Biology subjects

Loeuille, N.

Publications and source records attributed to Loeuille, N..

At least 19 recordsLinked to original sources

bioRxiv2026

Eco-evolutionary dynamics create extinction avalanches in mutualistic-antagonistic networks

Evolution has given rise to the diversity of life on Earth, but it can also cause species extinctions. While major extinction events are usually associated with external drivers, in this study, we show mechanistically how evolution can trigger abrupt extinction avalanches in ecological networks without any environmental change. In particular, we investigate an eco-evolutionary simulation model of a tripartite mutualistic-antagonistic network, such as a plant-pollinator-herbivore network, with additional intraguild competition. The prevalence of self-organised extinction avalanches depends on a subtle balance of the different interaction types, where antagonism and similarity-based competition are needed for initial diversification while mutualism and trait-independent competition foster evolutionarily driven extinction events. Extinction avalanches are triggered by a mutualist evolving to interact with plants that are not subject to sufficient antagonistic control. Subsequently, the mutualist, its plant partners and their main antagonist potentially outcompete the rest of the community. Our findings point out that evolutionary murder may claim many victims simultaneously and highlight the need to take different interaction types into account to gain a comprehensive understanding of the links between evolution and biodiversity in ecological communities.

evolutionary biology↗

bioRxiv2026

Pretty Good Yields allow the spatial management of multiple objectives in agricultural landscapes

In order to feed a growing global population without silencing nature, conceiving agricultural management strategies reconciling yield and conservation goals is key. Using numerical simulations of a metacommunity model, we explore the possibilities for compromise offered by spatial management strategies of farmed areas. Each strategy is characterized by its farming intensity, the proportion of farmed lands and their spatial aggregation. We show that achieving equitable yield-biodiversity compromise is difficult. While conciliatory strategies offering top yield and biodiversity are typically not possible, accepting slightly lower yields (ie, "Pretty Good Yield strategies") allows to recover substantial biodiversity. Such reconciliation possibilities are limited for species with small dispersal. Yield increases mainly through farmland expansion, whereas farming intensity strongly influences biodiversity, increasing it at low intensity before decreasing with further intensification. Finally, we demonstrate that reconciliation is easier if agricultural production relies on biodiversity through ecosystem services.

ecology↗

bioRxiv2026

Between Friends and Foes: Evolutionary Diversification in Mutualistic-Antagonistic Networks

Biotic interactions can drive evolutionary diversification, but the underlying mechanisms differ depending on the type of interaction. For instance, Ehrlich and Ravens escape-and-radiate coevolution provides a pathway of diversification in antagonistic interactions, whereas in mutualistic networks, coevolution is hypothesized to result in trait convergence rather than diversification. The combined effect of mutualism and antagonism on diversification remains unclear, even though organisms naturally engage in multiple types of interactions simultaneously. Using an eco-evolutionary simulation model, we investigate diversification in tripartite ecological networks such as plant-pollinator-herbivore networks. We find that diversification patterns vary according to the way mutualism and antagonism are connected on the trait level. If the two interactions are governed by uncorrelated plant traits, we observe little diversification in the mutualistic and substantial diversification in the antagonistic subnetwork. By contrast, if the same plant trait mediates both mutualism and antagonism (an example of ecological pleiotropy), diversification rates in all guilds become interdependent. In this case, even the mutualistic guild diversifies considerably when antagonism is strong, while strong mutualism restricts diversification also in the antagonistic guild. Our study underlines that the inclusion of multiple interaction types is necessary to advance our understanding of evolutionary dynamics in ecological networks.

evolutionary biology↗

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↗

bioRxiv2026

Direct and community-driven selection jointly drive body size evolution in harvested predator-prey systems

Fisheries-induced evolution (FIE) affects multiple life-history traits, most notably body size. This evolutionary response is often examined at the single-species level and attributed to direct size-selective harvesting. However, fishing also targets other community members, reshaping trophic interactions and thereby modifying evolutionary constraints due to community changes. Here, we disentangle two forms of fishing-induced selection on body size - direct, arising from size-selective harvesting within species individuals, and indirect, emerging from fishing-induced changes in community structure - and investigate how their interplay shapes evolutionary trajectories. Using an adaptive dynamics framework within a predator-prey model, we show that (i) community destructuring can either amplify or dampen the effects of intraspecific size-selectivity on body-size evolution, (ii) predator evolution is primarily driven by direct selection, whereas prey evolution is mostly constrained indirectly by community structure. We then extend our analysis using a stochastic framework and show that (iii) prey evolution allows the evolutionary rescue of predators, underscoring the importance of community context. Our results demonstrate that eco-evolutionary feedbacks can profoundly alter both community structure and fishery yields, strengthening calls to incorporate evolution into ecosystem-based fisheries management.

