Biology subjects

Levin, S. A.

Publications and source records attributed to Levin, S. A..

11 recordsLinked to original sources

bioRxiv2025

Spatio-temporal modelling of in vitro viral infection: the impact of defective interfering particles on type I interferon response

Defective interfering particles (DIPs) are incomplete viral genomes that modulate infection by competing with wild-type viruses and activating innate immunity. How DIPs interact with type I interferon (IFN) in spatially structured environments remains unclear. Focusing initially on influenza A, we developed a spatially explicit, stochastic model of in vitro viral infection integrating virus and DIP replication, IFN signalling, and alternative dispersal modes. We find that: (1) our model captures the ring-like and patchy plaque morphologies observed experimentally; (2) IFN production peaks at an intermediate DIP ratio, reflecting a trade-off between early immune activation and sufficient co-infection; and (3) even a small fraction of long-range spread of virus and DIPs escape containment despite longer IFN ranges; this causes stronger antiviral responses but earlier peaks in lysis at similar levels of cell loss. The model is available as an interactive platform: https://shiny-spatial-infection-app-production.up.railway.app/.

systems biology↗

bioRxiv2024

Global Stability and Tipping Point Prediction of the Coral Reef Ecosystem

Coral reef ecosystems are remarkable for their biodiversity and ecological significance, exhibiting the capacity to exist in different stable configurations with possible abrupt shifts between these alternative stable states. This study applies landscape-flux theory to analyze how these complex systems behave when subjected to random environmental disturbances. We use this theory to formulate and investigate several early warning indicators of ecosystem transitions in a well-known coral-reef model. We studied a number of specific indicators, including the average flux (the driving force when the system is out of equilibrium), the entropy production rate, the nonequilibrium free energy and the time irreversibility of the cross-correlation functions. These indicators demonstrate a distinctive advantage when compared to classical indicators based on the phenomenon of critical slowing down; they exhibit turning points midway between two bifurcations, enabling them to forecast transitions in both directions substantially earlier than conventional methods. In contrast, early warning indicators based on the critical slowing down phenomenon typically only become apparent when the system approaches the actual bifurcation or tipping point(s). Our findings offer improved tools for anticipating critical transitions in coral reef and other at-risk ecosystems, with the potential to enhance conservation and management strategies.

ecology↗

bioRxiv2024

A unifying theoretical framework for tick-borne disease risk to explain conflicting results of exclosure experiments across scales

Disease ecology has focused greatly on determining how changes to biodiversity may drive infectious disease risk for humans. Fencing off experimental areas (exclosures) has been a common experimental approach to assess how removing large-bodied hosts may affect disease risk, especially with tick-borne pathogens (TBPs). However, exclosure experiments have found conflicting results based on the experiments scale, with smaller exclosures tending to increase tick densities inside the exclosure and larger exclosures tending to decrease tick densities inside. Previously, we have lacked a unifying theoretical framework able to reconcile the results of exclosure experiments across spatial scales. We present a spatially explicit model of TBP risk incorporating tick dispersal by small competent mammal hosts which can enter the exclosure and by large incompetent mammal hosts excluded from the exclosure. Our model reproduces the scale-dependence and spatial patterning observed in past exclosure experiments while elucidating their causal mechanisms. Specifically, the modeled exclosures produce high densities of infected ticks near their boundaries, with the densities decreasing towards the exclosures center. Empirical results have found lower tick densities at the exclosures edge than its center, a pattern we demonstrate can also be produced if we additionally allow ticks in their free-living questing stage to disperse.

ecology↗

bioRxiv2024

The development of ecological systems along paths of least resistance

A long-standing question in biology is whether there are common principles that characterize the development of ecological systems (the appearance of a group of taxa), regardless of organismal diversity and environmental context. Classic ecological theory holds that these systems develop following a sequenced orderly process that generally proceeds from fast-growing to slow-growing taxa and depends on life-history trade-offs. However, it is also possible that this developmental order is simply the path with the least environmental resistance for survival of the component species and hence favored by probability alone. Here, we use theory and data to show that the order from fast-to slow-growing taxa is the most likely developmental path for diverse systems when local taxon interactions self-organize to minimize environmental resistance. First, we demonstrate theoretically that a sequenced development is more likely than a simultaneous one, at least until the number of iterations becomes so large as to be ecologically implausible. We then show that greater diversity of taxa and life histories improves the likelihood of a sequenced order from fast-to slow-growing taxa. Using data from bacterial and metazoan systems, we present empirical evidence that the developmental order of ecological systems moves along the paths of least environmental resistance. The capacity of simple principles to explain the trend in the developmental order of diverse ecological systems paves the way to an enhanced understanding of the collective features characterizing the diversity of life.

