Biology subjects

Godoy, O.

Publications and source records attributed to Godoy, O..

At least 19 recordsLinked to original sources

bioRxiv2026

Coupling demography and interactions reshapes the structural stability of ecological communities

The assembly of ecological communities depends on both species' demography and the interactions among them. Ecological theory assumes that both ecological processes vary independently. However, empirical evidence demonstrates otherwise. How the structural stability of ecological communities changes when species' intrinsic growth rates and interactions are coupled remains unknown. To address this knowledge gap, we present several seemingly disconnected examples, such as the stress-gradient hypothesis, the covariance between environment and competition, higher-order interactions, and niche packing, that actually fall along a continuum of changes ranging from positive to negative interactions. Although the specific details of each scenario differ, they all share a common feature. When demography and interactions are coupled in multispecies models of population dynamics, the limits of structural stability in ecological communities shift non-linearly, and the domain of viability increases or decreases compared to a non-coupling scenario. We mathematically demonstrate that whether these changes are positive or negative depends on how the strength of intraspecific interactions shifts relative to interspecific interactions as species' growth rates increase. These new non-linear relationships imply two important shifts of thinking. Theoretically, the definition of structural stability must be generalized and its estimation requires the use of probabilistic measures based on ecological limits. Empirically, if abiotic and biotic barriers operate simultaneously, we need to account for such non-linear processes that can significantly modify population dynamics. Otherwise, we will not make accurate predictions of how ecological communities are assembled and biodiversity is maintained.

ecology↗

bioRxiv2025

Time-varying interactions drive species coexistence via rainfall variation

Species interactions are fundamental to maintaining diversity. However, it remains unclear how environmental variability modifies the structure, sign, and strength of species interactions that ultimately affect coexistence mechanisms. Here, we combined structural stability theory with time-varying population models to study the temporal variation of niche and fitness differences over nine years of annual plants in Mediterranean grasslands. Rainfall variation modulated species-specific responses in performance, and changed the magnitude of self-limitation and the variability in the strength of interspecific interactions for both competition and facilitation. These changes implied substantial variation in yearly niche and fitness differences, which ultimately impacted community stability. Additional simulations show that this full biological reorganization due to rainfall variation can maintain diversity by promoting temporal shifts in winners and losers compared to a single climatic year. Our results highlight the need to incorporate time-varying interactions to understand species coexistence under contrasting environmental conditions.

ecology↗

bioRxiv2025

Stably coexisting communities deliver higher ecosystem multifunctionality

Linking the processes determining species coexistence and effects of biodiversity on ecosystem functioning is important for a mechanistic understanding of how species loss impacts ecosystems1. There are good theoretical reasons to expect stably coexisting communities to deliver higher ecosystem functioning, as niche differences should promote coexistence and complementarity2, however, there is still little empirical evidence to demonstrate this relationship3. We present a novel experimental approach to tackle this question, in which we first measured interaction coefficients and intrinsic growth rates for 12 grassland species4 and used population models to estimate coexistence5. We then assembled 48 three-species communities, predicted to differ in their degree of coexistence and measured seven above and belowground functions. Here we extend findings demonstrating that biodiversity increases multifunctionality6,7 to show that amongst communities with the same initial diversity, multifunctionality is higher when all the species are predicted to coexist. Decomposing coexistence into the influence of niche and fitness differences showed that multifunctionality was high in niche differentiated communities but also in those with a single highly competitive species. We further examined the effect of indirect interactions, which provide an alternative mechanism of coexistence in multispecies communities, and found that they also provided an alternative route to high multifunctionality. Our results point the way to a unification of coexistence and biodiversity theory and to a more mechanistic understanding of the functional effects of biodiversity change.

ecology↗

bioRxiv2025

Species interactions are internally constrained despite large climatic variability

