Avian Foraging Behavior in Two Different Types of Coffee Agroecosystem in Chiapas, Mexico

This study describes the foraging ecology of birds during summer and winter in two different types of coffee agroecosystems in Chiapas, Mexico. Avian foraging behavior is documented in two agroecosystems of differing management intensity, structurally similar but with different levels of floristic diversity, during summer and winter seasons. The distribution of tree species used by birds was more even, and birds used a greater diversity of tree species, in the more diverse coffee shade system. Much of the variation in resource use derived from shifts in the use of flowers and fruit, highlighting the importance in resource phenology for birds. Insectivory was more frequent in winter than summer for the coffee layer, and in summer for the shade layer. Given the vegetative structural similarity of the two coffee agroecosystems included in this study, floristic differences probably accounted for much of the difference in the bird communities between the management systems, especially given the strong seasonal response to flowering and fruiting. This work suggests that plentiful and diverse food resources associated with the high diversity of plant species may facilitate coexistence of the high number of bird species found in shade-grown coffee agroecosystems.     

Defaunation leads to interaction deficits,not interaction compensation,in an island seed dispersal network

Following defaunation, the loss of interactions with mutualists such as pollinators or seed dispersers may be compensated through increased interactions with remaining mutualists, ameliorating the negative cascading impacts on biodiversity. Alternatively, remaining mutualists may respond to altered competition by reducing the breadth or intensity of their interactions, exacerbating negative impacts on biodiversity. Despite the importance of these responses for our understanding of the dynamics of mutualistic networks and their response to global change, the mechanism and magnitude of interaction compensation within real mutualistic networks remains largely unknown. We examined differences in mutualistic interactions between frugivores and fruiting plants in two island ecosystems possessing an intact or disrupted seed dispersal network. We determined how changes in the abundance and behavior of remaining seed dispersers either increased mutualistic interactions (contributing to “interaction compensation”) or decreased interactions (causing an “interaction deficit”) in the disrupted network. We found a “rich‐get‐richer” response in the disrupted network, where remaining frugivores favored the plant species with highest interaction frequency, a dynamic that worsened the interaction deficit among plant species with low interaction frequency. Only one of five plant species experienced compensation and the other four had significant interaction deficits, with interaction frequencies 56–95% lower in the disrupted network. These results do not provide support for the strong compensating mechanisms assumed in theoretical network models, suggesting that existing network models underestimate the prevalence of cascading mutualism disruption after defaunation. This work supports a mutualist biodiversity‐ecosystem functioning relationship, highlighting the importance of mutualist diversity for sustaining diverse and resilient ecosystems.     

An invasive tree alters the structure of seed dispersal networks between birds and plants in French Polynesia

Aim We studied how the abundance of the highly invasive fruit‐bearing tree Miconia calvescens DC. influences seed dispersal networks and the foraging patterns of three avian frugivores. Location Tahiti and Moorea, French Polynesia. Methods Our study was conducted at six sites which vary in the abundance of M. calvescens. We used dietary data from three frugivores (two introduced, one endemic) to determine whether patterns of fruit consumption are related to invasive tree abundance. We constructed seed dispersal networks for each island to evaluate how patterns of interaction between frugivores and plants shift at highly invaded sites. Results Two frugivores increased consumption of M. calvescens fruit at highly invaded sites and decreased consumption of other dietary items. The endemic fruit dove, Ptilinopus purpuratus, consumed more native fruit than either of the two introduced frugivores (the red‐vented bulbul, Pycnonotus cafer, and the silvereye, Zosterops lateralis), and introduced frugivores showed a low potential to act as dispersers of native plants. Network patterns on the highly invaded island of Tahiti were dominated by introduced plants and birds, which were responsible for the majority of plant–frugivore interactions. Main conclusions Shifts in the diet of introduced birds, coupled with reduced populations of endemic frugivores, caused differences in properties of the seed dispersal network on the island of Tahiti compared to the less invaded island of Moorea. These results demonstrate that the presence of invasive fruit‐bearing plants and introduced frugivores can alter seed dispersal networks, and that the patterns of alteration depend both on the frugivore community and on the relative abundance of available fruit.     

