Biology subjects

Kefi, S.

Publications and source records attributed to Kefi, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Nutrient heterogeneity emerges from dynamical abiotic-biotic feedback in a spatially explicit plant-herbivore occupancy model

Spatial heterogeneity of abiotic resources is essential for species coexistence. Ecological theory often assumes predefined heterogeneity of resources that constrains community dynamics, but the recent developments of meta-ecosystem ecology and zoogeochemistry highlight nutrient patterns could result from the interactions between the activities and movements of organisms and their abiotic environment. Here we investigate the mechanisms by which biotic-abiotic feedbacks could generate nutrient spatial heterogeneity in a simple plant-herbivore occupancy model where populations forage, recycle, and disperse in a homogenous landscape. By systematically varying organisms ranges of foraging and dispersal, and recycling levels, we found that limited dispersal of plants plays a key role on the emergence of nutrient patchiness by favoring small clusters of vegetation that shape their environment through consumption and recycling. However, herbivores could also create nutrient spatial heterogeneity when large foraging and dispersal ranges, and high recycling, allow them to efficiently track plant hot spots and to increase population persistence. Unexpectedly, strong aggregation of herbivore populations did not necessarily result in nutrient clustering. Rather than via recycling, herbivores mainly affected nutrient distribution indirectly, through their top-down impact on plant distribution. When evenly spread in the landscape, herbivore populations with large foraging ranges created areas of strong herbivory pressure unfavorable to plant colonization where nutrient can accumulate. These results can help understand the dynamical feedback between biota and abiotic resources. In a context where human activities alter both nutrient distribution and species abundances, a better understanding of this biotic-abiotic feedback will be key to anticipate the response of ecosystems to current perturbations.

ecology↗

bioRxiv2025

On the energetic boundaries of trophic systems

Energy is the fundamental currency of life. Every organism requires a minimum intake to meet maintenance needs, and every trophic transfer dissipates part of the energy flow as heat. Classical theory has emphasized lower bounds on supply--the minimum resource level required for consumers to persist--yet the possible upper bounds and their role in limiting food-chain length remain unclear. We develop a thermodynamically grounded framework that reveals a triad of boundaries: (i) consumer thresholds, (ii) a basal protection limit that reframes the paradox of enrichment as a thermodynamic constraint, and (iii) environmental or physiological supply caps. We show that the intersection of these three boundaries determines the exact range of conditions under which a given ecosystem structure can occur, and that within this range trophic configurations arise as the unique solution that maximizes energy flow. As chain length increases, consumer thresholds rise while the basal protection limit falls, causing this range to contract and eventually disappear. Whether this limit is reached depends on the relative position of these two boundaries and the external supply cap. Their crossing defines an energetic ceiling: a thermodynamic bound on food-chain length beyond which no further level can be sustained. Our results show that feasibility conditions are directly shaped by thermodynamic laws, providing a mechanistic explanation for the emergence and limits of trophic systems.

ecology↗

bioRxiv2025

Beyond biomass: how interactions shape species' importance for ecosystem functioning

Assessing the functional role of species in a changing world is critical for effectively preserving ecosystems. Intuitively, this role should relate to how the loss of a species ultimately impacts a function. We introduce the notion of a species dynamic contribution, which takes into account biotic interactions as they develop in the community. Contrary to the static contribution --a measure of what a species directly does-- the dynamic contribution captures what the presence of the species causes. Using both model simulations and empirical data from a ciliate microcosm experiment, we demonstrate that dynamic and static contributions of species are generically unrelated. Our novel characterization of species functional contributions reveals that, due to biotic interactions, rare species that do not possess unique functional traits are just as likely as any other species to play an important role for ecosystem functioning.

