Species loss and secondary extinctions in simple and complex model communities

1. The loss of a species from an ecological community can trigger a cascade of secondary extinctions. Here we investigate how the complexity (connectance) of model communities affects their response to species loss. Using dynamic analysis based on a global criterion of persistence (permanence) and topological analysis we investigate the extent of secondary extinctions following the loss of different kinds of species. 2. We show that complex communities are, on average, more resistant to species loss than simple communities: the number of secondary extinctions decreases with increasing connectance. However, complex communities are more vulnerable to loss of top predators than simple communities. 3. The loss of highly connected species (species with many links to other species) and species at low trophic levels triggers, on average, the largest number of secondary extinctions. The effect of the connectivity of a species is strongest in webs with low connectance. 4. Most secondary extinctions are due to direct bottom-up effects: consumers go extinct when their resources are lost. Secondary extinctions due to trophic cascades and disruption of predator-mediated coexistence also occur. Secondary extinctions due to disruption of predator-mediated coexistence are more common in complex communities than in simple communities, while bottom-up and top-down extinction cascades are more common in simple communities. 5. Topological analysis of the response of communities to species loss always predicts a lower number of secondary extinctions than dynamic analysis, especially in food webs with high connectance.     

图论在RNA二级结构中的应用

图论是以图为研究对象的数学分支,是一门研究事物对象在图表示法中的特征与性质的学科。鉴于RNA二级结构在功能基因组研究中的重要地位,已发展了用二维图解表示法描述RNA二级结构。文章介绍了用于RNA二级结构图解表示法的两种图,即树图和对偶图的构造规则。并在树图表示基础上产生Laplacian矩阵和相应本征值谱。以有害突变预测和类RNA模体设计的例子,说明图论在RNA二级结构中的应用,同时对可能存在的一些问题做了讨论。     

Food web quantification using secondary production analysis: predaceous invertebrates of the snag habitat in a subtropical river

1. Secondary production was estimated for Plecoptera, Odonata and Megaloptera (mostly large predators) occurring on the snag habitat of a subtropical blackwater river in the southeastern U.S.A. Coastal Plain for 2 years. Production estimates and gut analyses were used in estimating species‐specific ingestion to construct a quantitative food web of the predator portion of the invertebrate assemblage. Neither basal resources (e.g. detritus) nor predaceous vertebrates (e.g. fishes) were considered in this analysis. A discharge‐specific model of snag‐habitat availability was used to convert values per m² of snag surface to values per m² of river bed.
2. These three orders included the major large predators on the snag habitat, as well as two detritivorous stoneflies. The major predators were the hellgrammite (Corydaluscornutus), five perlid stoneflies (Paragnetinakansensis, Perlestaplacida, Neoperlaclymene, Acroneuriaevoluta and Acroneuriaabnormis) and two dragonflies (Neurocorduliamolesta and Boyeriavinosa). The detritivores were Pteronarcysdorsata and Taeniopteryxlita.
3. Total predator production was high, but varied from only 7.1 to 7.4 g dry mass (DM) m^?2 y^?1 of snag surface (2.4–2.7 g DM m^?2 y^?1 of river bed) over two years. Corydalus was the largest predator and had the highest production (2.8–3.1 g DM m^?2 of snag surface). The most productive stoneflies were Perlesta (0.7–1.0 g DM m^?2 of snag surface) and Paragnetina (1.0–1.3 g DM m^?2 of snag surface). The most productive dragonfly was Neurocordulia (0.7–1.9 g DM m^?2 of snag surface). Production of the non‐predaceous stoneflies was 1.0–2.3 g DM m^?2 of snag surface. Production values per m² of river bed were 2–3.5 times lower than the values per m² snag surface.
4. Measurement of ingestion fluxes within the predator portion of the food web showed that predaceous invertebrates were primarily supported by chironomid and mayfly prey. However, the greatest consumption of chironomids and mayflies was by omnivorous hydropsychid caddisflies, which had a considerably higher production than the larger predators. There was a hierarchy of feeding with Corydalus as top predator consuming all other groups, followed in order by dragonflies, stoneflies and hydropsychids. Although the feeding hierarchy suggested the presence of four predatory trophic levels within the invertebrate assemblage, calculations of trophic position indicated there were less than two. With primary consumers (e.g. midges) having a trophic position of 2, Corydalus had a trophic position of only 3.5.
5. A relatively high fraction of invertebrate production was consumed by predaceous invertebrates, ranging from 9 to >100% for various primary consumer groups, with total consumption representing 52% of total production. Because these estimates do not include vertebrate consumption or emergence, it means that a high fraction of larval mortality is due to predation.     