evolutionary biology↗

bioRxiv2026

Potential and limits of the evolutionary rescue of harvested food webs

Fishing deeply alters marine food webs structure and can drive the evolution of species traits, whether the species are directly targeted or not. Yet, studies rarely account for fisheries-induced evolution, and consequences are generally interpreted at the single-species level. Theory however predicts that eco-evolutionary dynamics within food webs can either promote biodiversity maintenance or accelerate its decline. In this study, we investigate how evolution affects the robustness of trophic networks under fishing pressure. Modifying evolution speed and the allocation of fishing effort across 458 structurally distinct allometric networks enables us to show that evolution most often enhances robustness. Network evolutionary response however becomes more variable (and possibly negative) as evolutionary rates increase and when fishing preferentially targets predators. By contrast, fishing strategies that concentrate effort on lower trophic levels, or distribute it more evenly, promote network persistence through evolutionary rescue while substantially reducing the risk of evolutionary collapse. Moreover, our results appear to be sensitive to the main forces governing ecological dynamics within the network such as competition or predation intensity. Finally, the consequences of network evolution differ across trophic levels. Evolution often drives the collapse of higher trophic levels while simultaneously promoting evolutionary rescue and enhancing diversity at lower levels through increased diversification, thereby generating a trade-off between vertical diversity (number of trophic levels) and total diversity. This highlights the importance of accounting for evolutionary dynamics and food web functioning in fisheries management, and suggests that reducing predator mortality may help prevent network evolutionary collapse.

evolutionary biology↗

bioRxiv2026

Applying a metaweb approach to reserve design: large, well protected areas are crucial to maintain food webs

Establishing protected areas is a promising tool to address the accelerating loss of biodiversity. However, protection levels are often low, and there is an ongoing debate over the most effective spatial configuration of reserves. This debate rarely considers trophic structure and ignores biodiversity outside protected areas. In this study, we investigate which reserve configurations best support species diversity and the persistence of high trophic levels, across systems and spatial scales, both inside and outside protected areas. Using a spatially explicit stochastic model, we assess how reserve architecture influences multiple conservation objectives across 27 empirical terrestrial, freshwater, and marine food webs. Specifically, we explore reserve architecture along three dimensions: the aggregation of protected areas, their proportion at the landscape scale, and the effectiveness level of protection measures. Our results show that having few but larger protected areas enhances all conservation metrics within reserves, while diversity within and outside reserves is relatively insensitive to reserve aggregation. Smaller and more dispersed reserves improve the overall abundance of species off-reserves through spillover effects. Reconciling all objectives inside and outside reserves becomes feasible when protection effectiveness is sufficiently high. Increasing the efficiency of protection allows for a reduction in the total amount of protected land without compromising conservation outcomes. Moreover, higher species dispersal facilitates the achievement of multiple conservation goals, supporting the implementation of architectures that enhance connectivity among reserves. These findings highlight the importance of an integrated approach combining spatial ecology and trophic functioning to optimize protected area planning under multiple objectives.

ecology↗

bioRxiv2026

Eco-evolutionary dynamics of planktonic calcifying communities under ocean acidification

Increasing emissions of CO2 into the atmosphere are causing ocean acidification, threatening calcifying organisms. In this study, we model the physiological responses of coccolithophorids to acidification to understand the ecological and evolutionary outcomes of a system in interaction with zooplankton. Assuming a trade-off between growth and protection against grazing, we show that calcification has bivalent effects on transfers between two trophic levels and that acidity can strongly alter energy transfers. Taking into account the evolution of calcifying phenotypes in response to acidification, we show that the system outcome contrasts with previous results. While the effect of evolution depends on how calcification affects grazing, it nevertheless follows that acidification leads to a decrease in calcifying capacity. This evolutionary decrease may be progressive, but can also lead to tipping points where abrupt shifts may occur. Such a counter-selection of calcification in turn affects ecosystem functioning, enhancing energy transfers within the system and modifying carbon fluxes. We discuss how such eco-evolutionary changes may impact food webs integrity, carbon sequestration into the deep ocean and therefore endanger the carbon pump stability.

