Browsing by Author "Genin, Alexandre"

Now showing 1 - 6 of 6
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    Easy, fast and reproducible Stochastic Cellular Automata with chouca
    (2024) Genin, Alexandre; Dupont, Guillaume; Valencia, Daniel; Zucconi, Mauro; Avila-Thiem, M. Isidora; Navarrete, Sergio A.; Wieters, Evie A.
    Stochastic cellular automata (SCA) are models that describe spatial dynamics using a grid of cells that switch between discrete states over time. They are widely used to understand how small-scale processes scale up to affect ecological dynamics at larger spatial scales, and have been applied to a wide diversity of theoretical and applied problems in all systems, such as arid ecosystems, coral reefs, forests, bacteria, or urban growth. Despite their wide applications, SCA implementations are often ad-hoc, lacking performance, guarantees of correctness and poorly reproducible. De novo implementation of SCA for each specific system and application also represents a major barrier for many practitioners. To provide a unifying, well-tested technical basis to this class of models and facilitate their implementation, we built chouca, an R package that translates definitions of SCA models into compiled code, and runs simulations in an efficient way. chouca supports SCA based on rectangular grids where transition probabilities are defined for each cell, with performance typically two to three orders of magnitude above typical implementations in interpreted languages (e.g. R, Python), all while maintaining an intuitive interface in the R environment. Exact and mean-field simulations can be run, and both numerical and graphical results can be easily exported. Besides providing better reproducibility and accessibility, a fast engine for SCA unlocks novel, computationally intensive statistical approaches, such as simulation-based inference of ecological interactions from field data, which represents by itself an important avenue for research. By providing an easy and efficient entry point to SCAs, chouca lowers the bar to the use of this class of models for ecologists, managers and general practitioners, providing a leveled-off reproducible platform while opening novel methodological approaches.
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    Emergent Spatial Patterns Can Indicate Upcoming Regime Shifts in a Realistic Model of Coral Community
    (2024) Genin, Alexandre; Navarrete, Sergio A.; Garcia-Mayor, Angeles; Wieters, Evie A.
    Increased stress on coastal ecosystems, such as coral reefs, seagrasses, kelp forests, and other habitats, can make them shift toward degraded, often algae-dominated or barren communities. This has already occurred in many places around the world, calling for new approaches to identify where such regime shifts may be triggered. Theoretical work predicts that the spatial structure of habitat-forming species should exhibit changes prior to regime shifts, such as an increase in spatial autocorrelation. However, extending this theory to marine systems requires theoretical models connecting field-supported ecological mechanisms to data and spatial patterns at relevant scales. To do so, we built a spatially explicit model of subtropical coral communities based on experiments and long-term datasets from Rapa Nui (Easter Island, Chile), to test whether spatial indicators could signal upcoming regime shifts in coral communities. Spatial indicators anticipated degradation of coral communities following increases in frequency of bleaching events or coral mortality. However, they were generally unable to signal shifts that followed herbivore loss, a widespread and well-researched source of degradation, likely because herbivory, despite being critical for the maintenance of corals, had comparatively little effect on their self-organization. Informative trends were found under both equilibrium and nonequilibrium conditions but were determined by the type of direct neighbor interactions between corals, which remain relatively poorly documented. These inconsistencies show that while this approach is promising, its application to marine systems will require detailed information about the type of stressor and filling current gaps in our knowledge of interactions at play in coral communities.
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    Monitoring the fabric of nature: using allometric trophic network models and observations to assess policy effects on biodiversity
    (2023) Navarrete, Sergio A.; Avila-Thieme, M. Isidora; Valencia, Daniel; Genin, Alexandre; Gelcich, Stefan
    Species diversity underpins all ecosystem services that support life. Despite this recognition and the great advances in detecting biodiversity, exactly how many and which species co-occur and interact, directly or indirectly in any ecosystem is unknown. Biodiversity accounts are incomplete; taxonomically, size, habitat, mobility or rarity biased. In the ocean, the provisioning of fish, invertebrates and algae is a fundamental ecosystem service. This extracted biomass depends on a myriad of microscopic and macroscopic organisms that make up the fabric of nature and which are affected by management actions. Monitoring them all and attributing changes to management policies is daunting. Here we propose that dynamic quantitative models of species interactions can be used to link management policy and compliance with complex ecological networks. This allows managers to qualitatively identify 'interaction-indicator' species, which are highly impacted by management policies through propagation of complex ecological interactions. We ground the approach in intertidal kelp harvesting in Chile and fishers' compliance with policies. Results allow us to identify sets of species that respond to management policy and/or compliance, but which are often not included in standardized monitoring. The proposed approach aids in the design of biodiversity programmes that attempt to connect management with biodiversity change.This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.
