Population models of genomic imprinting. II. Maternal and fertility selection

Under several hypotheses for the evolutionary origin of imprinting, genes with maternal and reproductive effects are more likely to be imprinted. We thus investigate the effect of genomic imprinting in single-locus diallelic models of maternal and fertility selection. First, the model proposed by Gavrilets for maternal selection is expanded to include the effects of genomic imprinting. This augmented model exhibits novel behavior for a single-locus model: long-period cycling between a pair of Hopf bifurcations, as well as two-cycling between conjoined pitchfork bifurcations. We also examine several special cases: complete inactivation of one allele and when the maternal and viability selection parameters are independent. Second, we extend the standard model of fertility selection to include the effects of imprinting. Imprinting destroys the "sex-symmetry" property of the standard model, dramatically increasing the number of degrees of freedom of the selection parameter set. Cycling in all these models is rare in parameter space.     

Ecoepidemic models with prey group defense and feeding saturation

In this paper we consider a model for the herd behavior of prey, that are subject to attacks by specialist predators. The latter are affected by a transmissible disease. With respect to other recently introduced models of the same nature, we focus here our attention to the possible feeding satiation phenomenon. The system dynamics is thoroughly investigated, to show the occurrence of several types of bifurcations. In addition to the transcritical and Hopf bifurcation that occur commonly in predator–prey system also a zero-Hopf and a global bifurcation occur. The Hopf and the global bifurcation occur only in the disease-free (so purely demographic) system. The latter is a heteroclinic connection for the between saddle equilibrium points where a stable limit cycle is disrupted and where the system disease-free collapses while in a parameter space region the endemic system exists stably.     

Effects of quarantine in six endemic models for infectious diseases

Thresholds, equilibria, and their stability are found for SIQS and SIQR epidemiology models with three forms of the incidence. For most of these models, the endemic equilibrium is asymptotically stable, but for the SIQR model with the quarantine-adjusted incidence, the endemic equilibrium is an unstable spiral for some parameter values and periodic solutions arise by Hopf bifurcation. The Hopf bifurcation surface and stable periodic solutions are found numerically.     

Critical slowing down as an indicator of transitions in two-species models

Transitions in ecological systems often occur without apparent warning, and may represent shifts between alternative persistent states. Decreasing ecological resilience (the size of the basin of attraction around a stable state) can signal an impending transition, but this effect is difficult to measure in practice. Recent research has suggested that a decreasing rate of recovery from small perturbations (critical slowing down) is a good indicator of ecological resilience. Here we use analytical techniques to draw general conclusions about the conditions under which critical slowing down provides an early indicator of transitions in two-species predator-prey and competition models. The models exhibit three types of transition: the predator-prey model has a Hopf bifurcation and a transcritical bifurcation, and the competition model has two saddle-node bifurcations (in which case the system exhibits hysteresis) or two transcritical bifurcations, depending on the parameterisation. We find that critical slowing down is an earlier indicator of the Hopf bifurcation in predator-prey models in which prey are regulated by predation rather than by intrinsic density-dependent effects and an earlier indicator of transitions in competition models in which the dynamics of the rare species operate on slower timescales than the dynamics of the common species. These results lead directly to predictions for more complex multi-species systems, which can be tested using simulation models or real ecosystems.     

Population models of genomic imprinting. I. Differential viability in the sexes and the analogy with genetic dominance

Many single-locus, two-allele selection models of genomic imprinting have been shown to reduce formally to one-locus Mendelian models with a modified parameter for genetic dominance. One exception is the model where selection at the imprinted locus affects the sexes differently. We present two models of maternal inactivation with differential viability in the sexes, one with complete inactivation, and the other with a partial penetrance for inactivation. We show that, provided dominance relations at the imprintable locus are the same in both sexes, a globally stable polymorphism exists for a range of viabilities that is independent of the penetrance of imprinting. The conditions for a polymorphism are the same as in previous models with differential viability in the sexes but without imprinting and in a model of the paternal X-inactivation system in marsupials. The model with incomplete inactivation is used to illustrate the analogy between imprinting and dominance by comparing equilibrium bifurcation plots for fixed values of dominance and penetrance. We also derive a single expression for the dominance parameter that leaves the frequency and stability of equilibria unchanged for all levels of inactivation. Although an imprinting model with sex differences does not formally reduce to a nonimprinting scheme, close theoretical parallels clearly exist.     

