Treatment outcome in an SI model with evolutionary resistance: a Darwinian model for the evolution of resistance.

We consider a Darwinian (evolutionary game theoretic) version of a standard susceptible-infectious SI model in which the resistance of the disease causing pathogen to a treatment that prevents death to infected individuals is subject to evolutionary adaptation. We determine the existence and stability of all equilibria, both disease-free and endemic, and use the results to determine conditions under which the treatment will succeed or fail. Of particular interest are conditions under which a successful treatment in the absence of resistance adaptation (i.e. one that leads to a stable disease-free equilibrium) will succeed or fail when pathogen resistance is adaptive. These conditions are determined by the relative breadths of treatment effectiveness and infection transmission rate distributions as functions of pathogen resistance.

A bifurcation theorem for Darwinian matrix models and an application to the evolution of reproductive life-history strategies.

We prove bifurcation theorems for evolutionary game theoretic (Darwinian dynamic) versions of nonlinear matrix equations for structured population dynamics. These theorems generalize existing theorems concerning the bifurcation and stability of equilibrium solutions when an extinction equilibrium destabilizes by allowing for the general appearance of the bifurcation parameter. We apply the theorems to a Darwinian model designed to investigate the evolutionary selection of reproductive strategies that involve either low or high post-reproductive survival (semelparity or iteroparity). The model incorporates the phenotypic trait dependence of two features: population density effects on fertility and a trade-off between inherent fertility and post-reproductive survival. Our analysis of the model determines conditions under which evolution selects for low or for high reproductive survival. In some cases (notably an Allee component effect on newborn survival), the model predicts multiple attractor scenarios in which low or high reproductive survival is initial condition dependent.

Discrete time darwinian dynamics and semelparity versus iteroparity.

We derive and analyze a Darwinian dynamic model based on a general di erence equation population model under the assumption of a trade-o between fertility and survival. Both inherent and density dependent terms are functions of a phenotypic trait (subject to Darwinian evolution) and its population mean. We prove general theorems about the existence and stability of extinction equilibria and the bifurcation of positive equilibria when extinction equilibria destabilize. We apply these results, together with the Evolutionarily Stable Strategy (ESS) Maximum Principle, to the model when both semelparous and iteroparous traits are available to individuals in the population. We find that if the density terms in the population model are trait independent, then only semelparous equilibria are ESS. When density terms do depend on the trait, then in a neighborhood of a bifurcation point it is again the case that only semelparous equilibria are ESS. However, we also show by simulations that ESS iteroparous (and also non-ESS semelparous) equilibria can arise outside a neighborhood of bifurcation points when density e ects depend in a hierarchical manner on the trait.

Difference equations as models of evolutionary population dynamics.

We describe the evolutionary game theoretic methodology for extending a difference equation population dynamic model in a way so as to account for the Darwinian evolution of model coefficients. We give a general theorem that describes the familiar transcritical bifurcation that occurs in non-evolutionary models when theextinction equilibrium destabilizes. This bifurcation results in survival (positive) equilibria whose stability depends on the direction of bifurcation. We give several applications based on evolutionary versions of some classic equations, such as the discrete logistic (Beverton-Holt) and Ricker equations. In addition to illustrating our theorems, these examples also illustrate other biological phenomena, such as strong Allee effects, time-dependent adaptive landscapes, and evolutionary stable strategies.

Periodic matrix models for seasonal dynamics of structured populations with application to a seabird population.

For structured populations with an annual breeding season, life-stage interactions and behavioral tactics may occur on a faster time scale than that of population dynamics. Motivated by recent field studies of the effect of rising sea surface temperature (SST) on within-breeding-season behaviors in colonial seabirds, we formulate and analyze a general class of discrete-time matrix models designed to account for changes in behavioral tactics within the breeding season and their dynamic consequences at the population level across breeding seasons. As a specific example, we focus on egg cannibalism and the daily reproductive synchrony observed in seabirds. Using the model, we investigate circumstances under which these life history tactics can be beneficial or non-beneficial at the population level in light of the expected continued rise in SST. Using bifurcation theoretic techniques, we study the nature of non-extinction, seasonal cycles as a function of environmental resource availability as they are created upon destabilization of the extinction state. Of particular interest are backward bifurcations in that they typically create strong Allee effects in population models which, in turn, lead to the benefit of possible (initial condition dependent) survival in adverse environments. We find that positive density effects (component Allee effects) due to increased adult survival from cannibalism and the propensity of females to synchronize daily egg laying can produce a strong Allee effect due to a backward bifurcation.

