Does Habitat Variability Really Promote Metabolic Network Modularity?

The hypothesis that variability in natural habitats promotes modular organization is widely accepted for cellular networks. However, results of some data analyses and theoretical studies have begun to cast doubt on the impact of habitat variability on modularity in metabolic networks. Therefore, we re-evaluated this hypothesis using statistical data analysis and current metabolic information. We were unable to conclude that an increase in modularity was the result of habitat variability. Although horizontal gene transfer was also considered because it may contribute for survival in a variety of environments, closely related to habitat variability, and is known to be positively correlated with network modularity, such a positive correlation was not concluded in the latest version of metabolic networks. Furthermore, we demonstrated that the previously observed increase in network modularity due to habitat variability and horizontal gene transfer was probably due to a lack of available data on metabolic reactions. Instead, we determined that modularity in metabolic networks is dependent on species growth conditions. These results may not entirely discount the impact of habitat variability and horizontal gene transfer. Rather, they highlight the need for a more suitable definition of habitat variability and a more careful examination of relationships of the network modularity with horizontal gene transfer, habitats, and environments.     

Structure of trophic and mutualistic networks across broad environmental gradients

This study aims to understand how inherent ecological network structures of nestedness and modularity vary over large geographic scales with implications for community stability. Bipartite networks from previous research from 68 locations globally were analyzed. Using a meta‐analysis approach, we examine relationships between the structure of 22 trophic and 46 mutualistic bipartite networks in response to extensive gradients of temperature and precipitation. Network structures varied significantly across temperature gradients. Trophic networks showed decreasing modularity with increasing variation in temperature within years. Nestedness of mutualistic networks decreased with increasing temperature variability between years. Mean annual precipitation and variability of precipitation were not found to have significant influence on the structure of either trophic or mutualistic networks. By examining changes in ecological networks across large‐scale abiotic gradients, this study identifies temperature variability as a potential environmental mediator of community stability. Understanding these relationships contributes to our ability to predict responses of biodiversity to climate change at the community level.     

Convergent evolution of modularity in metabolic networks through different community structures

ABSTRACT: BACKGROUND: It has been reported that the modularity of metabolic networks of bacteria is closely relatedto the variability of their living habitats. However, given the dependency of the modularityscore on the community structure, it remains unknown whether organisms achieve certainmodularity via similar or different community structures. RESULTS: In this work, we studied the relationship between similarities in modularity scores andsimilarities in community structures of the metabolic networks of 1021 species. Bothsimilarities are then compared against the genetic distances. We revisited the associationbetween modularity and variability of the microbial living environments and extended theanalysis to other aspects of their life style such as temperature and oxygen requirements. Wealso tested both topological and biological intuition of the community structures identifiedand investigated the extent of their conservation with respect to the taxomony. CONCLUSIONS: We find that similar modularities are realized by different community structures. We findthat such convergent evolution of modularity is closely associated with the number of(distinct) enzymes in the organism's metabolome, a consequence of different life styles ofthe species. We find that the order of modularity is the same as the order of the number ofthe enzymes under the classification based on the temperature preference but not on theoxygen requirement. Besides, inspection of modularity-based communities reveals thatthese communities are graph-theoretically meaningful yet not reflective of specificbiological functions. From an evolutionary perspective, we find that the communitystructures are conserved only at the level of kingdoms. Our results call for moreinvestigation into the interplay between evolution and modularity: how evolution shapesmodularity, and how modularity affects evolution (mainly in terms of fitness andevolvability). Further, our results call for exploring new measures of modularity andnetwork communities that better correspond to functional categorizations.     

Availability of food resources and habitat structure shape the individual‐resource network of a Neotropical marsupial

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A Big World Inside Small-World Networks

Real networks, including biological networks, are known to have the small-world property, characterized by a small “diameter”, which is defined as the average minimal path length between all pairs of nodes in a network. Because random networks also have short diameters, one may predict that the diameter of a real network should be even shorter than its random expectation, because having shorter diameters potentially increases the network efficiency such as minimizing transition times between metabolic states in the context of metabolic networks. Contrary to this expectation, we here report that the observed diameter is greater than the random expectation in every real network examined, including biological, social, technological, and linguistic networks. Simulations show that a modest enlargement of the diameter beyond its expectation allows a substantial increase of the network modularity, which is present in all real networks examined. Hence, short diameters appear to be sacrificed for high modularities, suggesting a tradeoff between network efficiency and advantages offered by modularity (e.g., multi-functionality, robustness, and/or evolvability).     