Biomass and biodiversity in species-rich tritrophic communities

We consider a tritrophic system with one basal and one top species and a large number of primary consumers, and derive upper and lower bounds for the total biomass of the middle trophic level. These estimates do not depend on dynamical regime, holding for fixed point, periodic, or chaotic dynamics. We have two kinds of estimates, depending on whether the predator abundance is zero. All these results are uniform in a self-limitation parameter, which regulates prey diversity in the system. For strong self-limitation, diversity is large; for weak self-limitation, it is small. Diversity depends on the variance of species’ parameter values. The larger this variance, the lower the diversity, and vice versa. Moreover, variation in the parameters of the Holling type II functional response changes the bifurcation character, with the equilibrium state with nonzero predator abundance losing stability. If that variation is small then the bifurcation can lead to oscillations (the Hopf bifurcation). Under certain conditions, there exists a supercritical Hopf bifurcation. We then find a connection between diversity and Hopf bifurcations. We also show that the system exhibits top-down regulation and a hump-shaped diversity-productivity curve.We then extend the model by allowing species to experience self-regulation. For this extended model, explicit estimates of prey diversity are obtained. We study the dynamics of this system and find the following. First, diversity and system dynamics crucially depend on variation in species parameters. We show that under certain conditions, the system undergoes a supercritical Hopf bifurcation. We also establish a connection between diversity and Hopf bifurcations. For strong self-limitation, diversity is large and complex dynamics are absent. For weak self-limitation, diversity is small and the equilibrium with non-zero predator abundance is unstable.     

Stability analysis of pathogen-immune interaction dynamics

The paper considers models of dynamics of infectious disease in vivo from the standpoint of the mathematical analysis of stability. The models describe the interaction of the target cells, the pathogens, and the humoral immune response. The paper mainly focuses on the interior equilibrium, whose components are all positive. If the model ignores the absorption of the pathogens due to infection, the interior equilibrium is always asymptotically stable. On the other hand, if the model does consider it, the interior equilibrium can be unstable and a simple Hopf bifurcation can occur. A sufficient condition that the interior equilibrium is asymptotically stable is obtained. The condition explains that the interior equilibrium is asymptotically stable when experimental parameter values are used for the model. Moreover, the paper considers the models in which uninfected cells are involved in the immune response to pathogens, and are removed by the immune complexes. The effect of the involvement strongly affects the stability of the interior equilibria. The results are shown with the aid of symbolic calculation software.     

Modelling autonomous oscillations in the human pupil light reflex using non-linear delay-differential equations

Neurophysiological and anatomical observations are used to derive a non-linear delay-differential equation for the pupil light reflex with negative feedback. As the gain or the time delay in the reflex is increased, a supercritical Hopf bifurcation occurs from a stable fixed point to a stable limit cycle oscillation in pupil area. A Hopf bifurcation analysis is used to determine the conditions for instability and the period and amplitude of these oscillations. The more complex waveforms typical of the occurrence of higher order bifurcations were not seen in numerical simulations of the model. This model provides a general framework to study the different types of dynamical behaviors which can be produced by the pupil light reflex, e.g. edge-light pupil cycling.     

