PubMed Health⌕ Search

Biomedical subjects

Simon A Levin

Publications and source records attributed to Simon A Levin.

At least 19 recordsLinked to original sources
PubMed2007

Epidemic enhancement in partially immune populations.

We observe that a pathogen introduced into a population containing individuals with acquired immunity can result in an epidemic longer in duration and/or larger in size than if the pathogen were introduced into a naive population. We call this phenomenon "epidemic enhancement," and use simple dynamical models to show that it is a realistic scenario within the parameter ranges of many common infectious diseases. This finding implies that repeated pathogen introduction or intermediate levels of vaccine coverage can lead to pathogen persistence in populations where extinction would otherwise be expected.

Adaptive Immunity↗
PubMed2006

Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites.

The fixation of a new allele can be driven by Darwinian positive selection or can be due to random genetic drift. Identifying instances of positive selection is a difficult task, because its impact is routinely obscured by the action of negative selection. The nature of the genetic code dictates that positive selection in favor of an amino acid replacement should often cause a burst of two or three nucleotide substitutions at a single codon site, because a large fraction of amino acid replacements cannot be achieved after just one nucleotide substitution. Here, we study pairs of successive nonsynonymous substitutions at one codon in the course of evolution of HIV-1 genes within HIV-1 populations inhabiting infected individuals. Such pairs are more numerous and more clumped than expected if different substitutions were independent and than what is observed for pairs of successive synonymous substitutions. Bursts of nonsynonymous substitutions in HIV-1 evolution cannot be explained by mutational biases and must, therefore, be due to positive selection. Both reversals, exact or imprecise, of fixed deleterious mutations and acquisitions of amino acids with new properties are responsible for the bursts. Temporal clumping is strongest at codon sites with a low overall rate of nonsynonymous evolution, implying that a substantial fraction of replacements of conservative amino acids are driven by positive selection. We identified many conservative sites of HIV-1 proteins that occasionally experience positive selection.

Amino Acid Substitution↗
PubMed2006

Evolutionary escape from the prisoner's dilemma.

The classic prisoner's dilemma model of game theory is modified by introducing occasional variations on the options available to players. Mutation and selection of game options reliably change the game matrix, gradually, from a prisoner's dilemma game into a byproduct mutualism one, in which cooperation is stable, and "temptation to defect" is replaced by temptation to cooperate. This result suggests that when there are many different potential ways of interacting, exploring those possibilities may make escape from prisoner's dilemmas a common outcome in the world. A consequence is that persistent prisoner's dilemma structures may be less common than one might otherwise expect.

Animals↗
PubMed2006

A neutral metapopulation model of biodiversity in river networks.

In this paper, we develop a stochastic, discrete, structured metapopulation model to explore the dynamics and patterns of biodiversity of riparian vegetation. In the model, individual plants spread along a branched network via directional dispersal and undergo neutral ecological drift. Simulation results suggest that in comparison to 2-D landscapes with non-directional dispersal, river networks with directional dispersal have lower local (alpha) and overall (gamma) diversities, but higher between-community (beta) diversity, implying that riparian species are distributed in a more localized pattern and more vulnerable to local extinction. The relative abundance patterns also change, such that higher percentages of species are in low-abundance, or rare, classes, accompanied by concave rank-abundance curves. In contrast to existing theories, the results suggest that in river networks, increased directional dispersal reduces alpha diversity. These altered patterns and trends result from the combined effects of directionality of dispersal and river network structure, whose relative importance is in need of continuing study. In addition, riparian communities obeying neutral dynamics seem to exhibit abrupt changes where large tributaries confluence; this pattern may provide a signature to identify types of interspecific dynamics in river networks.

Biodiversity↗
PubMed2006

The evolution of resource adaptation: how generalist and specialist consumers evolve.

Why and how specialist and generalist strategies evolve are important questions in evolutionary ecology. In this paper, with the method of adaptive dynamics and evolutionary branching, we identify conditions that select for specialist and generalist strategies. Generally, generalist strategies evolve if there is a switching benefit; specialists evolve if there is a switching cost. If the switching cost is large, specialists always evolve. If the switching cost is small, even though the consumer will first evolve toward a generalist strategy, it will eventually branch into two specialists.

Biological Evolution↗
PubMed2006

Global asymptotic coherence in discrete dynamical systems.

