The spatio-temporal dynamics of neutral genetic diversity

The notions of pulled and pushed solutions of reaction-dispersal equations introduced by Garnier et al. (2012) and Roques et al. (2012) are based on a decomposition of the solutions into several components. In the framework of population dynamics, this decomposition is related to the spatio-temporal evolution of the genetic structure of a population. The pulled solutions describe a rapid erosion of neutral genetic diversity, while the pushed solutions are associated with a maintenance of diversity. This paper is a survey of the most recent applications of these notions to several standard models of population dynamics, including reaction-diffusion equations and systems and integro-differential equations. We describe several counterintuitive results, where unfavorable factors for the persistence and spreading of a population tend to promote diversity in this population. In particular, we show that the Allee effect, the existence of a competitor species, as well as the presence of climate constraints are factors which can promote diversity during a colonization. We also show that long distance dispersal events lead to a higher diversity, whereas the existence of a nonreproductive juvenile stage does not affect the neutral diversity in a range-expanding population.     

Gene surfing in expanding populations

Large scale genomic surveys are partly motivated by the idea that the neutral genetic variation of a population may be used to reconstruct its migration history. However, our ability to trace back the colonization pathways of a species from their genetic footprints is limited by our understanding of the genetic consequences of a range expansion. Here, we study, by means of simulations and analytical methods, the neutral dynamics of gene frequencies in an asexual population undergoing a continual range expansion in one dimension. During such a colonization period, lineages can fix at the wave front by means of a "surfing" mechanism [Edmonds, C.A., Lillie, A.S., Cavalli-Sforza, L.L., 2004. Mutations arising in the wave front of an expanding population. Proc. Natl. Acad. Sci. 101, 975-979]. We quantify this phenomenon in terms of (i) the spatial distribution of lineages that reach fixation and, closely related, (ii) the continual loss of genetic diversity (heterozygosity) at the wave front, characterizing the approach to fixation. Our stochastic simulations show that an effective population size can be assigned to the wave that controls the (observable) gradient in heterozygosity left behind the colonization process. This effective population size is markedly higher in the presence of cooperation between individuals ("pushed waves") than when individuals proliferate independently ("pulled waves"), and increases only sub-linearly with deme size. To explain these and other findings, we develop a versatile analytical approach, based on the physics of reaction-diffusion systems, that yields simple predictions for any deterministic population dynamics. Our analytical theory compares well with the simulation results for pushed waves, but is less accurate in the case of pulled waves when stochastic fluctuations in the tip of the wave are important.     

Effect of environmental fluctuations on invasion fronts

We determine the density profile and velocity of invasion fronts in one-dimensional infinite habitats in the presence of environmental fluctuations. The population dynamics is reformulated in terms of a stochastic reaction-diffusion equation and is reduced to a deterministic equation that incorporates the systematic contributions of the noise. We obtain analytical expressions for the front profile and velocity by constructing a variational principle. The effect of the noise differs, depending on whether it affects the density-independent growth rate, the intraspecific competition term or the Allee threshold. Fluctuations in the density-independent growth rate increase the invasion velocity and the population density of the invaded area. Fluctuations in the competition term also change the population density of the invaded area, but modify the invasion velocity only for certain initial conditions. Fluctuations in the Allee threshold can induce pulled or pushed invasion fronts as well as invasion failure. We compare our analytical results with numerical solutions of the stochastic partial differential equations and show that our procedure proves useful in dealing with reaction-diffusion equations with multiplicative noise.     

一个具有年龄结构的单种群离散反应扩散模型的波前解

利用上下解方法研究了一个具有年龄结构的单种群离散反应扩散模型波前解的存在性,并证明了存在具有临界波速的波前解.     

Modeling Spatial Spread of Infectious Diseases with a Fixed Latent Period in a Spatially Continuous Domain

In this paper, with the assumptions that an infectious disease in a population has a fixed latent period and the latent individuals of the population may diffuse, we formulate an SIR model with a simple demographic structure for the population living in a spatially continuous environment. The model is given by a system of reaction-diffusion equations with a discrete delay accounting for the latency and a spatially non-local term caused by the mobility of the individuals during the latent period. We address the existence, uniqueness, and positivity of solution to the initial-value problem for this type of system. Moreover, we investigate the traveling wave fronts of the system and obtain a critical value c ^* which is a lower bound for the wave speed of the traveling wave fronts. Although we can not prove that this value is exactly the minimal wave speed, numeric simulations seem to suggest that it is. Furthermore, the simulations on the PDE model also suggest that the spread speed of the disease indeed coincides with c ^*. We also discuss how the model parameters affect c ^*.     

