Diversity indices for ecological networks: a unifying framework using Hill numbers

Describing how ecological interactions change over space and time and how they are shaped by environmental conditions is crucial to understand and predict ecosystem trajectories. However, it requires having an appropriate framework to measure network diversity locally, regionally and between samples (α‐, γ‐ and β‐diversity). Here, we propose a unifying framework that builds on Hill numbers and accounts both for the probabilistic nature of biotic interactions and the abundances of species or groups. We emphasise the importance of analysing network diversity across different species aggregation levels (e.g. from species to trophic groups) to get a better understanding of network structure. We illustrate our framework with a simulation experiment and an empirical analysis using a global food‐web database. We discuss further usages of the framework and show how it responds to recent calls on comparing ecological networks and analysing their variation across environmental gradients and time.     

Species richness and trophic diversity increase decomposition in a co-evolved food web

Ecological communities show great variation in species richness, composition and food web structure across similar and diverse ecosystems. Knowledge of how this biodiversity relates to ecosystem functioning is important for understanding the maintenance of diversity and the potential effects of species losses and gains on ecosystems. While research often focuses on how variation in species richness influences ecosystem processes, assessing species richness in a food web context can provide further insight into the relationship between diversity and ecosystem functioning and elucidate potential mechanisms underpinning this relationship. Here, we assessed how species richness and trophic diversity affect decomposition rates in a complete aquatic food web: the five trophic level web that occurs within water-filled leaves of the northern pitcher plant, Sarracenia purpurea. We identified a trophic cascade in which top-predators--larvae of the pitcher-plant mosquito--indirectly increased bacterial decomposition by preying on bactivorous protozoa. Our data also revealed a facultative relationship in which larvae of the pitcher-plant midge increased bacterial decomposition by shredding detritus. These important interactions occur only in food webs with high trophic diversity, which in turn only occur in food webs with high species richness. We show that species richness and trophic diversity underlie strong linkages between food web structure and dynamics that influence ecosystem functioning. The importance of trophic diversity and species interactions in determining how biodiversity relates to ecosystem functioning suggests that simply focusing on species richness does not give a complete picture as to how ecosystems may change with the loss or gain of species.     

Temporal and spatial changes in benthic invertebrate trophic networks along a taxonomic richness gradient

Species interactions underlie most ecosystem functions and are important for understanding ecosystem changes. Representing one type of species interaction, trophic networks were constructed from biodiversity monitoring data and known trophic links to assess how ecosystems have changed over time. The Baltic Sea is subject to many anthropogenic pressures, and low species diversity makes it an ideal candidate for determining how pressures change food webs. In this study, we used benthic monitoring data for 20 years (1980–1989 and 2010–2019) from the Swedish coast of the Baltic Sea and Skagerrak to investigate changes in benthic invertebrate trophic interactions. We constructed food webs and calculated fundamental food web metrics evaluating network horizontal and vertical diversity, as well as stability that were compared over space and time. Our results show that the west coast of Sweden (Skagerrak) suffered a reduction in benthic invertebrate biodiversity by 32% between the 1980s and 2010s, and that the number of links, generality of predators, and vulnerability of prey have been significantly reduced. The other basins (Bothnian Sea, Baltic Proper, and Bornholm Basin) do not show any significant changes in species richness or consistent significant trends in any food web metrics investigated, demonstrating resilience at a lower species diversity. The decreased complexity of the Skagerrak food webs indicates vulnerability to further perturbations and pressures should be limited as much as possible to ensure continued ecosystem functions.     