Parasites reduce food web robustness because they are sensitive to secondary extinction as illustrated by an invasive estuarine snail

A robust food web is one in which few secondary extinctions occur after removing species. We investigated how parasites affected the robustness of the Carpinteria Salt Marsh food web by conducting random species removals and a hypothetical, but plausible, species invasion. Parasites were much more likely than free-living species to suffer secondary extinctions following the removal of a free-living species from the food web. For this reason, the food web was less robust with the inclusion of parasites. Removal of the horn snail, Cerithidea californica, resulted in a disproportionate number of secondary parasite extinctions. The exotic Japanese mud snail, Batillaria attramentaria, is the ecological analogue of the native California horn snail and can completely replace it following invasion. Owing to the similarities between the two snail species, the invasion had no effect on predator–prey interactions. However, because the native snail is host for 17 host-specific parasites, and the invader is host to only one, comparison of a food web that includes parasites showed significant effects of invasion on the native community. The hypothetical invasion also significantly reduced the connectance of the web because the loss of 17 native trematode species eliminated many links.     

Cascading extinctions and community collapse in model food webs

Species loss in ecosystems can lead to secondary extinctions as a result of consumer–resource relationships and other species interactions. We compare levels of secondary extinctions in communities generated by four structural food-web models and a fifth null model in response to sequential primary species removals. We focus on various aspects of food-web structural integrity including robustness, community collapse and threshold periods, and how these features relate to assumptions underlying different models, different species loss sequences and simple measures of diversity and complexity. Hierarchical feeding, a fundamental characteristic of food-web structure, appears to impose a cost in terms of robustness and other aspects of structural integrity. However, exponential-type link distributions, also characteristic of more realistic models, generally confer greater structural robustness than the less skewed link distributions of less realistic models. In most cases for the more realistic models, increased robustness and decreased levels of web collapse are associated with increased diversity, measured as species richness S, and increased complexity, measured as connectance C. These and other results, including a surprising sensitivity of more realistic model food webs to loss of species with few links to other species, are compared with prior work based on empirical food-web data.     

Regime shifts in marine communities: a complex systems perspective on food web dynamics

Species composition and habitats are changing at unprecedented rates in the world''s oceans, potentially causing entire food webs to shift to structurally and functionally different regimes. Despite the severity of these regime shifts, elucidating the precise nature of their underlying processes has remained difficult. We address this challenge with a new analytic approach to detect and assess the relative strength of different driving processes in food webs. Our study draws on complexity theory, and integrates the network-centric exponential random graph modelling (ERGM) framework developed within the social sciences with community ecology. In contrast to previous research, this approach makes clear assumptions of direction of causality and accommodates a dynamic perspective on the emergence of food webs. We apply our approach to analysing food webs of the Baltic Sea before and after a previously reported regime shift. Our results show that the dominant food web processes have remained largely the same, although we detect changes in their magnitudes. The results indicate that the reported regime shift may not be a system-wide shift, but instead involve a limited number of species. Our study emphasizes the importance of community-wide analysis on marine regime shifts and introduces a novel approach to examine food webs.     