ecology↗

bioRxiv2024

Variation in season length and development time is sufficient to drive the emergence and coexistence of social and solitary behavioral strategies

Season length and its associated variables can influence the expression of social behaviors, including the occurrence of eusociality in insects. Eusociality can vary widely across environmental gradients, both within and between different species. Numerous theoretical models have been developed to examine the life history traits that underlie the emergence and maintenance of eusociality, yet the impact of seasonality on this process is largely uncharacterized. Here, we present a theoretical model that incorporates season length and offspring development time into a single, individual-focused model to examine how these factors can shape the costs and benefits of social living. We find that longer season lengths and faster brood development times are sufficient to favor the emergence and maintenance of a social strategy, while shorter seasons favor a solitary one. We also identify a range of season lengths where social and solitary strategies can coexist. Moreover, our theoretical predictions are well-matched to the natural history and behavior of two flexibly-eusocial bee species, suggesting our model can make realistic predictions about the evolution of different social strategies. Broadly, this work reveals the crucial role that environmental conditions can have in shaping social behavior and its evolution and underscores the need for further models that explicitly incorporate such variation to study evolutionary trajectories of eusociality.

evolutionary biology↗

bioRxiv2023

Can higher-order interactions resolve the species coexistence paradox?

Most ecological models are based on the assumption that species interact in pairs. Emerging in diverse communities, however, are higher-order interactions, in which two or more species jointly impact the growth of a third species. A pitfall of the pairwise approach is that it misses the higher-order interactions potentially responsible for maintaining diversity in nature. Here, we explore how well higher-order interactions enable coexistence when pairwise interactions are insufficient to do so. Specifically, we explore the stability properties of systems where higher-order interactions guarantee that a specified set of abundances are a feasible equilibrium of the dynamics. Even these higher-order interactions do not necessarily produce robust coexistence. We find that facilitative higher-order interactions that counter pairwise competitive interactions are less likely to generate stable equilibria than competitive interactions countering pairwise facilitation. In both cases the system is more likely to be stable when the pairwise interactions are weak, and when the equilibrium abundances are near those produced by the pairwise interactions. Last, we show that correlations between the pairwise and higher-order interactions permit robust coexistence in diverse systems. Our work reveals the challenges in generating stable coexistence through higher-order interactions, but also uncovers higher-order interaction patterns that can enable diversity.

ecology↗

bioRxiv2023

Integrating coexistence and invasion theories under a probabilistic framework

The dynamics of ecological communities in nature are typically characterized by probabilistic processes involving invasion dynamics. Because of technical challenges, however, the majority of theoretical and experimental studies have focused on coexistence dynamics. Therefore, it has become central to understand the extent to which coexistence outcomes can be used to predict analogous invasion outcomes relevant to systems in nature. Here, we study the limits to this predictability under a geometric and probabilistic Lotka-Volterra framework. We show that while survival probability in coexistence dynamics can be fairly closely translated into colonization probability in invasion dynamics, the translation is less precise between community persistence and community augmentation, and worse between exclusion probability and replacement probability. These results provide a guiding and testable theoretical framework regarding the translatability of outcomes between coexistence and invasion outcomes when communities are represented by Lotka-Volterra dynamics under environmental uncertainty.

ecology↗

bioRxiv2022

Coexistence in diverse communities with higher-order interactions

A central assumption in most ecological models is that the interactions in a community operate only between pairs of species. However, the interaction between two species may be fundamentally changed by the presence of others. Although interactions among three or more species, called higher-order interactions, have the potential to modify our theoretical understanding of coexistence, ecologists lack clear expectations for how these interactions shape community structure. Here, we analytically predict and numerically confirm how the variability and strength of higher-order interactions affect species coexistence. We found that, as higher-order interaction strengths become more variable across species, fewer species coexist, echoing the behavior of pairwise models. If inter-specific higher-order interactions become too harmful relative to self-regulation, coexistence was destabilized, but coexistence was also lost when these interactions were too weak and mutualistic effects became prevalent. Last, we showed that more species rich communities structured by higher-order interactions lose species more readily than their species poor counterparts, generalizing classic results for community stability. Our work provides needed theoretical expectation for how higher-order interactions impact species coexistence in diverse communities.