Compensatory ability to null mutation in metabolic networks

Robustness is an inherent property of biological system. It is still a limited understanding of how it is accomplished at the cellular or molecular level. To this end, this article analyzes the impact degree of each reaction to others, which is defined as the number of cascading failures of following and/or forward reactions when an initial reaction is deleted. By analyzing more than 800 organism's metabolic networks, it suggests that the reactions with larger impact degrees are likely essential and the universal reactions should also be essential. Alternative metabolic pathways compensate null mutations, which represents that average impact degrees for all organisms are small. Interestingly, average impact degrees of archaea organisms are smaller than other two categories of organisms, eukayote and bacteria, indicating that archaea organisms have strong robustness to resist the various perturbations during the evolution process. The results show that scale‐free feature and reaction reversibility contribute to the robustness in metabolic networks. The optimal growth temperature of organism also relates the robust structure of metabolic network. Biotechnol. Bioeng. 2009;103: 361–369. © 2008 Wiley Periodicals, Inc.     

The ecological significance of extremely large flocks of birds

Population size is generally limited by resource availability during and outside the breeding season. Therefore, maximum size of flocks may provide important information on population regulation and the influence of diet and trophic level on maximal degree of sociality. We hypothesized that (a) flock size should increase with nutrient availability; (b) flock size should decrease with latitude because productivity is higher at lower latitude; (c) aquatic habitats should have larger flocks than terrestrial habitats because the former are less accessible; (d) smaller species should have larger flocks because they require overall less food; (e) human‐impacted species that live in perturbed habitats should have smaller flocks than other species; (f) flock size should decrease with increasing trophic level because there is a reduction in biomass due to conversion at each trophic level; and (g) flocks of species depending on ancestral landscapes should have decreased in size in recent years due to human impact (e.g., land‐use). We obtained 1564 observations of flocks that exceeded 100,000 individuals in order to test the predictions listed above. Most effect sizes were small to medium accounting for 1%–9% of the variance, while large effects accounting for 25% or more were only found for total nitrogen used per km² and area used for agriculture. Changes in large bird flocks were caused by habitat degradation and persecution, and temporal decline in size of large flocks revealed changes in nutrient use, reductions in nutrient cycling, and changes in flock size linked to trophic level.     

Stable resource polymorphism along the benthic littoral–pelagic axis in an invasive crayfish

Although intraspecific variability is now widely recognized as affecting evolutionary and ecological processes, our knowledge on the importance of intraspecific variability within invasive species is still limited. This is despite the fact that understanding the linkage between within‐population morphological divergences and the use of different trophic or spatial resources (i.e., resource polymorphism) can help to better predict their ecological impacts on recipient ecosystems. Here, we quantified the extent of resource polymorphism within populations of a worldwide invasive crayfish species, Procambarus clarkii, in 16 lake populations by comparing their trophic (estimated using stable isotope analyses) and morphological characteristics between individuals from the littoral and pelagic habitats. Our results first demonstrated that crayfish occured in both littoral and pelagic habitats of seven lakes and that the use of pelagic habitat was associated with increased abundance of littoral crayfish. We then found morphological (i.e., body and chelae shapes) and trophic divergence (i.e., reliance on littoral carbon) among individuals from littoral and pelagic habitats, highlighting the existence of resource polymorphism in invasive populations. There was no genetic differentiation between individuals from the two habitats, implying that this resource polymorphism was stable (i.e., high gene flow between individuals). Finally, we demonstrated that a divergent adaptive process was responsible for the morphological divergence in body and chela shapes between habitats while difference in littoral reliance neutrally evolved under genetic drift. These findings demonstrated that invasive P. clarkii can display strong within‐population phenotypic variability in recent populations, and this could lead to contrasting ecological impacts between littoral and pelagic individuals.     