A bifurcation theorem for evolutionary matrix models with multiple traits.

One fundamental question in biology is population extinction and persistence, i.e., stability/instability of the extinction equilibrium and of non-extinction equilibria. In the case of nonlinear matrix models for structured populations, a bifurcation theorem answers this question when the projection matrix is primitive by showing the existence of a continuum of positive equilibria that bifurcates from the extinction equilibrium as the inherent population growth rate passes through 1. This theorem also characterizes the stability properties of the bifurcating equilibria by relating them to the direction of bifurcation, which is forward (backward) if, near the bifurcation point, the positive equilibria exist for inherent growth rates greater (less) than 1. In this paper we consider an evolutionary game theoretic version of a general nonlinear matrix model that includes the dynamics of a vector of mean phenotypic traits subject to natural selection. We extend the fundamental bifurcation theorem to this evolutionary model. We apply the results to an evolutionary version of a Ricker model with an added Allee component. This application illustrates the theoretical results and, in addition, several other interesting dynamic phenomena, such as backward bifurcation induced strong Allee effects.

A juvenile-adult population model: climate change, cannibalism, reproductive synchrony, and strong Allee effects.

We study a discrete time, structured population dynamic model that is motivated by recent field observations concerning certain life history strategies of colonial-nesting gulls, specifically the glaucous-winged gull (Larus glaucescens). The model focuses on mechanisms hypothesized to play key roles in a population's response to degraded environment resources, namely, increased cannibalism and adjustments in reproductive timing. We explore the dynamic consequences of these mechanics using a juvenile-adult structure model. Mathematically, the model is unusual in that it involves a high co-dimension bifurcation at [Formula: see text] which, in turn, leads to a dynamic dichotomy between equilibrium states and synchronized oscillatory states. We give diagnostic criteria that determine which dynamic is stable. We also explore strong Allee effects caused by positive feedback mechanisms in the model and the possible consequence that a cannibalistic population can survive when a non-cannibalistic population cannot.

The puzzle of partial migration: Adaptive dynamics and evolutionary game theory perspectives.

We consider the phenomenon of partial migration which is exhibited by populations in which some individuals migrate between habitats during their lifetime, but others do not. First, using an adaptive dynamics approach, we show that partial migration can be explained on the basis of negative density dependence in the per capita fertilities alone, provided that this density dependence is attenuated for increasing abundances of the subtypes that make up the population. We present an exact formula for the optimal proportion of migrants which is expressed in terms of the vital rates of migrant and non-migrant subtypes only. We show that this allocation strategy is both an evolutionary stable strategy (ESS) as well as a convergence stable strategy (CSS). To establish the former, we generalize the classical notion of an ESS because it is based on invasion exponents obtained from linearization arguments, which fail to capture the stabilizing effects of the nonlinear density dependence. These results clarify precisely when the notion of a "weak ESS", as proposed in Lundberg (2013) for a related model, is a genuine ESS. Secondly, we use an evolutionary game theory approach, and confirm, once again, that partial migration can be attributed to negative density dependence alone. In this context, the result holds even when density dependence is not attenuated. In this case, the optimal allocation strategy towards migrants is the same as the ESS stemming from the analysis based on the adaptive dynamics. The key feature of the population models considered here is that they are monotone dynamical systems, which enables a rather comprehensive mathematical analysis.

The many guises of R0 (a didactic note).

The basic reproduction number R0 is, by definition, the expected life time number of offspring of a newborn individual. An operationalization entails a specification of what events are considered as "reproduction" and what events are considered as "transitions from one individual-state to another". Thus, an element of choice can creep into the concretization of the definition. The aim of this note is to clearly expose this possibility by way of examples from both population dynamics and infectious disease epidemiology.

Backward bifurcations and strong Allee effects in matrix models for the dynamics of structured populations.

In nonlinear matrix models, strong Allee effects typically arise when the fundamental bifurcation of positive equilibria from the extinction equilibrium at r=1 (or R0=1) is backward. This occurs when positive feedback (component Allee) effects are dominant at low densities and negative feedback effects are dominant at high densities. This scenario allows population survival when r (or equivalently R0) is less than 1, provided population densities are sufficiently high. For r>1 (or equivalently R0>1) the extinction equilibrium is unstable and a strong Allee effect cannot occur. We give criteria sufficient for a strong Allee effect to occur in a general nonlinear matrix model. A juvenile-adult example model illustrates the criteria as well as some other possible phenomena concerning strong Allee effects (such as positive cycles instead of equilibria).