Spatial synchrony (coherence) in dynamical systems is of both theoretical and applied importance. We address this problem for a generalization of coupled map lattices (CMLs). In the systems we study, which we term "meta-CMLs," the map at each lattice point may be multidimensional (corresponding, for example, to multispecies ecological systems in which all species have the same dispersal pattern). Most previous work on coherence of CMLs has focused on local stability. Here, we prove a global theorem that provides a useful sufficient condition guaranteeing decay of incoherence in meta-CMLs regardless of initial conditions and regardless of the nature of the attractors of the system. This result facilitates useful analyses of a variety of applied problems, including conservation of endangered species and eradication of pests or infectious diseases.

Journal Article↗
PubMed2006

Global stability in a chemostat with multiple nutrients.

We study a single species in a chemostat, limited by two nutrients, and separate nutrient uptake from growth. For a broad class of uptake and growth functions it is proved that a nontrivial equilibrium may exist. Moreover, if it exists it is unique and globally stable, generalizing a result in [15].

Algorithms↗
PubMed2006

The SIRC model and influenza A.

We develop a simple ordinary differential equation model to study the epidemiological consequences of the drift mechanism for influenza A viruses. Improving over the classical SIR approach, we introduce a fourth class (C) for the cross-immune individuals in the population, i.e., those that recovered after being infected by different strains of the same viral subtype in the past years. The SIRC model predicts that the prevalence of a virus is maximum for an intermediate value of R(0), the basic reproduction number. Via a bifurcation analysis of the model, we discuss the effect of seasonality on the epidemiological regimes. For realistic parameter values, the model exhibits a rich variety of behaviors, including chaos and multi-stable periodic outbreaks. Comparison with empirical evidence shows that the simulated regimes are qualitatively and quantitatively consistent with reality, both for tropical and temperate countries. We find that the basins of attraction of coexisting cycles can be fractal sets, thus predictability can in some cases become problematic even theoretically. In accordance with previous studies, we find that increasing cross-immunity tends to complicate the dynamics of the system.

Antigenic Variation↗
PubMed2006

Size and scaling of predator-prey dynamics.

We propose a scaled version of the Rosenzweig-MacArthur model using both Type I and Type II functional responses that incorporates the size dependence of interaction rates. Our aim is to link the energetic needs of organisms with the dynamics of interacting populations, for which survival is a result of a game-theoretic struggle for existence. We solve the scaled model of predator-prey dynamics and predict population level characteristics such as the scaling of coexistence size ranges and the optimal predator-prey size ratio. For a broad class of such models, the optimal predator-prey size ratio given available prey of a fixed size is constant. We also demonstrate how scaling predictions of prey density differ under resource limitation vs. predator drawdown. Finally, we show how evolution of predator size can destabilize population dynamics, compare scaling of predator-prey cycles to previous work, as well as discuss possible extensions of the model to multispecies communities.

Animals↗
PubMed2006

Building resilience and adaptation to manage Arctic change.

Unprecedented global changes caused by human actions challenge society's ability to sustain the desirable features of our planet. This requires proactive management of change to foster both resilience (sustaining those attributes that are important to society in the face of change) and adaptation (developing new socioecological configurations that function effectively under new conditions). The Arctic may be one of the last remaining opportunities to plan for change in a spatially extensive region where many of the ancestral ecological and social processes and feedbacks are still intact. If the feasibility of this strategy can be demonstrated in the Arctic, our improved understanding of the dynamics of change can be applied to regions with greater human modification. Conditions may now be ideal to implement policies to manage Arctic change because recent studies provide the essential scientific understanding, appropriate international institutions are in place, and Arctic nations have the wealth to institute necessary changes, if they choose to do so.

Adaptation, Physiological↗
PubMed2005

Age structure, residents, and transients of Miocene rodent communities.

The age structures of two successive rodent communities are studied on the basis of a rich record from well-dated Miocene sections (17-10 Ma) in north-central Spain. Community age is defined as the mean of the residence times of the community members at the time of the locality age. Community ages are negatively correlated with the numbers of community members. These members are divided into residents (with continuous membership times > or =1.54 million years) and transients (with membership times <1.54 million years). During episodes of species loss, there is a preferential disappearance of transients while residents are retained, a pattern referred to as the "seniority rule." The residents define the studied communities. They are associated with early successional stages of vegetation, and transients are associated with later stages. Under stable conditions, early arrivals in succession are "transient" and replaced by competitive later arrivals. The reversed roles of transients and residents in the studied fossil record are explained by assuming high degrees of disturbance. We view the system within the context of nonequilibrium metapopulation theory, in which competitively superior species become transients because of their dependence on ephemeral late successional habitats.