Analysis of a hyper-diverse seed dispersal network: modularity and underlying mechanisms

Mutualistic interactions involving pollination and ant-plant mutualistic networks typically feature tightly linked species grouped in modules. However, such modularity is infrequent in seed dispersal networks, presumably because research on those networks predominantly includes a single taxonomic animal group (e.g. birds). Herein, for the first time, we examine the pattern of interaction in a network that includes multiple taxonomic groups of seed dispersers, and the mechanisms underlying modularity. We found that the network was nested and modular, with five distinguishable modules. Our examination of the mechanisms underlying such modularity showed that plant and animal trait values were associated with specific modules but phylogenetic effect was limited. Thus, the pattern of interaction in this network is only partially explained by shared evolutionary history. We conclude that the observed modularity emerged by a combination of phylogenetic history and trait convergence of phylogenetically unrelated species, shaped by interactions with particular types of dispersal agents.     

Do asynchronies in extinction debt affect the structure of trophic networks? A case study of antagonistic butterfly larvae–plant networks

Habitat loss and fragmentation affect species richness in fragmented habitats and can lead to immediate or time‐delayed species extinctions. Asynchronies in extinction and extinction debt between interacting species may have severe effects on ecological networks. However, these effects remain largely unknown. We evaluated the effects of habitat patch and landscape changes on antagonistic butterfly larvae–plant trophic networks in Mediterranean grasslands in which previous studies had shown the existence of extinction debt in plants but not in butterflies. We sampled current species richness of habitat‐specialist and generalist butterflies and vascular plants in 26 grasslands. We assessed the direct effects of historical and current patch and landscape characteristics on species richness and on butterfly larvae–plant trophic network metrics and robustness. Although positive species‐ and interactions–area relationships were found in all networks, structure and robustness was only affected by patch and landscape changes in networks involving the subset of butterfly specialists. Larger patches had more species (butterflies and host plants) and interactions but also more compartments, which decreased network connectance but increased network stability. Moreover, most likely due to the rescue effect, patch connectivity increased host‐plant species (but not butterfly) richness and total links, and network robustness in specialist networks. On the other hand, patch area loss decreased robustness in specialist butterfly larvae–plant networks and made them more prone to collapse against host plant extinctions. Finally, in all butterfly larvae–plant networks we also detected a past patch and landscape effect on network asymmetry, which indicates that there were different extinction rates and extinction debts for butterflies and host plants. We conclude that asynchronies in extinction and extinction debt in butterfly–plant networks provoked by patch and landscape changes caused changes in species richness and network links in all networks, as well as changes in network structure and robustness in specialist networks.     

Intercolony variation in growth of black brant goslings on the Yukon-Kuskokwim Delta,Alaska

Recent declines in black brant (Branta bernicla nigricans) are likely the result of low recruitment. In geese, recruitment is strongly affected by habitat conditions experienced by broods because gosling growth rates are indicative of forage conditions during brood rearing and strongly influence future survival and productivity. In 2006–2008, we studied gosling growth at 3 of the 4 major colonies on the Yukon-Kuskokwim Delta, Alaska. Estimates of age-adjusted gosling mass at the 2 southern colonies (approx. 30% of the world population of breeding black brant) was low (gosling mass at 30.5 days ranged 346.7 ± 42.5 g to 627.1 ± 15.9 g) in comparison to a third colony (gosling mass at 30.5 days ranged 640.0 ± 8.3 g to 821.6 ± 13.6 g) and to most previous estimates of age-adjusted mass of brant goslings. Thus, our results are consistent with the hypothesis that poor gosling growth is negatively influencing the brant population. There are 2 non-mutually exclusive explanations for the apparent growth rates we observed. First, the population decline may have been caused by density-independent factors and habitat capacity has declined along with the population as a consequence of the unique foraging feedback between brant and their grazing habitats. Alternatively, a reduction in habitat capacity, as a result of changes to the grazing system, may have negatively influenced gosling growth, which is contributing to the overall long-term population decline. We found support for both explanations. For colonies over habitat capacity we recommend management to enhance foraging habitat, whereas for colonies below habitat capacity we recommend management to increase nesting productivity. © 2010 The Wildlife Society.     