Understanding how vital rates and species interactions vary over time is crucial for predicting community responses to environmental change. Considerable progress has been made in understanding the drivers of variation in vital rates. However, the question of whether interactions are highly plastic and context-dependent, or strongly constrained by internal (e.g., species traits and composition) and/or external factors (e.g., environmental conditions) remains unclear. We applied a theoretical approach based on the feasibility domain --the range of conditions allowing coexistence-- to a nine-year dataset of time-changing interactions between annual plants under large variability in annual precipitation. Using subcommunities of three species, we found that species interactions are strongly constrained, forming a "core-periphery" structure of consistently feasible combinations across years. This main finding means that species sample repeatedly a restricted range of opportunities for coexistence. Similar findings were obtained for subcommunities of four species. Crucially, the constraints to variation in biotic interactions are determined by species identity (internal constraints) rather than precipitation or temporal autocorrelation (external environmental factors). Furthermore, we found a contrasting effect of precipitation on the feasibility of subcommunities. While wetter years increase similarity between subcommunities and reduce the overall feasible range, drier years increase dissimilarity between subcommunities and increase the probability of coexistence when the conditions seem harsher. These findings suggest that constraints to biotic interactions tend to be alike across species in wetter years, but more context dependency occurs across species in drier years. Our findings challenge the assumption of highly plastic species interactions even in a highly dynamic system of annual plants. Our results also highlight the critical importance of internal constraints generated by species identity in mediating community persistence and predicting community responses to environmental change.

ecology↗

bioRxiv2025

Neighbor density-dependent facilitation promotescoexistence and internal oscillation

The ability of species to form diverse communities is not fully understood. Species are known to interact in various ways with their neighborhood. Despite this, common models of species coexistence assume that per capita interactions are constant and competitive, even as the environment changes. In this study, we investigate how neighbor density-dependent variation in the strength and sign of species interactions changes species and community dynamics. We show that by including these sources of variation, predictions of ecological dynamics are significantly improved compared to outcomes of typical models that hold interaction strengths constant. We compared how well models based on different functions of neighbor density and identity did in describing population trajectories (i.e., persistence over time) and community dynamics (i.e., temporal stability, synchrony and degree of oscillation) in simulated two-species communities and a real diverse annual plant system. In our simulated communities, we found the highest level of coexistence between species pairs when species interactions varied from competitive to facilitative according to neighbor density (i.e., following a sigmoid function). Introducing within-guild facilitation through a nonlinear bounded function allowed populations, both simulated and empirical, to avoid extinction or runaway growth. In fact, nonlinear bounded functions (i.e., exponential and sigmoid functions) predicted population trends over time within the range of abundances observed over the last 10 years. With the sigmoid function, the simulated communities of two species displayed a higher probability of synchrony and oscillation than other functional forms. These simulated communities did not always show temporal stability but were predicted to coexist. Overall, varying species interactions lead to realistic ecological trajectories and community dynamics when bounded by asymptotes based on neighbor density. These findings are important for advancing our understanding of how diverse communities are sustained and for operationalizing ecological theory in the study of the real world.

ecology↗

bioRxiv2025

A general framework for cycles in ecology

Theory predicts that indirect interactions in ecological networks sustain species diversity through oscillatory dynamics. However, a framework linking interaction structure to these cycles is lacking. We develop an analytical toolbox combining assembly graphs with a mathematical decomposition of interaction matrices into symmetric and anti-symmetric components. We find that assembly cycles--closed loops of species invasions--are suppressed when symmetric interactions dominate, reflecting strong intraspecific competition. Conversely, anti-symmetric dominance, indicating competitive asymmetries, leads to cycles like rock-paper-scissors and novel multispecies invasion patterns. As asymmetries increase, new cycles emerge involving both sequential and simultaneous invasions. Applying this approach to 21 plant community interaction matrices, we find few cycles due to prevalent self-limiting effects. Our work clarifies when indirect interactions drive cycles and introduces a simple ratio assessing symmetric versus anti-symmetric contributions, constraining cycle emergence, and species coexistence in nature. Significant statementUncertainties of the fundamental blocks that maintain biodiversity hinder our understanding of the dynamics we can observe in ecological communities. By applying a well-known mathematical approach to decomposing interactions among species within ecological communities, we discover great potential for observing rock-paper-scissors and more complex cyclic dynamics in nature. However, we predict and confirm analyzing multiple datasets that cyclic dynamics are rare because of two phenomena that pervade ecological communities. These are differences in species performance and the dominance of self-limiting effects. Our framework underscores the importance of studying simple properties of biotic interactions to predict complex ecological dynamics.