evolutionary biology↗

bioRxiv2026

A graphical approach of the interplay of eco-evolutionary dynamics and coexistence

Given the accumulation of evidence that evolution can affect ecological dynamics, especially under global change scenarios, a key question is how such ecoevolutionary dynamics may change the coexistence of species and biodiversity in general. In the present article, we propose a graphical approach allowing to simultaneously discuss ecological coexistence and phenotype evolution. Our graphical approach allows tackling the two aspects in the same parameter space, allowing direct links between ecological and evolutionary perspectives. While evolution is often thought positive for the resilience of ecological systems, we first highlight it does not usually allow for better coexistence for the system as a whole. Even when focusing on the fate of the species that is evolving, evolution often leads to greater vulnerability. The graphical approach we propose is flexible and can be applied to all interaction types and covers variations in trade-off structures. Using this flexibility, we highlight how evolutionary effects can be positive or negative for coexistence, depending on these two components. Finally, we illustrate how the approach can be applied, using empirical examples derived from the literature. We thereby highlight the critical ingredients needed to inform the graphical approach, its potential use for proposing testable scenarios, but also clarify its limits.

ecology↗

bioRxiv2025

Interplay of immigration and coevolution constrains the structure of specialist-generalist communities

Species and populations in nature fall along a specialist-generalist continuum in habitat preferences and resource use. However, most studies focusing on assembly, niche packing and diversification have considered solely niche positions within a community. We study how the co-evolution of niche position and degree of specialization affects packing, coexistence, and properties of the resulting communities under different modes of community assembly. We observe that evolution can lead to diversification and spontaneous emergence of asymmetric configurations of generalist and specialist phenotypes. Moreover, there exist multiple alternative evolutionarily stable states, with either many specialists or fewer generalists, some of which are only locally uninvadable. Contingency on assembly history shows that both local evolutionary adaptation and dispersal processes influence community-level eco-evolutionary dynamics and the structure of communities. By comparing communities along a continuum of assembly modes going from pure coevolution to pure dispersal, we find that high rates of evolution constrain richness while promoting generalism, partly because pure evolutionary communities become trapped at local evolutionary optima. In contrast, communities shaped by strong immigration tend to be rich in specialist species. Finally, high rates of evolution decrease invasion success in mixed assembly scenarios, a pattern consistent with the phenomenon of community monopolization.

ecology↗

bioRxiv2025

Overexploitation counteracts top-down control and the paradox of enrichment in simple food chains.

Overexploitation, the depletion of a resource by its consumer on a short timescale, is widespread in nature but its general implications for biomass control and community stability are not clear. Most approaches investigating the interactions between trophic levels and variations in biomass patterns or in population dynamics generally ignore overexploitation. Here we use a resource-plant-herbivore food chain model allowing for overexploitation (i.e. the plant can overexploit the resource and/or the herbivore can overexploit the plant). We uncover the conditions under which either type of overexploitation occurs and show that they qualitatively change ecological patterns, mainly by suppressing top-down control when interaction strength is high. When plant productivity increases, top-down control patterns are suppressed above the level when the plant starts to overexploit resources. Similarly, when herbivory intensity increases, top-down control patterns disappear when plants become overex-ploited. Overexploitation also prevents enrichment-driven destabilization by capping the energy fluxes in the community. These findings connect top-down and bottom-up controls in a single framework, and highlight the role overexploitation can play in structuring and stabilizing food chains via the modulation of interaction strengths.

ecology↗

bioRxiv2025

Urbanisation and habitat fragmentation favour thermophilic and monogynous ant species

