Biology subjects

Valdovinos, F. S.

Publications and source records attributed to Valdovinos, F. S..

At least 19 recordsLinked to original sources

bioRxiv2026

Correlated traits generate the structure and stability of multiplex ecological networks

Ecological stability and function emerge from the many and diverse types of interactions among species. Ecological networks represent the structure and strength of species interactions, but their study is often restricted to single interaction-types, likely due to an absence of models for plausibly (i.e., nonrandomly) structured 'multiplex networks' of multiple interaction types. Here, we present a general but mechanistic model that simulates multiplex networks using the different, but correlated, traits that determine different species interactions. We show that ecological stability varies systematically with these trait correlations by controlling the emergent complexity and positioning of strong interactions in the community. Our model provides a flexible but power tool to study multiplex networks under alternative trait-based hypotheses, offering new insights into the structure and stability of complex natural systems.

ecology↗

bioRxiv2026

Cross-scale persistence analysis in mutualistic networks unifies extinction thresholds and invasibility

Cross-scale integration remains a persistent challenge in ecology. Mechanistic network models have advanced this integration by linking individual behavior to community dynamics. Their complexity, however, often limits exploration to numerical simulations, which tend to be insufficient for fully unveiling the fundamental rules governing system behavior. Extracting these rules requires moving beyond numerical observation to establish exact, analytical constraints. Here, a complete mathematical analysis of a mechanistically detailed plant--pollinator model is presented. This cross-scale analysis decouples transient and equilibrium dynamics, proving that pollination strictly gates plant persistence while recruitment competition caps equilibrium abundance. The precise behavioral mechanisms scaling up to determine network stability are determined: nestedness stabilizes communities by generating floral reward gradients that guide adaptive foraging, whereas connectance destabilizes by eroding these rescue pathways. Additionally, native community persistence and biological invasions are conceptually unified; a single, multi-scale reward threshold (R^*) is shown to govern both native survival and alien establishment. These analytical derivations are distilled into conceptual frameworks and visual summaries accessible for empiricists interested in theory and conceptual unification. By translating numerical observations into rigorous, trait-grounded proofs, this analysis demonstrates that complex, cross-scale networks are tractable, revealing the precise conditions under which communities assemble, persist, and collapse.

ecology↗

bioRxiv2026

Large language models unlock the ecology of species interactions

Species interactions shape population dynamics, geographic distributions, evolutionary trajectories, and responses to environmental change. Yet data on these interactions remain scarce across broad spatial, temporal, and taxonomic scales because they are difficult to collect in the field. One promising source of interaction data is citizen science platforms, which contain billions of biodiversity observations, often accompanied by unstructured text comments that may document interactions among organisms. Advances in large language models (LLMs) make it increasingly feasible to identify, extract, and categorize biotic interactions from these unstructured data at scale. Here, we present an LLM workflow that collects species interaction observations from multilingual citizen science comments. Using two case studies--bird-bird and plant-pollinator interactions--we show that LLMs can rapidly extract interaction types and participating species with high accuracy. These data can greatly expand the spatial, temporal, and taxonomic coverage and resolution of species interactions data, enable new tests of long-standing ecological questions, and improve our ability to track ecological changes. With appropriate validation, expert review, and attention to data privacy for both users and sensitive species, this approach opens new opportunities to characterize, forecast, and conserve biodiversity under global change.

ecology↗

bioRxiv2025

The equalizing effect of adaptive foraging increases plant coexistence in plant-pollinator networks

The role of pollination in plant coexistence remains contested, with studies using Lotka-Volterra models suggesting pollination hinders while consumer-resource approaches indicating it can promote plant coexistence. Through the lens of modern coexistence theory, we analyze how network nestedness and pollinator foraging behavior influence plant coexistence via stabilizing (increasing the relative effect of intraspecific to interspecific competition) or equalizing (reducing fitness differences) mechanisms. Our findings reveal that while nestedness alone threatens specialist plant persistence, adaptive foraging by pollinators generates equalizing mechanisms by benefiting specialist over generalist plants which promotes plant coexistence, helping explain the contrasting conclusions from previous studies.

ecology↗

bioRxiv2024

Effect of network structure and adaptive foraging on pollination services of species-rich plant-pollinator communities