一类含时滞的Logistic反应扩散方程的波前解

研究一类含时滞的Logistic滞反应扩散方程的波前解．通过构造合适的上下解,证明了当时滞充分小时,方程存在波前解．用线性化方法,给出了存在波前解的时滞τ取值范围的一个估计．     

A mathematical analysis on public goods games in the continuous space

We consider the population dynamics of two competing species sharing the same resource, which is modeled by the carrying capacity term of logistic equation. One species (farmer) increases the carrying capacity in exchange for a decreased survival rate, while the other species (exploiter) does not. As the carrying capacity is shared by both species, farmer is altruistic. The effect of continuous spatial structure on the performance of such strategies is studied using the reaction diffusion equations. Mathematical analysis on the traveling wave solution of the system revealed; (1) Farmers can never expel exploiters in any traveling wave solution. (2) The expanding velocity of the exploiter population invading the farmer population can be analytically determined and it depends only on a cost of altruism and the diffusion coefficients while it is independent of the benefit of altruism. (3) When the effect of altruism is small, the dynamics of the invasion of exploiters obeys the Fisher-KPP equation. Numerical calculations confirm these results.     

Integrodifference equations in the presence of climate change: persistence criterion,travelling waves and inside dynamics

To understand the effects that the climate change has on the evolution of species as well as the genetic consequences, we analyze an integrodifference equation (IDE) models for a reproducing and dispersing population in a spatio-temporal heterogeneous environment described by a shifting climate envelope. Our analysis on the IDE focuses on the persistence criterion, travelling wave solutions, and the inside dynamics. First, the persistence criterion, characterizing the global dynamics of the IDE, is established in terms of the basic reproduction number. In the case of persistence, a unique travelling wave is found to govern the global dynamics. The effects of the size and the shifting speed of the climate envelope on the basic reproduction number, and hence, on the persistence criterion, are also investigated. In particular, the critical domain size and the critical shifting speed are found in certain cases. Numerical simulations are performed to complement the theoretical results. In the case of persistence, we separate the travelling wave and general solutions into spatially distinct neutral fractions to study the inside dynamics. It is shown that each neutral genetic fraction rearranges itself spatially so as to asymptotically achieve the profile of the travelling wave. To measure the genetic diversity of the population density we calculate the Shannon diversity index and related indices, and use these to illustrate how diversity changes with underlying parameters.

     

Sea-urchin feeding fronts

Sea-urchin feeding fronts are a striking example of spatial pattern formation in an ecological system. If it is assumed that urchins are asocial, and that they move randomly, then the formation of these dense fronts is an apparent paradox. The key lies in observations that urchins move further in areas where their algal food is less plentiful. This naturally leads to the accumulation of urchins in areas with abundant algae. If urchin movement is represented as a random walk, with a step size that depends on algal concentration, then their movement may be described by a Fokker–Planck diffusion equation. For certain combinations of algal growth and urchin grazing, traveling wave solutions are obtained. Two-dimensional simulations of urchin algal dynamics show that an initially uniformly distributed urchin population, grazing on an alga with a smoothly varying density, may form a propagating front separating two sharply delineated regions. On one side of the front algal density is uniformly low, and on the other side of the front algal density is uniformly high. Bounds on when stable fronts will form are obtained in terms of urchin density and grazing, and algal growth.     

Dynamics of prostate cancer stem cells with diffusion and organism response

We develop a systems based model for prostate cancer, as a sub-system of the organism. We accomplish this in two stages. We first start with a general ODE that includes organism response terms. Then, to account for normally observed spatial diffusion of cell populations, the ODE is extended to a PDE that includes spatial terms. Numerical solutions of the full PDE are provided, and are indicative of traveling wave fronts. This motivates the use of a well known transformation to derive a canonically related (non-linear) system of ODEs for traveling wave solutions. For biological feasibility, we show that the non-negative cone for the traveling wave system is time invariant. We also prove that the traveling waves have a unique global attractor. Biologically, the global attractor would be the limit for the avascular tumor growth. We conclude with comments on clinical implications of the model.     

