Food-web assembly during a classic biogeographic study: species’“trophic breadth” corresponds to colonization order

The Non-Dereliction in Evolution: Trophic Specialisation Drives Convergence in the Radiation of Red Devil Spiders (Araneae: Dysderidae) in the Canary Islands

Natural selection plays a key role in deterministic evolution, as clearly illustrated by the multiple cases of repeated evolution of ecomorphological characters observed in adaptive radiations. Unlike most spiders, Dysdera species display a high variability of cheliceral morphologies, which has been suggested to reflect different levels of specialization to feed on isopods. In this study, we integrate geometric morphometrics and experimental trials with a fully resolved phylogeny of the highly diverse endemic species from the Canary Islands to 1) quantitatively delimit the different cheliceral morphotypes present in the archipelago, 2) test their association with trophic specialization, as reported for continental species, 3) reconstruct the evolution of these ecomorphs throughout the diversification of the group, 4) test the hypothesis of convergent evolution of the different morphotypes, and 5) examine whether specialization constitutes a case of evolutionary irreversibility in this group. We show the existence of 9 cheliceral morphotypes and uncovered their significance for trophic ecology. Further, we demonstrate that similar ecomorphs evolved multiple times in the archipelago, providing a novel study system to explain how convergent evolution and irreversibility due to specialization may be combined to shape phenotypic diversification in adaptive radiations.

Stochastic block models reveal a robust nested pattern in healthy human gut microbiomes

A key question in human gut microbiome research is what are the robust structural patterns underlying its taxonomic composition. Herein, we use whole metagenomic datasets from healthy human guts to show that such robust patterns do exist, albeit not in the conventional enterotype sense. We first introduce the concept of mixed-membership enterotypes using a network inference approach based on stochastic block models. We find that gut microbiomes across a group of people (hosts) display a nested structure, which has been observed in a number of ecological systems. This finding led us to designate distinct ecological roles to both microbes and hosts: generalists and specialists. Specifically, generalist hosts have microbiomes with most microbial species, while specialist hosts only have generalist microbes. Moreover, specialist microbes are only present in generalist hosts. From the nested structure of microbial taxonomies, we show that these ecological roles of microbes are generally conserved across datasets. Our results show that the taxonomic composition of healthy human gut microbiomes is associated with robustly structured combinations of generalist and specialist species.

Biotic filtering by species' interactions constrains food-web variability across spatial and abiotic gradients

Despite intensive research on species dissimilarity patterns across communities (i.e. β-diversity), we still know little about their implications for variation in food-web structures. Our analyses of 50 lake and 48 forest soil communities show that, while species dissimilarity depends on environmental and spatial gradients, these effects are only weakly propagated to the networks. Moreover, our results show that species and food-web dissimilarities are consistently correlated, but that much of the variation in food-web structure across spatial, environmental, and species gradients remains unexplained. Novel food-web assembly models demonstrate the importance of biotic filtering during community assembly by (1) the availability of resources and (2) limiting similarity in species' interactions to avoid strong niche overlap and thus competitive exclusion. This reveals a strong signature of biotic filtering processes during local community assembly, which constrains the variability in structural food-web patterns across local communities despite substantial turnover in species composition.

Addressing the Eltonian shortfall with trait-based interaction models

We have very limited knowledge of how species interact in most communities and ecosystems despite trophic relationships being fundamental for linking biodiversity to ecosystem functioning. A promising approach to fill this gap is to predict interactions based on functional traits, but many questions remain about how well we can predict interactions for different taxa, ecosystems and amounts of input data. Here, we built a new traits-based model of trophic interactions for European vertebrates and found that even models calibrated with 0.1% of the interactions (100 out of 71 k) estimated the full European vertebrate food web reasonably well. However, predators were easier to predict than prey, especially for some clades (e.g. fowl and storks) and local food web connectance was consistently overestimated. Our results demonstrate the ability to rapidly generate food webs when empirical data are lacking-an important step towards a more complete and spatially explicit description of food webs.