Network science has had a great impact on ecology by providing tools to characterize the structure of species interactions in communities and evaluate the effect of such network structure on community dynamics. This has been particularly the case for the study of plant-pollinator communities, which has experienced a tremendous growth with the adoption of network analyses. Here, I build on such body of research to evaluate how network structure and adaptive foraging of pollinators affect ecosystem services of plant-pollinator communities. Specifically, I quantify -- using model simulations -- pollen deposition in networks that exhibit structures like the ones of empirical networks (hereafter empirically connected networks) and those with higher connectance and lower nestedness than empirical networks, for scenarios where pollinators are fixed foragers and scenarios where they are adaptive foragers. I found that empirically connected networks with adaptive foraging exhibit the highest pollen deposition rate. Increased network connectance reduces pollen deposition as increased number of interactions lead to greater conspecific pollen dilution in the absence of other mechanisms such as pollinator floral constancy. High nestedness in moderately connected networks increases the proportion of pollinators visiting only one or two plant species, which are associated with the highest quality visits. Adaptive foraging allows pollinators to quantitatively specialize on specialist plant species which increases conspecific pollen deposition. This research advances pollination biology by elucidating how population dynamics, consumer-resource interactions, adaptive foraging, and network structure affects pollen deposition in a network context.

ecology↗

bioRxiv2023

A highly resolved multiplex network reveals the structural role of insects and plants in terrestrial food webs

Comparative studies suggest remarkable similarities among food webs across habitats, including systematic changes in their structure with diversity and complexity (scale-dependence). However, historic aboveground terrestrial food webs (ATFWs) have coarsely grouped plants and insects such that these webs are generally small, and herbivory is disproportionately underrepresented compared to vertebrate predator-prey interactions. Furthermore, terrestrial herbivory is thought to be structured by unique processes compared to size-structured feeding in other systems. Here, we present the richest ATFW to date, including [~]580,000 feeding links among [~]3,800 taxonomic species, sourced from [~]27,000 expert-vetted interaction records annotated as feeding upon one of six different resource types: leaves, flowers, seeds, wood, prey, and carrion. By comparison to historical ATFWs and null ecological hypotheses, we show that our temperate forest web displays a potentially unique structure characterized by two properties: a) a large fraction of carnivory interactions dominated by a small number of hyper-generalist, opportunistic bird and bat predators, and b) a smaller fraction of herbivory interactions dominated by a hyper-rich community of insects with variably-sized but highly-specific diets. We attribute our findings to the large-scale, even resolution of vertebrate, insect, and plant guilds in our food web.

ecology↗

bioRxiv2023

A general trait-based model for multiplex ecological networks

Ecological networks can represent the structure of food webs, energy flow, and the many and diverse types of interactions between species in ecosystems. Despite its tremendous importance for understanding biodiversity, stability, ecosystem functioning, research on ecological networks has traditionally been restricted to subsets of the species or interactions in ecosystems, i.e., "subnetworks" such as pollination networks or food webs. As a result, the structure of "multiplex" networks that include multiple interaction types is mostly unknown and there is no robust, underlying theory to support their study. Some ecological traits, such as body size or length of mouth parts, are well-known as key predictors of different species interactions. These traits are often strongly related to each other due to evolutionary history, allometry, and selection, and this relatedness may constrain the structure of ecological multiplex networks. We use this idea to develop a model that simulates multiplex ecological networks by interconnecting subnetworks using correlated traits. Our model predicts how multiplex network structure, measured as the overlaps between species functional roles, is affected by neutral processes, interaction rules, and trait constraints, while the structure of individual subnetworks is independent of these trait correlations. Additionally, our model accurately predicts the structure of an observed multiplex network using existing knowledge on species trait correlations and basic features of known ecological subnetworks. This work will stimulate new studies of the structure and dynamics of complex ecosystems by providing a null expectation for how multiplex ecological networks are structured under different ecological conditions.

ecology↗

bioRxiv2023

Modeling time-varying phytoplankton subsidy reveals at-risk species in a Chilean intertidal ecosystem

