Modeling the ecology of parasitic plasmids

Plasmids are autonomous genetic elements that can be exchanged between microorganisms via horizontal gene transfer (HGT). Despite the central role they play in antibiotic resistance and modern biotechnology, our understanding of plasmids’ natural ecology is limited. Recent experiments have shown that plasmids can spread even when they are a burden to the cell, suggesting that natural plasmids may exist as parasites. Here, we use mathematical modeling to explore the ecology of such parasitic plasmids. We first develop models of single plasmids and find that a plasmid’s population dynamics and optimal infection strategy are strongly determined by the plasmid’s HGT mechanism. We then analyze models of co-infecting plasmids and show that parasitic plasmids are prone to a “tragedy of the commons” in which runaway plasmid invasion severely reduces host fitness. We propose that this tragedy of the commons is averted by selection between competing populations and demonstrate this effect in a metapopulation model. We derive predicted distributions of unique plasmid types in genomes—comparison to the distribution of plasmids in a collection of 17,725 genomes supports a model of parasitic plasmids with positive plasmid–plasmid interactions that ameliorate plasmid fitness costs or promote the invasion of new plasmids.

Stochasticity-induced stabilization weakens in diverse communities.

Environmental stochasticity and the temporal variations of demographic rates associated with it are ubiquitous in nature. The ability of these fluctuations to stabilize a coexistence state of competing populations (sometimes known as the storage effect) is a counterintuitive feature that has aroused much interest. Here we consider the performance of environmental stochasticity as a stabilizer in diverse communities. We show that the effect of stochasticity is buffered because of the differential response of populations to environmental variations, and its stabilizing effect disappears as the number of populations increases. Of particular importance is the ratio between the autocorrelation time of the environment and the generation time. Species richness grows with stochasticity only when this ratio is smaller than the inverse of the fundamental biodiversity parameter. When stochasticity impedes coexistence and lowers the species richness, the ratio between the strength of environmental variations and the speciation (or migration) rate governs its effect.

Terraforming and Eco-Economics in the Mars Trilogy

In Red Mars (1992), Green Mars (1993), and Blue Mars (1996), Robinson uses the speculative science of terraforming an alien world to explore the complex relationships between planetary ecology--the interlocking, autopoietic systems that allow life to flourish--and political economy, the distribution of scarce resources among competing populations and interests. At the center of the trilogy lies what Robinson calls “eco-economics,” his challenge to the default assumption that economics means the exploitation, degradation, and eventual exhaustion of natural resources. Terraforming transforms Mars over the course of the three novels and becomes a means to imagine the birth of a new planetary order that confronts head-on the obstacles to utopian progress: socioeconomic conflict, environmental degradation, racial and religious antagonisms, state violence, and corporate greed. As it undergoes its sea-change from red to green to blue, Mars offers its citizens (and the novels’ readers) a means to imagine a utopian future that replaces the politics of scarcity and desperation with hard-won forms of cooperation, ecological stewardship, democracy, and diversity.

Studying the dynamics of nonlinear interaction between enterprise populations

The article highlights the results of a study of the dynamic evolutionary processes of trophic relations between populations of enterprises. A model based on differential equations is constructed, which describes the economic system and takes into account the dynamics of the specific income of competing populations of enterprises in relations of protocooperation, nonlinearity of growth and competition. This model can be used to analyze the dynamics of transient processes in various life cycle scenarios and predict the synergistic effect of mergers and acquisitions. A bifurcation analysis of possible scenarios of dynamic modes of merger and acquisition processes using the neural network system of pattern recognition was carried out. To this end, a Kohonen self-organizing map has been constructed, which recognizes phase portraits of bifurcation diagrams of enterprises life cycle into five separate classes in accordance with the scenarios of their development. As a result of the experimental study, characteristic modes of the evolution of economic systems were revealed, and also conclusions were made on the mechanisms of influence of the external environment and internal structure on the regime of evolution of populations of enterprises.

Resilience Analysis for Competing Populations

Ecological resilience refers to the ability of a system to retain its state when subject to state variables perturbations or parameter changes. While understanding and quantifying resilience is crucial to anticipate the possible regime shifts, characterizing the influence of the system parameters on resilience is the first step towards controlling the system to avoid undesirable critical transitions. In this paper, we apply tools of qualitative theory of differential equations to study the resilience of competing populations as modeled by the classical Lotka-Volterra system. Within the high interspecific competition regime, such model exhibits bistability, and the boundary between the basins of attraction corresponding to exclusive survival of each population is the stable manifold of a saddle-point. Studying such manifold and its behavior in terms of the model parameters, we characterized the populations resilience: while increasing competitiveness leads to higher resilience, it is not always the case with respect to reproduction. Within a pioneering context where both populations initiate with few individuals, increasing reproduction leads to an increase in resilience; however, within an environment previously dominated by one population and then invaded by the other, an increase in resilience is obtained by decreasing the reproduction rate. Besides providing interesting insights for the dynamics of competing population, this work brings near to each other the theoretical concepts of ecological resilience and the mathematical methods of differential equations and stimulates the development and application of new mathematical tools for ecological resilience.