Environmental context determines multi‐trophic effects of consumer species loss

Loss of biodiversity and nutrient enrichment are two of the main human impacts on ecosystems globally, yet we understand very little about the interactive effects of multiple stressors on natural communities and how this relates to biodiversity and ecosystem functioning. Advancing our understanding requires the following: (1) incorporation of processes occurring within and among trophic levels in natural ecosystems and (2) tests of context‐dependency of species loss effects. We examined the effects of loss of a key predator and two groups of its prey on algal assemblages at both ambient and enriched nutrient conditions in a marine benthic system and tested for interactions between the loss of functional diversity and nutrient enrichment on ecosystem functioning. We found that enrichment interacted with food web structure to alter the effects of species loss in natural communities. At ambient conditions, the loss of primary consumers led to an increase in biomass of algae, whereas predator loss caused a reduction in algal biomass (i.e. a trophic cascade). However, contrary to expectations, we found that nutrient enrichment negated the cascading effect of predators on algae. Moreover, algal assemblage structure varied in distinct ways in response to mussel loss, grazer loss, predator loss and with nutrient enrichment, with compensatory shifts in algal abundance driven by variation in responses of different algal species to different environmental conditions and the presence of different consumers. We identified and characterized several context‐dependent mechanisms driving direct and indirect effects of consumers. Our findings highlight the need to consider environmental context when examining potential species redundancies in particular with regard to changing environmental conditions. Furthermore, non‐trophic interactions based on empirical evidence must be incorporated into food web‐based ecological models to improve understanding of community responses to global change.     

Delineating reef fish trophic guilds with global gut content data synthesis and phylogeny

Understanding species’ roles in food webs requires an accurate assessment of their trophic niche. However, it is challenging to delineate potential trophic interactions across an ecosystem, and a paucity of empirical information often leads to inconsistent definitions of trophic guilds based on expert opinion, especially when applied to hyperdiverse ecosystems. Using coral reef fishes as a model group, we show that experts disagree on the assignment of broad trophic guilds for more than 20% of species, which hampers comparability across studies. Here, we propose a quantitative, unbiased, and reproducible approach to define trophic guilds and apply recent advances in machine learning to predict probabilities of pairwise trophic interactions with high accuracy. We synthesize data from community-wide gut content analyses of tropical coral reef fishes worldwide, resulting in diet information from 13,961 individuals belonging to 615 reef fish. We then use network analysis to identify 8 trophic guilds and Bayesian phylogenetic modeling to show that trophic guilds can be predicted based on phylogeny and maximum body size. Finally, we use machine learning to test whether pairwise trophic interactions can be predicted with accuracy. Our models achieved a misclassification error of less than 5%, indicating that our approach results in a quantitative and reproducible trophic categorization scheme, as well as high-resolution probabilities of trophic interactions. By applying our framework to the most diverse vertebrate consumer group, we show that it can be applied to other organismal groups to advance reproducibility in trait-based ecology. Our work thus provides a viable approach to account for the complexity of predator–prey interactions in highly diverse ecosystems.

The diversity of life on our planet has produced a remarkable variety of biological traits that characterize different species, and such traits are widely considered an alternative to taxonomy to increase our understanding of biodiversity and ecosystem functioning. This study presents an unbiased and fully reproducible framework to delineate trophic guilds in reef fishes.     

Trophic complementarity drives the biodiversity–ecosystem functioning relationship in food webs

The biodiversity–ecosystem functioning (BEF) relationship is central in community ecology. Its drivers in competitive systems (sampling effect and functional complementarity) are intuitive and elegant, but we lack an integrative understanding of these drivers in complex ecosystems. Because networks encompass two key components of the BEF relationship (species richness and biomass flow), they provide a key to identify these drivers, assuming that we have a meaningful measure of functional complementarity. In a network, diversity can be defined by species richness, the number of trophic levels, but perhaps more importantly, the diversity of interactions. In this paper, we define the concept of trophic complementarity (TC), which emerges through exploitative and apparent competition processes, and study its contribution to ecosystem functioning. Using a model of trophic community dynamics, we show that TC predicts various measures of ecosystem functioning, and generate a range of testable predictions. We find that, in addition to the number of species, the structure of their interactions needs to be accounted for to predict ecosystem productivity.     