格上时滞Lotka-Volterra合作系统的波前解

研究了定义在格上并具有时滞的Lotka-Volterra合作系统的波前解.通过构造上下解得到了波前解的存在性,借助于比较原理和渐近传播理论得到了波前解的不存在性,进而在得到了波前解最小波速的充分条件.     

Landscape mosaic induces traveling waves of insect outbreaks

The effect of landscape mosaic on recurrent traveling waves in spatial population dynamics was studied via simulation modeling across a theoretical landscape with varying levels of connectivity. Phase angle analysis was used to identify locations of wave epicenters on patchy landscapes. Simulations of a tri-trophic model of the larch budmoth (Zeiraphera diniana) with cyclic population dynamics on landscapes with a single focus of high-density habitat produced traveling waves generally radiating outwardly from single and multiple foci and spreading to isolated habitats. We have proposed two hypotheses for this result: (1) immigration subsidies inflate population growth rates in the high connectivity habitat and, thus, reduce the time from valleys to peaks in population cycles; (2) populations in the high connectivity habitat crash from peaks to valleys faster than in an isolated habitat due to over-compensatory density dependence. While population growth rates in the high connectivity habitat benefitted from immigration subsidies, times from population valleys to peaks were greater in high connectivity habitat due to a greater magnitude of fluctuations. Conversely, the mean time of the crash from population peaks to valleys was shorter in high connectivity habitat, supporting the second hypothesis. Results of this study suggest over-compensatory density dependence as an underlying mechanism for recurrent traveling waves originating in high connectivity habitats aggregated around a single focus.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Two-sex population dynamics in space: effects of gestation time on persistence.

Most single-species population models assume either that one sex dominates the growth dynamics (usually the female), or that the life cycles of the two sexes are identical; however, sexual differences in ontogenetic features can render this assumption invalid. Further, the interaction between sexes is necessarily nonlinear, and the dependence of dynamic behavior on sexual interactions can be complicated. Here we examine a two-sex population model, related to the well-known logistic model, with explicit sexual interactions. The model is bistable and, by the addition of diffusion, admits traveling wave solutions. Dominance of states via this spatial dynamic are examined. A simple condition for neutral dominance is obtained; sexual interactions inhibit the dominance of the nonzero population, making persistence more difficult.     

Spreading speed, traveling waves, and minimal domain size in impulsive reaction-diffusion models

How growth, mortality, and dispersal in a species affect the species' spread and persistence constitutes a central problem in spatial ecology. We propose impulsive reaction-diffusion equation models for species with distinct reproductive and dispersal stages. These models can describe a seasonal birth pulse plus nonlinear mortality and dispersal throughout the year. Alternatively, they can describe seasonal harvesting, plus nonlinear birth and mortality as well as dispersal throughout the year. The population dynamics in the seasonal pulse is described by a discrete map that gives the density of the population at the end of a pulse as a possibly nonmonotone function of the density of the population at the beginning of the pulse. The dynamics in the dispersal stage is governed by a nonlinear reaction-diffusion equation in a bounded or unbounded domain. We develop a spatially explicit theoretical framework that links species vital rates (mortality or fecundity) and dispersal characteristics with species' spreading speeds, traveling wave speeds, as well as minimal domain size for species persistence. We provide an explicit formula for the spreading speed in terms of model parameters, and show that the spreading speed can be characterized as the slowest speed of a class of traveling wave solutions. We also give an explicit formula for the minimal domain size using model parameters. Our results show how the diffusion coefficient, and the combination of discrete- and continuous-time growth and mortality determine the spread and persistence dynamics of the population in a wide variety of ecological scenarios. Numerical simulations are presented to demonstrate the theoretical results.     

Effects of long-range taxis and population pressure on the range expansion of invasive species in heterogeneous environments

We consider a new model for biological invasions in periodic patchy environments, in which long-range taxis and population pressure are incorporated in the framework of reaction-diffusion-advection equations. We assume that long-range taxis is induced by a weighted integral of stimuli within a certain sensing range. Population pressure is incorporated in the diffusion coefficient that linearly increases with population density. We first analyze the model in the absence of population pressure and demonstrate how the sensing length of long-range taxis influences the range expansion pattern of invasive species and its rate of spread. The effects of population pressure are examined for both homogeneous and periodic patchy environments. For the homogeneous environment, an exact and explicit traveling wave solution and the spreading speed are obtained. For the periodic patchy environment, we find numerically that a population starting from any localized distribution evolves to a traveling periodic wave if the null solution of the RDA equation is locally unstable, and that the traveling wave speed significantly increases with increasing population pressure. Furthermore, the population pressure and taxis intensity synergistically enhance the spreading speed when they are increased together.     