Non-native mammals are weak candidates to substitute ecological function of native avian seed dispersers in an island ecosystem

Although prominent examples exist of non-native species causing substantial ecological harm, many have neutral or positive effects, including filling surrogate roles once performed by extinct native organisms. We tested the ecological roles of two non-native mammals as seed dispersers or seed predators in Guåhan, which, due to invasive brown tree snakes (Boiga irregularis), is devoid of native seed dispersers–birds and bats. We conducted feeding trials with captive rats (Rattus spp.), which are present but uncommon due to predation by snakes, and pigs (Sus scrofa), which are abundant. We examined if and how they interacted with common forest fruits. We then compared how any gut-passed or animal-handled seeds germinated compared to seeds left in whole fruit or depulped seeds. Rats and pigs interacted with most of the fruits and seeds (>80%) that they were fed. Of those, most seeds were destroyed—78% for rats and 90% for pigs, across both native and non-native plant species. Compared to seeds germinating within whole fruits, rats improved germination of the seeds that they handled without ingesting, while pigs diminished the germination of seeds that they handled. The small percentage of seeds (approximately 1.5% for rats and 5% for pigs) that survived gut passage germinated in higher proportions than those in whole fruits. Percentages of seed survival to germination are lower than found in similar studies with native avian frugivores. Our results indicate that pigs and rats have mixed effects on seeds, but are not suitable surrogates for native seed dispersers.     

Avian fruit consumption and seed dispersal in a temperate Australian woodland

Abstract The effectiveness of avian fruit consumers as seed dispersers of fleshy‐fruited plants was studied in a temperate woodland community. As a consequence of the short and overlapping fruiting phenologies of fleshy‐fruited plant species in temperate regions of Australia, there are very few avian species that are true specialist frugivores. The relative importance of bird species as fruit consumers was investigated, and how their foraging activities, movements and gut treatment of seeds affected dispersal of viable seeds away from the parent plant was examined. Fruit consumption and consumer seed dispersal capacity were assessed in this study through faecal analyses and by testing the viability of seeds that had passed through the gut of avian consumers. Behavioural observations enabled us to determine the consumption rates of, and quantities of fruit consumed by, various bird species and the amount of time spent feeding. Silvereyes (Zosterops lateralis) were the dominant fruit consumers in the community, although 19 bird species were either observed consuming fruit or provided faecal samples that contained fruit. Silvereyes had a high local abundance at the site and more than 90% of silvereyes’faecal samples contained the seeds of fruiting plants (n = 409). Large numbers of fruit were consumed per visit by silvereyes, particularly for Rhagodia parabolica (fragrant saltbush). Silvereyes consumed an average of four R. parabolica fruit per 5 s and up to a maximum 40 fruit per visit. Viability was high for seeds recovered from silvereyes’faeces (R. parabolica, 94.4% viable; Hymenanthera dentata, 100% viable). However, the number of seeds per faecal sample was high for R. parabolica, which may result in density‐dependent seed mortality. Gut passage rate for silvereyes fed R. parabolica fruit in captivity was 31.5 ± 1.9 min. Silvereyes remained at fruiting plants for very short periods (average 50‐60 s) and in most cases moved away from the parent plant, primarily toward canopy trees. Given the short visit duration of silvereyes, individuals would have left the parent plant well before seeds passed through the gut. Rhagodia parabolica fruit was consumed by a large number of bird species in the community, including species often thought of as exclusively insectivorous or nectarivorous. These species are likely to disperse viable R. parabolica seeds into microhabitats different from those visited by silvereyes.     