Deciphering trophic interactions in a mid-Cambrian assemblage

Exceptionally preserved fossil sites have allowed specimen-based identification of trophic interactions to which network analyses have been applied. However, network analyses of the fossil record suffer from incomplete and indirect data, time averaging that obscures species coexistence, and biases in preservation. Here, we present a high-resolution fossil data set from Raymond Quarry member of the mid-Cambrian Burgess Shale (7,549 specimens, 61 taxa, ∼510 Mya) and formulate a measure of "preservation bias" that aids identification of assemblage subsets to which network analyses can be reliably applied. For these sections, abundance correlation network analyses predicted longitudinally consistent trophic and competitive interactions. Our analyses predicted previously postulated trophic interactions with 83.5% accuracy and demonstrated a shift from specialist interaction-dominated assemblages to ones dominated by generalist and competitive interactions. This approach provides a robust, taphonomically corrected framework to explore and predict in detail the existence and ecological character of putative interactions in fossil data sets.

Diverse interactions and ecosystem engineering can stabilize community assembly

The complexity of an ecological community can be distilled into a network, where diverse interactions connect species in a web of dependencies. Species interact directly with each other and indirectly through environmental effects, however to our knowledge the role of these ecosystem engineers has not been considered in ecological network models. Here we explore the dynamics of ecosystem assembly, where species colonization and extinction depends on the constraints imposed by trophic, service, and engineering dependencies. We show that our assembly model reproduces many key features of ecological systems, such as the role of generalists during assembly, realistic maximum trophic levels, and increased nestedness with mutualistic interactions. We find that ecosystem engineering has large and nonlinear effects on extinction rates. While small numbers of engineers reduce stability by increasing primary extinctions, larger numbers of engineers increase stability by reducing primary extinctions and extinction cascade magnitude. Our results suggest that ecological engineers may enhance community diversity while increasing persistence by facilitating colonization and limiting competitive exclusion.

Tracking the assembly of nested parasite communities: Using β-diversity to understand variation in parasite richness and composition over time and scale

Community composition is driven by a few key assembly processes: ecological selection, drift and dispersal. Nested parasite communities represent a powerful study system for understanding the relative importance of these processes and their relationship with biological scale. Quantifying β-diversity across scales and over time additionally offers mechanistic insights into the ecological processes shaping the distributions of parasites and therefore infectious disease. To examine factors driving parasite community composition, we quantified the parasite communities of 959 amphibian hosts representing two species (the Pacific chorus frog, Pseudacris regilla and the California newt, Taricha torosa) sampled over 3 months from 10 ponds in California. Using additive partitioning, we estimated how much of regional parasite richness (γ-diversity) was composed of within-host parasite richness (α-diversity) and turnover (β-diversity) at three biological scales: across host individuals, across species and across habitat patches (ponds). We also examined how β-diversity varied across time at each biological scale. Differences among ponds comprised the majority (40%) of regional parasite diversity, followed by differences among host species (23%) and among host individuals (12%). Host species supported parasite communities that were less similar than expected by null models, consistent with ecological selection, although these differences lessened through time, likely due to high dispersal rates of infectious stages. Host individuals within the same population supported more similar parasite communities than expected, suggesting that host heterogeneity did not strongly impact parasite community composition and that dispersal was high at the individual host-level. Despite the small population sizes of within-host parasite communities, drift appeared to play a minimal role in structuring community composition. Dispersal and ecological selection appear to jointly drive parasite community assembly, particularly at larger biological scales. The dispersal ability of aquatic parasites with complex life cycles differs strongly across scales, meaning that parasite communities may predictably converge at small scales where dispersal is high, but may be more stochastic and unpredictable at larger scales. Insights into assembly mechanisms within multi-host, multi-parasite systems provide opportunities for understanding how to mitigate the spread of infectious diseases within human and wildlife hosts.

A test of trophic and functional island biogeography theory with the avifauna of a continental archipelago