ecology↗

bioRxiv2024

TOP-DOWN CLIMATIC PROCESSES MODULATE BIODIVERSITY-FUNCTIONING RELATIONSHIPS ACROSS NORTH AMERICAN FORESTS

Experimental evidence indicates that more diverse communities sustain higher levels of ecosystem functioning. Generally, bottom-up processes accounting for community selection and complementarity effects on biodiversity are used to explain biodiversity effects on ecosystem functioning. However, top-down macroecological processes can also influence the distribution of ecosystem functions across large environmental gradients and, importantly, biodiversity patterns. Here, we tested whether past climate instability, current climate, and climate-driven species abundance explain tree richness gradients, and therefore, determine the relationship between species richness and ecosystem functioning using 137,808 forest inventory plots across continental extents including forests of Canada, the US, and Mexico. Consistent with previous research, we found a positive monotonic relationship between species richness and biomass (measured as level stand basal area) across North American forests. However, structural equation models revealed that the indirect effect of past climate instability, current climate conditions, and climate-driven individuals abundance underlie species richness patterns and the positive covariation between species richness and biomass. The importance of top-down climatic processes varied from boreal to tropical regions, yet their significant effects were pervasive across all forest types, indicating that climate strongly modulates the strength of the relationships between species richness and basal area. Our results help to understand the assembly processes driving the ubiquitous positive monotonic relationship between species richness and basal area across continental extents. This knowledge, obtained from adopting a macroecological perspective, helps understanding biodiversity-functioning relationships, which are usually explained by mechanisms at the community level. Significance statementMore biodiverse communities sustain higher levels of ecosystem functions (BEF hypothesis). The role of biotic interactions among trees within ecological communities determining BEF has been widely studied, but it is not well known how past climatic variability, current climate, and species abundance determine BEF. Using 137,808 forest inventory plots across North American forests located in Canada, the US, and Mexico, we document a positive relationship between tree species richness and stand basal area. Detailed analysis revealed that the positive BEF relationship is underlined by a strong and indirect effect of past and current climate. Our results highlight the importance of top-down climate processes operating at macroecological scales to understand biodiversity-functioning relationships.

ecology↗

bioRxiv2024

Cooperation maximizes biodiversity

Cooperation, the mutual benefit that individuals of different species obtain when they interact together, is ubiquitous in nature. Despite their importance, most of all current ecological theories have been formalized focusing on negative interactions such as competition or predation. The role of cooperation, or other types of positive interactions including facilitation and mutualism, has not been fully addressed, or, if so, always in combination with negative interactions. This fact limits our understanding of the unique features by which cooperation as opposed to competition promotes biodiversity. To address this gap, we introduce here cooperation into structural stability, a general framework to understand how species interactions and environmental variability determine the long-term persistence of species within communities. Compared to a pure competitive case, cooperation promotes three distinctive features. First, cooperation increases the opportunities for species to coexist. This feature increases the persistence of species with contrasted phylogenetic, functional, and demographic strategies that the environment would otherwise filter. Second, cooperation creates intertwined biodiversity where the existence of some species begets the presence of others. Third, cooperation promotes multistability by changing the dynamics of community assembly due to variations in environmental conditions. In conclusion, we present a fully operational framework to understand the unique ecological roles of cooperation in nature. It indicates that cooperation as opposed to competition maximizes the maintenance of biodiversity.

ecology↗

bioRxiv2023

Sex in the kitchen: non-additive effects of competition for food and reproductive interference on coexistence outcomes between closely related species.