Darwinian dynamics of a juvenile-adult model.

The bifurcation that occurs from the extinction equilibrium in a basic discrete time, nonlinear juvenile-adult model for semelparous populations, as the inherent net reproductive number R0 increases through 1, exhibits a dynamic dichotomy with two alternatives: an equilibrium with overlapping generations and a synchronous 2-cycle with non-overlapping generations. Which of the two alternatives is stable depends on the intensity of competition between juveniles and adults and on the direction of bifurcation. We study this dynamic dichotomy in an evolutionary setting by assuming adult fertility and juvenile survival are functions of a phenotypic trait u subject to Darwinian evolution. Extinction equilibria for the Darwinian model exist only at traits u• that are critical points of R0(u). We establish the simultaneous bifurcation of positive equilibria and synchronous 2-cycles as the value of R0(u•) increases through 1 and describe how the stability of these dynamics depend on the direction of bifurcation, the intensity of between-class competition, and the extremal properties of R0(u) at u•. These results can be equivalently stated in terms of the inherent population growth rate r(u).

Stable bifurcations in semelparous Leslie models.

In this paper, we consider nonlinear Leslie models for the dynamics of semelparous age-structured populations. We establish stability and instability criteria for positive equilibria that bifurcate from the extinction equilibrium at R (0)=1. When the bifurcation is to the right (forward or super-critical), the criteria consist of inequalities involving the (low-density) between-class and within-class competition intensities. Roughly speaking, stability (respectively, instability) occurs if between-class competition is weaker (respectively, stronger) than within-class competition. When the bifurcation is to the left (backward or sub-critical), the bifurcating equilibria are unstable. We also give criteria that determine whether the boundary of the positive cone is an attractor or a repeller. These general criteria contribute to the study of dynamic dichotomies, known to occur in lower dimensional semelparous Leslie models, between equilibration and age-cohort-synchronized oscillations.

A net reproductive number for periodic matrix models.

We give a definition of a net reproductive number R (0) for periodic matrix models of the type used to describe the dynamics of a structured population with periodic parameters. The definition is based on the familiar method of studying a periodic map by means of its (period-length) composite. This composite has an additive decomposition that permits a generalization of the Cushing-Zhou definition of R (0) in the autonomous case. The value of R (0) determines whether the population goes extinct (R (0)<1) or persists (R (0)>1). We discuss the biological interpretation of this definition and derive formulas for R (0) for two cases: scalar periodic maps of arbitrary period and periodic Leslie models of period 2. We illustrate the use of the definition by means of several examples and by applications to case studies found in the literature. We also make some comparisons of this definition of R (0) with another definition given recently by Bacaër.

Evolutionary dynamics and strong Allee effects.

We describe the dynamics of an evolutionary model for a population subject to a strong Allee effect. The model assumes that the carrying capacity k(u), inherent growth rate r(u), and Allee threshold a(u) are functions of a mean phenotypic trait u subject to evolution. The model is a plane autonomous system that describes the coupled population and mean trait dynamics. We show bounded orbits equilibrate and that the Allee basin shrinks (and can even disappear) as a result of evolution. We also show that stable non-extinction equilibria occur at the local maxima of k(u) and that stable extinction equilibria occur at local minima of r(u). We give examples that illustrate these results and demonstrate other consequences of an Allee threshold in an evolutionary setting. These include the existence of multiple evolutionarily stable, non-extinction equilibria, and the possibility of evolving to a non-evolutionary stable strategy (ESS) trait from an initial trait near an ESS.

Life stages: interactions and spatial patterns.

In many stage-structured species, different life stages often occupy separate spatial niches in a heterogeneous environment. Life stages of the giant flour beetle Tribolium brevicornis (Leconte), in particular adults and pupae, occupy different locations in a homogeneous habitat. This unique spatial pattern does not occur in the well-studied stored grain pests T. castaneum (Herbst) and T. confusum (Duval). We propose density dependent dispersal as a causal mechanism for this spatial pattern. We model and explore the spatial dynamics of T. brevicornis with a set of four density dependent integrodifference and difference equations. The spatial model exhibits multiple attractors: a spatially uniform attractor and a patchy attractor with pupae and adults spatially separated. The model attractors are consistent with experimental observations.