Context dependency of animal resource subsidies

The transport of resource subsidies by animals has been documented across a range of species and ecosystems. Although many of these studies have shown that animal resource subsidies can have significant effects on nutrient cycling, ecosystem productivity, and food‐web structure, there is a great deal of variability in the occurrence and strength of these effects. Here we propose a conceptual framework for understanding the context dependency of animal resource subsidies, and for developing and testing predictions about the effects of animal subsidies over space and time. We propose a general framework, in which abiotic characteristics and animal vector characteristics from the donor ecosystem interact to determine the quantity, quality, timing, and duration (QQTD) of an animal input. The animal input is translated through the lens of recipient ecosystem characteristics, which include both abiotic and consumer characteristics, to yield the QQTD of the subsidy. The translated subsidy influences recipient ecosystem dynamics through effects on both trophic structure and ecosystem function, which may both influence the recipient ecosystem's response to further inputs and feed back to influence the donor ecosystem. We present a review of research on animal resource subsidies across ecosystem boundaries, placed within the context of this framework, and we discuss how the QQTD of resource subsidies can influence trophic structure and ecosystem function in recipient ecosystems. We explore the importance of understanding context dependency of animal resource subsidies in increasingly altered ecosystems, in which the characteristics of both animal vectors and donor and recipient ecosystems may be changing rapidly. Finally, we make recommendations for future research on animal resource subsidies, and resource subsidies in general, that will increase our understanding and predictive capacity about their ecosystem effects.     

Biodiversity and ecosystem functioning in food webs: the vertical diversity hypothesis

One challenge in merging community and ecosystem ecology is to integrate the complexity of natural multitrophic communities into concepts of ecosystem functioning. Here, we combine food‐web and allometry theories to demonstrate that primary production, as measured by the total nutrient uptake of the multitrophic community, is determined by vertical diversity (i.e. food web's maximum trophic level) and structure (i.e. distributions of species and their abundances and metabolic rates across trophic levels). In natural ecosystems, the community size distribution determines all these vertical patterns and thus the total nutrient uptake. Our model suggests a vertical diversity hypothesis (VDH) for ecosystem functioning in complex food webs. It predicts that, under a given nutrient supply, the total nutrient uptake increases exponentially with the maximum trophic level in the food web and it increases with its maximum body size according to a power law. The VDH highlights the effect of top–down regulation on plant nutrient uptake, which complements traditional paradigms that emphasised the bottom–up effect of nutrient supply on vertical diversity. We conclude that the VDH contributes to a synthetic framework for understanding the relationship between vertical diversity and ecosystem functioning in food webs and predicting the impacts of global changes on multitrophic ecosystems.     

An ecosystem organization model explaining diversity at an ecosystem level: Coevolution of primary producer and decomposer

Ecological complexity of species interactions and habitat heterogeneity creates and maintains biodiversity at a trophic level in an ecosystem. This biodiversity simultaneously serves as raw material on which selective forces for organizing ecosystems operate. As a result of this organization process, differences in structure and functioning of ecosystems (diversity at ecosystem level) are generated. Although understanding diversity at the ecosystem level has attracted great interest, recent theoretical advances toward this aim have not been fully appreciated yet. Following Higashi et al. (1993), this report presents a theoretical framework that deals with the organization process of an ecosystem as a consequence of the interactions among its biotic components and their modification of ecological traits. Specifically, the ecosystem organization process of a terrestrial ecosystem is analyzed, including primary producers and decomposers. This model sheds new insight into the differences between temperate and tropical forest ecosystems.     

淡水鱼类功能生态学研究进展

在全球变化和人类活动的影响下,生物多样性正以前所未有的速度丧失,全球生物正经受第六次生物多样性危机。淡水生态系统是最脆弱的生态系统之一。淡水鱼类作为淡水生态系统的重要组成部分,承受着日趋严重的气候变化、栖息地退化、生物入侵和过度捕捞等压力,面临巨大的威胁。在此背景下,如何准确评估鱼类种群和群落对环境变化的响应,以及鱼类群落结构和功能的变化对生态系统功能的影响是淡水鱼类多样性和淡水生态系统保护的关键问题。近年来,淡水鱼类功能生态学的快速发展为解答这一问题提供了一个框架。系统地介绍了淡水鱼类功能生态学主要研究内容、方法、进展及其应用,并着重介绍了淡水鱼类功能特征及其与环境的关系、环境变化下的功能生态学响应研究。据此提出了淡水鱼类功能生态学未来的重点研究方向,指出了其在鱼类多样性保护和资源利用等领域的应用前景。     