种间互作网络的结构、生态系统功能及稳定性机制研究

生态群落中不同物种间发生多样化的相互作用, 形成了复杂的种间互作网络。复杂生态网络的结构如何影响群落的生态系统功能及稳定性是群落生态学的核心问题之一。种间互作直接影响到物质和能量在生态系统不同组分之间的流动和循环以及群落构建过程, 使得网络结构与生态系统功能和群落稳定性密切相关。在群落及生态系统水平上开展种间互作网络研究将为群落的构建机制、生物多样性维持、生态系统稳定性、物种协同进化和性状分化等领域提供新的视野。当前生物多样性及生态系统功能受到全球变化的极大影响, 研究种间互作网络的拓扑结构、构建机制、稳定性和生态功能也可为生物多样性的保护和管理提供依据。该文从网络结构、构建机制、网络结构和稳定性关系、种间互作对生态系统功能的影响等4个方面综述当前种间网络研究进展, 并提出在今后的研究中利用机器学习和多层网络等来探究环境变化对种间互作网络结构和功能的影响, 并实现理论和实证研究的有效整合。     

Avian responses to an emergent,wetland weed

African boxthorn (Lycium ferocissimum Solanaceae) is a Weed of National Significance in Australia. It is particularly problematic in Victoria and is thought to not only threaten native wildlife but also provide important habitat, particularly to birds, when there is no native alternative. In a wetland ecosystem such as a saltmarsh, boxthorn has the potential to increase structural complexity because it can stand as an emergent above surrounding vegetation. We compared bird assemblages and behaviour in saltmarsh vegetation with and without boxthorn in a coastal wetland in south‐east Australia. Species assemblage, but not richness, changed with the presence of boxthorn. The presence of singing honeyeaters (Lichenostomus virescens) and white‐fronted chats (Epthianura albifrons), the two most common native bird species (based on numerical and spatial dominance), appeared to drive these differences; singing honeyeaters preferred boxthorn while white‐fronted chats avoided it. The presence of boxthorn increased the seasonal availability of fruit and flowers, which was reflected by a high frequency of foraging for fruit and nectar where boxthorn was present. In saltmarshes without boxthorn, there was a higher frequency of foraging for insects. Some, but not all, species responded to increased structural complexity and fruit/floral resources provided by boxthorn. Consequently, management by reducing boxthorn is likely to alter bird communities and the usage of sites by some native species, thus management success should consider fine‐scale biodiversity objectives, such as managing for particular types or species of birds.     

Antagonism and bistability in protein interaction networks

A protein interaction network (PIN) is a set of proteins that modulate one another's activities by regulated synthesis and degradation, by reversible binding to form complexes, and by catalytic reactions (e.g., phosphorylation and dephosphorylation). Most PINs are so complex that their dynamical characteristics cannot be deduced accurately by intuitive reasoning alone. To predict the properties of such networks, many research groups have turned to mathematical models (differential equations based on standard biochemical rate laws, e.g., mass-action, Michaelis-Menten, Hill). When using Michaelis-Menten rate expressions to model PINs, care must be exercised to avoid making inconsistent assumptions about enzyme-substrate complexes. We show that an appealingly simple model of a PIN that functions as a bistable switch is compromised by neglecting enzyme-substrate intermediates. When the neglected intermediates are put back into the model, bistability of the switch is lost. The theory of chemical reaction networks predicts that bistability can be recovered by adding specific reaction channels to the molecular mechanism. We explore two very different routes to recover bistability. In both cases, we show how to convert the original 'phenomenological' model into a consistent set of mass-action rate laws that retains the desired bistability properties. Once an equivalent model is formulated in terms of elementary chemical reactions, it can be simulated accurately either by deterministic differential equations or by Gillespie's stochastic simulation algorithm.     

