Isolated populations ultimately go extinct because of the intrinsic noise of elementary processes. In multi-population systems extinction of a population may occur via more than one route. We investigate this generic situation in a simple predator-prey (or infected-susceptible) model. The predator and prey populations may coexist for a long time but ultimately both go extinct. In the first extinction route the predators go extinct first, whereas the prey thrive for a long time and then also go extinct. In the second route the prey go extinct first causing a rapid extinction of the predators. Assuming large sub-population sizes in the coexistence state, we compare the probabilities of each of the two extinction routes and predict the most likely path of the sub-populations to extinction. We also suggest an effective three-state master equation for the probabilities to observe the coexistence state, the predator-free state and the empty state.
Many populations in nature are fragmented: they consist of local populations occupying separate patches. A local population is prone to extinction due to the shot noise of birth and death processes. A migrating population from another patch can dramatically delay the extinction. What is the optimal migration rate that minimizes the extinction risk of the whole population? Here we answer this question for a connected network of model habitat patches with different carrying capacities.
Extinction of a long-lived isolated stochastic population can be described as an exponentially slow decay of quasi-stationary probability distribution of the population size. We address extinction of a population in a two-population system in the case when the population turnover -- renewal and removal -- is much slower than all other processes. In this case there is a time scale separation in the system which enables one to introduce a short-time quasi-stationary extinction rate W_1 and a long-time quasi-stationary extinction rate W_2, and develop a time-dependent theory of the transition bet…
Established populations often exhibit oscillations in their sizes. If a population is isolated, intrinsic stochasticity of elemental processes can ultimately bring it to extinction. Here we study extinction of oscillating populations in a stochastic version of the Rosenzweig-MacArthur predator-prey model. To this end we extend a WKB approximation (after Wentzel, Kramers and Brillouin) of solving the master equation to the case of extinction from a limit cycle in the space of population sizes. We evaluate the extinction rates and find the most probable paths to extinction by applying Floquet th…
This paper deals with extinction of an isolated population caused by intrinsic noise. We model the population dynamics in a "refuge" as a Markov process which involves births and deaths on discrete lattice sites and random migrations between neighboring sites. In extinction scenario I the zero population size is a repelling fixed point of the on-site deterministic dynamics. In extinction scenario II the zero population size is an attracting fixed point, corresponding to what is known in ecology as Allee effect. Assuming a large population size, we develop WKB (Wentzel-Kramers-Brillouin) approx…
We consider a stochastic population model where the intrinsic or demographic noise causes cycling between states before the population eventually goes extinct. A master equation approach coupled with a WKB (Wentzel-Kramers-Brillouin) approximation is used to construct the optimal path to extinction. In addition, a probabilistic argument is used to understand the pre-extinction dynamics and approximate the mean time to extinction. Analytical results agree well with numerical Monte Carlo simulations. A control method is implemented to decrease the mean time to extinction. Analytical results quan…
Many types of bacteria can survive under stress by switching stochastically between two different phenotypes: the "normals" who multiply fast, but are vulnerable to stress, and the "persisters" who hardly multiply, but are resilient to stress. Previous theoretical studies of such bacterial populations have focused on the \emph{fitness}: the asymptotic rate of unbounded growth of the population. Yet for an isolated population of established (and not very large) size, a more relevant measure may be the population \emph{extinction risk} due to the interplay of adverse extrinsic variations and int…
We study the extinction risk of a fragmented population residing on a network of patches coupled by migration, where the local patch dynamics include the Allee effect. We show that mixing between patches dramatically influences the population's viability. Slow migration is shown to always increase the population's global extinction risk compared to the isolated case. At fast migration, we demonstrate that synchrony between patches minimizes the population's extinction risk. Moreover, we discover a critical migration rate that maximizes the extinction risk of the population, and identify an ear…
We study the combined impact of a colored environmental noise and demographic noise on the extinction risk of a long-lived and well-mixed isolated stochastic population which exhibits the Allee effect. The environmental noise modulates the population birth and death rates. Assuming that the Allee effect is strong, and the environmental noise is positively correlated and Gaussian, we derive a Fokker-Planck equation for the joint probability distribution of the population sizes and environmental fluctuations. In WKB approximation this equation reduces to an effective two-dimensional Hamiltonian …
Environmental noise can cause an exponential reduction in the mean time to extinction (MTE) of an isolated population. We study this effect on an example of a stochastic birth-death process with rates modulated by a colored Gaussian noise. A path integral formulation yields a transparent way of evaluating the MTE and finding the optimal realization of the environmental noise that determines the most probable path to extinction. The population-size dependence of the MTE changes from exponential in the absence of the environmental noise to a power law for a short-correlated noise and to no depen…
We study simple stochastic scenarios, based on birth-and-death Markovian processes, that describe populations with Allee effect, to account for the role of demographic stochasticity. In the mean-field deterministic limit we recover well-known deterministic evolution equations widely employed in population ecology. The mean-time to extinction is in general obtained by the Wentzel-Kramers-Brillouin (WKB) approximation for populations with strong and weak Allee effects. An exact solution for the mean time to extinction can be found via a recursive equation for special cases of the stochastic dyna…
The extinction time of an isolated population can be exponentially reduced by a periodic modulation of its environment. We investigate this effect using, as an example, a stochastic branching-annihilation process with a time-dependent branching rate. The population extinction is treated in eikonal approximation, where it is described as an instanton trajectory of a proper reaction Hamiltonian. The modulation of the environment perturbs this trajectory and synchronizes it with the modulation phase. We calculate the corresponding change in the action along the instanton using perturbation techni…