Three stage semelparous Leslie models.

Nonlinear Leslie matrix models have a long history of use for modeling the dynamics of semelparous species. Semelparous models, as do nonlinear matrix models in general, undergo a transcritical equilibrium bifurcation at inherent net reproductive number R(0) = 1 where the extinction equilibrium loses stability. Semelparous models however do not fall under the purview of the general theory because this bifurcation is of higher co-dimension. This mathematical fact has biological implications that relate to a dichotomy of dynamic possibilities, namely, an equilibration with over lapping age classes as opposed to an oscillation in which age classes are periodically missing. The latter possibility makes these models of particular interest, for example, in application to the well known outbreaks of periodical insects. While the nature of the bifurcation at R(0) = 1 is known for two-dimensional semelparous Leslie models, only limited results are available for higher dimensional models. In this paper I give a thorough accounting of the bifurcation at R(0) = 1 in the three-dimensional case, under some monotonicity assumptions on the nonlinearities. In addition to the bifurcation of positive equilibria, there occurs a bifurcation of invariant loops that lie on the boundary of the positive cone. I describe the geometry of these loops, classify them into three distinct types, and show that they consist of either one or two three-cycles and heteroclinic orbits connecting (the phases of) these cycles. Furthermore, I determine stability and instability properties of these loops, in terms of model parameters, as well as those of the positive equilibria. The analysis also provides the global dynamics on the boundary of the cone. The stability and instability conditions are expressed in terms of certain measures of the strength and the symmetry/asymmetry of the inter-age class competitive interactions. Roughly speaking, strong inter-age class competitive interactions promote oscillations (not necessarily periodic) with separated life-cycle stages, while weak interactions promote stable equilibration with overlapping life-cycle stages. Methods used include the theory of planar monotone maps, average Lyapunov functions, and bifurcation theory techniques.

Modeling frequency-dependent selection with an application to cichlid fish.

Negative frequency-dependent selection is a well known microevolutionary process that has been documented in a population of Perissodus microlepis, a species of cichlid fish endemic to Lake Tanganyika (Africa). Adult P. microlepis are lepidophages, feeding on the scales of other living fish. As an adaptation for this feeding behavior P. microlepis exhibit lateral asymmetry with respect to jaw morphology: the mouth either opens to the right or left side of the body. Field data illustrate a temporal phenotypic oscillation in the mouth-handedness, and this oscillation is maintained by frequency-dependent selection. Since both genetic and population dynamics occur on the same time scale in this case, we develop a (discrete time) model for P. microlepis populations that accounts for both dynamic processes. We establish conditions on model parameters under which the model predicts extinction and conditions under which there exists a unique positive (survival) equilibrium. We show that at the positive equilibrium there is a 1:1 phenotypic ratio. Using a local stability and bifurcation analysis, we give further conditions under which the positive equilibrium is stable and conditions under which it is unstable. Destabilization results in a bifurcation to a periodic oscillation and occurs when frequency-dependent selection is sufficiently strong. This bifurcation is offered as an explanation of the phenotypic frequency oscillations observed in P. microlepis. An analysis of the bifurcating periodic cycle results in some interesting and unexpected predictions.

Coexistence of competing juvenile-adult structured populations.

The Leslie-Gower model is a discrete time analog of the competition Lotka-Volterra model and is known to possess the same dynamic scenarios of that famous model. The Leslie-Gower model played a historically significant role in the history of competition theory in its application to classic laboratory experiments of two competing species of flour beetles (carried out by Park in the 1940s-1960s). While these experiments generally supported what became the Competitive Exclusion Principle, Park observed an anomalous coexistence case. Recent literature has discussed Park's 'coexistence case' by means of non-Lotka-Volterra, non-equilibrium dynamics that occur in a high dimensional model with life cycle stages. We study this dynamic possibility in the lowest possible dimension, that is to say, by means of a model involving only two species each with two life cycle stages. We do this by extending the Leslie-Gower model so as to describe the competitive interaction of two species with juvenile and adult classes. We give a complete account of the global dynamics of the resulting model and show that it allows for non-equilibrium competitive coexistence as competition coefficients are increased. We also show that this phenomenon occurs in a general class of models for competing populations structured by juvenile and adult life cycle stages.