Fine‐tuning the nested structure of pollination networks by adaptive interaction switching,biogeography and sampling effect in the Galápagos Islands

The structure of pollination networks, particularly its nestedness, contain important information on network assemblages. However, there is still limited understanding of the mechanisms underlying nested pollination network structures. Here, we investigate the role of adaptive interaction switching (AIS), island area, isolation, age and sampling effort in explaining the nestedness of pollination networks across ten Galápagos Islands. The AIS algorithm is inspired by Wallace's elimination of the unfit, where a species constantly replaces its least profitable mutualistic partner with a new partner selected at random. To explain network structures, we first use a dynamic model that includes functional response of pollination and AIS, with only species richness and binary connectance as input (hereafter the AIS model). Thereafter, other explanatory variables (isolation, area, age and sampling effort) were added to the model. In four out of ten islands, the pollination network was significantly nested, and predictions from the AIS model correlated with observed structures, explaining 69% variation in nestedness. Overall, in terms of independent contribution from hierarchical partitioning of variation in observed nestedness, the AIS model predictions contributed the most (37%), followed by sampling effort (28%) and island area (22%), with only trivial contributions from island isolation and age. Therefore, adaptive switching of biotic interactions seems to be key to ensure network function, with island biogeographic factors being only secondary. Although large islands could harbour more diverse assemblages and thus foster more nested structures, sufficient sampling proves to be essential for detecting non‐random network structures.     

Seed Dispersal Distances and Plant Migration Potential in Tropical East Asia

Most predictions of vegetation responses to anthropogenic climate change over the next 100 yr are based on plant physiological tolerances and do not account for the ability of plant species to migrate over the distances required in the time available, or the impact of habitat fragmentation on this ability. This review assesses the maximum routine dispersal distances achievable in tropical East Asia and their vulnerability to human impacts. Estimates for various plant–vector combinations range from < 10 m, for species dispersed by ants or mechanical means, to > 10 km for some species dispersed by wind (tiny seeds), water, fruit pigeons, large fruit bats (tiny seeds), elephants, rhinoceroses, and people. Most plant species probably have maximum dispersal distances in the 100–1000 m range, but the widespread, canopy-dominant Dipterocarpaceae and Fagaceae are normally dispersed < 100 m. Large fruit bats and fruit pigeons are particularly important for long-distance dispersal in fragmented landscapes and should be protected from hunting. The maximum seed dispersal distances estimated in this study are potentially sufficient for many plant species to track temperature changes in steep topography, but are far too small for a significant role in mitigating climate change impacts in the lowlands, where temperature and rainfall gradients are much more shallow.     

Dispersal of non-native plants by introduced bison in an island ecosystem

An understanding of the mechanisms of seed dispersal is critical to effectively managing populations of non-native plants. We investigated whether introduced bison on Santa Catalina Island, California, have the potential to spread non-native plants through the shedding of clumps of seed-laden hair and/or ingesting and later excreting seeds. We collected clumps of hair shaved from bison during a roundup and dislodged by wallowing activity. Greenhouse and field trials were used to test for seed viability and persistence of hair clumps in wallows. In addition to trials with bison hair, we collected samples of bison dung and tested for seed germination in a greenhouse. The majority of seeds extracted from bison hair clumps were of non-native forbs. There was a significant positive relationship between the size of hair clumps and the number of seeds extracted from the clumps, suggesting that managing the introduced bison population at a lower level will help minimize the spread of non-native plants by the species. Seeds of non-native plants were capable of germinating under conditions similar to those on Santa Catalina Island. Clumps of bison hair persisted in wallows, but did not remain intact and lost nearly 40% of their original mass. The number of germinable seeds contained in bison dung was low: 18 seeds germinated from 6 of 18 dung samples. Introduced bison appear to facilitate the dispersal of non-native plants over native plants on Santa Catalina Island. Our study suggests that a comprehensive strategy to control non-native plants must involve the management of the animal agents of plant dispersal.     

Reciprocal specialization in ecological networks

Theories suggest that food webs might consist of groups of species forming 'blocks', 'compartments' or 'guilds'. We consider ecological networks – subsets of complete food webs – involving species at adjacent trophic levels. Reciprocal specializations occur when (say) a pollinator (or group of pollinators) specializes on a particular flower species (or group of such species) and vice versa. Such specializations tend to group species into guilds. We characterize the level of reciprocal specialization for both antagonistic interactions – particularly parasitoids and their hosts – and mutualistic ones – such as insects and the flowers that they pollinate. We also examine whether trophic patterns might be 'palimpsests'– that is, there might be reciprocal specialization within taxonomically related species within a network, but these might be obscured when these relationships are combined. Reciprocal specializations are rare in all these systems when tested against the most conservative null model.     