Competition for food and reproductive interference (negative interspecific sexual interactions) have been identified as major drivers of species exclusion. Still, how these biotic interactions jointly determine competitive dominance remains largely unknown. We tackle this by coupling population models and laboratory experiments with two sibling species of spider mites. Using experiments specifically designed to measure the single and combined effects of food competition and reproductive interference, we first show that the strength and symmetry of reproductive interference between species changes in presence of food competition. Next, we show that population models incorporating each type of interaction alone lead to markedly different predictions, from exclusion of the inferior competitor for food, to priority effects instead favouring the latter under the sole effect of reproductive interference. Moreover, accounting for the observed reduction in the strength of reproductive interference in the presence of food competition changes the threshold frequency determining the dominant competitor when both interactions are at play, from equal chances for the two species to exclude the other depending on their initial frequency, to favouring the superior competitor for food except when it is extremely rare. Finally, we showed that the model generates accurate predictions for population dynamics in an independent population cage experiment, indicating that our approach captures the most relevant processes governing the outcome of interactions between competing spider mite species. Altogether, our results suggest that trophic interactions can modulate sexual interactions, significantly impacting population dynamics and competitive outcomes. Hence, the joint consideration of food competition and reproductive interference is critical to accurately predict and understand species coexistence.

ecology↗

bioRxiv2023

Fast-slow traits predict competition network structure and its response to resources and enemies.

Plants interact in complex networks but how their structure depends on resources, natural enemies and species resource-use strategy remains poorly understood. Here, we quantified competition networks among 18 plants varying in fast-slow strategy, by testing how increased nutrient availability and reduced foliar pathogens affected intra- and inter-specific interactions. Our results show that nitrogen and pathogens altered several aspects of network structure, often in unexpected ways due to fast and slow growing species responding differently. Nitrogen addition increased competition asymmetry in slow growing networks, as expected, but decreased it in fast growing networks. Pathogen reduction made networks more even and less skewed because pathogens targeted weaker competitors. Surprisingly, pathogens and nitrogen dampened each others effect. Our results show that plant growth strategy is key to understand how competition respond to resources and enemies, a prediction from classic theories which has rarely been tested by linking functional traits to competition networks.

ecology↗

bioRxiv2023

Evolution in abiotic environments shapes coexistence between two spider mite species

Adaptation to abiotic stresses generally relies on traits that are not independent from those affecting species interactions. Still, the impact of such evolutionary processes on coexistence remains elusive. Here, we studied two spider mite species evolving separately on tomato plants that hyper-accumulated cadmium, a stressful environment for herbivores, or on plants without cadmium. Through experimental evolution and structural stability theory, we found that both species coexist in the cadmium environment, but evolution of a single species in cadmium leads to exclusion. However, when both species evolve in cadmium they can coexist. This shift occured due to a simultaneous increase in intra and a decrease in interspecific competition in that environment. These predictions were further confirmed with complementary experiments of population dynamics. Therefore, population shifts to novel environments, even in absence of interspecific competitors, may have unforeseen evolutionary consequences for community composition and the maintenance of species diversity.

evolutionary biology↗

bioRxiv2023

Effects of ploidy and genetic diversity on competitive outcomes.

O_LIGenetic diversity affects evolutionary trajectories but their ultimate effects on ecological interactions and community dynamics remains poorly understood. It has been hypothesized that phenotypic novelties produced by ploidy and heterozygosity modify the ecological interactions between novel genotypes and more ancient locally adapted ones, and therefore, their opportunities to coexist. C_LIO_LIWe performed a greenhouse competition experiment with three taxa of the Erysimum incanum species complex differing in ploidy (2x, 4x and 6x) and heterozygosity (high and low). This experiment allows us to parameterize a population model to test the effect of genetic diversity on modulating the ecological forces that determine the outcome of competition, niche and fitness differences. C_LIO_LIDepending on whether ploidy variation and the level of heterozygosity made interspecific competition greater or smaller than intraspecific competition, we predicted either priority effects or coexistence. Such competitive outcome differences were explained by the phenotypic expression in the number of stalks (plant size surrogate) with genotypes under priority effects showing more stalks. C_LIO_LIAltogether, our results show that non-polyploid plants can coexist with polyploids contravening theoretical expectations of polyploidy dominance under stable conditions. However, historical contingency such as order of arrival promotes priority effects when adaptive phenotypic optimums strongly compete for space. C_LI

ecology↗

bioRxiv2023

Structural asymmetry in biotic interactions as a tool to understand and forecast ecological persistence