Impact of fear effect on the growth of prey in a predator-prey interaction model

Several field data and experiments on a terrestrial vertebrates exhibited that the fear of predators would cause a substantial variability of prey demography. Fear for predator population enhances the survival probability of prey population, and it can greatly reduce the reproduction of prey population. Based on the experimental evidence, we proposed and analyzed a prey-predator system introducing the cost of fear into prey reproduction with Holling type-II functional response. We investigate all the biologically feasible equilibrium points, and their stability is analyzed in terms of the model parameters. Our mathematical analysis exhibits that for strong anti-predator responses can stabilize the prey-predator interactions by ignoring the existence of periodic behaviors. Our model system undergoes Hopf bifurcation by considering the birth rate r₀ as a bifurcation parameter. For larger prey birth rate, we investigate the transition to a stable coexisting equilibrium state, with oscillatory approach to this equilibrium state, indicating that the greatest characteristic eigenvalues are actually a pair of imaginary eigenvalues with real part negative, which is increasing for r₀. We obtained the conditions for the occurrence of Hopf bifurcation and conditions governing the direction of Hopf bifurcation, which imply that the prey birth rate will not only influence the occurrence of Hopf bifurcation but also alter the direction of Hopf bifurcation. We identify the parameter regions associated with the extinct equilibria, predator-free equilibria and coexisting equilibria with respect to prey birth rate, predator mortality rates. Fear can stabilize the predator-prey system at an interior steady state, where all the species can exists together, or it can create the oscillatory coexistence of all the populations. We performed some numerical simulations to investigate the relationship between the effects of fear and other biologically related parameters (including growth/decay rate of prey/predator), which exhibit the impact that fear can have in prey-predator system. Our numerical illustrations also demonstrate that the prey become less sensitive to perceive the risk of predation with increasing prey growth rate or increasing predators decay rate.     

Multilocus selection in subdivided populations I. Convergence properties for weak or strong migration

The dynamics and equilibrium structure of a deterministic population-genetic model of migration and selection acting on multiple multiallelic loci is studied. A large population of diploid individuals is distributed over finitely many demes connected by migration. Generations are discrete and nonoverlapping, migration is irreducible and aperiodic, all pairwise recombination rates are positive, and selection may vary across demes. It is proved that, in the absence of selection, all trajectories converge at a geometric rate to a manifold on which global linkage equilibrium holds and allele frequencies are identical across demes. Various limiting cases are derived in which one or more of the three evolutionary forces, selection, migration, and recombination, are weak relative to the others. Two are particularly interesting. If migration and recombination are strong relative to selection, the dynamics can be conceived as a perturbation of the so-called weak-selection limit, a simple dynamical system for suitably averaged allele frequencies. Under nondegeneracy assumptions on this weak-selection limit which are generic, every equilibrium of the full dynamics is a perturbation of an equilibrium of the weak-selection limit and has the same stability properties. The number of equilibria is the same in both systems, equilibria in the full (perturbed) system are in quasi-linkage equilibrium, and differences among allele frequencies across demes are small. If migration is weak relative to recombination and epistasis is also weak, then every equilibrium is a perturbation of an equilibrium of the corresponding system without migration, has the same stability properties, and is in quasi-linkage equilibrium. In both cases, every trajectory converges to an equilibrium, thus no cycling or complicated dynamics can occur.      

Multiple limit cycles in the standard model of three species competition for three essential resources

We consider the dynamics of the standard model of 3 species competing for 3 essential (non-substitutable) resources in a chemostat using Liebig's law of the minimum functional response. A subset of these systems which possess cyclic symmetry such that its three single-population equilibria are part of a heteroclinic cycle bounding the two-dimensional carrying simplex is examined. We show that a subcritical Hopf bifurcation from the coexistence equilibrium together with a repelling heteroclinic cycle leads to the existence of at least two limit cycles enclosing the coexistence equilibrium on the carrying simplex- the ``inside' one is an unstable separatrix and the ``outside' one is at least semi-stable relative to the carrying simplex. Numerical simulations suggest that there are exactly two limit cycles and that almost every positive solution approaches either the stable limit cycle or the stable coexistence equilibrium, depending on initial conditions. Bifurcation diagrams confirm this picture and show additional features. In an alternative scenario, we show that the subcritical Hopf together with an attracting heteroclinic cycle leads to an unstable periodic orbit separatrix. This research was partially supported by NSF grant DMS 0211614. KY 40292, USA. This author's research was supported in part by NSF grant DMS 0107160     

Bifurcation Analysis of Models with Uncertain Function Specification: How Should We Proceed?