Biodiversity and ecosystem function: the consumer connection

Proposed links between biodiversity and ecosystem processes have generated intense interest and controversy in recent years. With few exceptions, however, empirical studies have focused on grassland plants and laboratory aquatic microbial systems, whereas there has been little attention to how changing animal diversity may influence ecosystem processes. Meanwhile, a separate research tradition has demonstrated strong top‐down forcing in many systems, but has considered the role of diversity in these processes only tangentially. Integration of these research directions is necessary for more complete understanding in both areas. Several considerations suggest that changing diversity in multi‐level food webs can have important ecosystem effects that can be qualitatively different than those mediated by plants. First, extinctions tend to be biased by trophic level: higher‐level consumers are less diverse, less abundant, and under stronger anthropogenic pressure on average than wild plants, and thus face greater risk of extinction. Second, unlike plants, consumers often have impacts on ecosystems disproportionate to their abundance. Thus, an early consequence of declining diversity will often be skewed trophic structure, potentially reducing top‐down influence. Third, where predators remain abundant, declining diversity at lower trophic levels may change effectiveness of predation and penetrance of trophic cascades by reducing trait diversity and the potential for compensation among species within a level. The mostly indirect evidence available provides some support for this prediction. Yet effects of changing animal diversity on functional processes have rarely been tested experimentally. Evaluating impacts of biodiversity loss on ecosystem function requires expanding the scope of current experimental research to multi‐level food webs. A central challenge to doing so, and to evaluating the importance of trophic cascades specifically, is understanding the distribution of interaction strengths within natural communities and how they change with community composition. Although topology of most real food webs is extremely complex, it is not at all clear how much of this complexity translates to strong dynamic linkages that influence aggregate biomass and community composition. Finally, there is a need for more detailed data on patterns of species loss from real ecosystems (community “disassembly” rules).     

Functional diversity can facilitate the collapse of an undesirable ecosystem state

Biodiversity may increase ecosystem resilience. However, we have limited understanding if this holds true for ecosystems that respond to gradual environmental change with abrupt shifts to an alternative state. We used a mathematical model of anoxic–oxic regime shifts and explored how trait diversity in three groups of bacteria influences resilience. We found that trait diversity did not always increase resilience: greater diversity in two of the groups increased but in one group decreased resilience of their preferred ecosystem state. We also found that simultaneous trait diversity in multiple groups often led to reduced or erased diversity effects. Overall, our results suggest that higher diversity can increase resilience but can also promote collapse when diversity occurs in a functional group that negatively influences the state it occurs in. We propose this mechanism as a potential management approach to facilitate the recovery of a desired ecosystem state.     

Rethinking experiments that explore multiple global change factors

Our current capacity to predict the responses of ecosystem functions under global change factors is limited. We propose new and more efficient approaches to experimental design and modeling that utilize interactions between ecosystem functions to improve our understanding of their sensitivity to global change factors.     

Trophic-dynamic considerations in relating species diversity to ecosystem resilience

Complexity in the networks of interactions among and between the living and abiotic components forming ecosystems confounds the ability of ecologists to predict the economic consequences of perturbations such as species deletions in nature. Such uncertainty hampers prudent decision making about where and when to invest most intensively in species conservation programmes. Demystifying ecosystem responses to biodiversity alterations may be best achieved through the study of the interactions allowing biotic communities to compensate internally for population changes in terms of contributing to ecosystem function, or their intrinsic functional redundancy. Because individual organisms are the biologically discrete working components of ecosystems and because environmental changes are perceived at the scale of the individual, a mechanistic understanding of functional redundancy will hinge upon understanding how individuals' behaviours influence population dynamics in the complex community setting. Here, I use analytical and graphical modelling to construct a conceptual framework for predicting the conditions under which varying degrees of interspecific functional redundancy can be found in dynamic ecosystems. The framework is founded on principles related to food web successional theory, which provides some evolutionary insights for mechanistically linking functional roles of discrete, interacting organisms with the dynamics of ecosystems because energy is the currency both for ecological fitness and for food web commerce. Net productivity is considered the most contextually relevant ecosystem process variable because of its socioeconomic significance and because it ultimately subsumes all biological processes and interactions. Redundancy relative to productivity is suggested to manifest most directly as compensatory niche shifts among adaptive foragers in exploitation ecosystems, facilitating coexistence and enhancing ecosystem recovery after disturbances which alter species' relative abundances, such as extinctions. The framework further explicates how resource scarcity and environmental stochasticity may constitute 'ecosystem legacies' influencing the emergence of redundancy by shaping the background conditions for foraging behaviour evolution and, consequently, the prevalence of compensatory interactions. Because it generates experimentally testable predictions for a priori hypothesis testing about when and where varying degrees of functional redundancy are likely to be found in food webs, the framework may be useful for advancing toward the reliable knowledge of biodiversity and ecosystem function relations necessary for prudent prioritization of conservation programmes. The theory presented here introduces explanation of how increasing diversity can have a negative influence on ecosystem sustainability by altering the environment for biotic interactions and thereby changing functional compensability among biota--under particular conditions.     