A waterfowl seed-dispersal network from the Neotropical region is nested and modular

Seed dispersal by vertebrates is fundamental for the persistence of plant species, forming networks of interactions that are often nested and modular. Networks involving angiosperms and frugivorous birds are relatively well-studied in the Neotropical region, but there are no previous studies of networks involving waterbirds. Here, we describe the structure of a Neotropical waterfowl seed-dispersal network and identify the species that have an important role for the network structure. We used information on 40 plant taxa found in fecal samples of five common waterfowl species to calculate the nestedness (NODF), weighted nestedness (WNODF), modularity, and weighted modularity of the network. We found that the network was nested, with yellow-billed teal showing the highest contribution both to nestedness and weighted nestedness. Twenty-four plant species contributed positively to weighted nestedness, with Salzmann's mille graines presenting the highest influence both to nestedness and weighted nestedness. The network was modular, but the weighted modularity was not significant. These results need to be considered with caution due to incomplete interaction sampling for two species. Ringed teal, Brazilian teal, and yellow-billed teal were considered hub modular species. Among plants, beak sedges and water snowflake were considered modular hub species, while Salzmann's mille graines and spikerush were network connectors. The structure of this Neotropical waterbird seed-dispersal network differed from the only previous waterfowl network study, from Europe, which found similar level of nestedness but no significant modularity. We include several possible explanations for this discrepancy and identified priorities for future research into waterbird–plant interaction networks. Abstract in Portuguese is available with online material.     

Coastal Habitats as Surrogates for Taxonomic,Functional and Trophic Structures of Benthic Faunal Communities

Due to human impact, there is extensive degradation and loss of marine habitats, which calls for measures that incorporate taxonomic as well as functional and trophic aspects of biodiversity. Since such data is less easily quantifiable in nature, the use of habitats as surrogates or proxies for biodiversity is on the rise in marine conservation and management. However, there is a critical gap in knowledge of whether pre-defined habitat units adequately represent the functional and trophic structure of communities. We also lack comparisons of different measures of community structure in terms of both between- (β) and within-habitat (α) variability when accounting for species densities. Thus, we evaluated a priori defined coastal habitats as surrogates for traditional taxonomic, functional and trophic zoobenthic community structure. We focused on four habitats (bare sand, canopy-forming algae, seagrass above- and belowground), all easily delineated in nature and defined through classification systems. We analyzed uni- and multivariate data on species and trait diversity as well as stable isotope ratios of benthic macrofauna. A good fit between habitat types and taxonomic and functional structure was found, although habitats were more similar functionally. This was attributed to within-habitat heterogeneity so when habitat divisions matched the taxonomic structure, only bare sand was functionally distinct. The pre-defined habitats did not meet the variability of trophic structure, which also proved to differentiate on a smaller spatial scale. The quantification of trophic structure using species density only identified an epi- and an infaunal unit. To summarize the results we present a conceptual model illustrating the match between pre-defined habitat types and the taxonomic, functional and trophic community structure. Our results show the importance of including functional and trophic aspects more comprehensively in marine management and spatial planning.     

Modularity of trophic network is driven by phylogeny and migration in a steppe ecosystem

Evidence is mounting that the structures of trophic networks are governed by migratory movements of interacting species and also by their phylogenetic relationships. Using the largest available trophic network of a large steppe ecosystem, we tested that steppe trophic networks including migratory species are associated with (i) migratory strategy and (ii) phylogenetic relatedness of interacting species: (1) whole graph-level metrics, estimated as modularity, and (2) species-level network metrics, measured as node degree (number of interacting partners), and centrality metrics. We found that (1) a substantial number of links were established by migrant taxa; (2) the phylogenetic signal in network structure was moderate for both consumer and prey nodes; (3) both consumer and prex phylogenies affected modularity, which was modulated by migration strategy; and (4) all species-level graph properties significantly differed between networks including and excluding migratory taxa. In sum, here we show that the structure of steppe trophic networks is primarily governed by migratory strategies and to a lesser extent, by phylogenetic relatedness, using the largest available food web representative for steppe ecology and migration biology.     