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    Self- organization as a mechanism of resilience in dryland ecosystems
    (2024) Kefi, Sonia; Genin, Alexandre; Garcia-Mayor, Angeles; Guirado, Emilio; Cabral, Juliano S.; Berdugo, Miguel; Guerber, Josquin; Sole, Ricard; Maestre, Fernando T.
    Self- organized spatial patterns are a common feature of complex systems, ranging from microbial communities to mussel beds and drylands. While the theoretical implications of these patterns for ecosystem - level processes, such as functioning and resilience, have been extensively studied, empirical evidence remains scarce. To address this gap, we analyzed global drylands along an aridity gradient using remote sensing, field data, and modeling. We found that the spatial structure of the vegetation strengthens as aridity increases, which is associated with the maintenance of a high level of soil multifunctionality, even as aridity levels rise up to a certain threshold. The combination of these results with those of two individual - based models indicate that self- organized vegetation patterns not only form in response to stressful environmental conditions but also provide drylands with the ability to adapt to changing conditions while maintaining their functioning, an adaptive capacity which is lost in degraded ecosystems. Self- organization thereby plays a vital role in enhancing the resilience of drylands. Overall, our findings contribute to a deeper understanding of the relationship between spatial vegetation patterns and dryland resilience. They also represent a significant step forward in the development of indicators for ecosystem resilience, which are critical tools for managing and preserving these valuable ecosystems in a warmer and more arid world.
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    Species diversity promotes facilitation under stressful conditions
    (2024) Danet, Alain; Bautista, Susana; Genin, Alexandre; Beckerman, Andrew P.; Anthelme, Fabien; Kefi, Sonia
    Climate change is expected to lead to a drier world, with more frequent and severe droughts, constituting a growing threat to biodiversity, especially in drylands. Positive plant-plant interactions, such as nurse plants facilitating beneficiary communities in their understorey, could mitigate such climate-induced stress. However, testing the real-world relevance of nurse facilitation under drought requires accounting for interactions within the diverse beneficiary communities, which may reduce, or amplify the buffering effect of a nurse. Here, we investigated when and how the interactions among nurse plants and beneficiary community members buffered drought effects in a Mediterranean semiarid abandoned cropland. We transplanted sapling beneficiary communities of either one or three species either under a nurse or in open microsites for different soil moisture levels through watering. Net facilitative effects on survival and biomass were only observed when beneficiary communities were species-diverse and under drought (without watering), meaning that under these conditions, facilitation provided by the nurse had larger positive effects than the negative effects stemming from competition with the nurse and among beneficiary species. Nurses appear to be generating these increases in survival and biomass in drought conditions via two mechanisms commonly associated with watering in open sites: they generate complementarity among the beneficiaries and shift traits to lower stress profiles. Contrasting with watering, which was found to enhance competitive hierarchy, our study shows that nurses appear to alter species dominance, favouring the less competitive species. Our results highlight three mechanisms (complementarity, competitive dominance, and trait plasticity) by which nurse species could mitigate the loss of biodiversity and biomass production due to water stress. Maintaining and supporting nurse species is thus a potentially pivotal approach in the face of projected increase in drought conditions for many drylands across the world.Keywords: biodiversity, dryland, ecosystem functioning, facilitation, functional traits, plant-plant interactions
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    Unveiling functional linkages between habitats and organisms: Macroalgal habitats as influential factors of fish functional traits
    (2024) Sanabria-Fernandez, Jose A.; Genin, Alexandre; Dakos, Vasilis
    Understanding the relationship between the characteristics of habitats and their associated community is essential to comprehend the functioning of ecological systems and prevent their degradation. This is particularly relevant for in decline, habitat-forming species, such as macroalgae, which support diverse communities of fish in temperate rocky reefs. To understand the link between the functional habitats of macroalgae and the functional dimension of their associated fish communities, we used a standardized underwater visual census to quantify the macroalgal functional diversity, as well as the functional diversity, redundancy, and richness of fish communities in 400 sites scattered in three southern temperate marine realms. Our findings reveal that functional macroalgal habitats can be classified into three groups that shape the functional diversity, redundancy, and richness of fish when considering trait commonness. These results enhance our comprehension of the functional connections between the habitat and coexisting fish within marine ecosystems, providing valuable insights for the preser-vation of these habitats.