The probabilistic niche model reveals substantial variation in the niche structure of empirical food webs

The structure of food webs, complex networks of interspecies feeding interactions, plays a crucial role in ecosystem resilience and function, and understanding food web structure remains a central problem in ecology. Previous studies have shown that key features of empirical food webs can be reproduced by low-dimensional "niche" models. Here we examine the form and variability of food web niche structure by fitting a probabilistic niche model to 37 empirical food webs, a much larger number of food webs than used in previous studies. The model relaxes previous assumptions about parameter distributions and hierarchy and returns parameter estimates for each species in each web. The model significantly outperforms previous niche model variants and also performs well for several webs where a body-size-based niche model performs poorly, implying that traits other than body size are important in structuring these webs' niche space. Parameter estimates frequently violate previous models' assumptions: in 19 of 37 webs, parameter values are not significantly hierarchical, 32 of 37 webs have nonuniform niche value distributions, and 15 of 37 webs lack a correlation between niche width and niche position. Extending the model to a two-dimensional niche space yields networks with a mixture of one- and two-dimensional niches and provides a significantly better fit for webs with a large number of species and links. These results confirm that food webs are strongly niche-structured but reveal substantial variation in the form of the niche structuring, a result with fundamental implications for ecosystem resilience and function.     

Coexistence of the niche and neutral perspectives in community ecology

The neutral theory for community structure and biodiversity is dependent on the assumption that species are equivalent to each other in all important ecological respects. We explore what this concept of equivalence means in ecological communities, how such species may arise evolutionarily, and how the possibility of ecological equivalents relates to previous ideas about niche differentiation. We also show that the co-occurrence of ecologically similar or equivalent species is not incompatible with niche theory as has been supposed, because niche relations can sometimes favor coexistence of similar species. We argue that both evolutionary and ecological processes operate to promote the introduction and to sustain the persistence of ecologically similar and in many cases nearly equivalent species embedded in highly structured food webs. Future work should focus on synthesizing niche and neutral perspectives rather than dichotomously debating whether neutral or niche models provide better explanations for community structure and biodiversity.     

The models of niche and their application

Having studied the definitions of niche proposed by different ecologists, I have proposed a quantitative method of niche which can be applied to plants. Accordingly, the niche of an operational taxonomic unit (OTU) has been described by a mapping from its environmental set to the unit interval [0, 1], which enables a model of niche to be mathematically operational. The concepts of fundamental niche, realized niche, time niche, etc., may be described by using mathematical models related to each other, and the geometrical relationships between them can be revealed by a multi-dimensional surface. The uni-factor models are built upon the condition that the other factors are optimal for OTU, which are particular cases of the multi-factor models. The establishment of the quantitative relationship between these two kinds of models makes it possible to find out the plants' fundamental niche by doing uni-factor experiments. This may simplify the experiments in which the parameters in a practically applied model are to be estimated. The niche index introduced in this paper is related to average level and aftereffect of plant responses to the effects of its environment (i.e. “inertia”), thus it should be the basis of the simulation of plant seed yield and of its environmental evaluation. Accordingly, models of niche index, of plant seed yield, of plant growth and of environmental evaluation have been built which can be applied to the environmental evaluation or the prediction and management of plant (crop) production, etc.As an example of application, the models of wheat yield and its environmental assessment have been established and practically tested. The results of testing the model of wheat yield showed that the relative errors are 8% and 7.2%, respectively, in 1984 and 1986. The results of the environmental assessment of wheat reveal the fact that the insufficiency of the soil moisture at the 2th and 3th stages is the main restriction of the production of the wheat in Dinxi, Gansu Province, China.     

Can variations in the spatial distribution at sea and isotopic niche width be associated with consistency in the isotopic niche of a pelagic seabird species?