The allometric trophic network (ATN) framework for modeling population dynamics has provided numerous insights into ecosystem functioning in recent years. Herein we extend ATN modeling of the intertidal ecosystem off the central coast of Chile to include empirical data on pelagic chlorophyll-a concentration. This intertidal community requires subsidy of primary productivity to support its rich ecosystem. Previous work models this subsidy using a constant rate of phytoplankton input to the system. However, data shows pelagic subsidies exhibit short-term, highly variable, pulse-like behavior. Incorporating this variable input into ATN modeling is the primary contribution of this work and provides several new insights into this ecosystems response to pulses of offshore phytoplankton, including: (1) closely related sea snails show differential responses to pulses of phytoplankton that are explained by underlying network structure; (2) increasing the rate of pelagic-intertidal mixing increases fluctuations in species biomasses that may increase the risk of local extirpation; (3) predators are the most sensitive species to phytoplankton biomass fluctuations, putting these species at greater risk of extirpation than others. Finally, our work provides a straightforward way to incorporate empirical, time-series data into the ATN framework that will expand this powerful methodology to new applications.

ecology↗

bioRxiv2023

A century of sampling at an ecological preserve reveals declining diversity of wild bees

We analyzed the wild bee community from 1921 to 2018 at a nature preserve in southern Michigan, USA using museum records and found significant shifts in the bee community. Across the near century of records, species richness peaked in the 1970s and 1980s. There was an intensive bee survey completed by F.C. Evans in 1972 and 1973. We attempted to replicate his effort in 2017 and 2018, and again found a significant decline in species richness and evenness. There was also evidence of declining abundance in many of the more common species. We also conducted traits analyses using neural networks, revealing that oligolectic ground-nesting bees and cleptoparasitic bees were more likely to be extirpated whereas polylectic cavity-nesting bees were more likely to have persisted. Additionally, larger body size was associated with increased probability of local extirpation for polylectic cavity-nesting species. Larger phenological range was associated with increased chances of persistence for polylectic species, while it was associated with extirpation for oligolectic ground-nesting species. Species in the contemporary samples also had a more southerly overall distribution compared to the historic one. Open Research StatementData used for analyses in this manuscript, including Evans original dataset from 1972/1973 with updated species nomenclature, will be permanently archived at the USDA Ag Data Commons after the acceptance of this manuscript and will be citable and accessible here: https://data.nal.usda.gov/dataset/century-sampling-ecological-preserve-reveals-declining-diversity-wild-bees. Complete instructions on how to access all data referenced in this manuscript can be found in Appendix S1.

ecology↗

bioRxiv2022

Through the Random Forest: Ontogeny as a study system to connect prediction to explanation

As modeling tools and approaches become more advanced, ecological models are becoming more complex and must be investigated with novel methods of analysis. Machine learning approaches are a powerful toolset for exploring such complexity. While these approaches are powerful, results may suffer from well-known trade-offs between predictive and explanatory power. We employ an empirically rooted ontogenetically stage-structured consumer-resource model to investigate how machine learning can be used as a tool to root model analysis in mechanistic ecological principles. Applying random forest models to model output using simulation parameters as feature inputs, we extended established feature analysis into a simple graphical analysis. We used this graphical analysis to reduce model behavior to a linear function of three ecologically based mechanisms. From this model, we find that stability depends on the interaction between internal plant demographics that control the distribution of plant density across ontogenetic stages and the distribution of consumer pressure across ontogenetic stages. Predicted outcomes from these linear models rival accuracy achieved by our random forests, while explaining results as a function of ecological interactions.

ecology↗

bioRxiv2021

Dynamics of pollination and seed dispersal mutualisms at low density

Pollination and seed dispersal mutualisms are critical for biodiversity and ecosystem services yet face mounting threats from anthropogenic perturbations that cause their populations to decline. Characterizing the dynamics of these mutualisms when populations are at low density is important to anticipate consequences of these perturbations. We developed simple population dynamic models detailed enough to distinguish different mechanisms by which plant populations benefit from animal pollination or seed dispersal. We modeled benefits as functions of foraging rate by animals on plant rewards and specified whether they affected plant seed set, germination, or negative density dependence during recruitment. We found that pollination and seed dispersal mutualisms are stable at high density but exhibit different dynamics at low density, depending on plant carrying capacity, animal foraging efficiency, and whether populations are obligate upon their partners for persistence. Under certain conditions, all mutualisms experience destabilizing thresholds in which one population declines because its partner is too rare. Plants additionally experience Allee effects when obligate upon pollinators. Finally, pollination mutualisms can exhibit bistable coexistence at low or high density when plants are facultative upon pollinators. Insights from our models can inform conservation efforts, as mutualist populations continue to decline globally.