ecology↗

bioRxiv2025

Emergent coexistence and the limits of reductionism in ecological communities

Understanding if pairwise interactions explain the species composition of communities is a central goal in ecology. This question has been challenged by the observation of emergent coexistence, where microbial communities contain species that cannot coexist in pairs, suggesting the presence of non-pairwise mechanisms. Instead, we show that emergent coexistence arises naturally in species-rich models with pairwise interactions. Strikingly, this phenomenon does not require additional mechanisms like intransitive or higher-order interactions; rather, coexistence arises from dense networks of indirect effects. As diversity increases, we show that indirect effects become so intricate that pairwise interactions no longer predict community composition, revealing a fundamental limit to reductionist explanations of coexistence. Like chaos emerging from simple rules, our findings provide theoretical foundations to understand how unexpected species coexistence can emerge from pairwise interactions.

ecology↗

bioRxiv2025

Revealing the organization of species stability in ecological communities

Ecological communities are often composed of many species, each interacting in complex ways. This complexity makes predictions of species responses to disturbances challenging. Here, we analyze dynamical community models and reveal an unexpectedly simple principle: species stability is governed by a single metric--self-regulation loss (SL). SL quantifies the importance of self-regulatory processes in species population dynamics. In effect, SL captures a collective outcome of species interactions, organizing how individual species respond to disturbances. When applied to data from protist community experiments, SL accurately forecasts species responses to temperature changes. Our work reveals that, despite the complexity of ecological systems, species stability follows a remarkably simple organizing principle.

ecology↗

bioRxiv2024

Ecological networks across interaction types are modular and highly driven by sampling intensity at biogeographical scales

Understanding how the structure of ecological communities varies across biotic and abiotic dimensions is a fundamental goal in ecology. This challenge is now approachable due to the increasing availability of data on community structure across the globe. Ecological communities are often defined with respect to the guilds considered and the interactions they engage in, but it is unclear whether interactions of different types respond similarly to large-scale environmental gradients. Therefore, we lack a deeper understanding of how the emergent structure of interaction networks varies across biogeographical gradients, and how this effect may change depending on their constituent interaction types. Here, using a unique dataset of 952 networks across the globe, we provide a first comparison of network structural metrics and their large-scale variability for five overarching interaction types (feeding, frugivory, herbivory, parasitism and pollination). We show that degree distribution, but not connectance alone, helps us understand the observed network structures, and this pattern is maintained across interaction types (with the partial exception of food webs). Moreover, degree distribution descriptors are generally explained by differences across studies, which represent a proxy for variability in sampling and network construction methods. Environ-mental factors show weaker but robust effects on network degree distribution, and food webs are generally more sensitive to changes in environmental factors than networks of other interaction types. By analysing common descriptors of the degree distributions of ecological networks, this study underscores for the first time generalities and differences across networks of different interaction types and their response to environmental and anthropogenic factors.

ecology↗

bioRxiv2024

Response diversity is a major driver of temporal stability in complex food webs

Global change constitutes a major threat to biodiversity and ecosystem functioning which can materialise in the temporal stability of ecological communities. However, the majority of research on stability has focused on single trophic level communities and has not yet integrated classic theory about species richness and food web structure with more recent theory centred on response diversity and stochasticity. Using a stochastic, bioenergenetic food web model, we integrate these multiple bodies of theory to reveal that response diversity is a major driver of community stability. Moreover, our integrated theory reveals that positive stability-richness relationships emerge only in the presence of response diversity. In contrast to previous work, food web structure is only a secondary driver of community stability, but interacts with response diversity to determine the sign of the stability-richness relationship. Our study reveals identifiable pathways by which food web structure and response diversity drive community stability, and raises concerns about how the loss of response diversity (biotic homogenisation) may lead to a breakdown of community stability.

ecology↗

bioRxiv2024

Unpacking sublinear growth: diversity, stability and coexistence

How can many species coexist in natural ecosystems remains a fundamental question in ecology. Theory suggests that competition for space and resources should maintain the number of coexisting species far below the staggering diversity commonly found in nature. A recent model finds that, when sublinear growth rates of species are coupled with competition, species diversity can stabilize community dynamics. This, in turn, is suggested to explain the coexistence of many species in natural ecosystems. In this brief note we clarify why the sublinear growth (SG) model does not solve the long standing paradox of species coexistence. This is because in the SG model coexistence emerges from an unrealistic property, in which species per-capita growth rate diverges at low abundance, preventing species from ever going extinct. When infinite growth at low abundance is reconciled with more realistic assumptions, the SG model recovers the expected paradox: increasing diversity leads to competitive exclusion and species extinctions.