This study tested for fluctuations on short-term consistency (within about 1 month) in the isotopic niche of a pelagic seabird species. Short-term consistency in the isotopic niche was assessed using a wide-ranging apex predator, the Cory’s shearwaters Calonectris diomedea, along a 3-year study (2010–2012), during both the pre-laying and chick-rearing periods, with markedly inter- and intra-annual differences in the foraging spatial distribution at sea and isotopic niche width. We used individual movement data and stable isotope data, analysed using recent metrics based in a Bayesian framework, of 69 adults breeding on a small neritic island in the North Atlantic (39°24′N, 009°30′W). As expected, our results confirm that isotopic niche expansion could arise via increased variation in spatial distribution at sea among individuals. Results suggest fluctuations on short-term consistency in the isotopic niche of Cory’s shearwaters related to their different foraging patterns among periods and, ultimately, to presumably temporal changes in the availability and predictability of food resources. Short-term consistency in the isotopic niche was higher and persistent during periods when the population showed an intermediate isotopic niche width and absent when isotopic niche was either smaller or larger during the study period. These results suggest that consistency in the isotopic niche is an important characteristic of this population during the breeding period that may fluctuate depending on resources availability and should be important to understand the dynamics of foraging ecology of pelagic seabirds in general.     

Mapping the niche space of soil microorganisms using taxonomy and traits

The biodiversity of microbial communities has important implications for the stability and functioning of ecosystem processes. Yet, very little is known about the environmental factors that define the microbial niche and how this influences the composition and activity of microbial communities. In this study, we derived niche parameters from physiological response curves that quantified microbial respiration for a diverse collection of soil bacteria and fungi along a soil moisture gradient. On average, soil microorganisms had relatively dry optima (0.3 MPa) and were capable of respiring under low water potentials (-2.0 MPa). Within their limits of activity, microorganisms exhibited a wide range of responses, suggesting that some taxa may be able to coexist by partitioning the moisture niche axis. For example, we identified dry-adapted generalists that tolerated a broad range of water potentials, along with wet-adapted specialists with metabolism restricted to less-negative water potentials. These contrasting ecological strategies had a phylogenetic signal at a coarse taxonomic level (phylum), suggesting that the moisture niche of soil microorganisms is highly conserved. In addition, variation in microbial responses along the moisture gradient was linked to the distribution of several functional traits. In particular, strains that were capable of producing biofilms had drier moisture optima and wider niche breadths. However, biofilm production appeared to come at a cost that was reflected in a prolonged lag time prior to exponential growth, suggesting that there is a trade-off associated with traits that allow microorganisms to contend with moisture stress. Together, we have identified functional groups of microorganisms that will help predict the structure and functioning of microbial communities under contrasting soil moisture regimes.     

Scenarios of change in the realized climatic niche of mountain carnivores and ungulates

Mountains are among the natural systems most affected by climate change, and mountain mammals are considered particularly imperiled, given their high degree of specialization to narrow tolerance bands of environmental conditions. Climate change mitigation policies, such as the Paris Agreement, are essential to stem climate change impacts on natural systems. But how significant is the Paris Agreement to the survival of mountain mammals? We investigated how alternative emission scenarios may determine change in the realized climatic niche of mountain carnivores and ungulates in 2050. We based our predictions of future change in species niches based on how species have responded to past environmental changes, focusing on the probabilities of niche shrink and niche stability. We found that achieving the Paris Agreement's commitments would substantially reduce climate instability for mountain species. Specifically, limiting global warming to below 1.5°C would reduce the probability of niche shrinkage by 4% compared with a high-emission scenario. Globally, carnivores showed greater niche shrinkage than ungulates, whereas ungulates were more likely to shift their niches (i.e., face a level of climate change that allows adaptation). Twenty-three species threatened by climate change according to the IUCN Red List had greater niche contraction than other species we analyzed (3% higher on average). We therefore argue that climate mitigation policies must be coupled with rapid species-specific conservation intervention and sustainable land-use policies to avoid high risk of loss of already vulnerable species.     