Organic contaminant exposure in the Lake St. Clair food web

Chemical concentrations and distributions in an aquatic food web were studied to quantify the relative importance of chemical properties versus food web processes in determining exposure dynamics of organic contaminants in aquatic ecosystems. Five organochlorines were measured (Pentachlorobenzene QCB, Hexachlorobenzene HCB, Octachlorostyrene OCS, Dichlorodiphenyldichloroethylene DDE and Polychlorinated Biphenyls PCBs) in the food web of Lake St. Clair. Levels of QCB in aquatic organisms ranged from 1.0 to 25 µg kg^–1 lipid, and levels of HCB ranged from 10 to 410 µg kg^–1 lipid. More elevated concentrations of OCS (13 to 392 µg kg^–1 lipid), DDE (162 to 11 986 µg kg^–1 lipid) and PCB (650 to 64 900 µg kg^–1 lipid) were observed. Organism — water equilibrium ratios were calculated for all species sampled to quantify the importance of food web processes in regulating contaminant exposure dynamics. Correlations of organism — water equilibrium ratios with body size were not significant for QCB, HCB and OCS (P>0.1), but were found to be significant for DDE and PCB (P<0.01).Results support the conclusion that both chemical properties and food web dynamics regulate the distribution and concentration of organochlorines in aquatic ecosystems. Food web processes are important, however, for chemicals, that are not metabolized and have octanol — water partition coefficients (log K _ow) greater than 5.5.     

Species-rich ecosystems are vulnerable to cascading extinctions in an increasingly variable world

Global warming leads to increased intensity and frequency of weather extremes. Such increased environmental variability might in turn result in increased variation in the demographic rates of interacting species with potentially important consequences for the dynamics of food webs. Using a theoretical approach, we here explore the response of food webs to a highly variable environment. We investigate how species richness and correlation in the responses of species to environmental fluctuations affect the risk of extinction cascades. We find that the risk of extinction cascades increases with increasing species richness, especially when correlation among species is low. Initial extinctions of primary producer species unleash bottom-up extinction cascades, especially in webs with specialist consumers. In this sense, species-rich ecosystems are less robust to increasing levels of environmental variability than species-poor ones. Our study thus suggests that highly species-rich ecosystems such as coral reefs and tropical rainforests might be particularly vulnerable to increased climate variability.     

Local adaptation to temperature conserves top-down control in a grassland food web

A fundamental limitation in many climate change experiments is that tests represent relatively short-term 'shock' experiments and so do not incorporate the phenotypic plasticity or evolutionary change that may occur during the gradual process of climate change. However, capturing this aspect of climate change effects in an experimental design is a difficult challenge that few studies have accomplished. I examined the effect of temperature and predator climate history in food webs composed of herbaceous plants, generalist grasshopper herbivores and spider predators across a natural 4.8°C temperature gradient spanning 500 km in northeastern USA. In these grasslands, the effects of rising temperatures on the plant community are indirect and arise via altered predator-herbivore interactions. Experimental warming had no direct effect on grasshoppers, but reduced predation risk effects by causing spiders from all study sites to seek thermal refuge lower in the plant canopy. However, spider thermal tolerance corresponded to spider origin such that spiders from warmer study sites tolerated higher temperatures than spiders from cooler study sites. As a consequence, the magnitude of the indirect effect of spiders on plants did not differ along the temperature gradient, although a reciprocal transplant experiment revealed significantly different effects of spider origin on the magnitude of top-down control. These results suggest that variation in predator response to warming may maintain species interactions and associated food web processes when faced with long term, chronic climate warming.     

Linearity in the aggregate effects of multiple predators in a food web

Theory in community ecology often assumes that predator species have similar indirect effects and thus can be treated mathematically as a single functional unit (e.g. guild or trophic level). This assumption is questionable biologically because predator species typically differ in their effects, creating the potential for nonlinearities when they coexist. We evaluated the nature of indirect effects caused by three species of hunting spider predators, singly and in multiple species combinations, on grass and herb plants in experimental old-field food webs. Despite the potential for nonlinearity, indirect effects in different multiple predator combinations consistently did not differ significantly from the respective means of the single species effects. Thus, for this experimental system, the whole was simply the average of the parts. Consequently, models which abstract predator species as single trophic levels would successfully predict indirect effects in this system regardless of the composition of the predator fauna.     

