Trophic niche-space imaging,using resource and consumer traits

The strength of trophic (feeding) links between two species depends on the traits of both the consumer and the resource. But which traits of consumer and resource have to be measured to predict link strengths, and how many? A novel theoretical framework for systematically determining trophic traits from empirical data was recently proposed. Here we demonstrate this approach for a group of 14 consumer fish species (Labeobarbus spp., Cyprinidae) and 11 aquatic resource categories coexisting in Lake Tana in northern Ethiopia, analysing large sets of phenotypic consumer and resource traits with known roles in feeding ecology. We systematically reconstruct structure and geometry of trophic niche space, in which link strengths are predicted by the distances between consumers and resources. These distances are then represented graphically resulting in an image of trophic niche space and its occupancy. We find trophic niche to be multidimensional. Among the models we analysed, one with two resource and two consumer traits had the highest predictive power for link strength. Results further suggest that trophic niche space has a pseudo-Euclidean geometry, meaning that link strength decays with distance in some dimensions of trophic niche space, while it increases with distance in other dimensions. Our analysis not only informs theory and modelling but may also be helpful for predicting trophic link strengths for pairs of other, similar species.     

High intraspecific variability in the functional niche of a predator is associated with ontogenetic shift and individual specialization

Investigations on the functional niche of organisms have primarily focused on differences among species and tended to neglect the potential effects of intraspecific variability despite the fact that its potential ecological and evolutionary importance is now widely recognized. In this study, we measured the distribution of functional traits in an entire population of largemouth bass (Micropterus salmoides) to quantify the magnitude of intraspecific variability in functional traits and niche (size, position, and overlap) between age classes. Stable isotope analyses (δ¹³C and δ¹⁵N) were also used to determine the association between individual trophic ecology and intraspecific functional trait variability. We observed that functional traits were highly variable within the population (mean coefficient variation: 15.62% ± 1.78% SE) and predominantly different between age classes. In addition, functional and trophic niche overlap between age classes was extremely low. Differences in functional niche between age classes were associated with strong changes in trophic niche occurring during ontogeny while, within age classes, differences among individuals were likely driven by trophic specialization. Each age class filled only a small portion of the total functional niche of the population and age classes occupied distinct portions in the functional space, indicating the existence of ontogenetic specialists with different functional roles within the population. The high amplitude of intraspecific variability in functional traits and differences in functional niche position among individuals reported here supports the recent claims for an individual‐based approach in functional ecology.     

A multivariate approach reveals diversity of ontogenetic niche shifts across taxonomic and functional groups

1. Shifts in the fundamental and realised niche of individuals during their ontogeny are ubiquitous in nature, but we know little about what aspects of the niche change and how these changes vary across species within communities. However, this knowledge is essential to predict the dynamics of populations and communities and how they respond to environmental change.
2. Here I introduce a range of metrics to describe different aspects of shifts in the realised trophic niche of individuals based on stable isotopes. Applying this multi-variate approach to 2,272 individuals from 13 taxonomic and functional distinct species (Amphibia, Hemiptera, Coleoptera, Odonata) sampled in natural pond communities allowed me to: (1) describe and quantify the diversity of trophic niche shift patterns over ontogeny in multi-dimensional space, and (2) identify what aspects of ontogenetic shifts vary across taxa, and functional groups.
3. Results revealed that species can differ substantially in which aspects of the trophic niche change and how they change over ontogeny. Interestingly, patterns of ontogenetic niche shifts grouped in distinct taxonomic clusters in multi-variate space, including two distinct groups of predators (Hemiptera versus Odonata). Given the differences in traits (especially feeding mode) across groups, this suggests that differences in ontogenetic niche shifts across species could at least partially be explained by variation in traits and functional roles of species.
4. These results emphasise the importance of a multivariate approach to capture the large diversity of trophic niche shifts patterns possible in natural communities and suggest that differences in ontogenetic niche shifts follow general patterns.