The classical MacArthur-Wilson theory of island biogeography (TIB) emphasizes the role of island area and isolation in determining island biotas, but is neutral with respect to species differences that could affect community assembly and persistence. Recent extensions of island biogeography theory address how functional differences among species may lead to non-random community assembly processes and different diversity-area scaling patterns. First, the trophic TIB considers how diversity scaling varies across trophic position in a community, with species at higher trophic levels being most strongly influenced by island area. Second, further extensions have predicted how trait distributions, and hence functional diversity, should scale with area. Trait-based theory predicts richness-corrected functional diversity should be low on small islands but converge to null on larger islands. Conversely, competitive assembly predicts high diversity on small islands converging to null with increasing size. However, despite mounting interest in diversity-area relationships across different dimensions of diversity, these predictions derived from theory have not been extensively tested across taxa and island systems. Here, we develop and test predictions of the trophic TIB and extensions to functional traits, by examining the diversity-area relationship across multiple trophic ranks and dimensions of avian biodiversity in the Ryūkyū archipelago of Japan. We find evidence for a positive species- and phylogenetic diversity-area relationship, but functional diversity was not strongly affected by island area. Counter to the trophic TIB, we found no differences in the slopes of species-area relationships among trophic ranks, although slopes varied among trophic guilds at the same rank. We revealed differential assembly of trophic ranks, with evidence of trait-based assembly of intermediate predators but otherwise neutral community assembly. Our results suggest that niche space differs among trophic guilds of birds, but that differences are mostly not predicted by current extensions of island biogeography theory. While predicted patterns do not fit the empirical data well in this case, the development of such theory provides a useful framework to analyse island patterns from new perspectives. The application of empirical datasets such as ours should help provide a basis for developing further iterations of island biogeography theory.

Analysing ecological networks of species interactions

Network approaches to ecological questions have been increasingly used, particularly in recent decades. The abstraction of ecological systems - such as communities - through networks of interactions between their components indeed provides a way to summarize this information with single objects. The methodological framework derived from graph theory also provides numerous approaches and measures to analyze these objects and can offer new perspectives on established ecological theories as well as tools to address new challenges. However, prior to using these methods to test ecological hypotheses, it is necessary that we understand, adapt, and use them in ways that both allow us to deliver their full potential and account for their limitations. Here, we attempt to increase the accessibility of network approaches by providing a review of the tools that have been developed so far, with - what we believe to be - their appropriate uses and potential limitations. This is not an exhaustive review of all methods and metrics, but rather, an overview of tools that are robust, informative, and ecologically sound. After providing a brief presentation of species interaction networks and how to build them in order to summarize ecological information of different types, we then classify methods and metrics by the types of ecological questions that they can be used to answer from global to local scales, including methods for hypothesis testing and future perspectives. Specifically, we show how the organization of species interactions in a community yields different network structures (e.g., more or less dense, modular or nested), how different measures can be used to describe and quantify these emerging structures, and how to compare communities based on these differences in structures. Within networks, we illustrate metrics that can be used to describe and compare the functional and dynamic roles of species based on their position in the network and the organization of their interactions as well as associated new methods to test the significance of these results. Lastly, we describe potential fruitful avenues for new methodological developments to address novel ecological questions.

Identifying a common backbone of interactions underlying food webs from different ecosystems

Although the structure of empirical food webs can differ between ecosystems, there is growing evidence of multiple ways in which they also exhibit common topological properties. To reconcile these contrasting observations, we postulate the existence of a backbone of interactions underlying all ecological networks—a common substructure within every network comprised of species playing similar ecological roles—and a periphery of species whose idiosyncrasies help explain the differences between networks. To test this conjecture, we introduce a new approach to investigate the structural similarity of 411 food webs from multiple environments and biomes. We first find significant differences in the way species in different ecosystems interact with each other. Despite these differences, we then show that there is compelling evidence of a common backbone of interactions underpinning all food webs. We expect that identifying a backbone of interactions will shed light on the rules driving assembly of different ecological communities.

The structure of ecological networks can vary dramatically, yet there may be common features across networks from different ecosystem types. Here, Bramon Mora et al. use network alignment to demonstrate that there is a common backbone of interactions underlying empirical food webs.