When we investigate the bifurcation structure of models of natural phenomena, we usually assume that all model functions are mathematically specified and that the only existing uncertainty is with respect to the parameters of these functions. In this case, we can split the parameter space into domains corresponding to qualitatively similar dynamics, separated by bifurcation hypersurfaces. On the other hand, in the biological sciences, the exact shape of the model functions is often unknown, and only some qualitative properties of the functions can be specified: mathematically, we can consider that the unknown functions belong to a specific class of functions. However, the use of two different functions belonging to the same class can result in qualitatively different dynamical behaviour in the model and different types of bifurcation. In the literature, the conventional way to avoid such ambiguity is to narrow the class of unknown functions, which allows us to keep patterns of dynamical behaviour consistent for varying functions. The main shortcoming of this approach is that the restrictions on the model functions are often given by cumbersome expressions and are strictly model-dependent: biologically, they are meaningless. In this paper, we suggest a new framework (based on the ODE paradigm) which allows us to investigate deterministic biological models in which the mathematical formulation of some functions is unspecified except for some generic qualitative properties. We demonstrate that in such models, the conventional idea of revealing a concrete bifurcation structure becomes irrelevant: we can only describe bifurcations with a certain probability. We then propose a method to define the probability of a bifurcation taking place when there is uncertainty in the parameterisation in our model. As an illustrative example, we consider a generic predator–prey model where the use of different parameterisations of the logistic-type prey growth function can result in different dynamics in terms of the type of the Hopf bifurcation through which the coexistence equilibrium loses stability. Using this system, we demonstrate a framework for evaluating the probability of having a supercritical or subcritical Hopf bifurcation.     

Mathematical modeling of the population dynamics of a distinct interactions type system with local dispersal

Distinct biotic interactions in multi-species communities are a ubiquitous force in the natural ecosystem, and this force is an essential determinant of community stability and species coexistence outcomes. We conduct numerical simulations and bifurcation analysis of partial differential equations to gain better understanding and ecological insights into how predation (a), predator handling time (h), and local dispersal affect multi-species community dynamics. This system consists of resource-mutualist-exploiter-competitor interactions and local dispersal. From the inspection of our numerical simulations and co-dimension one bifurcation analysis findings, we discover several critical values that correspond to transcritical bifurcation, subcritical and supercritical Hopf bifurcations. This occurs as we vary the bifurcation parameters a and h in this complex ecological system under symmetric and asymmetric dispersal scenarios. Furthermore, the interplay between these local bifurcation points results in an exciting co-dimension two bifurcations, i.e., Bogdanov-Takens and cusp bifurcation points, respectively, which act as the synchronization points in this complex ecological system. From an ecological viewpoint, we find that (i) the effect of the no-dispersal scenario supports the maintenance of species biodiversity when the predation strength is moderate; (ii) symmetric dispersal induces both subcritical and supercritical Hopf bifurcation and support species diversity for moderate predation strength; and (iii) asymmetric dispersal promotes species diversity as it simplifies the bifurcation changes in dynamics by eliminating the subcritical bifurcations that trigger uncertainty, and this dispersal mechanism mediates species coexistence outcomes. Fundamentally, stable limit cycles have been reported as predator handling time varies in some ecological models; however, we observed in our bifurcation analysis the emergence of the unstable limit cycle as predator handling time changes. We discover that intense predator handling time destabilizes this complex ecological community. In general, our results demonstrate the influential roles of predation, predator handling time, and local dispersal in determining this system’s coexistence dynamics. This knowledge provides a better understanding of species conservation and biological control management.     

Oscillations in a patchy environment disease model

For a single patch SIRS model with a period of immunity of fixed length, recruitment-death demographics, disease related deaths and mass action incidence, the basic reproduction number R(0) is identified. It is shown that the disease-free equilibrium is globally asymptotically stable if R(0)<1. For R(0)>1, local stability of the endemic equilibrium and Hopf bifurcation analysis about this equilibrium are carried out. Moreover, a practical numerical approach to locate the bifurcation values for a characteristic equation with delay-dependent coefficients is provided. For a two patch SIRS model with travel, it is shown that there are several threshold quantities determining its dynamic behavior and that travel can reduce oscillations in both patches; travel may enhance oscillations in both patches; or travel can switch oscillations from one patch to another.     

Bifurcation analysis of the Nowak-Bangham model in CTL dynamics

This paper investigates the local bifurcations of a CTL response model published by Nowak and Bangham [M.A. Nowak, C.R.M. Bangham, Population dynamics of immune responses to persistent viruses, Science 272 (1996) 74]. The Nowak-Bangham model can have three equilibria depending on the basic reproduction number, and generates a Hopf bifurcation through two bifurcations of equilibria. The main result shows a sufficient condition for the interior equilibrium to have a unique bifurcation point at which a simple Hopf bifurcation occurs. For this proof, some new techniques are developed in order to apply the method established by Liu [W.M. Liu, Criterion of Hopf bifurcations without using eigenvalues, J. Math. Anal. Appl. 182 (1) (1994) 250]. In addition, to demonstrate the result obtained theoretically, some bifurcation diagrams are presented with numerical examples.     