人工封育区沙化草地植被生态位研究

采用样线和样方结合法对宁夏人工封育草原进行野外调查,运用重要值、Levins生态宽度指数和Pianka生态位重叠指数对封育外围区、边缘区、核心区3种不同措施下的植物生态位宽度及生态位重叠进行分析,以揭示人工封育区沙化草地植被生态位变化规律。结果表明：在整个人工封育区,重要值之和较大的为黑沙蒿（Artemisia ordosica Krasch.）和刺沙蓬（Salsolaruthenica IIjin.）,分别为689.53、455.83。外围区与边缘区生态位宽度最大的均为黑沙蒿,生态位宽度分别为0.846、0.790,核心区生态位宽度最大的是阿尔泰狗娃花（Heteropappus altaicus（Willd.）Novopokr.）,生态位宽度为0.640,是人工封育区的优势种。生态位重叠计测结果表明,植被的生态位宽度和生态位重叠并不存在直接的线性关系;生态位重叠度平均值和重叠对百分数表现为外围区〉核心区〉边缘区。不同封育措施间生态位宽度和生态位重叠度的差异表明适度封育有利于草地植被恢复,但随着封育时间延长,植物的再生和幼苗的形成会受到一定程度抑制。     

宁夏盐池不同封育措施下的植物生态位研究

运用Levins生态位宽度指数及Pianka生态位重叠指数,对宁夏盐池柳林堡人工封育草场不同措施（老封育区、新封育区、对照区）下的植物生态位宽度及生态位重叠度进行计算,从生态位角度揭示不同措施下的植被恢复情况。结果表明：老封育区、新封育区和对照区的主要建群种生态位宽度均有较大的差异,老封育区宽度值最大的是耐旱性极强的阿尔泰狗哇花（Heteropappus altaicus（Willd.）Novopokr.）、丝叶山苦荬（Lxeris chinensis var.graminifolia（Ledeb.）H.C.Fu）、叉枝鸦葱（Scorzonera divaricata Turcz.）,说明随着封育时间的延长,封育区植被有旱生化方向发展的趋势;新封育区的优势种是丝叶山苦荬、黑沙蒿（Artemisia ordosica Krasch.）、苦豆子（Sophora alopecuroides）、刺沙蓬（S.ruthenica Iljin）,且4种植物生态位宽度接近,对资源环境的利用更为均衡;对照区的优势种是黑沙蒿、苦豆子、刺沙蓬,宽度值分别为0.729、0.666、0.540。同时,3种措施的生态位重叠结果均表明,生态位宽度大的物种不一定和其他物种有大的重叠指数,较高的生态位宽度和较高的生态位重叠度之间并不存在直接的线性关系。这一现象从另外一个角度说明植被恢复过程中环境资源存在着高度的空间异质性。     

Short- and long-term consistency in the foraging niche of wandering albatrosses

The wandering albatross (Diomedea exulans) is regarded as a generalist predator, but can it be consistent in its foraging niche at an individual level? This study tested short- and long-term consistency in the foraging niche in terms of habitat use, trophic level and, by inference, prey selection. Fieldwork was carried out at Bird Island, South Georgia, in May–October 2009, during the chick-rearing period. Blood (plasma and cells) and feathers for stable isotope analyses (δ¹³C and δ¹⁵N) were sampled from 35 adults on their return from a foraging trip during which they carried stomach temperature, activity and global positioning system loggers. Results suggest short-term consistency in foraging niche in relation to both oceanic water mass and trophic level, and long-term consistency in use of habitat. Consistent differences between individuals partly reflected sex-specific habitat preferences. The proportion of consistent individuals (i.e., with a narrow foraging niche) was estimated at c. 40?% for short-term habitat and trophic level (prey) preferences and 29?% for longer-term habitat preference, suggesting this is an important characteristic of this population and potentially of pelagic seabirds in general. Foraging consistency was not related to body condition or level of breeding experience; instead, it may reduce intraspecific competition.     

The ecological niche of Daphnia magna characterized using population growth rate

The concept of an organism's niche is central to ecological theory, but an operational definition is needed that allows both its experimental delineation and interpretation of field distributions of the species. Here we use population growth rate (hereafter, pgr) to define the niche as the set of points in niche space where pgr > 0. If there are just two axes to the niche space, their relationship to pgr can be pictured as a contour map in which pgr varies along the axes in the same way that the height of land above sea level varies with latitude and longitude. In laboratory experiments we measured the pgr of Daphnia magna over a grid of values of pH and Ca2+, and so defined its "laboratory niche" in pH-Ca2+ space. The position of the laboratory niche boundary suggests that population persistence is only possible above 0.5 mg Ca2+/L and between pH 5.75 and pH 9, though more Ca2+ is needed at lower pH values. To see how well the measured niche predicts the field distribution of D. magna, we examined relevant field data from 422 sites in England and Wales. Of the 58 colonized water bodies, 56 lay within the laboratory niche. Very few of the sites near the niche boundary were colonized, probably because pgr there is so low that populations are vulnerable to extinction by other factors. Our study shows how the niche can be quantified and used to predict field distributions successfully.     