     

The potential of and limitations to marine population prognosis

Following the 19th century recognition and definition of basic ecological entities, functional analysis has been the highlight of this century. The synthesis of these findings enables ecological prognosis. The population as the basic functional unit has been repeatedly treated; in the marine field, fisheries management approaches developed into multi-species population analysis. As in planktology, theoretical ecology, and classic biocoenotic research, the population interactions are of increasing scientific interest. A mathematical model is suggested that combines these extrinsic and intrinsic functional relationships in order to define the fit of the ecological niche to the environment, the decisive measure of the expected population success, and thus of the probable population development needed for prognostic purposes. It is discussed in how far the orientation towards the predictive power or — with respect to the “skill” of meteorological prognoses — the “ecological prognostic skill” improvement may serve as a means to choose the best investigative strategy.     

Linking intraspecific variability in trophic and functional niches along an environmental gradient

1. Intraspecific trophic variability has important ecological and evolutionary implications, and is driven by multiple interacting factors. Functional traits and environmental conditions are important in mediating the trophic niche of individuals because they determine their ability to consume certain prey, their energetic requirements, and resource availability. In this study, we aimed at investigating the interacting effects of functional traits and environmental conditions on several attributes of trophic niche in natural populations.
2. Here, we quantified intraspecific variability in the trophic niche of 12 riverine populations of European minnow (Phoxinus phoxinus) using stable isotope analyses. Functional traits (i.e. morpho-anatomical traits) and environmental conditions (i.e. upstream–downstream gradient, forest cover) were quantified to identify the determinants of (1) trophic position and resource origin, (2) trophic niche size, and (3) trophic differentiation (β-diversity) among populations.
3. We demonstrated that trophic position and resource origin covaried with functional traits related to body size and locomotion performance, and that the strength and shape of these relationships varied according to local environmental conditions. The trophic niche size also differed among populations, although no determinant was identified. Finally, trophic β-diversity was correlated to environmental differentiation among sites.
4. Overall, the determinants of intraspecific variability in trophic niche appeared highly context-dependent, and related to the interactions between functional traits and environmental conditions. Because populations are currently facing important environmental changes, understanding this context-dependency is important for predicting food web structure and ecosystem dynamics in a changing world.

     

The effects of morphology,phylogeny and prey availability on trophic resource partitioning in an anuran community

Several factors influence the partitioning of trophic resources in ecological communities, such as morphology, evolutionary history, and resource availability. Although the effects of morphology, phylogeny, and resource availability on trophic ecology have long been explored by theoretical studies, little has been done to empirically test these relationships. Here, we tested whether phylogenetic and morphological distances correlate with trophic niche overlap using a path analysis of multiple partial regression of distance matrices. Also, we tested whether niche breadth is influenced by body size using Phylogenetic Generalized Least Squares analysis. Trophic niche overlap was better explained by morphology per se than by the phylogenetic distance. We also found that predator's body size influences niche breadth calculated considering prey traits and availability, but not when we do not include these availability data. Additionally, trophic niche breadth was usually smaller when we considered prey traits and availability, differently from niche overlap, whose values increased when we did not consider these data. Our findings show that the interpretation of trophic niche in communities changes if we consider availability data, affecting inferences about coexistence and trophic specialization. Our study contributes to understanding trophic specialization and emphasizes the importance of incorporating prey availability and their traits into diet analysis.     

Linking habitat specialization with species' traits in European birds

Ecological specialization provides information about adaptations of species to their environment. However, identification of traits representing the relevant dimensions of ecological space remains challenging. Here we endeavoured to explain how complex habitat specializations relate to various ecological traits of European birds. We employed phylogenetic generalized least squares and information theoretic approach statistically controlling for differences in geographic range size among species. Habitat specialists had narrower diet niche, wider climatic niche, higher wing length/tail length ratio and migrated on shorter distances than habitat generalists. Our results support an expected positive link between habitat and diet niche breadth estimates, however a negative relationship between habitat and climate niche breadths is surprising. It implies that habitat specialists occur mostly in spatially restricted environments with high climatic variability such as mountain areas. This, however, complicates our understanding of predicted impacts of climatic changes on avian geographical distributions. Our results further corroborate that habitat specialization reflects occupation of morphological space, when specialists depend more on manoeuvrability of the flight and are thus more closely associated to open habitats than habitat generalists. Finally, our results indicate that long distance movements might hamper narrow habitat preferences. In conclusion, we have shown that species’ distributions across habitats are informative about their positions along other axes of ecological space and can explain states of particular functional traits, however, our results also reveal that the links between different niche estimates cannot be always straightforwardly predicted.     