Enhancing the structural diversity between forest patches—A concept and real-world experiment to study biodiversity,multifunctionality and forest resilience across spatial scales

Intensification of land use by humans has led to a homogenization of landscapes and decreasing resilience of ecosystems globally due to a loss of biodiversity, including the majority of forests. Biodiversity–ecosystem functioning (BEF) research has provided compelling evidence for a positive effect of biodiversity on ecosystem functions and services at the local (α-diversity) scale, but we largely lack empirical evidence on how the loss of between-patch β-diversity affects biodiversity and multifunctionality at the landscape scale (γ-diversity). Here, we present a novel concept and experimental framework for elucidating BEF patterns at α-, β-, and γ-scales in real landscapes at a forest management-relevant scale. We examine this framework using 22 temperate broadleaf production forests, dominated by Fagus sylvatica. In 11 of these forests, we manipulated the structure between forest patches by increasing variation in canopy cover and deadwood. We hypothesized that an increase in landscape heterogeneity would enhance the β-diversity of different trophic levels, as well as the β-functionality of various ecosystem functions. We will develop a new statistical framework for BEF studies extending across scales and incorporating biodiversity measures from taxonomic to functional to phylogenetic diversity using Hill numbers. We will further expand the Hill number concept to multifunctionality allowing the decomposition of γ-multifunctionality into α- and β-components. Combining this analytic framework with our experimental data will allow us to test how an increase in between patch heterogeneity affects biodiversity and multifunctionality across spatial scales and trophic levels to help inform and improve forest resilience under climate change. Such an integrative concept for biodiversity and functionality, including spatial scales and multiple aspects of diversity and multifunctionality as well as physical and environmental structure in forests, will go far beyond the current widely applied approach in forestry to increase resilience of future forests through the manipulation of tree species composition.     

Intraspecific diversity loss in a predator species alters prey community structure and ecosystem functions

Loss in intraspecific diversity can alter ecosystem functions, but the underlying mechanisms are still elusive, and intraspecific biodiversity–ecosystem function (iBEF) relationships have been restrained to primary producers. Here, we manipulated genetic and functional richness of a fish consumer (Phoxinus phoxinus) to test whether iBEF relationships exist in consumer species and whether they are more likely sustained by genetic or functional richness. We found that both genotypic and functional richness affected ecosystem functioning, either independently or interactively. Loss in genotypic richness reduced benthic invertebrate diversity consistently across functional richness treatments, whereas it reduced zooplankton diversity only when functional richness was high. Finally, losses in genotypic and functional richness altered functions (decomposition) through trophic cascades. We concluded that iBEF relationships lead to substantial top-down effects on entire food chains. The loss of genotypic richness impacted ecological properties as much as the loss of functional richness, probably because it sustains “cryptic” functional diversity.

Global change is expected to generate a loss of intraspecific diversity worldwide. This mesocosm study explores whether loss of genetic and functional diversity in a predator species affects community and ecosystem functioning of lower trophic levels in pond ecosystems, revealing that diversity loss in a single consumer species can impact an entire ecosystem, reducing its functionality.     

Functional trait diversity across trophic levels determines herbivore impact on plant community biomass

Understanding the consequences of trophic interactions for ecosystem functioning is challenging, as contrasting effects of species and functional diversity can be expected across trophic levels. We experimentally manipulated functional identity and diversity of grassland insect herbivores and tested their impact on plant community biomass. Herbivore resource acquisition traits, i.e. mandible strength and the diversity of mandibular traits, had more important effects on plant biomass than body size. Higher herbivore functional diversity increased overall impact on plant biomass due to feeding niche complementarity. Higher plant functional diversity limited biomass pre‐emption by herbivores. The functional diversity within and across trophic levels therefore regulates the impact of functionally contrasting consumers on primary producers. By experimentally manipulating the functional diversity across trophic levels, our study illustrates how trait‐based approaches constitute a promising way to tackle existing links between trophic interactions and ecosystem functioning.     