The relative importance of herbivory and carnivory on the distribution of energy in a stochastic tri-trophic food web

A three-state, discrete-time Markov chain is used to model the dynamics of energy flow in a tri-trophic food web. The distribution of energy in the three trophic levels is related to the rates of flow between the trophic levels and calculated for the entire range of possible flow values. These distributions are then analysed for stability and used to test the idea that plants are resource-limited and herbivores are predation-limited. Low rates of death and decomposition, when coupled with low rates of herbivory and carnivory, tend to destabilize this food web. Food webs with higher rates of death and decomposition are relatively more stable regardless of rates of herbivory and carnivory. Plants are more prone to resource-limitation and herbivores are, in general, limited by their predators, which supports Hairston et al. (Am. Nat. 94 (1960) 421). The rate of decomposition often mediates the roles of top-down and bottom-up control of energy flow in the food web.     

Pelagic food web interactions among benthic invertebrates and trout in mountain lakes

1. Benthic chironomid larvae and the amphipod Gammarus lacustris have been observed in the pelagic habitats of many mountain lakes. The main goal of this study was to determine if chironomid larvae and gammarids potentially affect predator–prey and nutrient dynamics in pelagic food webs of mountain lakes. 2. Eighty‐six mountain lakes were surveyed in Alberta and eastern British Columbia during the years 1965–1984, 1991–2004 and 2005–2007. Pelagic chironomid larvae were found in 86% of these lakes, and pelagic gammarids were found in 29% of lakes. Densities of pelagic chironomid larvae were 92% lower in lakes with pelagic gammarids and 76% lower in lakes with trout (P < 0.05). Intraguild predation of trout on gammarids appeared to reduce predation pressure on chironomid larvae. Gammarids consumed in vitro about 1 chironomid per gammarid per day or about 20% of their body mass in chironomid biomass per day. 3. Concentrations of total dissolved P and N, particulate C, and chlorophyll‐a increased with increasing densities of pelagic gammarids and chironomid larvae in situ (R² = 0.14 ± 0.19 SD, P < 0.1) and in vitro (P < 0.001). 4. Our findings suggest that gammarids and chironomid larvae are linked as predators and prey in pelagic food webs, possibly stimulating phytoplankton abundance via nutrient release.     

Vertical planktonic structure in the central basin of Lake Baikal in summer 1999, with special reference to the microbial food web

Planktonic microbial interactions in the central basin of Lake Baikal were examined on a summer day in 1999. The subsurface maxima of bacterial abundance and chlorophyll concentration were recorded at the same depth, whereas the vertical distribution of heterotrophic nanoflagellates was the inverse of those of bacteria and picophytoplankton. Release of extracellular organic car-bon (EOC) from phytoplankton was estimated by the NaH¹⁴CO₃ method as 2.4µgCl^–1day^–1. Bacterial production (4.3µgCl^–1day^–1), estimated in a bottle incubation experiment using size-fractionated water samples, exceeded the EOC released. Thus, other supplying sources of organic matter are needed for the bacterial production. Grazing (2.6µgCl^–1day^–1) was also estimated in the experiment and accounted for 60% of the bacterial production. This is the first report on the microbial food web in the central basin of Lake Baikal.     