Anthropogenic fragmentation of landscapes: mechanisms for eroding the specificity of plant-herbivore interactions

Reduced ecological specialization is an emerging, general pattern of ecological networks in fragmented landscapes. In plant-herbivore interactions, reductions in dietary specialization of herbivore communities are consistently associated with fragmented landscapes, but the causes remain poorly understood. We propose several hypothetical bottom-up and top-down mechanisms that may reduce the specificity of plant-herbivore interactions. These include empirically plausible applications and extensions of theory based on reduced habitat patch size and isolation (considered jointly), and habitat edge effects. Bottom-up effects in small, isolated habitat patches may limit availability of suitable hostplants, a constraint that increases with dietary specialization. Poor hostplant quality due to inbreeding in such fragments may especially disadvantage dietary specialist herbivores even when their hostplants are present. Size and isolation of habitat patches may change patterns of predation of herbivores, but whether such putative changes are associated with herbivore dietary specialization should depend on the mobility, size, and diet breadth of predators. Bottom-up edge effects may favor dietary generalist herbivores, yet top-down edge effects may favor dietary specialists owing to reduced predation. An increasingly supported edge effect is trophic ricochets generated by large grazers/browsers, which remove key hostplant species of specialist herbivores. We present empirical evidence that greater deer browsing in small forest fragments disproportionately reduces specialist abundances in lepidopteran assemblages in northeastern USA. Despite indirect evidence for these mechanisms, they have received scant direct testing with experimental approaches at a landscape scale. Identifying their relative contributions to reduced specificity of plant-herbivore interactions in fragmented landscapes is an important research goal.

Winter is coming: Food web structure and seasonality in a subtropical freshwater coastal lake

Food web studies provide a useful tool to assess the organization and complexity of natural communities. Nevertheless, the seasonal dynamics of food web properties, their environmental correlates, and potential association with community diversity and stability remain poorly studied. Here, we condensed an incomplete 6-year community dataset of a subtropical coastal lake to examine how monthly variation in diversity impacts food web structure over an idealized time series for an averaged year. Phytoplankton, zooplankton, macroinvertebrates, and fish were mostly resolved to species level (n = 120 trophospecies). Our results showed that the seasonal organization of the food web could be aggregated into two clusters of months grouped here as 'summer' and 'winter'. During 'winter', the food web decreases in size and complexity, with the number of trophospecies dropping from 106 to 82 (a 22.6% decrease in the number of nodes) and the trophic interactions from 1,049 to 637 between month extremes (a 39.3% drop in the number of links). The observed simplification in food web structure during 'winter' suggests that community stability is more vulnerable to the impact of any change during this period.

Effects of spatial scale of sampling on food web structure

This study asks whether the spatial scale of sampling alters structural properties of food webs and whether any differences are attributable to changes in species richness and connectance with scale. Understanding how different aspects of sampling effort affect ecological network structure is important for both fundamental ecological knowledge and the application of network analysis in conservation and management. Using a highly resolved food web for the marine intertidal ecosystem of the Sanak Archipelago in the Eastern Aleutian Islands, Alaska, we assess how commonly studied properties of network structure differ for 281 versions of the food web sampled at five levels of spatial scale representing six orders of magnitude in area spread across the archipelago. Species (S) and link (L) richness both increased by approximately one order of magnitude across the five spatial scales. Links per species (L/S) more than doubled, while connectance (C) decreased by approximately two-thirds. Fourteen commonly studied properties of network structure varied systematically with spatial scale of sampling, some increasing and others decreasing. While ecological network properties varied systematically with sampling extent, analyses using the niche model and a power-law scaling relationship indicate that for many properties, this apparent sensitivity is attributable to the increasing S and decreasing C of webs with increasing spatial scale. As long as effects of S and C are accounted for, areal sampling bias does not have a special impact on our understanding of many aspects of network structure. However, attention does need be paid to some properties such as the fraction of species in loops, which increases more than expected with greater spatial scales of sampling.

Highly resolved early Eocene food webs show development of modern trophic structure after the end-Cretaceous extinction

Generalities of food web structure have been identified for extant ecosystems. However, the trophic organization of ancient ecosystems is unresolved, as prior studies of fossil webs have been limited by low-resolution, high-uncertainty data. We compiled highly resolved, well-documented feeding interaction data for 700 taxa from the 48 million-year-old latest early Eocene Messel Shale, which contains a species assemblage that developed after an interval of protracted environmental and biotal change during and following the end-Cretaceous extinction. We compared the network structure of Messel lake and forest food webs to extant webs using analyses that account for scale dependence of structure with diversity and complexity. The Messel lake web, with 94 taxa, displays unambiguous similarities in structure to extant webs. While the Messel forest web, with 630 taxa, displays differences compared to extant webs, they appear to result from high diversity and resolution of insect–plant interactions, rather than substantive differences in structure. The evidence presented here suggests that modern trophic organization developed along with the modern Messel biota during an 18 Myr interval of dramatic post-extinction change. Our study also has methodological implications, as the Messel forest web analysis highlights limitations of current food web data and models.