Environmental changes such as urbanisation and related habitat loss and fragmentation profoundly impact ecological communities by altering habitats, resources, and microclimates. Yet, the impacts of the resulting environmental conditions on metacommunity dynamics, ranging from species sorting to mass effects, remain a subject of debate. Ants, with diverse life histories and strong ecological effects, are ideal model species to study these pressures. We investigated the response of ant communities, including taxonomic and functional diversity, to urbanisation and habitat fragmentation in the Paris region, comparing wooded areas in 25 urban parks vs. 24 rural forests outside the city. We found a clear difference in species composition between urban and rural environments, with a higher prevalence of thermophilic species and a tendency for monogyny in the city. Forest communities were homogeneous across the size levels we studied, while park communities differed noticeably depending on park size, with larger parks harbouring more species. Our findings suggest that urbanisation selects specific ant traits and favours more thermophilic species, thereby increasing the mean thermal preference of urban communities. These selective effects influence which species can colonise and survive in different patches, shaping metacommunity structure and potentially affecting the resilience of ant communities under climate change.

ecology↗

bioRxiv2025

The role of pathogens in creating and maintaining host polymorphism

Terrestrial and marine ecosystems exhibit remarkable species diversity and richness. Among the hypotheses put forward to explain this diversity --its origins and the forces sustaining it-- one prominent hypothesis posits that pathogens could be pivotal in generating and maintaining species diversity within ecosystems. To explore this hypothesis, we analyzed a host-pathogen system, examining the specific conditions that might facilitate pathogen-driven diversification within the host population, with a focus on both the emergence and persistence of diversity. By applying a fecundity-transmission trade-off in which a non-evolving pathogen influences its evolving host, we observed that pathogens only infrequently drive host diversification, and only around intermediate trade-off conditions. Furthermore, while these rare diversification events result in stable coexistence, evolved diversity is low, consisting of two coexisting host morphs. Because the sole evolution of hosts in response to pathogens offers limited opportunity for diversification, we propose additional mechanisms that could foster higher levels of diversity within the system.

ecology↗

bioRxiv2025

The strength of the fecundity-immunity trade-off modulates host evolutionary dynamics, pathogen propagation, and host abundance

In most species, life history trade-offs generate conflicts between biological functions because of resource allocation constraints. During pathogenic infections, hosts can deploy various immune defenses, but these responses usually carry fitness costs, most often expressed as reduced fertility. This fecundity-immunity trade off has been widely studied for its evolutionary implications, yet its effects on other emergent properties --such as host abundance and pathogen spread-- remain poorly understood. Here, we develop an SIR model incorporating three immune strategies --reduced host susceptibility, increased host recovery, and reduced pathogen virulence-- and show that the evolutionary impact of the fecundity-immunity trade off depends on both its shape and the specific immune mechanism under selection. For reduced susceptibility and increased recovery, disease spread and host abundance evolve in opposite directions along evolutionary trajectories, such that when disease spread increases, host abundance decreases, and vice versa. For reduced virulence, however, this relationship is more complex and does not follow a simple pattern. Across all three mechanisms, trade offs with low cost intensity, whether concave or convex, favor the joint evolution of high fecundity and high immunity. In contrast, concave or convex trade offs incurring high cost consistently select for high fecundity at the expense of immunity. Trade offs with moderate cost intensity generate two alternative outcomes: one strategy with high fecundity and low immunity, and another combining low fecundity with enhanced immunity. Together, these findings underscore the importance of accounting for the specific immune mechanism evolving and the associated cost intensity when predicting the eco-evolutionary consequences of fecundity-immunity trade-offs. HighlightsO_LIImpacts of host evolution on R0 and total host abundance N are rarely investigated C_LIO_LIHost evolution accessed under various components of a fecundity-immunity trade-off C_LIO_LIWeak fecundity-susceptibility / recovery trade-offs decrease R0 and increase N C_LIO_LIStrong fecundity-susceptibility / recovery trade-offs increase R0 and decrease N C_LIO_LIMore complex patterns are observed for the fecundity-virulence trade-off C_LI

ecology↗

bioRxiv2025

Managing risks and trade-offs in multispecies fisheries: the role of trophic control and price asymmetry