不同鸟类生境网络复合与优化——以苏锡常地区白鹭、鸳鸯、雉鸡为例

通过复合优化不同焦点物种的生境网络表征多数物种生境网络实现物种多样性保护,具有重要理论价值和实践意义。以苏锡常地区为研究区域,以白鹭、鸳鸯和雉鸡3种鸟类为焦点物种,通过采用生境斑块约束条件模型与最小成本路径法相结合的方法识别出生境网络;从满足集合覆盖问题视角出发,通过采用网络构成要素复合的方法进行网络复合,其中廊道与廊道的复合通过采用评价生态系统服务价值的方法实现;通过采用观测数据为生境斑块和迁移廊道增补依据的方法进行复合生境网络优化。结果表明:生境网络经过复合,廊道总面积、总长度及生态系统服务价值在分别减少了16%、68%和10%的情况下,保持了斑块间的连接度、兼顾到经济效益和生态效益最大化、覆盖了占总数86%以上的75处观测点;复合生境网络经过优化,覆盖了2010年及以后所有84处观测点,廊道总面积、总长度及生态系统服务价值分别增加了19%、21%和27%;说明生境网络复合优化定量分析方法和思路具有可行性,为网络复合研究提供了借鉴。     

Influence of lateral gradients of hydrologic connectivity on trophic positions of fishes in the Upper Mississippi River

1. Riverscapes consist of the main channel and lateral slackwater habitats along a gradient of hydrological connectivity from maximum connection in main channel habitats to minimum connection in backwaters. Spatiotemporal differences in water currents along this gradient produce dynamic habitat conditions that influence species diversity, population densities and trophic interactions of fishes. 2. We examined the importance of lateral connectivity gradients for food web dynamics in the Upper Mississippi River during spring (high flow, moderately low temperatures) and summer (low flow, higher temperatures). We used literature information and gut contents analyses to determine feeding guilds and stable isotope analysis to estimate mean trophic position of local fish assemblages. During June and August 2006, we collected over 1000 tissue samples from four habitats (main channel, secondary channels, tertiary channels and backwaters) distributed within four hydrologic connectivity gradients. 3. Mean trophic position differed among feeding guilds and seasons, with highest values in spring. Mean trophic position of fish assemblages, variability in trophic position and food chain length (maximum trophic position) of the two dominant piscivore species (Micropterus salmoides and M. dolomieu) in both seasons were significantly associated with habitat along the lateral connectivity gradient. Food chain length peaked in tertiary channels in both seasons, probably due to higher species diversity of prey at these habitats. We infer that food chain length and trophic position of fish assemblages were lower in backwater habitats in the summer mainly because of the use of alternative food sources in these habitats. 4. A greater number of conspecifics exhibited significant among‐habitat variation in trophic position during the summer, indicating that low river stages can constrain fish movements in the Upper Mississippi River. 5. Results of this study should provide a better understanding of the fundamental structure of large river ecosystems and an improved basis for river rehabilitation and management through knowledge of the importance of lateral complexity in rivers.     

Metabolic patch dynamics in small headwater streams: exploring spatial and temporal variability in benthic processes

1. To gain a better understanding of the heterotrophic nature of small headwater streams in forested landscapes we explored the spatial and temporal variability of in‐stream organic matter processes. Three methods were used to measure the benthic metabolism of different in‐stream habitats in seven streams throughout a calendar year. This allowed us to analyse the contribution of various metabolic habitats (i.e. sediment, leaf litter, cobbles) to in‐stream metabolism during a natural flow regime. Furthermore, it allowed us to define in‐stream patchiness based on functional rather than structural elements. 2. Bacterial growth, measured using a leucine assay, displayed a quadratic relationship over time with a peak in warmer months and consistently higher bacterial growth in fine depositional (3.00–710.64 mg C m^?2 day^?1) than coarse gravel (38.84–582.85 mg C m^?2 day^?1) sediments. 3. Community metabolism, measured using dissolved oxygen chambers, showed distinct diel patterns and consistently greater net daily metabolism in leaf packs (?261.76 to ?24.50 mg C m^?2 day^?1) than fine depositional sediments (?155.00 to ?15.56 mg C m^?2 day^?1). Coarse gravel sediments (?49.55 to ?16.88 mg C m^?2 day^?1) and cobble habitats (?151.98 to 55.38 mg C m^?2 day^?1) exhibited the lowest metabolic rates. Modelled whole‐stream metabolism was highly variable among streams and temporal patterns appeared driven by temperature and the relative contribution of patch configuration as a function of flow. 4. Cellulose decomposition potential showed higher rates of microbial activity in fine depositional compared to coarse gravel sediments (30.5 and 29.1 kg average cotton tensile strength loss respectively), though there were higher rates of thread loss indicative of macroinvertebrate activity in gravel compared to depositional sediment (21% and 13% average thread loss respectively), with a slight quadratic trend. The high variability among habitats, streams and over time in this integrative measure may be explained by variability in local microbial activity as well as the potential for macroinvertebrates to contribute across patches. 5. There were strong relationships among benthic processes and habitat structure, nutrient status, stream temperature and flow. Different habitats had distinct metabolic characteristics and these characteristics appear to influence stream food webs and biogeochemical cycling depending on the relative abundance of habitats. Generally, within habitat variability was less than among habitat variability and among stream variability was less than temporal variability. Hence, in terms of the spatial and temporal heterogeneity of benthic processes, these small headwater streams showed predictable metabolic patterns. However, there were few correlations between differing measures of benthic metabolism at the same patch and this suggests that caution should be taken when attempting to infer the rates of one level of metabolic activity (e.g. whole community metabolism) based on another (e.g. bacterial productivity).     