The significance of tree-tree interactions for forest ecosystem functioning

Global change exposes forest ecosystems to many risks including novel climatic conditions, increased frequency of climatic extremes and sudden emergence and spread of pests and pathogens. At the same time, forest landscape restoration has regained global attention as an integral strategy for climate change mitigation. Owing to unpredictable future risks and the need for new forests that provide multiple ecosystem services, mixed-species forests have been advocated for this purpose. However, the successful establishment of mixed forests requires intrinsic knowledge of biodiversity's role for forest ecosystem functioning. In this respect, a better understanding of tree-tree interactions and how they contribute to observed positive tree species richness effects on key ecosystem functions is critical. Here, we review the current knowledge of the underlying mechanisms of tree-tree interactions and argue that positive net biodiversity effects at the community scale may emerge from the dominance of positive over negative interactions at the local neighbourhood scale. In a second step, we demonstrate how tree-tree interactions and the immediate tree neighbourhood's role can be systematically assessed in a tree diversity experiment. The expected results will improve predictions about the effects of tree interactions on ecosystem functioning based on general principles. We argue that this knowledge is urgently required to guide the design of tree species mixtures for the successful establishment of newly planted forests.     

Human‐aided admixture may fuel ecosystem transformation during biological invasions: theoretical and experimental evidence

Biological invasions can transform our understanding of how the interplay of historical isolation and contemporary (human‐aided) dispersal affects the structure of intraspecific diversity in functional traits, and in turn, how changes in functional traits affect other scales of biological organization such as communities and ecosystems. Because biological invasions frequently involve the admixture of previously isolated lineages as a result of human‐aided dispersal, studies of invasive populations can reveal how admixture results in novel genotypes and shifts in functional trait variation within populations. Further, because invasive species can be ecosystem engineers within invaded ecosystems, admixture‐induced shifts in the functional traits of invaders can affect the composition of native biodiversity and alter the flow of resources through the system. Thus, invasions represent promising yet under‐investigated examples of how the effects of short‐term evolutionary changes can cascade across biological scales of diversity. Here, we propose a conceptual framework that admixture between divergent source populations during biological invasions can reorganize the genetic variation underlying key functional traits, leading to shifts in the mean and variance of functional traits within invasive populations. Changes in the mean or variance of key traits can initiate new ecological feedback mechanisms that result in a critical transition from a native ecosystem to a novel invasive ecosystem. We illustrate the application of this framework with reference to a well‐studied plant model system in invasion biology and show how a combination of quantitative genetic experiments, functional trait studies, whole ecosystem field studies and modeling can be used to explore the dynamics predicted to trigger these critical transitions.     

植物遗传多样性与生态系统功能关系的研究进展

全球变化和人类活动导致物种生境的萎缩, 造成很多植物种群数量缩减, 遗传多样性快速丧失。对于物种多样性低的生态系统, 优势种的遗传多样性可能比物种多样性对生态系统功能产生更大的影响。因此, 了解遗传多样性和生态系统功能的关系(GD-EF)及其机制对生物多样性保护、应对环境变化和生态修复具有指导意义。该文综述了植物遗传多样性对生态系统结构(高营养级生物群落结构)和生态系统功能(初级生产力、养分循环和稳定性)的影响及机制、功能多样性对GD-EF的影响、遗传多样性效应和物种多样性效应的比较, 以及GD-EF在生态修复等实际应用的研究进展。最后指出当前研究的不足之处, 以期为后续研究提供参考: 1)还需深入研究GD-EF机制; 2)未评估遗传多样性对生态系统多功能性的影响; 3)不同遗传多样性测度对生态系统功能的影响不明确; 4)缺少长期的和多空间尺度结合的GD-EF实验; 5)遗传多样性效应相对于其他因子的作用不清楚。