Analyzing trophic ecosystem functions with the interaction functional space

Quantifying the vulnerability of ecosystems to global change requires a better understanding of how trophic ecosystem functions emerge. So far, trophic ecosystem functions have been studied from the perspective of either functional diversity or network ecology. To integrate these two perspectives, we propose the interaction functional space (IFS) a conceptual framework to simultaneously analyze the effects of traits and interactions on trophic functions. We exemplify the added value of our framework for seed dispersal and wood decomposition and show how species interactions influence the relationship between functional trait diversity and trophic functions. We propose future applications for a range of functions where the IFS can help to elucidate mechanisms underpinning trophic functions and facilitate understanding of functional changes in ecosystems amidst global change.     

Ecological memory at millennial time-scales: the importance of data constraints,species longevity and niche features

Ecological memory describes how antecedent conditions drive the dynamics of an ecological system. Palaeoecological records are paramount to understand ecological memory at millennial time-scales, but the concept is widely neglected in the literature, and a formal approach is lacking. Here, we fill such a gap by introducing a quantitative framework for ecological memory in palaeoecology, and assessing how data constraints and taxa traits shape ecological memory patterns. We simulate the population dynamics and pollen abundance of 16 virtual taxa with different life and niche traits as a response to an environmental driver. The data is processed to mimic a realistic sediment deposition and sampled at increasing depth intervals. We quantify ecological memory with Random Forests, and assess how data properties and taxa traits shape ecological memory. We find that life-span and niche features modulate the relative importance of the antecedent values of the driver and the pollen abundance over periods of 240 yr and longer. Additionally, we find that accumulation rate and decreasing pollen-sampling resolution inflate the importance of antecedent pollen abundance. Our results suggest that: 1) ecological memory patterns are sensitive to varying accumulation rates. A better understanding on the numerical basis of this effect may enable the assimilation of ecological memory concepts and methods in palaeoecology; 2) incorporating niche theory and models is essential to better understand the nature of ecological memory patterns at millennial time-scales. 3) Long-lived generalist taxa are highly decoupled from the environmental signal. This finding has implications on how we interpret the abundance-environment relationship of real taxa with similar traits, and how we use such knowledge to forecast their distribution or reconstruct past climate.     

Regeneration niche differentiates functional strategies of desert woody plant species

Plant communities vary dramatically in the number and relative abundance of species that exhibit facilitative interactions, which contributes substantially to variation in community structure and dynamics. Predicting species’ responses to neighbors based on readily measurable functional traits would provide important insight into the factors that structure plant communities. We measured a suite of functional traits on seedlings of 20 species and mature plants of 54 species of shrubs from three arid biogeographic regions. We hypothesized that species with different regeneration niches—those that require nurse plants for establishment (beneficiaries) versus those that do not (colonizers)—are functionally different. Indeed, seedlings of beneficiary species had lower relative growth rates, larger seeds and final biomass, allocated biomass toward roots and height at a cost to leaf mass fraction, and constructed costly, dense leaf and root tissues relative to colonizers. Likewise at maturity, beneficiaries had larger overall size and denser leaves coupled with greater water use efficiency than colonizers. In contrast to current hypotheses that suggest beneficiaries are less “stress-tolerant” than colonizers, beneficiaries exhibited conservative functional strategies suited to persistently dry, low light conditions beneath canopies, whereas colonizers exhibited opportunistic strategies that may be advantageous in fluctuating, open microenvironments. In addition, the signature of the regeneration niche at maturity indicates that facilitation expands the range of functional diversity within plant communities at all ontogenetic stages. This study demonstrates the utility of specific functional traits for predicting species’ regeneration niches in hot deserts, and provides a framework for studying facilitation in other severe environments.     