ecology↗

bioRxiv2024

EcologicalNetworksDynamics.jl: A Julia package to simulate the temporal dynamics of complex ecological networks

O_LISpecies interactions play a crucial role in shaping biodiversity, species coexistence, population dynamics, community stability and ecosystem functioning. Our understanding of the role of the diversity of species interactions driving these species, community and ecosystem features is limited because current approaches often focus only on trophic interactions. This is why a new modelling framework that includes a greater diversity of interactions between species is crucially needed. C_LIO_LIWe developed a modular, user-friendly, and extensible Julia package that delivers the core functionality of the bio-energetic food web model. Moreover, it embeds several ecological interaction types alongside the capacity to manipulate external drivers of ecological dynamics like temperature. These new features represent important processes known to influence biodiversity, coexistence, functioning and stability in natural communities. Specifically, they include: a) an explicit multiple nutrient intake model for producers, b) competition among producers, c) temperature dependence implemented via the Boltzmann-Arhennius rule, and d) the ability to model several non-trophic interactions including competition for space, plant facilitation, predator interference and refuge provisioning. C_LIO_LIThe inclusion of the various features provides users with the ability to ask questions about multiple simultaneous processes and stressor impacts, and thus develop theory relevant to real world scenarios facing complex ecological communities in the Anthropocene. It will allow researchers to quantify the relative importance of different mechanisms to stability and functioning of complex communities. C_LIO_LIThe package was build for theoreticians seeking to explore the effects of different types of species interactions on the dynamics of complex ecological communities, but also for empiricists seeking to confront their empirical findings with theoretical expectations. The package provides a straightforward framework to model explicitly complex ecological communities or provide tools to generate those communities from few parameters. C_LI

ecology↗

bioRxiv2024

Estimating distance to tipping point from dryland ecosystem images

Resource-limited ecosystems, such as drylands, can exhibit self-organized spatial patterns. Theory suggests that these patterns can reflect increasing degradation levels as ecosystems approach possible tipping points to degradation. However, we still lack ways of estimating a distance to degradation points that is comparable across sites. Here, we present an approach to do just that from images of ecosystem landscapes. After validating the approach on simulated landscapes, we applied it to a global dryland dataset, estimated the distance of each of the sites to their degradation point and investigated the drivers of that distance. Crossing this distance with aridity projections makes it possible to pinpoint the most fragile sites among those studied. Our approach paves the way for a risk assessment method for spatially-organized ecosystems.

ecology↗

bioRxiv2024

The interplay of facilitation and competition drives the emergence of multistability in dryland plant communities

Species are wrapped in a set of feedbacks within communities and with their abiotic environment, which can can generate alternative stable states. So far, research on alternative stable states has mostly focused on systems with a small number of species and a limited diversity of interaction types. Here, we analyze a spatial model of plant community dynamics in drylands, where each species is characterized by a strategy, and interact through facilitation and competition. Our work identifies three different types of multistability emerging from the interplay of competition and facilitation. Under low-stress levels, the community organizes in small groups of coexisting species maintained by space and facilitation, while under higher stress levels, positive feedbacks from competition and facilitation lead to the dominance of a single species before desertification happens. Our study paves the way for bridging community ecology and alternative states theory in a common framework.