ecology↗

bioRxiv2020

Asynchrony between virus diversity and antibody selection limits influenza virus evolution

Seasonal influenza viruses create a persistent global disease burden by evolving to escape immunity induced by prior infections and vaccinations. New antigenic variants have a substantial selective advantage at the population level, but these variants are rarely selected within-host, even in previously immune individuals. Using a mathematical model, we show that the temporal asynchrony between within-host virus exponential growth and antibody-mediated selection could limit within-host antigenic evolution. If selection for new antigenic variants acts principally at the point of initial virus inoculation, where small virus populations encounter well-matched mucosal antibodies in previously infected individuals, there can exist protection against reinfection that does not regularly produce observable new antigenic variants within individual infected hosts. Our results provide a theoretical explanation for how virus antigenic evolution can be highly selective at the global level but nearly neutral within host. They also suggest new avenues for improving influenza control.

evolutionary biology↗

bioRxiv2018

Cascading regime shifts within and across scales

Regime shifts are large, abrupt and persistent critical transitions in the function and structure of systems (1, 2). Yet it is largely unknown how these transitions will interact, whether the occurrence of one will increase the likelihood of another, or simply correlate at distant places. Here we explore two types of cascading effects: domino effects create one-way dependencies, while hidden feedbacks produce two-way interactions; and compare them with the control case of driver sharing which can induce correlations. Using 30 regime shifts described as networks, we show that 45% of the pair-wise combinations of regime shifts present at least one plausible structural interdependence. Driver sharing is more common in aquatic systems, while hidden feedbacks are more commonly found in terrestrial and Earth systems tipping points. The likelihood of cascading effects depends on cross-scale interactions, but differs for each cascading effect type. Regime shifts should not be studied in isolation: instead, methods and data collection should account for potential teleconnections.

ecology↗

bioRxiv2017

Mobility can promote the evolution of cooperation via emergent self-assortment dynamics

The evolution of costly cooperation, where cooperators pay a personal cost to benefit others, requires that cooperators interact more frequently with other cooperators. This condition, called positive assortment, is known to occur in spatially-structured viscous populations, where individuals typically have low mobility and limited dispersal. However many social organisms across taxa, from cells and bacteria, to birds, fish and ungulates, are mobile, and live in populations with considerable inter-group mixing. In the absence of information regarding others traits or conditional strategies, such mixing may inhibit assortment and limit the potential for cooperation to evolve. Here we employ spatially-explicit individual-based evolutionary simulations to incorporate costs and benefits of two coevolving costly traits: cooperative and local cohesive tendencies. We demonstrate that, despite possessing no information about others traits or payoffs, mobility (via self-propulsion or environmental forcing) facilitates assortment of cooperators via a dynamically evolving difference in the cohesive tendencies of cooperators and defectors. We show analytically that this assortment can also be viewed in a multilevel selection framework, where selection for cooperation among emergent groups can overcome selection against cooperators within the groups. As a result of these dynamics, we find an oscillatory pattern of cooperation and defection that maintains cooperation even in the absence of well known mechanisms such as kin interactions, reciprocity, local dispersal or conditional strategies that require information on others strategies or payoffs. Our results offer insights into differential adhesion based mechanisms for positive assortment and reveal the possibility of cooperative aggregations in dynamic fission-fusion populations.\n\nAuthor SummaryCooperation among animals is ubiquitous. In a cooperative interaction, the cooperator confers a benefit to its partner at a personal cost. How does natural selection favour such a costly behaviour? Classical theories argue that cooperative interactions among genetic relatives, reciprocal cooperators, or among individuals within groups in viscous population structures are necessary to maintain cooperation. However, many organisms are mobile, and live in dynamic (fission-fusion) groups that constantly merge and split. In such populations, the above mechanisms may be inadequate to explain cooperation. Here, we develop a minimal model that explicitly accounts for mobility and cohesion among organisms. We find that mobility can support cooperation via emergent dynamic groups, even in the absence of previously known mechanisms. Our results may offer insights into the evolution of cooperation in animals that live in fission fusion groups, such as birds, fish or mammals, or microbes living in turbulent media, such as in oceans or in the bloodstreams of animal hosts.

evolutionary biology↗