蛋白质网络聚类算法分析平台的设计与实现

蛋白质网络聚类是识别功能模块的重要手段,不仅有利于理解生物系统的组织结构,对预测蛋白质功能也具有重要的意义。针对目前蛋白质网络聚类算法缺乏有效分析软件的事实,本文设计并实现了一个新的蛋白质网络聚类算法分析平台ClusterE。该平台实现了查全率、查准率、敏感性、特异性、功能富集分析等聚类评估方法,并且集成了FAG-EC、Dpclus、Monet、IPC-MCE、IPCA等聚类算法,不仅可以对蛋白质网络聚类分析结果进行可视化,并且可以在不同聚类分析指标下对多个聚类算法进行可视化比较与分析。该平台具有良好的扩展性,其中聚类算法以及聚类评估方法都是以插件形式集成到系统中。     

Understand ecosystem regime shifts by modelling ecosystem development using Boolean networks

Complex ecosystems are difficult to model and are still poorly understood. In spite of the long lasting efforts to predict them, we still lack a real integrated framework to grasp their behaviours. In this paper, the concept of ecosystem development is proposed to understand the sharp regime shifts they cumulate over the long term. To handle regime shifts, we develop an integrated model merging the physical, biological and social components and interactions (processes) of an ecosystem into a single graph representation. We then formalize sharp structural (topological) changes of the system with Boolean networks. We illustrate this theoretical approach borrowed from discrete model formalisms on some ecosystems assumed to be representative of most ecosystems: the eusocial (termite and ant) insect colonies and their associated interactions.Boolean networks, combined with rigorous production/rewriting rules and syntax, simulate the ecosystem's responses to strong perturbations. This deterministic and qualitative approach allows identifying fragile components, analysing ecosystem resilience to perturbations and to map out every lethal trajectory of the ecosystem. In our models, termite colonies appear to be almost six times less vulnerable to perturbations than ant colonies, and need (8%) more time steps to collapse. This robust result was partly due to the higher number of essential nodes in ant ecosystems, and partly due to interactions related to the ants' vertebrate predators. The rigorous and parsimonious abilities of such discrete models pave the way in reinterpreting and managing a wide range of ecosystems.     

Comparing species interaction networks along environmental gradients

Knowledge of species composition and their interactions, in the form of interaction networks, is required to understand processes shaping their distribution over time and space. As such, comparing ecological networks along environmental gradients represents a promising new research avenue to understand the organization of life. Variation in the position and intensity of links within networks along environmental gradients may be driven by turnover in species composition, by variation in species abundances and by abiotic influences on species interactions. While investigating changes in species composition has a long tradition, so far only a limited number of studies have examined changes in species interactions between networks, often with differing approaches. Here, we review studies investigating variation in network structures along environmental gradients, highlighting how methodological decisions about standardization can influence their conclusions. Due to their complexity, variation among ecological networks is frequently studied using properties that summarize the distribution or topology of interactions such as number of links, connectance, or modularity. These properties can either be compared directly or using a procedure of standardization. While measures of network structure can be directly related to changes along environmental gradients, standardization is frequently used to facilitate interpretation of variation in network properties by controlling for some co‐variables, or via null models. Null models allow comparing the deviation of empirical networks from random expectations and are expected to provide a more mechanistic understanding of the factors shaping ecological networks when they are coupled with functional traits. As an illustration, we compare approaches to quantify the role of trait matching in driving the structure of plant–hummingbird mutualistic networks, i.e. a direct comparison, standardized by null models and hypothesis‐based metaweb. Overall, our analysis warns against a comparison of studies that rely on distinct forms of standardization, as they are likely to highlight different signals. Fostering a better understanding of the analytical tools available and the signal they detect will help produce deeper insights into how and why ecological networks vary along environmental gradients.