Experimental verification of ecological niche modeling in a heterogeneous environment

The current range of ecological habitats occupied by a species reflects a combination of the ecological tolerance of the species, dispersal limitation, and competition. Whether the current distribution of a species accurately reflects its niche has important consequences for the role of ecological niche modeling in predicting changes in species ranges as the result of biological invasions and climate change. We employed a detailed data set of species occurrence and spatial variation in biotic and abiotic attributes to model the niche of a native California annual plant, Collinsia sparsiflora. We tested the robustness of our model for both the realized and fundamental niche by planting seeds collected from four populations, representing two ecotypes, into plots that fully represented the five-dimensional niche space described by our model. The model successfully predicted which habitats allowed for C. sparsiflora persistence, but only for one of the two source ecotypes. Our results show that substantial niche divergence has occurred in our sample of four study populations, illustrating the importance of adequately sampling and describing within-species variation in niche modeling.     

Herbivores and edaphic factors constrain the realized niche of a native plant

Biotic interactions, such as competition and herbivory, can limit plant species ranges to a subset of edaphically suitable habitats, termed the realized niche. Here we explored the role that herbivores play in restricting the niche of serpentine ecotypes of the native California annual Collinsia sparsiflora. We planted seeds from four populations into a range of natural field environments that varied in the presence/absence of naturally occurring C. sparsiflora and in predicted suitability for growth and survival of the serpentine ecotype of C. sparsiflora. Path analysis was then used to model the direct and herbivore-mediated indirect effects of environmental variables on the survival of C. sparsiflora serpentine ecotypes. We found that C. sparsiflora received more herbivory when planted into areas where serpentine ecotypes of C. sparsiflora were not predicted to persist, and that increased herbivory was associated with decreased survival, suggesting that herbivores may limit the distribution of C. sparsiflora serpentine ecotypes. Additionally, we demonstrated that edaphic environmental variables impacted the survival of C. sparsiflora serpentine ecotypes both directly and indirectly, by altering interactions with herbivores. These indirect effects were probably trait-mediated and probably occurred because edaphic factors may influence plant traits that, in turn, alter attractiveness to herbivores. Although the magnitude of direct effects exceeded the magnitude of indirect effects, many strong herbivore-mediated indirect effects were detected. Thus, interactions between the abiotic environment and insect herbivory contributed to restricting the niche of C. sparsiflora serpentine ecotypes to a subset of available habitat.     

Effects of photoacclimation on the light niche of corals: a process-based approach

The ecology of photosynthetic organisms is influenced by the need to adjust the photosynthetic apparatus to variable light environments (photoacclimation). In this study, we quantified different components of the photoacclimation process for a reef-building coral (Turbinaria mesenterina, Lamarck, 1816): including, variation in absorption cross-section, size of photosynthetic units, turnover time, chlorophyll content, and colony respiration. We used these calibrations to characterize this species’ light niche, and to determine the sensitivity of the niche boundaries to different processes of photoacclimation. Results showed that the breadth of the light niche was most sensitive to the size of the photosynthetic unit, absorption cross-section, and rates of respiration. Habitats with the highest light availability did not lead to maximal energy acquisition. This was because, although corals acclimated to high light have high rates of photosynthesis per unit chlorophyll, their chlorophyll content was strongly reduced. This suggests that potential energetic benefits that could be achieved through increased light harvesting (i.e., increased chlorophyll content) in high-light habitats are outweighed by costs associated with photoprotection. Such costs appear to place an upper bound on the habitat distributions of coral species. Our approach reveals how the photophysiological processes involved in photoacclimation interact to determine the light niche.     