Some simple models of cannibalism

A sequence of mathematical models for a species which engages in cannibalism are investigated. The models treat the species as age-structured, and assume that adults consume the unhatched eggs of their own kind. The McKendrick or von Foerster partial differential equation model is first converted into a set of three coupled, nonlinear ordinary differential equations, and then adjusted to describe cannibalism. Some rather unusual dynamical effects are discovered. These include both a Hopf bifurcation and a catastrophic transition from an asymptotically stable equilibrium point to a stable limit cycle.     

On local bifurcations in neural field models with transmission delays

Neural field models with transmission delays may be cast as abstract delay differential equations (DDE). The theory of dual semigroups (also called sun-star calculus) provides a natural framework for the analysis of a broad class of delay equations, among which DDE. In particular, it may be used advantageously for the investigation of stability and bifurcation of steady states. After introducing the neural field model in its basic functional analytic setting and discussing its spectral properties, we elaborate extensively an example and derive a characteristic equation. Under certain conditions the associated equilibrium may destabilise in a Hopf bifurcation. Furthermore, two Hopf curves may intersect in a double Hopf point in a two-dimensional parameter space. We provide general formulas for the corresponding critical normal form coefficients, evaluate these numerically and interpret the results.     

Resilience and local stability in a nutrient-limited resource-consumer system

The “paradox of enrichment” predicts that increasing the growth rate of the resource in a resource-consumer dynamic system, by nutrient enrichment, for example, can lead to local instability of the system—that is, to a Hopf bifurcation. The approach to the Hopf bifurcation is accompanied by a decrease in resilience (rate of return to equilibrium). On the other hand, studies of nutrient cycling in food webs indicate that an increase in the nutrient input rate usually results in increased resilience. Here these two apparently conflicting theoretical results are reconciled with a model of a nutrient-limited resource-consumer system in which the tightly recycled limiting nutrient is explicitly modelled. It is shown that increasing nutrient input may at first lead to increased resilience and that resilience decreases sharply only immediately before the Hopf bifurcation is reached.     

Dynamics of an HIV-1 therapy model of fighting a virus with another virus

In this paper, we rigorously analyse an ordinary differential equation system that models fighting the HIV-1 virus with a genetically modified virus. We show that when the basic reproduction ratio ?(0)<1, then the infection-free equilibrium E (0) is globally asymptotically stable; when ?(0)>1, E (0) loses its stability and there is the single-infection equilibrium E (s). If ?(0)∈(1, 1+δ) where δ is a positive constant explicitly depending on system parameters, then the single-infection equilibrium E (s) that is globally asymptotically stable, while when ?(0)>1+δ, E (s) becomes unstable and the double-infection equilibrium E (d) comes into existence. When ?(0) is slightly larger than 1+δ, E (d) is stable and it loses its stability via Hopf bifurcation when ?(0) is further increased in some ways. Through a numerical example and by applying a normal form theory, we demonstrate how to determine the bifurcation direction and stability, as well as the estimates of the amplitudes and the periods of the bifurcated periodic solutions. We also perform numerical simulations which agree with the theoretical results. The approaches we use here are a combination of analysis of characteristic equations, fluctuation lemma, Lyapunov function and normal form theory.     

Effect of a sharp change of the incidence function on the dynamics of a simple disease

We investigate two cases of a sharp change of incidencec functions on the dynamics of a susceptible-infective-susceptible epidemic model. In the first case, low population levels have mass action incidence, while high population levels have proportional incidence, the switch occurring when the total population reaches a certain threshold. Using a modified Dulac theorem, we prove that this system has a single equilibrium which attracts all solutions for which the disease is present and the population remains bounded. In the second case, an increase of the number of infectives leads to a mass action term being added to a standard incidence term. We show that this allows a Hopf bifurcation to occur, with periodic orbits being generated when a locally asymptotically stable equilibrium loses stability.