Biology subjects

Capitan, J. A.

Publications and source records attributed to Capitan, J. A..

7 recordsLinked to original sources

bioRxiv2026

A quantitative approach to species occupancy across communities: the co-occurrence-occupancy curve

Species tolerating the same environmental conditions can potentially colonize and thrive in the same habitats and eco-regions. Are any pair of those species equally probable to co-occur in the same community? Can we quantify the propensity of two species to co-occur together? Here, we focus on a simple but largely overlooked community-level pattern: the co-occurrence-occupancy curve, which relates the tendency of species to co-occur with others to their total occupancy across sites. We first define this empirical curve and then derive its expected shape under a random null model that assumes site equivalence and species independence. Building on these results, we introduce the Species Association Index (SAI), an occupancy-standardized measure that quantifies the tendency of a species to associate with others independently of its overall frequency of occurrence. The SAI enables meaningful comparisons among species with contrasting occupancies and provides a transparent benchmark against which departures from neutrality can be assessed. We illustrate the approach using two contrasting systems--tropical rain forest trees on Barro Colorado Island and organisms from Mediterranean rocky shores--highlighting both the generality of the co-occurrence-occupancy framework and its limitations.

ecology↗

bioRxiv2026

Trait dimensionality in experimental and natural ecological communities

Classical niche theory predicts that species with more similar traits experience stronger competition, and thus, trait dimensionality, here defined as the number of independent traits per species in a community, plays a critical role in coexistence. Despite this, current studies often assume that communities are structured by only a few key traits. Here, we leveraged a theoretical framework that integrates phylogenetic information with repeated instances of community assembly to estimate the number of ecologically relevant traits required to support observed species richness in experimental and natural plant communities. We found that the inferred trait dimensionality is surprisingly high, often exceeding species richness, suggesting that many traits contribute to coexistence. Furthermore, we explored drivers of grassland trait dimensionality, and it depends in complex ways on area, species pool size, and latitude. Our findings indicate that local coexistence may rely on a larger number of traits than previously assumed, challenging low-dimensional trait-based views of community structure.

ecology↗

bioRxiv2025

The structure of pairwise competition is responsible for sudden regime shifts in a microbe-plasmid model

Plasmids play a crucial role in bacterial communities by facilitating the horizontal transfer of genetic material, particularly genes that confer resistance to different stressor agents. In this work, we introduce a microbe-plasmid model to study the conditions under which a plasmid-carrying bacterial strain can invade its corresponding plasmid-free counterpart, as well as those under which it can be eradicated from the population through potential intervention strategies. We reveal the variety of dynamic regimes of the model depending on the parameter values. In particular, we show that a heterogeneous structure of the competition between the two strains drives the possibility of coexistence of stationary states (i.e. bistability) which creates conditions for sudden regime shifts and hysteresis. We explore the implications of our results for the potential eradication of plasmid-mediated antibiotic resistance.

ecology↗

bioRxiv2022

Jaccard dissimilarity in stochastic community models based on the species-independence assumption

A fundamental problem in ecology is understanding the causes of change in species composition among sites (i.e. beta diversity). At present it is unclear how spatial heterogeneity in species occupancy across sites shapes these patterns. To address this question, we develop probabilistic models that consider two spatial or temporal sites, where presence probabilities vary both among species and between the sites. We derive analytical and approximate formulae for the expectation of pairwise beta-diversity. Using a novel graphical tool, Stochastic Incidence Plots (SIPs), which depict the presence probabilities in two sites across species labels, we develop a means to conceptualize the heterogeneity in presence probabilities: the steepness or unevenness of SIPs reflects species-level heterogeneity, while the degree of overlap between SIPs indicates site-level heterogeneity. Utilizing SIPs and a combinatorial approach in a two-species scenario, we demonstrate that beta-diversity is lower when SIPs are parallel compared to when they are anti-parallel. We also find that this prediction is testable with the well-known checkerboard pattern in incidence matrices. Finally, we applied the method to the species distribution models for five woodpecker species in Switzerland, showing that their spatial distributions will change significantly in the future. Overall, this work improves our understanding of how pairwise beta-diversity responds to occupancy heterogeneity.

ecology↗

bioRxiv2022

The implicit assumptions of classic functional responses and their multi-species extensions

Functional responses are central to describe consumer-resource interactions. Defined as the per capita average feeding rate of consumers, since Hollings seminal papers, they have been widely used in ecology. Hollings central observation was that they often saturate as resource density increases. If the interference between consumers is strong, they also decrease with consumer density. Here we emphasize the stochastic nature of the individual feeding processes and the associated probability distributions of the different behavioral types and show how they control population-averaged feeding rates. We do so by revisiting a classic approach based on the formulation of feeding interactions in terms of individual-based reaction schemes. We highlight the common assumptions underlying the different functional forms and discover a new predator-dependent functional response that should be considered the natural extension of the Holling type II functional response when consumers interference is considered. Our work has clear implications, on the one hand, for both model selection and parameter inference from feeding experiments, and, on the other, for the use of multi-species extensions of these functional responses in population-level food-web dynamic models.

ecology↗

bioRxiv2020

Effects of phylogeny on coexistence in model communities

A species traits influence the way in which it interacts with the environment. Thus, we expect traits to play a role in determining whether a given set of species coexists. Traits are, in turn, the outcome of an eco-evolutionary process summarized by a phylogenetic tree. Therefore, the phylogenetic tree associated with a set of species should encode information about the assembly properties of the community. Many studies have high-lighted the potentially complex ways in which phylogenetic information is translated into species ecological properties. However, much less emphasis has been placed on developing expectations for community properties under a particular hypothesis. In this work, we couple a simple model of trait evolution on a phylogenetic tree with local community dynamics governed by Lotka-Volterra equations. This allows us to derive properties of the community of coexisting species as a function of the number of traits, tree topology and the size of the species pool. Our results highlight how phylogenies and traits, in concert, affect the coexistence of a set of species. In this way, our work provides new baseline expectations for the ways in which phylogenetic information is reflected in the structure of and coexistence within local communities.

ecology↗

bioRxiv2020

Competitive dominance in plant communities: Modeling approaches and theoretical predictions

Understanding the main determinants of species coexistence across space and time is a central question in ecology. However, ecologists still know little about the scales and conditions at which biotic interactions matter and how these interact with the environment to structure species assemblages. Here we use recent theory developments to analyze plant distribution and trait data across Europe and find that plant height clustering is related to both evapotranspiration and gross primary productivity. This clustering is a signal of interspecies competition between plants, which is most evident in mid-latitude ecoregions, where conditions for growth (reflected in actual evapotranspiration rates and gross primary productivities) are optimal. Away from this optimum, climate severity likely overrides the effect of competition, or other interactions become increasingly important. Our approach bridges the gap between species-rich competition theories and large-scale species distribution data analysis.

ecology↗