ecology↗

bioRxiv2020

Ecological theory of mutualism: Models generalizing across different mechanisms

Mutualisms are ubiquitous in nature, provide important ecosystem services, and involve many species of interest for conservation. Theoretical progress on the population dynamics of mutualistic interactions, however, has comparatively lagged behind that of trophic and competitive interactions. Consequently, ecologists still lack a generalized framework to investigate the population dynamics of mutualisms. Here, we propose extensible models for two-species mutualisms focusing on nutritional, protection, and transportation mechanisms and evaluate the population-level consequences of those mechanisms. We introduce a novel theoretical framework that highlights characteristic dynamics when the effects of mutualism are directly dependent or independent of recipient density and when they saturate due to inter- or intra-specific density-dependence. We end by integrating our work into the broader historical context of population-dynamic models of mutualism and conclude that a general ecological theory of mutualism exists.

ecology↗

bioRxiv2020

Alteration of coastal productivity and artisanal fisheries interact to affect a marine food-web

Top-down and bottom-up forces determine ecosystem function and dynamics. Fisheries as a top-down force can shorten and destabilize food-webs, while climate-change driven effects can alter the bottom-up forces of primary productivity. We assessed the response of a highly-resolved intertidal food-web to these two global-change drivers, using network analysis and bioenergetic modelling. We quantified the relative importance of artisanal fisheries as another predator species, and evaluated the independent and combined effects of fisheries and plankton-productivity changes on food-web dynamics. The food-web was robust to the loss of all harvested species but sensible to plankton-productivity decline. Interestingly, fisheries dampened the negative impacts of decreasing plankton productivity on non-harvested species, while plankton-productivity decline increased the sensitivity of harvested species to fishing. Our results show that strategies for new scenarios caused by climate change are needed to protect marine ecosystems and the wellbeing of local communities dependent on their resources.

ecology↗

bioRxiv2020

NetworkExtinction: an R package to explore the propagation of extinctions through complex ecological networks

O_LIEarths biosphere is currently undergoing drastic reorganisation as a consequence of the sixth mass extinction brought on by the Anthropocene. Impacts of local and regional extirpation of species have been demonstrated to propagate through the complex interaction networks they are part of, subsequently leading to secondary extinctions, exacerbating biodiversity loss. Contemporary ecological theory has developed several measures to analyse the structure and robustness of ecological networks under biodiversity loss. However, a toolbox for direct simulation and quantification of extinction cascades and the creation of novel interactions (i.e. rewiring) remains absent. C_LIO_LIHere, we present NetworkExtinction - a novel R package which we have developed to explore the propagation of species extinctions sequences through ecological networks as well as quantify the effects of rewiring potential in response to primary species extinctions. With NetworkExtinction we have integrated ecological theory and computational simulations to develop functionality with which users may analyze and visualize the structure and robustness of ecological networks. The core functions introduced with NetworkExtinction focus on simulations of sequential primary extinctions and associated secondary extinctions while allowing for user-specified secondary extinction thresholds and realisation of rewiring potential. C_LIO_LIWith the package NetworkExtinction, users can estimate the robustness of ecological networks after performing species extinction routines based on several algorithms. Moreover, users can compare the number of simulated secondary extinctions against a null model of random extinctions. In-built visualizations enable graphing topological indices calculated by the deletion sequence functions after each simulation step. Finally, the user can define the degree distribution of the network by fitting different common distributions. Here, we illustrate the use of the package and its outputs by analyzing a Chilean coastal marine food web. C_LIO_LINetworkExtinction is a compact and easy-to-use R package with which users can quantify changes in ecological network structure in response to different patterns of species loss, thresholds, and rewiring potential. Therefore, this package is particularly useful to evaluate ecosystem responses to anthropogenic and environmental perturbations that produce non-random species extinctions. C_LI

ecology↗

bioRxiv2020

Phenology and flowering overlap drive specialization in pollinator networks

Variation in diet breadth and specialization stems from fundamental interactions species have with their environment1-3. Consequently, understanding the drivers of this variation is key to understanding ecological and evolutionary processes, and will facilitate the development of predictive tools as ecological networks respond to environmental change4,5. Diet breadth in wild bees has been an area of focus due to both their close mutualistic dependence on plants, and because both groups are under threat from global biodiversity loss6. Though many of the principles governing specialization for pollinators have been identified7,8, they remain largely unvalidated. Using mechanistic models of adaptive foraging in pollinators9,10, we show that while temporal resource overlap has little impact on specialization in pollinators with extended flight periods, reduced overlap increases specialization as pollinator flight periods decrease. These results are corroborated empirically using pollen load data taken from bees with shorter (genus Andrena) and longer (genus Lasioglossum) flight periods across environments with both high and low temporal resource overlap. This approach reveals how interacting phenologies structure plant-pollinator networks and drive pollinator diet breadth via the temporal overlap of floral resources.