ecology↗

bioRxiv2023

A taxonomy of multiple stable states in complex ecological communities

Many natural and man-made systems, from financial markets to ecosystems or the human brain, are built from multiple interconnected units. This complex high-dimensionality hinders our capacity to understand and predict the dynamics, functioning and fragility of these systems. One fragility scenario, particularly relevant to ecological communities of interacting species, concerns so-called regime shifts: abrupt and unexpected transitions from healthy, species-rich communities towards states of degraded ecosystem function and services. The accepted explanation for these shifts is that they arise as abrupt transitions between alternative stable states: multiple stable configurations of a system under the same internal and external conditions. These alternative states are well-understood in low-dimensional systems, but how they upscale with system complexity remains a debated question. In the present work we investigate the emergence of multiple stable states in a number of complex system models. We find that high-dimensional models with random interactions can unfold at least four different regimes of multistability, each emerging under a specific interaction scheme. More importantly, each multistability regime leaves a distinct and quantifiable fingerprint, providing a framework to analyze experimental evidence of abrupt shifts. By bridging previous results and studying multistability regimes, their fingerprints and their correlation with empirical evidence in ecology, our study helps define a common ground to understand and classify multiple stable states in complex systems.

ecology↗

bioRxiv2021

Landscape structure and dispersal rate drive large scale catastrophic shifts in spatially explicit metapopulations

Even when environments deteriorate gradually, ecosystems may shift abruptly from one state to another. Such catastrophic shifts are difficult to predict and reverse (hysteresis). While well studied in simplified contexts, we lack a general understanding of how catastrophic shifts spread in realistic spatial contexts. For different types of landscape structure, including typical terrestrial modular and riverine dendritic networks, we here investigate landscape-scale stability in metapopulations made of bistable patches. We find that such metapopulations usually exhibit large scale catastrophic shifts and hysteresis, and that the properties of these shifts depend strongly on metapopulation spatial structure and dispersal rate: intermediate dispersal rates and a riverine spatial structure can largely reduce hysteresis size. Interestingly, our study suggests that large-scale restoration is easier with spatially clustered restoration efforts and in populations characterized by an intermediate dispersal rate.

ecology↗

bioRxiv2021

The structure and Robustness of tripartite ecological networks

Until recently, most ecological network analyses have focused on a single interaction type. In nature, however, diverse interactions co-occur, each of them forming a layer of a multilayer network. Data including information on multiple interactions has recently started to emerge, giving us the opportunity to have a first glance at possible commonalities in the structure of these networks. We studied the structural features of 44 tripartite ecological networks from the literature, each composed of two layers of interactions (e.g. herbivory, parasitism, pollination), and investigated their fragility to species losses. We found that the way in which the different layers of interactions are connected to each other affect how perturbations spread in ecological communities. Our results highlight the importance of considering multiple interactions simultaneously to better gauge the robustness of ecological communities to species loss and to more reliably identify the species that are important for robustness.

ecology↗

bioRxiv2020

Spatial distribution of local patch extinctions drives recovery dynamics in metacommunities

Human activities lead more and more to the disturbance of plant and animal communities with local extinctions as a consequence. While these negative effects are clearly visible at a local scale, it is less clear how such local patch extinctions affect regional processes, such as metacommunity dynamics and the distribution of diversity in space. Since local extinctions may not be isolated events in space but rather cluster together, it is crucial to investigate their effects in a spatially explicit framework. Here, we use experimental microcosms and numerical simulations to understand the relationship between local patch extinctions and metacommunity dynamics. More specifically, we investigate the effects of the amount and spatial autocorrelation of extinctions in a full factorial design. Experimentally, we found that local patch extinctions increased inter-patch ({beta}-) diversity by creating differences between perturbed and unperturbed patches and at the same time increased local (-) diversity by delaying the competitive exclusion of inferior competitors. Most importantly, recolonization dynamics depended more strongly on the spatial distribution of patch extinctions than on the amount of extinctions per se. Clustered local patch extinctions reduced mixing between perturbed and unperturbed patches which led to slower recovery, lower -diversity in unperturbed patches and higher {beta}-diversity. Results from a metacommunity model matched the experimental observations qualitatively when the model included ranked competitive interactions, giving a hint at the underlying mechanisms. Our results highlight that local patch extinctions can increase the diversity within and between communities, that the strength of these effects depends on the spatial distribution of extinctions and that the effects of local patch extinctions can spread regionally, throughout a landscape. These findings are highly relevant for conservation and management of spatially structured communities under global change.

