thermal conditions strongly influence organism morphology, distribution, and activity patterns. However, few studies explore temperature as a mechanism driving ecological responses to fragmentation. Here we offer a conceptual framework that integrates thermal biology into fragmentation research to better understand individual, species, community, and ecosystem‐level responses to fragmentation. Specifically, the framework addresses how fragmentation changes temperature and how the effects of those temperature changes spread through the ecosystem, from organism response via thermal sensitivity, to changes in species distribution and activity patterns, to shifts in community structure following species' responses, and ultimately to changes in ecosystem functions. We place a strong emphasis on future research directions by outlining “Critical gaps” for each step of the framework. Empirical efforts to apply and test this framework promise new understanding of fragmentation's ecological consequences and new strategies for conservation in an increasingly fragmented and warmer world.     

克隆植物对种间竞争的适应策略

克隆植物种群因其寿命的持久性、空间上的可移动性和繁殖方式的多样化等特征与非克隆植物有很大区别, 在自然生态系统中占有重要地位, 甚至成为优势种或者建群种。该文通过归纳有关克隆植物的种间竞争适应策略研究案例, 阐述了克隆植物的竞争能力差异和影响竞争力的因素; 论述了克隆植物在构件形态、克隆构型、繁殖对策等方面对种间竞争的响应, 以及生理整合作用与种间竞争的关系; 分析了导致某些同类研究的结论不一致的原因, 认为实验对象差异、实验设计、生境条件与克隆植物形态及生理上的时空动态变化等都可能影响实验结果; 提出了全球变化背景下的克隆植物种间竞争及其分子生态学机制等可能是今后需要重点关注的问题。     

Spatial structure of an individual‐based plant–pollinator network

The influence of space on the structure (e.g. modularity) of complex ecological networks remains largely unknown. Here, we sampled an individual‐based plant–pollinator network by following the movements and flower visits of marked bumblebee individuals within a population of thistle plants for which the identities and spatial locations of stems were mapped in a 50 × 50 m study plot. The plant–pollinator network was dominated by parasitic male bumblebees and had a significantly modular structure, with four identified modules being clearly separated in space. This indicated that individual flower visitors opted for the fine‐scale division of resources, even within a local site. However, spatial mapping of network modules and movements of bumblebee individuals also showed an overlap in the dense center of the plant patch. Model selection based on Akaike information criterion with traits as predictor variables revealed that thistle stems with high numbers of flower heads and many close neighbours were particularly important for connecting individuals within the modules. In contrast, tall plants and those near the patch center were crucial for connecting the different modules to each other. This demonstrated that individual‐based plant–pollinator networks are influenced by both the spatial structure of plant populations and individual‐specific plant traits. Additionally, bumblebee individuals with long observation times were important for both the connectivity between and within modules. The latter suggests that bumblebee individuals will still show locally restricted movements within sub‐patches of plant populations even if they are observed over a prolonged time period. Our individual‐based and animal‐centered approach of sampling ecological networks opens up new avenues for incorporating foraging behaviour and intra‐specific trait variation into analyses of plant–animal interactions across space.     

A multi-scale looping approach to predict spatially dynamic patterns of functional species richness in changing landscapes

Land-use/land-cover (LU/LC) change is one of the main drivers of global biodiversity change. However, the lack of detailed data on species’ local distributions is frequently a major constraint to identify effective indicators of impact and to prescribe effective conservation and management measures. Here we aim to describe and demonstrate the applicability of a novel looping approach to predict spatially dynamic ecological responses to LU/LC changes. The methodology integrates statistical downscaling, multi-model inference, stochastic-dynamic modelling and simulations, and spatial projections under a common and interactive framework. We illustrate the approach with a study of passerine foraging groups and their potential indicator role under LU/LC change scenarios. Based on the coarse occurrence data from published atlases, this approach allowed transposing species richness to fine resolutions in order to assess regional ecological integrity by up scaling the local responses of those indicators again at the landscape level. Overall, our proposed framework was able to provide realistic patterns of passerine foraging responses to LU/LC changes, highlighting the usefulness of existing databases for model-based research in addressing complex emergent problems across scales. Comparative analysis between simulations and independent field data showed a promising model performance, with consistent projections of the local passerine functional composition for a significant number of point-counts tested. Our approach represents a contribution for more universal applications in the scope of conservation and landscape planning, especially when fine resolution data is difficult to obtain due to resources constraints.     