Insect-damaged fossil leaves record food web response to ancient climate change and extinction

Plants and herbivorous insects have dominated terrestrial ecosystems for over 300 million years. Uniquely in the fossil record, foliage with well-preserved insect damage offers abundant and diverse information both about producers and about ecological and sometimes taxonomic groups of consumers. These data are ideally suited to investigate food web response to environmental perturbations, and they represent an invaluable deep-time complement to neoecological studies of global change. Correlations between feeding diversity and temperature, between herbivory and leaf traits that are modulated by climate, and between insect diversity and plant diversity can all be investigated in deep time. To illustrate, I emphasize recent work on the time interval from the latest Cretaceous through the middle Eocene (67-47 million years ago (Ma)), including two significant events that affected life: the end-Cretaceous mass extinction (65.5 Ma) and its ensuing recovery; and globally warming temperatures across the Paleocene-Eocene boundary (55.8 Ma). Climatic effects predicted from neoecology generally hold true in these deep-time settings. Rising temperature is associated with increased herbivory in multiple studies, a result with major predictive importance for current global warming. Diverse floras are usually associated with diverse insect damage; however, recovery from the end-Cretaceous extinction reveals uncorrelated plant and insect diversity as food webs rebuilt chaotically from a drastically simplified state. Calibration studies from living forests are needed to improve interpretation of the fossil data.     

Trophic relationships in a tropical stream food web assessed by stable isotope analysis

1. Stable isotope analysis, coupled with dietary data from the literature, was used to investigate trophic patterns of freshwater fauna in a tropical stream food web (Guadeloupe, French West Indies).
2. Primary producers (biofilm, algae and plant detritus of terrestrial origin) showed distinct δ¹³C signatures, which allowed for a powerful discrimination of carbon sources. Both autochthonous (¹³C-enriched signatures) and allochthonous (¹³C-depleted signatures) resources enter the food web. The migrating behaviour of fishes and shrimps between marine and freshwater during their life cycles can be followed by carbon isotopes. Here, shrimp δ¹³C signatures were shown to shift from −16‰ (for juveniles under marine influence) to −24.7‰ (for adults in freshwater habitats). For resident species, δ¹³C values partly reflected the species' habitat preferences along the river continuum : species living in river mouths were ¹³C-enriched in comparison with those collected upstream.
3. Nitrogen isotopic ratios were also discriminating and defined three main trophic guilds among consumers. The δ¹⁵N values of herbivores/detritivores were 5.0–8.4‰, omnivores 8.8–10.2‰ and carnivores 11–12.7‰.
4. Mixing model equations were employed to calculate the possible range of contribution made by respective food sources to the diet of each species. The results revealed the importance of omnivorous species and the dependence of riverine biota on terrestrial subsidies, such as leaf detritus and fruits. Finally, the abundance of shrimps and their feeding habits placed in relief their key role in tropical freshwater food webs. Isotopic analysis provides a useful tool for assessing animal feeding patterns.     

Asymmetrical food web responses in trophic-level richness, biomass, and function following lake acidification

We tested for disproportional changes in annual and seasonal species richness and biomass among five trophic levels (phytoplankton, herbivorous, omnivorous, and carnivorous zooplankton, and fish) as well as altered trophic structure and ecosystem function following the 5-year experimental acidification of Little Rock Lake (Wisconsin, USA) from pH 6.1 to 4.7. Abiotic and biotic controls of trophic level response during acidification were also identified. Asymmetric reductions of species richness among trophic levels, separated by life stage and feeding type, were evident and changes in trophic structure were most pronounced by the end of the acidification period. Relative declines in richness of fish and zooplankton were greater than phytoplankton, which were generally unaffected, leading to a reduction of upper trophic level diversity. Each of the lower four trophic levels responded to a distinct combination of abiotic and biotic variables during acidification. pH was identified as a direct driver of change for only carnivorous zooplankton, while all other trophic levels were affected more by indirect interactions caused by acidification. Fluctuations in ecosystem function (zooplankton biomass and primary production) were also evident, with losses at all trophic levels only detected during the last year of acidification. The acidified basin displayed a tendency for greater variation in biomass for upper trophic levels relative to reference conditions implying greater unpredictability in ecosystem function. Together, these results suggest that trophic asymmetry may be an important and recurring feature of ecosystem response to anthropogenic stress.     