ecology↗

bioRxiv2020

Niche theory for mutualism: A graphical approach to plant-pollinator network dynamics

Contemporary Niche Theory is a useful framework for understanding how organisms interact with each other and with their shared environment. Its graphical representation, popularized by Tilman’s Resource Ratio Hypothesis, facilitates the analysis of the equilibrium structure of complex dynamical models including species coexistence. This theory has been applied primarily to resource competition since its early beginnings. Here, we integrate mutualism into niche theory by expanding Tilman’s graphical representation to the analysis of consumer-resource dynamics of plant-pollinator networks. We graphically explain the qualitative phenomena previously found by numerical simulations, including the effects on community dynamics of nestedness, adaptive foraging, and pollinator invasions. Our graphical approach promotes the unification of niche and network theories, and deepens the synthesis of different types of interactions within a consumer-resource framework.Secondary Abstract Teoría de Nicho para Mutualismos: Una aproximación gráfica a la dinámica de redes planta-polinizadorLa Teoría Contemporánea de Nicho es un marco útil para entender cómo los organismos interactúan entre ellos y con su ambiente compartido. Su representatión gráfica, popularizada por la Hipótesis de Razón de Recursos de Tilman, facilita el análisis de la estructura de equilibrio de modelos dinámicos complejos, incluyendo la coexistencia de especies. Esta teoría ha sido aplicada primariamente a competencia por recursos desde sus inicios. Aquí, integramos el mutualismo dentro de la teoría de nicho al expandir la representatión gráfica de Tilman al análisis de la dinámica consumidor-recurso de las redes planta-polinizador. Explicamos gráficamente fenómenos cualitativos encontrados previamente mediante simulaciones numéricas, incluyendo los efectos sobre la dinámica comunitaria del anidamiento, forrajeo adaptativo y de las invasiones por polinizadores. Nuestra aproximación gráfica promueve la unificatión de las teorías de nicho y de redes, y profundiza la síntesis de diferentes tipos de interacciones dentro de un marco de consumidor-recurso.Competing Interest StatementThe authors have declared no competing interest.View Full Text

ecology↗

bioRxiv2019

Integrating Economic dynamics into Ecological Networks: The case of fishery sustainability

Summary/AbstractUnderstanding and sustainably managing anthropogenic impact on ecosystems requires studying the integrated economic -ecological dynamics driving coupled human-natural systems. Here, we expand ecological network theory to study fishery sustainability by incorporating economic drivers into food-web models to evaluate the dynamics of thousands of single-species fisheries across hundreds of generated food-webs and two management strategies. Analysis reveals harvesting high population biomass species can initially support fishery persistence, but threatens long term economic and ecological sustainability by indirectly inducing extinction cascades in non-harvested species. This dynamic is exacerbated in open access fisheries where profit driven growth in fishing effort increases perturbation strength. Results demonstrate the unique insight into both ecological dynamics and sustainability garnered from considering economically dynamic fishing effort in the network. One Sentence SummaryIntegrating economic drivers into ecological networks reveal non-linear drivers of sustainability in fisheries.

ecology↗

bioRxiv2019

Pollinators in food webs: Mutualistic interactions increase diversity, stability, and function in multiplex networks

Ecosystems are composed of complex networks of many species interacting in different ways. While ecologists have long studied food webs of feeding interactions, recent studies increasingly focus on mutualistic networks including plants that exchange food for reproductive services provided by animals such as pollinators. Here, we synthesize both types of consumer-resource interactions to better understand the controversial effects of mutualism on ecosystems at the species, guild, and whole-community levels. We find that consumer-resource mechanisms underlying plant-pollinator mutualisms can increase the persistence, productivity, abundance, and temporal stability of both mutualists and non-mutualists in food webs. These effects strongly increase with floral reward productivity and are qualitatively robust to variation in the prevalence of mutualism and pollinators feeding upon resources in addition to rewards. This work advances the ability of mechanistic network theory to synthesize different types of interactions and illustrates how mutualism can enhance the diversity, stability, and function of complex ecosystems.

ecology↗