Nutritional composition of the diet of the western gorilla (Gorilla gorilla): Interspecific variation in diet quality

To meet nutritional needs, primates adjust their diets in response to local habitat differences, though whether these dietary modifications translate to changes in dietary nutrient intake is unknown. A previous study of two populations of the mountain gorilla (MG: Gorilla beringei) found no evidence for intraspecific variation in the nutrient composition of their diets, despite ecological and dietary differences between sites. One potential explanation is that nutritional variability in primate diets requires greater ecological divergence than what was captured between MG sites, underpinning environmental differences in the nutrient quality of plant foods. To test whether Gorilla exhibits interspecific variation in dietary composition and nutrient intake, we studied the composition and macronutrients of the western gorilla (WG: Gorilla gorilla) staple diets and compared them with published data from the two MG populations. We recorded feeding time and food intake of four adult female WGs from one habituated group over a period of 11 months (December 2004–October 2005) at the Mondika Research Center, Republic of Congo, allowing for assessment of seasonal patterns of nutrient intake. Staple diets of WGs and MGs diverged in their dietary and macronutrient composition. Compared to MGs, the staple diet of WGs (by intake) contained higher proportions of fruit (43%) and leaf (12%) and a lower proportion of herb (39%), resulting in a higher intake of total nonstructural carbohydrate and fiber and a lower intake of crude protein. Staple gorilla fruits and herbs differed in nutrient quality between sites. Gorillas exhibit nutritional flexibility that reflects ecological variation in the nutrient quality of plant foods. Since dietary quality typically affects rates of growth and reproduction in primates, our results suggest that interspecific differences in nutrient intake and food quality may shape differences in gorilla nutrient balancing and female life history strategies.     

Prospects for tropical forest biodiversity in a human-modified world

The future of tropical forest biodiversity depends more than ever on the effective management of human-modified landscapes, presenting a daunting challenge to conservation practitioners and land use managers. We provide a critical synthesis of the scientific insights that guide our understanding of patterns and processes underpinning forest biodiversity in the human-modified tropics, and present a conceptual framework that integrates a broad range of social and ecological factors that define and contextualize the possible future of tropical forest species. A growing body of research demonstrates that spatial and temporal patterns of biodiversity are the dynamic product of interacting historical and contemporary human and ecological processes. These processes vary radically in their relative importance within and among regions, and have effects that may take years to become fully manifest. Interpreting biodiversity research findings is frequently made difficult by constrained study designs, low congruence in species responses to disturbance, shifting baselines and an over-dependence on comparative inferences from a small number of well studied localities. Spatial and temporal heterogeneity in the potential prospects for biodiversity conservation can be explained by regional differences in biotic vulnerability and anthropogenic legacies, an ever-tighter coupling of human-ecological systems and the influence of global environmental change. These differences provide both challenges and opportunities for biodiversity conservation. Building upon our synthesis we outline a simple adaptive-landscape planning framework that can help guide a new research agenda to enhance biodiversity conservation prospects in the human-modified tropics.     

Why ecology fails at application: should we consider variability more than regularity?

Inability to solve applied ecological problems is argued to depend on inherent variability in intra- and interspecific interactions caused by individual utilisation of a variety of local environments, and on individual counter-adaptations towards limiting or regulating factors. Such biological diversification is largely a response to environmental heterogeneity. Empirical and theoretical analyses of ecological mechanisms in various gradients of interaction and adaptation should result in improved use of ecological insight. Due to the many gradients, to the locally determined processes and to covert genetic variation very precise predictions of the outcome of ecological interactions will never be possible. Instead of focussing on possible general laws, ecology may try to establish common responses in population and community dynamics to main environmental gradients, particularly with regard to habitats and ecosystems.     

The influence of species pools and local processes on the community structure: a test case with woody plant communities in China's mountains

Understanding how patterns of biodiversity vary among taxonomic levels can provide insights into the mechanisms that regulate the assembly of ecological communities. In this study, we examined the scale and environmental dependence of the relationship between number of species and number of genera/families in woody plant communities to investigate the influences of species pool and local ecological processes on the taxonomic structures of local communities. The data we used are based on a large number of forest plots collected across the eastern part of China and the globe. The results showed that the ratio of the number of genera/families:species and the taxonomic exponents, i.e. the exponents of the genus/family–species relationship, were generally lower than null expectations based on the regional species pool, suggesting that abiotic filtering (e.g. environmental filtering and dispersal limitation) is more important than interspecific competition in shaping local communities. The extent of species pool and the area sampled for local communities both influenced our ability to infer whether local ecological processes were important. In particular, the deviation of the taxonomic ratios and exponents between empirical and null patterns increased as the extent of species pool increased, and the taxonomic exponents declined as area of the local community increased, due partly to the reduced effect of interspecific competition. We conclude that regional species pools and local processes both influenced the taxonomic structure of local woody plant communities, but their effects vary substantially among spatial scales.     

Plant–soil feedback under drought: does history shape the future?

Plant–soil feedback (PSF) is widely recognised as a driver of plant community composition, but understanding of its response to drought remains in its infancy. Here, we provide a conceptual framework for the role of drought in PSF, considering plant traits, drought severity, and historical precipitation over ecological and evolutionary timescales. Comparing experimental studies where plants and microbes do or do not share a drought history (through co-sourcing or conditioning), we hypothesise that plants and microbes with a shared drought history experience more positive PSF under subsequent drought. To reflect real-world responses to drought, future studies need to explicitly include plant–microbial co-occurrence and potential co-adaptation and consider the precipitation history experienced by both plants and microbes.