The dynamics of assembling food webs

Community assembly is central to ecology, yet ecologists have amassed little quantitative information about how food webs assemble. Theory holds that colonisation rate is a primary driver of community assembly. We present new data from a mesocosm experiment to test the hypothesis that colonisation rate also determines the assembly dynamics of food webs. By manipulating colonisation rate and measuring webs through time, we show how colonisation rate governs structural changes during assembly. Webs experiencing different colonisation rates had stable topologies despite significant species turnover, suggesting that some features of network architecture emerge early and change little through assembly. But webs experiencing low colonisation rates showed less variation in the magnitudes of trophic fluxes, and were less likely to develop coupled fast and slow resource channels--a common feature of published webs. Our results reveal that food web structure develops according to repeatable trajectories that are strongly influenced by colonisation rate.

From projected species distribution to food-web structure under climate change

Climate change is inducing deep modifications in species geographic ranges worldwide. However, the consequences of such changes on community structure are still poorly understood, particularly the impacts on food-web properties. Here, we propose a new framework, coupling species distribution and trophic models, to predict climate change impacts on food-web structure across the Mediterranean Sea. Sea surface temperature was used to determine the fish climate niches and their future distributions. Body size was used to infer trophic interactions between fish species. Our projections reveal that 54 fish species of 256 endemic and native species included in our analysis would disappear by 2080-2099 from the Mediterranean continental shelf. The number of feeding links between fish species would decrease on 73.4% of the continental shelf. However, the connectance of the overall fish web would increase on average, from 0.26 to 0.29, mainly due to a differential loss rate of feeding links and species richness. This result masks a systematic decrease in predator generality, estimated here as the number of prey species, from 30.0 to 25.4. Therefore, our study highlights large-scale impacts of climate change on marine food-web structure with potential deep consequences on ecosystem functioning. However, these impacts will likely be highly heterogeneous in space, challenging our current understanding of climate change impact on local marine ecosystems.

A roadmap for bridging basic and applied research in forensic entomology

The National Research Council issued a report in 2009 that heavily criticized the forensic sciences. The report made several recommendations that if addressed would allow the forensic sciences to develop a stronger scientific foundation. We suggest a roadmap for decomposition ecology and forensic entomology hinging on a framework built on basic research concepts in ecology, evolution, and genetics. Unifying both basic and applied research fields under a common umbrella of terminology and structure would facilitate communication in the field and the production of scientific results. It would also help to identify novel research areas leading to a better understanding of principal underpinnings governing ecosystem structure, function, and evolution while increasing the accuracy of and ability to interpret entomological evidence collected from crime scenes. By following the proposed roadmap, a bridge can be built between basic and applied decomposition ecology research, culminating in science that could withstand the rigors of emerging legal and cultural expectations.

Community assembly, stability and signatures of dynamical constraints on food web structure

To understand the dynamics of natural species communities, a major challenge is to quantify the relationship between their assembly, stability, and underlying food web structure. To this end, two complementary aspects of food web structure can be related to community stability: sign structure, which refers to the distributions of trophic links irrespective of interaction strengths, and interaction strength structure, which refers to the distributions of interaction strengths with or without consideration of sign structure. In this paper, using data from a set of relatively well documented community food webs, I show that natural communities generally exhibit a sign structure that renders their stability sensitive to interaction strengths. Using a Lotka-Volterra type population dynamical model, I then show that in such communities, individual consumer species with high values of a measure of their total biomass acquisition rate, which I term "weighted generality", tend to undermine community stability. Thus consumer species' trophic modules (a species and all its resource links) should be "selected" through repeated immigrations and extinctions during assembly into configurations that increase the probability of stable coexistence within the constraints of the community's trophic sign structure. The presence of such constraints can be detected by the incidence and strength of certain non-random structural characteristics. These structural signatures of dynamical constraints are readily measurable, and can be used to gauge the importance of interaction-driven dynamical constraints on communities during and after assembly in natural communities.