A universal feature of ecological systems is that species do not interact with others with the same sign and strength. Yet, the consequences of this asymmetry in biotic interactions for the short- and long-term persistence of individual species and entire communities remains unclear. Here, we develop a set of metrics to evaluate how asymmetric interactions among species translate to asymmetries in their individual vulnerability to extinction under changing environmental conditions. These metrics, which solve previous limitations of how to independently quantify the size from the shape of the so-called feasibility domain, provide rigorous advances to understand simultaneously why some species and communities present more opportunities to persist than others. We further demonstrate that our shape-related metrics are useful to predict short-term changes in species relative abundances during seven years in a Mediterranean grassland. Our approach is designed to be applied to any ecological system regardless of the number of species and type of interactions. With it, we show that is possible to obtain both mechanistic and predictive information on ecological persistence for individual species and entire communities, paving the way for a stronger integration of theoretical and empirical research.

ecology↗

bioRxiv2022

Loss of species richness with land use intensity is explained by a reduction in niche differences.

Increases in land use intensity (LUI) reduce species richness. However, we have a poor understanding of how underlying coexistence mechanisms are altered by land use and whether diversity loss occurs due to changes in plant-plant interactions (competition and facilitation) or in species intrinsic growth rates. We expect that LUI could reduce stabilizing niche differences and the indirect interactions that promote coexistence (e.g., intransitivity), while increasing competitive inequalities between species. To test the importance of these different processes, we use 8-yr time series from 150 grasslands differing in LUI to evaluate the role of direct and indirect interactions in promoting coexistence between 50 plant species. We show that LUI reduces the number of coexisting species mostly by causing a non-linear reduction in niche differences, rather than by enhancing competitive inequalities. However, surprisingly, niche differences remained important in stabilizing coexistence between those species remaining at high LUI. Indirect interactions were generally less important than direct ones, and played a moderate role in promoting coexistence in smaller assemblages of species at intermediate LUI. Our models could accurately reproduce the decline in diversity seen with LUI, indicating that our time series approach captures the important interactions between species. By analyzing land use effects through recent advances in structural stability applied to community ecology we provide a more mechanistic understanding of its effects. Our results highlight the importance of identifying the niche differences that are lost with increasing LUI, to better predict and manage effects of land use on biodiversity. Significant statementHuman land use is a major threat to grassland biodiversity. Grasslands with high rates of fertilization, grazing and mowing, contain many fewer plant species. Knowing the underlying causes is necessary for a better management of biodiversity. Here we apply ecological theory to spatiotemporal data on changes in plant abundance in managed grasslands in central Europe. We show that the observed decline in diversity can be explained by how interactions among plant species change with increases in land use intensity. In particular, intensive land use removes the stabilizing effect of self-limiting processes that buffer species against extinction as well as limit competitive dominance. Therefore, actions to promote these stabilizing dynamics among interacting species seem key to restore plant diversity.

ecology↗

bioRxiv2022

Plant spatial aggregation modulates the interplay between plant competition and pollinator attraction with contrasting outcomes of plant fitness