Trait dimensionality and population choice alter estimates of phenotypic dissimilarity

The ecological niche is a multi‐dimensional concept including aspects of resource use, environmental tolerance, and interspecific interactions, and the degree to which niches overlap is central to many ecological questions. Plant phenotypic traits are increasingly used as surrogates of species niches, but we lack an understanding of how key sampling decisions affect our ability to capture phenotypic differences among species. Using trait data of ecologically distinct monkeyflower (Mimulus) congeners, we employed linear discriminant analysis to determine how (1) dimensionality (the number and type of traits) and (2) variation within species influence how well measured traits reflect phenotypic differences among species. We conducted analyses using vegetative and floral traits in different combinations of up to 13 traits and compared the performance of commonly used functional traits such as specific leaf area against other morphological traits. We tested the importance of intraspecific variation by assessing how population choice changed our ability to discriminate species. Neither using key functional traits nor sampling across plant functions and organs maximized species discrimination. When using few traits, vegetative traits performed better than combinations of vegetative and floral traits or floral traits alone. Overall, including more traits increased our ability to detect phenotypic differences among species. Population choice and the number of traits used had comparable impacts on discriminating species. We addressed methodological challenges that have undermined cross‐study comparability of trait‐based approaches. Our results emphasize the importance of sampling among‐population trait variation and suggest that a high‐dimensional approach may best capture phenotypic variation among species with distinct niches.     

Large-scale multi-trophic co-response models and environmental control of pelagic food webs in Québec lakes

Environmental heterogeneity plays a fundamental role in driving species distributions by, for one, fostering niche dimensionality. Within lake ecosystems, species distributions and concordance patterns are driven by both local and regional heterogeneity, though their relative importance across trophic levels has rarely been explored. We developed a statistical framework to compare responses of taxa from different trophic levels to abiotic factors and determine how this affected multi-trophic network structures. In particular, we used multi-species concordance modelling (concordance analysis and RV coefficient) to determine species associations and correlations within and among three trophic levels (phytoplankton, zooplankton and fish communities sampled across 49 southern Québec lakes, covering eight hydrological regions). We then used multiple factor analysis, latent variable modelling and local contributions of sites to beta diversity to assess the relative importance of major environmental gradients in structuring species co-responses and species interaction turnover across the landscape. Our analyses confirmed that concordant species within each trophic level varied jointly or segregated into different pelagic food webs in Québec lakes where important acidification and eutrophication took place. Some keynote species were indicators of different food web compartments and distinguished groups of lakes along multiple environmental niche dimensions. Among the three trophic levels examined, zooplankton depicted the highest proportion of species concordance and appeared to act as a trophic linkage between phytoplankton and fish. Ultimately, the losses or gains in species richness and species interactions were strongly driven by environmental gradients. This study provides for the first time a combined analysis of the effects of environmental heterogeneity on ecological communities belonging to three trophic levels sampled near simultaneously across an 800 km broad lacustrine landscape. The new framework developed in this study has a great potential to better understand the complex response of aquatic ecosystems in a world increasingly affected by multiple, cumulative stressors.     

Functional traits reveal the expansion and packing of ecological niche space underlying an elevational diversity gradient in passerine birds

Variation in species richness across environmental gradients may be associated with an expanded volume or increased packing of ecological niche space. However, the relative importance of these alternative scenarios remains unknown, largely because standardized information on functional traits and their ecological relevance is lacking for major diversity gradients. Here, we combine data on morphological and ecological traits for 523 species of passerine birds distributed across an Andes-to-Amazon elevation gradient. We show that morphological traits capture substantial variation in species dietary (75%) and foraging niches (60%) when multiple independent trait dimensions are considered. Having established these relationships, we show that the 14-fold increase in species richness towards the lowlands is associated with both an increased volume and density of functional trait space. However, we find that increases in volume contribute little to changes in richness, with most (78%) lowland species occurring within the range of trait space occupied at high elevations. Taken together, our results suggest that high species richness is mainly associated with a denser occupation of functional trait space, implying an increased specialization or overlap of ecological niches, and supporting the view that niche packing is the dominant trend underlying gradients of increasing biodiversity towards the lowland tropics.     