ecology↗

bioRxiv2020

Linking biotic homogenisation with large-scale changes of species associations

AimThe impact of global change on biodiversity is commonly assessed in terms of changes in species distributions, community richness and community composition. Whether and how much associations between species, i.e. the degree of correlation in their spatial co-occurrence, are also changing is much less documented and mostly limited to local studies of ecological networks. In this study, we quantify changes in large-scale patterns of species associations in bird communities in relation to changes in species composition. LocationFrance. Time period2001-2017. Major taxa studiedCommon breeding birds. MethodsWe use network approaches to build three community-aggregated indices reflecting complementary aspects of species association networks. We characterise the spatio-temporal dynamics of these indices using a large-scale and high-resolution dataset of bird co-abundances of 109 species monitored for 17 years (2001-2017) from 1,969 sites across France. We finally test whether spatial and temporal changes in species association networks are related to species homogenisation estimated as the spatio-temporal dynamics of {beta}-diversity and the proportion of habitat generalists. The consistency of these relationships is tested across three main habitats, namely woodland, grassland and human settlements. ResultsWe document a directional change in association-based indices in response to modifications in {beta}-diversity and in the proportion of generalists in space and time. Weaker associations and sparser networks were related to lower {beta}-diversity and a higher proportion of generalists, suggesting an overlooked aspect of biotic homogenisation affecting species associations. We report that this overall pattern is not constant across habitats, with opposite relationships between biotic homogenisation and change in species association networks in urban versus forest communities suggesting distinct homogenisation processes. Main ConclusionsAlthough species association contain only partial signatures of species interactions, our study highlights that biotic homogenisation translates to finer changes in community structure by affecting the number, strength and type of species associations.

ecology↗

bioRxiv2020

Scaling up biodiversity ecosystem functioning relationships: the role of environmental variability in space and time

The biodiversity and ecosystem functioning (BEF) relationship is expected to be scale-dependent. The autocorrelation of environmental heterogeneity is hypothesized to explain this scale dependence because it influences how quickly biodiversity accumulates over space or time. However, this link has yet to be demonstrated in a formal model. Here we use a Lotka-Volterra competition model to simulate community dynamics when environmental conditions vary across either space or time. Species differ in their optimal environmental conditions, which results in turnover in community composition. We vary biodiversity by modelling communities with different sized regional species pools and ask how the amount of biomass per unit area depends on the number of species present, and the spatial or temporal scale at which it is measured. We find that more biodiversity is required to maintain functioning at larger temporal and spatial scales. The number of species required increases quickly when environmental autocorrelation is low, and slowly when autocorrelation is high. Both spatial and temporal environmental heterogeneity led to scale dependence in BEF, but autocorrelation had larger impacts when environmental change was temporal. These findings show how the biodiversity required to maintain functioning is expected to increase over space and time.

ecology↗

bioRxiv2018

The diversity of interaction types drives the functioning of ecological communities

Ecological communities are undeniably diverse, both in terms of the species that compose them as well as the type of interactions that link species to each other. Despite this long-recognition of the coexistence of multiple interaction types in nature, little is known about the consequences of this diversity for community functioning. In the ongoing context of global change and increasing species extinction rates, it seems crucial to improve our understanding of the drivers of the relationship between species diversity and ecosystem functioning.\n\nHere, using a multispecies dynamical model of ecological communities including various interaction types (e.g. competition for space, predator interference, recruitment facilitation), we studied the role of the presence and the intensity of these interactions for species diversity, community functioning (biomass and production) and the relationship between diversity and functioning.\n\nTaken jointly, the diverse interactions have significant effects on species diversity, whose amplitude and sign depend on the type of interactions involved and their relative abundance. They however consistently increase the slope of the relationship between diversity and functioning, suggesting that species losses might have stronger effects on community functioning than expected when ignoring the diversity of interaction types and focusing on feeding interactions only.

ecology↗