Complex life cycles in a pond food web: effects of life stage structure and parasites on network properties,trophic positions and the fit of a probabilistic niche model

Most food webs use taxonomic or trophic species as building blocks, thereby collapsing variability in feeding linkages that occurs during the growth and development of individuals. This issue is particularly relevant to integrating parasites into food webs because parasites often undergo extreme ontogenetic niche shifts. Here, we used three versions of a freshwater pond food web with varying levels of node resolution (from taxonomic species to life stages) to examine how complex life cycles and parasites alter web properties, the perceived trophic position of organisms, and the fit of a probabilistic niche model. Consistent with prior studies, parasites increased most measures of web complexity in the taxonomic species web; however, when nodes were disaggregated into life stages, the effects of parasites on several network properties (e.g., connectance and nestedness) were reversed, due in part to the lower trophic generality of parasite life stages relative to free-living life stages. Disaggregation also reduced the trophic level of organisms with either complex or direct life cycles and was particularly useful when including predation on parasites, which can inflate trophic positions when life stages are collapsed. Contrary to predictions, disaggregation decreased network intervality and did not enhance the fit of a probabilistic niche model to the food webs with parasites. Although the most useful level of biological organization in food webs will vary with the questions of interest, our results suggest that disaggregating species-level nodes may refine our perception of how parasites and other complex life cycle organisms influence ecological networks.     

Rewiring and indirect effects underpin modularity reshuffling in a marine food web under environmental shifts

Species are characterized by physiological and behavioral plasticity, which is part of their response to environmental shifts. Nonetheless, the collective response of ecological communities to environmental shifts cannot be predicted from the simple sum of individual species responses, since co‐existing species are deeply entangled in interaction networks, such as food webs. For these reasons, the relation between environmental forcing and the structure of food webs is an open problem in ecology. To this respect, one of the main problems in community ecology is defining the role each species plays in shaping community structure, such as by promoting the subdivision of food webs in modules—that is, aggregates composed of species that more frequently interact—which are reported as community stabilizers. In this study, we investigated the relationship between species roles and network modularity under environmental shifts in a highly resolved food web, that is, a “weighted” ecological network reproducing carbon flows among marine planktonic species. Measuring network properties and estimating weighted modularity, we show that species have distinct roles, which differentially affect modularity and mediate structural modifications, such as modules reconfiguration, induced by environmental shifts. Specifically, short‐term environmental changes impact the abundance of planktonic primary producers; this affects their consumers’ behavior and cascades into the overall rearrangement of trophic links. Food web re‐adjustments are both direct, through the rewiring of trophic‐interaction networks, and indirect, with the reconfiguration of trophic cascades. Through such “systemic behavior,” that is, the way the food web acts as a whole, defined by the interactions among its parts, the planktonic food web undergoes a substantial rewiring while keeping almost the same global flow to upper trophic levels, and energetic hierarchy is maintained despite environmental shifts. This behavior suggests the potentially high resilience of plankton networks, such as food webs, to dramatic environmental changes, such as those provoked by global change.