Trait plasticity in species interactions: a driving force of community dynamics

Evolutionary community ecology is an emerging field of study that includes evolutionary principles such as individual trait variation and plasticity of traits to provide a more mechanistic insight as to how species diversity is maintained and community processes are shaped across time and space. In this review we explore phenotypic plasticity in functional traits and its consequences at the community level. We argue that resource requirement and resource uptake are plastic traits that can alter fundamental and realised niches of species in the community if environmental conditions change. We conceptually add to niche models by including phenotypic plasticity in traits involved in resource allocation under stress. Two qualitative predictions that we derive are: (1) plasticity in resource requirement induced by availability of resources enlarges the fundamental niche of species and causes a reduction of vacant niches for other species and (2) plasticity in the proportional resource uptake results in expansion of the realized niche, causing a reduction in the possibility for coexistence with other species. We illustrate these predictions with data on the competitive impact of invasive species. Furthermore, we review the quickly increasing number of empirical studies on evolutionary community ecology and demonstrate the impact of phenotypic plasticity on community composition. Among others, we give examples that show that differences in the level of phenotypic plasticity can disrupt species interactions when environmental conditions change, due to effects on realized niches. Finally, we indicate several promising directions for future phenotypic plasticity research in a community context. We need an integrative, trait-based approach that has its roots in community and evolutionary ecology in order to face fast changing environmental conditions such as global warming and urbanization that pose ecological as well as evolutionary challenges.     

Functional traits,convergent evolution,and periodic tables of niches

Ecology is often said to lack general theories sufficiently predictive for applications. Here, we examine the concept of a periodic table of niches and feasibility of niche classification schemes from functional trait and performance data. Niche differences and their influence on ecological patterns and processes could be revealed effectively by first performing data reduction/ordination analyses separately on matrices of trait and performance data compiled according to logical associations with five basic niche ‘dimensions’, or aspects: habitat, life history, trophic, defence and metabolic. Resultant patterns then are integrated to produce interpretable niche gradients, ordinations and classifications. Degree of scheme periodicity would depend on degrees of niche conservatism and convergence causing species clustering across multiple niche dimensions. We analysed a sample data set containing trait and performance data to contrast two approaches for producing niche schemes: species ordination within niche gradient space, and niche categorisation according to trait‐value thresholds. Creation of niche schemes useful for advancing ecological knowledge and its applications will depend on research that produces functional trait and performance datasets directly related to niche dimensions along with criteria for data standardisation and quality. As larger databases are compiled, opportunities will emerge to explore new methods for data reduction, ordination and classification.     

Temporal stability of niche use exposes sympatric Arctic charr to alternative selection pressures

There is now strong evidence that foraging niche specialisation plays a critical role in the very early stages of resource driven speciation. Here we test critical elements of models defining this process using a known polymorphic population of Arctic charr from subarctic Norway. We test the long-term stability of niche specialisation amongst foraging predators and discuss the possibility that contrasting foraging specialists are exposed to differing selection regimes. Inter-individual foraging niche stability was measured by combining two time-integrated ecological tracers of the foraging niche (each individual’s δ¹³C and δ¹⁵N stable isotope (SI) signatures and their food borne parasite fauna) with a short-term measure of foraging niche use (stomach contents composition). Three dietary subgroups of predators were identified, including zooplankton, gammarid and benthivore specialists foragers. Zooplanktivorous specialists had muscle low in δ ¹³C, a high abundance of parasites transmitted from pelagic copepods, a smaller head, longer snout and a more slender body-form than gammaridivorous specialist individuals which had muscle more enriched in δ ¹³C and high abundance of parasites transmitted from benthic Gammarus. Benthivorous individuals were intermediate between the other two foraging groups according to muscle SI-signals (δ¹³C) and loadings of parasites transmitted from both copepods and Gammarus. The close relationship between subgroups identified by stomach contents, time-integrated tracers of niche use (SI and parasites) and functional trophic morphology (niche adaptations) demonstrate a long-term temporally stable niche use of each individual predator. Differential habitat use and contrasting parasite communities and loadings, show differential exposure to different suites of selection pressures for different foraging specialists. Results also show that individual specialisation in trophic behaviour and thus exposure to different suites of selection pressures are stable over time, and thus provide a platform for disruptive selection to operate within this sympatric system.     