Ecosystem-based fisheries management (EBFM) aims to balance ecological and economic goals while employing precautionary measures to address uncertainties in knowledge and management. This study investigates fishing strategies to achieve this balance while minimizing the associated risks. Using a simplified prey-predator model, we explored various scenarios reflecting the diversity of global fisheries. The model integrates key ecological dynamics (bottom-up and top-down forces), economic factors (price structures), and aggregates the diversity of fishing practices by distributing fishing mortality across species. Our findings reveal that predators are always more affected by fishing than prey, regardless of the effort distribution. High yields are achieved by reducing predator densities--either maximizing predator catches when they are highly valued or reducing predation pressure to enhance prey harvests when prey prices are high. Such strategies result in significant ecological impacts, leading to systematic trade-offs. Elevated prey prices and top-down controlled systems intensify these trade-offs, increasing ecological risks. Regarding uncertainties, we demonstrate that maximizing yields poses risks to both biodiversity and profitability. Reconciliation is challenging but feasible when both species are fished. This balance can be achieved only in bottom-up controlled systems where prey valuation is not disproportionately high compared to predator prices.

ecology↗

bioRxiv2024

Spatial context allows the evolution the control of nitrification by plants

Some plant species inhibit or stimulate soil nitrification, the transformation of ammonium into nitrate by microorganisms. The control of nitrification may in turn alter ecosystem productivity and functioning. Given the potential positive impacts of nitrification control on plant fitness, we aim to determine the conditions under which nitrification control is likely to have been selected, and the consequences of that selection on ecosystem functioning. We investigate both the role of the abiotic context (nutrient availability and diffusion) and the role of other plant traits (mortality and dispersal). A first mean-field model shows that when nitrogen pools are shared among individuals within the plant population, the control of nitrification is counter-selected. A tragedy of the commons occurs because the costs of controlling nitrification (ie. of producing root exudates) only affect the controlling individuals while benefits are shared among all individuals. We then assume that the effects of the control of nitrification are spatially restricted to the rhizosphere, and we build a spatially explicit, individual-based model in which mutation of control of nitrification is possible. Plant capacity to control nitrification evolves when the plant environment is sufficiently private and generation time sufficiently long, leading to higher fitness benefits of the construction process. In such cases, plants evolve to inhibit nitrification when losses of nitrate are greater than losses of ammonium and evolve to stimulate nitrification when losses of ammonium are greater than losses of nitrate. Finally, biomass production tends to be maximal at the selected strategy when the diffusion of ammonium and nitrate is low. Our results help predict which strategies should be selected and likely to be found in different plants in different parts of the world.

ecology↗

bioRxiv2024

Diffusion of constructed resources and specialism promotes facilitation in spatial systems

Sessile organisms contend with locally limiting nutrients and neighbours. Increases in nutrient concentration due to niche construction and diffusion of resources change the interaction sign between neighbours usually thought to compete for resources. We investigate conditions under which the positive effect of niche construction outweighs the negative effect of resource consumption. Following the design of facilitation experiments, we model two patches connected by resource flows, and ask whether the presence of a niche constructor in one patch eases the colonisation of the other. Niche constructors positively affect neighbouring organisms when their niches are sufficiently differentiated, and when the constructed resource diffuses more than the non-constructed resource. Our work proposes mechanisms for the emergence of facilitation, which is increasingly recognised as a key process structuring plant and microbial communities. We discuss the implications for the spatial structure of communities and their functioning, including in an agricultural context.

ecology↗

bioRxiv2023

Group or solitary dispersal: worker presence and number favour the success of colony foundation in ants

Dispersal strategies are highly variable. Any strategy is associated to costs and benefits, and understanding which factors favour or disfavour a strategy is a key issue in ecology and evolution. Ants exhibit different dispersal and colony foundation strategies. Some species have winged queens that disperse solitarily and far by flight, and that found new colonies alone. Others have apterous queens that disperse with workers over short walking distances, and found new colonies as a group (colony fission). The putative benefits conferred by workers have been little studied and quantified, because comparing the costs and benefits of solitary vs. group dispersal and foundation is difficult when comparing different species. We did this using the ant Myrmecina graminicola, one of the few species that use both strategies. Young queens were mated and allowed to found new colonies in the laboratory, with either zero, two or four workers. We monitored the survival and growth of foundations over one year. The presence of workers increased both survival and growth, with more workers yielding higher growth. These results show the benefit of dispersing and founding in a group. The presence of few workers (as little as two workers) was sufficient to provide benefits, suggesting group foundation does not require a dramatic decrease in the number of propagules produced in M. graminicola. Our results support the hypothesis that the two strategies coexist along a competition-colonization trade-off, where solitary foundation offers a colonization advantage while group foundation has a competitive advantage.

ecology↗