Individual trophic specialisation and niche segregation explain the contrasting population trends of two sympatric otariids

Individual specialisation is increasingly recognised to be an ecological and evolutionary process having important consequences for population dynamics of vertebrates. The South American fur seal (SAFS) and the South American sea lion (SASL) are two otariid species with similar ecology that coexist in sympatry in the Uruguayan coast. These two species have contrasting trends and widely different population sizes. The underlying reasons for these population trends, unique in their geographical ranges, remain unknown. We studied the foraging ecology of these otariid species over 2 years at the individual- and population levels using the isotopic ratios (δ¹³C–δ¹⁵N) in whiskers of both sexes. We compared the isotope ratios between species and sexes and used several metrics to characterise the degree of overlap and distinctiveness in the use of isotopic niche space at the individual- and population levels. Interspecific trophic niche overlap was minimal, thus ruling out interspecific competition as the cause for the contrasting population trends of both species. At the intraspecific level, both species had sexual segregation in their foraging areas, but each species had a large overlap in the isotopic niches between sexes. While SAFS had a wider niche and generalist individuals, SASL had the narrower niche with a higher degree of individual specialisation. Behavioural constraints during the breeding season, intraspecific competition and a major dependence on resources of the Uruguayan coastal shelf may explain why SASL had a higher trophic individual specialisation and a larger vulnerability in a heavily exploited habitat by fisheries and, by consequence, a locally declining population trend.     

Rethinking receiver operating characteristic analysis applications in ecological niche modeling

The area under the curve (AUC) of the receiver operating characteristic (ROC) has become a dominant tool in evaluating the accuracy of models predicting distributions of species. ROC has the advantage of being threshold-independent, and as such does not require decisions regarding thresholds of what constitutes a prediction of presence versus a prediction of absence. However, we show that, comparing two ROCs, using the AUC systematically undervalues models that do not provide predictions across the entire spectrum of proportional areas in the study area. Current ROC approaches in ecological niche modeling applications are also inappropriate because the two error components are weighted equally. We recommend a modification of ROC that remedies these problems, using partial-area ROC approaches to provide a firmer foundation for evaluation of predictions from ecological niche models. A worked example demonstrates that models that are evaluated favorably by traditional ROC AUCs are not necessarily the best when niche modeling considerations are incorporated into the design of the test.     

Empirical realised niche models for British coastal plant species

Coastal environments host plant taxa adapted to a wide range of salinity conditions. Salinity, along with other abiotic variables, constrains the distribution of coastal plants in predictable ways, with relatively few taxa adapted to the most saline conditions. However, few attempts have been made to quantify these relationships to create niche models for coastal plants. Quantification of the effects of salinity, and other abiotic variables, on coastal plants is essential to predict the responses of coastal ecosystems to external drivers such as sea level rise. We constructed niche models for 132 coastal plant taxa in Great Britain based on eight abiotic variables. Paired measurements of vegetation composition and abiotic variables are rare in coastal habitats so four of the variables were defined using community mean values for Ellenberg indicators, i.e. scores assigned according to the typical alkalinity, fertility, moisture availability and salinity of sites where a species occurs. The remaining variables were the canopy height, annual precipitation, and maximum and minimum temperatures. Salinity and moisture indicator scores were significant terms in over 80 % of models, suggesting the distributions of most coastal species are at least partly determined by these variables. When the models were used to predict species occurrence against an independent dataset 64 % of models gave moderate to good predictions of species occurrence. This indicates that most models had successfully captured the key determinants of the niche. The models could potentially be applied to predict changes to habitats and species-dependent ecosystem services in response to rising sea levels.     

GIS-based niche modeling for mapping species' habitat

Ecological "niche modeling" using presence-only locality data and large-scale environmental variables provides a powerful tool for identifying and mapping suitable habitat for species over large spatial extents. We describe a niche modeling approach that identifies a minimum (rather than an optimum) set of basic habitat requirements for a species, based on the assumption that constant environmental relationships in a species' distribution (i.e., variables that maintain a consistent value where the species occurs) are most likely to be associated with limiting factors. Environmental variables that take on a wide range of values where a species occurs are less informative because they do not limit a species' distribution, at least over the range of variation sampled. This approach is operationalized by partitioning Mahalanobis D2 (standardized difference between values of a set of environmental variables for any point and mean values for those same variables calculated from all points at which a species was detected) into independent components. The smallest of these components represents the linear combination of variables with minimum variance; increasingly larger components represent larger variances and are increasingly less limiting. We illustrate this approach using the California Gnatcatcher (Polioptila californica Brewster) and provide SAS code to implement it.     