Animals↗
PubMed2005

The evolution of intergenerational discounting in offspring quality.

Intergenerational effects occur when an individual's actions affect not only its own survivorship and reproduction but also those of its offspring and possibly later descendants. In the presence of intergenerational effects, short-term and long-term measures of success (such as the expected numbers of surviving offspring and of farther descendants, respectively) may be in conflict. When such conflicts occur, life-history theory normally takes long-term measures to predict the outcome of selection. This ignores the fact that, because traits change in time--through mutation, sex, and recombination--long-term relations disintegrate. We study this issue with numerical simulations and analytical models combining intergenerational effects and evolutionary change. In the models, the parental investment per offspring, as well as the total reproductive effort, stand for investments in future generations. The models show that the rate of evolutionary change determines the level of those investments. Higher rates of mutation and of sexual as opposed to parthenogenetic reproduction favor lower parental investment per offspring and lower total reproductive effort. It follows that the level of investment of ancestors in descendants responds to the genetic relatedness between the generations of the lineage, in a manner unaccounted for by preexisting theory.

Animals↗
PubMed2005

Effective leadership and decision-making in animal groups on the move.

For animals that forage or travel in groups, making movement decisions often depends on social interactions among group members. However, in many cases, few individuals have pertinent information, such as knowledge about the location of a food source, or of a migration route. Using a simple model we show how information can be transferred within groups both without signalling and when group members do not know which individuals, if any, have information. We reveal that the larger the group the smaller the proportion of informed individuals needed to guide the group, and that only a very small proportion of informed individuals is required to achieve great accuracy. We also demonstrate how groups can make consensus decisions, even though informed individuals do not know whether they are in a majority or minority, how the quality of their information compares with that of others, or even whether there are any other informed individuals. Our model provides new insights into the mechanisms of effective leadership and decision-making in biological systems.

Animal Communication↗
PubMed2005

Strategic interactions in multi-institutional epidemics of antibiotic resistance.

The increasing frequency of antibiotic resistance in hospital-acquired infections is a major public health concern that has both biological and economic causes. Here we develop conceptual mathematical models that couple the economic incentives and population biology of hospital infection control (HIC). We show that the optimal investment by a hospital for HIC changes with the proportion of patients already colonized with antibiotic-resistant bacteria (ARB) at the time of admission. As that proportion increases, the optimal behavior of a hospital is to increase spending to control ARB with low transmissibility and decrease spending on those with high transmissibility. In some cases, the global optimum investment in HIC can shift discontinuously from one that contains transmission to a do-nothing policy once the proportion already colonized at the time of admission becomes too great. We also show that investments in HIC are determined by a strategic game when several hospitals share patients. Hospitals acting selfishly and rationally will free-ride on the investments of other hospitals, and the level of free-riding should increase with the number of other hospitals in the area. Thus, in areas with many hospitals, the rational strategy for each hospital is to spend less than in areas with few hospitals. Thus, we predict that transmission rates and the prevalence of ARB should be higher in urban hospitals, for instance, compared with rural hospitals. We conclude that regional coordination and planning for HIC is an essential element of public health planning for hospital-acquired infections.

Cross Infection↗
PubMed2005

Leaky prezygotic isolation and porous genomes: rapid introgression of maternally inherited DNA.

Accurate phylogenies are crucial for understanding evolutionary processes, especially species diversification. It is commonly assumed that "good" species are sufficiently isolated genetically that gene genealogies represent accurate phylogenies. However, it is increasingly clear that good species may continue to exchange genetic material through hybridization (introgression). Many studies of closely related species reveal introgression of some genes without others, often with more rapid introgression of maternally inherited chloroplast or mitochondrial DNA (cpDNA, mtDNA). We seek a general explanation for this biased introgression using simple models of common reproductive isolating barriers (RIBs). We compare empirically informed models of prezygotic isolation (for pre- and postinsemination mechanisms of both female choice and male competition) with postzygotic isolation and demonstrate that rate of introgression depends critically upon type of RIB and mode of genetic inheritance (maternal versus biparental versus paternal). Our frequency-dependent prezygotic RIBs allow much more rapid introgression of biparentally and maternally inherited genes than do commonly modeled postzygotic RIBs (especially maternally inherited DNA). After considering the specific predictions in the context of empirical observations, we conclude that our model of prezygotie RIBs is a general explanation for biased introgression of maternally inherited genomic components. These findings suggest that we should use extreme caution when interpreting single gene genealogies as species phylogenies, especially for cpDNA and mtDNA.

Animals↗