Speeds of invasion in a model with strong or weak Allee effects

We study an invasion model based on a reaction-diffusion equation with an Allee effect. We use a special, piecewise-linear, population growth rate. This function allows us to obtain traveling wave solutions and to compute wave speeds for a full range of Allee effects, including weak Allee effects. Some investigators claim that linearization fails to give the correct speed of invasion if there is an Allee effect. We show that the minimum speed for a sufficiently weak Allee may, in fact, be the same as that derived by means of linearization.     

Changes over time in the spatiotemporal dynamics of cyclic populations of field voles (Microtus agrestis L.)

We demonstrate changes over time in the spatial and temporal dynamics of an herbivorous small rodent by analyzing time series of population densities obtained at 21 locations on clear cuts within a coniferous forest in Britain from 1984 to 2004. Changes had taken place in the amplitude, periodicity, and synchrony of cycles and density-dependent feedback on population growth rates. Evidence for the presence of a unidirectional traveling wave in rodent abundance was strong near the beginning of the study but had disappeared near the end. This study provides empirical support for the hypothesis that the temporal (such as delayed density dependence structure) and spatial (such as traveling waves) dynamics of cyclic populations are closely linked. The changes in dynamics were markedly season specific, and changes in overwintering dynamics were most pronounced. Climatic changes, resulting in a less seasonal environment with shorter winters near the end of the study, are likely to have caused the changes in vole dynamics. Similar changes in rodent dynamics and the climate as reported from Fennoscandia indicate the involvement of large-scale climatic variables.     

The rate of beneficial mutations surfing on the wave of a range expansion

Many theoretical and experimental studies suggest that range expansions can have severe consequences for the gene pool of the expanding population. Due to strongly enhanced genetic drift at the advancing frontier, neutral and weakly deleterious mutations can reach large frequencies in the newly colonized regions, as if they were surfing the front of the range expansion. These findings raise the question of how frequently beneficial mutations successfully surf at shifting range margins, thereby promoting adaptation towards a range-expansion phenotype. Here, we use individual-based simulations to study the surfing statistics of recurrent beneficial mutations on wave-like range expansions in linear habitats. We show that the rate of surfing depends on two strongly antagonistic factors, the probability of surfing given the spatial location of a novel mutation and the rate of occurrence of mutations at that location. The surfing probability strongly increases towards the tip of the wave. Novel mutations are unlikely to surf unless they enjoy a spatial head start compared to the bulk of the population. The needed head start is shown to be proportional to the inverse fitness of the mutant type, and only weakly dependent on the carrying capacity. The precise location dependence of surfing probabilities is derived from the non-extinction probability of a branching process within a moving field of growth rates. The second factor is the mutation occurrence which strongly decreases towards the tip of the wave. Thus, most successful mutations arise at an intermediate position in the front of the wave. We present an analytic theory for the tradeoff between these factors that allows to predict how frequently substitutions by beneficial mutations occur at invasion fronts. We find that small amounts of genetic drift increase the fixation rate of beneficial mutations at the advancing front, and thus could be important for adaptation during species invasions.     

具时滞的人口模型的行波解

研究具时滞的人口模型的行波解存在性问题,利用[5]中的方法,鹕行波解的存在性问题转化为寻找上下解的问题。     

Traveling wave solutions in a plant population model with a seed bank

We propose an integro-difference equation model to predict the spatial spread of a plant population with a seed bank. The formulation of the model consists of a nonmonotone convolution integral operator describing the recruitment and seed dispersal and a linear contraction operator addressing the effect of the seed bank. The recursion operator of the model is noncompact, which poses a challenge to establishing the existence of traveling wave solutions. We show that the model has a spreading speed, and prove that the spreading speed can be characterized as the slowest speed of a class of traveling wave solutions by using an asymptotic fixed point theorem. Our numerical simulations show that the seed bank has the stabilizing effect on the spatial patterns of traveling wave solutions.