Ecosystem functions such as seed production are the result of a complex interplay between competitive plant-plant interactions and mutualistic pollinator-plant interactions. In this interplay, spatial plant aggregation could work in two different directions: it could increase intra- and interspecific competition, thus reducing seed production; but it could also attract pollinators increasing plant fitness. To shed light on how plant spatial arrangement modulates this balance, we conducted a field study in a Mediterranean annual grassland with three focal plant species with different phenology (Chamaemelum fuscatum (early phenology), Leontodon maroccanus (middle phenology) and Pulicaria paludosa (late phenology)) and a diverse guild of pollinators (flies, bees, beetles, and butterflies). All three species showed spatial aggregation of conspecific individuals. Additionally, we found that the two mechanisms were working simultaneously: crowded neighborhoods reduced individual seed production via plant-plant competition, but they also made individual plants more attractive for some pollinator guilds, increasing visitation rates and plant fitness. The balance between these two forces varied depending on the focal species and the spatial scale considered. Therefore, our results indicate that mutualistic interactions not always effectively compensate for competitive interactions in situations of spatial aggregation of flowering plants, at least in our study system. We highlight the importance of explicitly considering the spatial structure at different spatial scales of multitrophic interactions to better understand individual plant fitness and community dynamics.

ecology↗

bioRxiv2022

Predicting and prioritizing species coexistence: learning outcomes via experiments

Community assembly provides the foundation for applications in biodiversity conservation, climate change, invasion ecology, restoration ecology, and synthetic ecology. Predicting and prioritizing community assembly outcomes remains challenging. We address this challenge via a mechanism-free LOVE (Learning Outcomes Via Experiments) approach suitable for cases where little data or knowledge exist: we carry out actions (randomly-sampled combinations of species additions), measure abundance outcomes, and then train a model to predict arbitrary outcomes of actions, or prioritize actions that would yield the most desirable outcomes. When trained on <100 randomly-selected actions, LOVE predicts outcomes with 2-5% error across datasets, and prioritizes actions for maximizing richness, maximizing abundance, or minimizing abundances of unwanted species, with 94-99% true positive rate and 12-83% true negative rate across tasks. LOVE complements existing approaches for community ecology by providing a foundation for additional mechanism-first study, and may help address numerous ecological applications.

ecology↗

bioRxiv2021

The non-random structure of multi-trophic ecological interactions maximizes species coexistence within ecologically realistic constraints

Theory posits that the persistence of species in ecological communities is shaped by their interactions within and across trophic guilds. However, we lack empirical evaluations of how the structure, strength, and sign of biotic interactions drive the potential to coexist in diverse multi-trophic communities. Here we model community feasibility domains, a theoretically-informed measure of multi-species coexistence probability, from grassland communities comprising more than 45 species on average from three trophic guilds (plants, pollinators, and herbivores). Contrary to our hypothesis, increasing community complexity, measured either as the number of guilds or community richness, did not decrease community feasibility. Rather, we observed that high degrees of species self-regulation and niche partitioning allow maintaining larger levels of community feasibility and higher species persistence in more diverse communities. Our results show that biotic interactions within and across guilds are not random in nature and both structures significantly contribute to maintaining multi-trophic diversity.

ecology↗

bioRxiv2021

Multitrophic higher-order interactions modulate species persistence

There is growing recognition that interactions between species pairs are modified in a multispecies context by the density of a third species. However, how these higher-order interactions (HOIs) affect species persistence remains poorly understood. To explore the effect of HOIs steaming from multiple trophic layers on plant persistence, we experimentally built a mutualistic system containing three plants and three pollinators species with two contrasting network structures. For both structures, we first estimated the statistically supported HOIs on plant species, in addition to the pairwise interactions among plants and plant-pollinators. Following a structuralist approach, we then assessed the effects of the supported HOIs on the persistence probability of each of the three competing plant species and their combinations. HOIs produced substantial effects on the strength and sign of per capita interactions between plant species to such an extent that predictions of species persistence differ from a non-HOIs scenario. Changes in network structure due to removing a plant-pollinator link further modulated the species persistence probabilities by reorganizing per capita interaction strengths of both pairwise interactions and HOIs. Our study provides empirical evidence of the joint importance of HOIs and network structure for determining the probability of species to persist within diverse communities.

ecology↗