Duckling response to changes in the trophic web of acidified lakes

We reared American Black Duck (Anas rubripes Brewster) and Common Goldeneye (Bucephala clangula Linnaeus) ducklings on two Quebec laurentian lakes in which we manipulated brook trout populations (Salvelinus fontinalis Mitchill), lake acidity and lake productivity to relate waterfowl foraging to trophic status of lakes. We developed a preliminary model to assess the effects of lake acidity and productivity, fish predation and interspecific fish/duck competition in relation to available food (aquatic invertebrates). We then validated the model using a factorial analysis of the relationships between the variables pertaining to the diet of the fish and ducklings, and the environmental characteristics of the lakes (acidity, biological production and fish predation).The first factorial axis can be interpreted in terms of biological productivity, while the second axis illustrates the effect that fish have on the quantity and type of food available to ducklings. Two different trends appear to occur depending on whether the carrying capacity of the lake is reduced by acidification of the water or increase through liming or fertilization. In the first case, fish predation appears to have a marked effect on available food, whereas in the second case, interspecific fish/duck competition is apparently to blame for changes in the diet of ducklings. In both instances, but to a lesser extent, fish compete increasingly (exploitation and/or interference) with the ducklings, forcing them to feed to a greater extent in riparian sites that are less accessible to fish.     

Structure of planktonic microbial food web in a brackish stratified Siberian lake

The distribution of primary components of the microbial community (autotrophic pico- and nanoplankton, phototrophic bacteria, heterotrophic bacteria, microscopic fungi, heterotrophic flagellates, ciliates and heliozoa) in the water column of Lake Shira, a steppe brackish-water, stratified lake in Khakasia, Siberia (Russia), were assessed in midsummer. Bacterioplankton was the main component of the planktonic microbial community, accounting for 65.3 to 75.7% of the total microbial biomass. The maximum concentration of heterotrophic bacteria were recorded in the monimolimnion of the lake. Autotrophic microorganisms contributed more significantly to the total microbial biomass in the pelagic zone (20.2–26.5%) than in the littoral zone of the lake (8.7–14.9%). First of all, it is caused by development of phototrophic sulphur bacteria at the oxic-anoxic boundary. The concentrations of most aerobic phototrophic and heterotrophic microorganisms were maximal in the upper mixolimnion. Heterotrophic flagellates dominated the protozoan populations. Ciliates were minor component of the planktonic microbial community of the lake. Heterotrophic flagellates were the most diverse group of planktonic eucaryotes in the lake, which represented by 36 species. Facultative and obligate anaerobic flagellates were revealed in the monimolimnion. There were four species of Heliozoa and only three of ciliates in the lake.     

Trophic interactions within the microbial food web in the South China Sea revealed by size-fractionation method

To define nanoflagellate-bacteria interactions and potential trophic levels within the microbial food web in the oligotrophic South China Sea, we conducted fourteen size-fractionation experiments in which seawater was filtered through 1, 2, 5, 10, 20, 60, and 200 μm membranes or meshes and the growth of four groups of picoplankton, Prochlorococcus, Synechococcus, high DNA heterotrophic bacteria, and low DNA heterotrophic bacteria were monitored in each filtrate after 24 hours of incubation. Removing grazers by filtration would relieve the grazing pressure on lower trophic levels which finally influenced the net growth rates of picoplankton. The growth patterns of Prochlorococcus and Synechococcus were similar, with higher growth rates in the < 1 μm or < 2 μm treatments, a second peak in the < 10 μm treatments and often a third peak in the < 200 μm treatments. The net growth rates of low DNA heterotrophic bacteria were little influenced by size-fractionation. Due to a subgroup of high DNA heterotrophic bacteria with larger size and higher DNA content which appeared to resist the grazing by < 5 μm nanoflagellates, the net growth rates of high DNA heterotrophic bacteria were higher in the < 2 μm or < 5 μm treatments with a second peak in the < 60 μm treatments. A general pattern of five potential trophic levels (< 2 μm, 2-5 μm, 5-10 μm, 10-60 μm, 60-200 μm) was revealed combining all the experiments, confirming the existence of multiple trophic levels within the microbial food web in the oligotrophic South China Sea.