Niche evolution in Australian terrestrial mammals? Clarifying scale-dependencies in phylogenetic and functional drivers of co-occurrence

Interactive forces between competition and habitat filtering drive many biogeographic patterns over evolutionary time scales. However, the responsiveness of assemblages to these two forces is highly influenced by spatial scale, forming complex patterns of niche separation. We explored these spatial dependencies by quantifying the influence of phylogeny and functional traits in shaping present day native terrestrial mammal assemblages at multiple scales, principally by identifying the spatial scales at which niche evolution operates. We modelled the distribution of 53 native terrestrial mammal species across New South Wales, Australia. Using predicted distributions, we estimated the range overlap between each pair of species at increasing grain sizes (~0.8, 5.1, 20, 81, 506, 2,025, 8,100 km²). We employed a decision tree to identify how interactions among functional traits and phylogenetic relatedness translated to levels of sympatry at increasing spatial scales. We found that Australian terrestrial mammals displayed phylogenetic over-dispersion that was inversely related to spatial scale, suggesting that ecological processes were more influential than biogeographic sympatry patterns in defining assemblages of species. While the contribution of phylogenetic relatedness to patterns of co-occurrence decreased as spatial scale increased, the reverse was true for habitat preferences. At the same time, functional traits also operated at different scales, as dietary preferences dominated at local spatial scales (<10 km²) while body mass has a stronger effect at larger spatial scales. Our findings show that ecological and evolutionary processes operate at different scales and that Australian terrestrial mammals diverged slower along their micro-scale niche compared to their macro-scale niche. By combining phylogenetic and niche methods through the modelling of species distributions, we assessed whether specific traits were related to a particular niche. More importantly, conducting multi-scale spatial analysis avoids categorical assignment of traits-to-niches, providing a clearer relationship between traits and a species ecological niche and a more precise scaling for the axes of niche evolution.     

Are species' responses to global change predicted by past niche evolution?

Predicting how and when adaptive evolution might rescue species from global change, and integrating this process into tools of biodiversity forecasting, has now become an urgent task. Here, we explored whether recent population trends of species can be explained by their past rate of niche evolution, which can be inferred from increasingly available phylogenetic and niche data. We examined the assemblage of 409 European bird species for which estimates of demographic trends between 1970 and 2000 are available, along with a species-level phylogeny and data on climatic, habitat and trophic niches. We found that species'' proneness to demographic decline is associated with slow evolution of the habitat niche in the past, in addition to certain current-day life-history and ecological traits. A similar result was found at a higher taxonomic level, where families prone to decline have had a history of slower evolution of climatic and habitat niches. Our results support the view that niche conservatism can prevent some species from coping with environmental change. Thus, linking patterns of past niche evolution and contemporary species dynamics for large species samples may provide insights into how niche evolution may rescue certain lineages in the face of global change.     

Boundaries that demarcate structural and functional domains of chromatin

Understanding of how the eukaryotic genome is packaged into chromatin and what the functional consequences of this organization are has begun to emerge recently. The concept of ‘chromatin domains’ — the topologically independent structural unit — is the basis of higher order chromatin organization. The idea that this structural unit may also coincide with the functional unit, offers a useful framework in dissecting the structure-function relationship. Boundaries that define these domains have been identified and several assays have been developed to test themin vivo. We have used genetic means to identify and analyse such boundary elements in the bithorax complex ofDrosophila melanogaster. In this review we discuss chromatin domain boundaries identified in several systems using different means. Although there is no significant sequence conservation among various chromatin domain boundaries, these elements show functional conservation across the species. Finally, we discuss mechanistic aspects of how chromatin domain boundaries may function in organizing and regulating eukaryotic genome.