Food resource partitioning in a Mediterranean demersal fish assemblage: the effect of body size and niche width

We investigated the effects of body size, feeding strategy and depth distribution on the trophic resource partitioning among the 26 dominant fish consumers in a fish assemblage on the central Mediterranean shelf-break. The fish assemblage was structured in two major trophic guilds: epibenthic and zooplanktonic feeders, according to the position of each predator along the benthos–plankton gradient. Within each main guild, the species were segregated along a prey-size or fish-size gradient into five further guilds. Fish size and prey size were strongly correlated, indicating that the prey-size niche can be well explained by predator size. Fish consumers showed a significant negative correlation between the similarity in prey type and the similarity in depth distribution; most species with similar trophic preferences segregated along the depth dimension. The only predators overlapping in both food and depth preferences were those with a more specialist trophic behavior. These results suggest that fish body size and depth preferences are the two main niche dimensions, explaining a large part of the coexistence between the Mediterranean shelf-break fish consumers.     

Estimating the spatio-temporal risk of disease epidemics using a bioclimatic niche model

There are presently few tools available for estimating epidemic risks from forest pathogens, and hence informing pro-active disease management. In this study we demonstrated that a bioclimatic niche model can be used to examine questions of epidemic risk in temperate eucalypt plantations. The bioclimatic niche model, CLIMEX, was used to identify regional variation in climate suitability for Mycosphaerella leaf disease (MLD), a major cause of foliage damage in temperate eucalypt plantations around the world. Using historical observations of MLD damage, we were able to convert the relative score of climatic suitability generated by CLIMEX into a severity ranking ranging from low to high, providing for the first time a direct link between risk and impact, and allowing us to explore disease severity in a way meaningful to forest managers. We determined that the ‘Compare Years’ function in CLIMEX could be used for site-specific risk assessment to identify severity, frequency and seasonality of MLD epidemics. We explored appropriate scales of risk assessment for forest managers. Applying the CLIMEX model of MLD using a 0.25° or coarser grid size to areas of sharp topographic relief frequently misrepresented the risk posed by MLD, because considerable variation occurred between individual forest sites encompassed within a single grid cell. This highlighted the need for site-specific risk assessment to address many questions pertinent to managing risk in plantations.     

Consequences of niche overlap for ecosystem functioning: an experimental test with pond grazers

While the number of studies investigating the effects of species diversity on ecosystem properties continues to expand, few have explicitly examined how ecosystem functioning depends quantitatively on the degree of niche complementarity among species. We report the results of a microcosm experiment where similarity in habitat use among aquatic snail species was evaluated as a predictor of changes in community and ecosystem properties due to increasing species richness. Replicate microcosms with all possible one- and two-species combinations of a guild of six snail species were stocked with identical initial snail biomass. Microcosms with two species of snails had greater final snail biomass, lower attached algae biomass, and less total organic matter than monocultures. Snail species differed in their use of five distinct habitat types in the microcosms. Similarity in habitat use between a species pair was negatively related to the magnitude of change (e.g., deltaEF [change in ecosystem function]) in dissolved oxygen. periphyton biomass, and accrual of organic matter with a change in diversity. However, using the most stringent criterion for complementarity effects (e.g., Dmax [proportional deviation of the total polyculture yield from the highest yielding monoculture]), a relationship between species' niche similarity and changes in function with increasing species richness was only observed for dissolved oxygen. The identity of snail species present in the microcosms had strong effects on total organic matter, snail biomass, dissolved oxygen, periphyton biomass, and sedimentation rate. In this study, herbivore identity, sampling effects, and niche complementarity all appear to contribute to species richness effects on pond ecosystem properties and community structure. The analytical approach employed here may profitably be used in other systems to quantify the role of niche complementarity in species richness-ecosystem function relationships.