How high should be the rate of immigration into a stochastic population in order to significantly reduce the probability of observing the population extinct? Is there any relation between the population size distributions with and without immigration? Under what conditions can one justify the simple patch occupancy models which ignore the population distribution and its dynamics in a patch, and treat a patch simply as either occupied or empty? We address these questions by exactly solving a simple stochastic model obtained by adding a steady immigration to a variant of the Verhulst model: a pr…
We consider non-demographic noise in the form of uncertainty in the reaction step size, and reveal a dramatic effect this noise may have on the stability of self-regulating populations. Employing the reaction scheme mA->kA, but allowing, e.g., the product number k to be a-priori unknown and sampled from a given distribution, we show that such non-demographic noise can greatly reduce the population's extinction risk compared to the fixed k case. Our analysis is tested against numerical simulations, and by using empirical data of different species, we argue that certain distributions may be more…
We investigate extinction of a long-lived self-regulating stochastic population, caused by intrinsic (demographic) noise. Extinction typically occurs via one of two scenarios depending on whether the absorbing state n=0 is a repelling (scenario A) or attracting (scenario B) point of the deterministic rate equation. In scenario A the metastable stochastic population resides in the vicinity of an attracting fixed point next to the repelling point n=0. In scenario B there is an intermediate repelling point n=n_1 between the attracting point n=0 and another attracting point n=n_2 in the vicinity o…
We investigate how a catastrophic event (modeled as a temporary fall of the reproduction rate) increases the extinction probability of an isolated self-regulated stochastic population. Using a variant of the Verhulst logistic model as an example, we combine the probability generating function technique with an eikonal approximation to evaluate the exponentially large increase in the extinction probability caused by the catastrophe. This quantity is given by the eikonal action computed over "the optimal path" (instanton) of an effective classical Hamiltonian system with a time-dependent Hamilto…
Many species are unsustainable at small population densities (Allee Effect), i.e., below a threshold named Allee threshold, the population decreases instead of growing. In a closed local population, environmental fluctuations always lead to extinction. Here, we show how, in spatially extended habitats, dispersal can lead to a sustainable population in a region, provided the amplitude of environmental fluctuations is below an extinction threshold. We have identified two types of sustainable populations: high-density and low-density populations (through a mean-field approximation, valid in the l…
Mathematical models of population extinction have a variety of applications in such areas as ecology, paleontology and conservation biology. Here we propose and investigate two types of sub-exponential models of population extinction.The results of performed analysis show that the principle of minimum of information loss is the underlying law for the evolution of a broad class of models of population extinction. Finally, we propose a possible application of this modeling framework to mechanisms underlying time perception.
In recent years non-demographic variability has been shown to greatly affect dynamics of stochastic populations. For example, non-demographic noise in the form of a bursty reproduction process with an a-priori unknown burst size, or environmental variability in the form of time-varying reaction rates, have been separately found to dramatically impact the extinction risk of isolated populations. In this work we investigate the extinction risk of an isolated population under the combined influence of these two types of non-demographic variation. Using the so-called momentum-space WKB approach we…
We study a generic reaction-diffusion model for single-species population dynamics that includes reproduction, death, and competition. The population is assumed to be confined in a refuge beyond which conditions are so harsh that they lead to certain extinction. Standard continuum mean field models in one dimension yield a critical refuge length L_c such that a population in a refuge larger than this is assured survival. Herein we extend the model to take into account the discreteness and finiteness of the population, which leads us to a stochastic description. We present a particular critical…
Population genetics struggles to model extinction; standard models track the relative rather than absolute fitness of genotypes, while the exceptions describe only the short-term transition from imminent doom to evolutionary rescue. But extinction can result from failure to adapt not only to catastrophes, but also to a backlog of environmental challenges. We model long-term evolution to long series of small challenges, where fitter populations reach higher population sizes. The population's long-term fitness dynamic is well approximated by a simple stochastic Markov chain model. Long-term pers…
Multiple-scale mobility is ubiquitous in nature and has become instrumental for understanding and modeling animal foraging behavior. However, the impact of individual movements on the long-term stability of populations remains largely unexplored. We analyze deterministic and stochastic Lotka Volterra systems, where mobile predators consume scarce resources (prey) confined in patches. In fragile systems (that is, those unfavorable to species coexistence), the predator species has a maximized abundance and is resilient to degraded prey conditions when individual mobility is multiple scaled. With…
We consider control of reaction and population systems by deterministically imposed transitions between the states with different numbers of particles or individuals. Even where the imposed transitions are significantly less frequent than spontaneous transitions, they can exponentially strongly modify the rates of rare events, including switching between metastable states or population extinction. We also study optimal control of rare events, and specifically, optimal control of disease extinction for a limited vaccine supply. A comparison is made with control of rare events by modulating the …
Species extinction occurs regularly and unavoidably in ecological systems. The time scales for extinction can broadly vary and inform on the ecosystem's stability. We study the spatio-temporal extinction dynamics of a paradigmatic population model where three species exhibit cyclic competition. The cyclic dynamics reflects the non-equilibrium nature of the species interactions. While previous work focusses on the coarsening process as a mechanism that drives the system to extinction, we found that unexpectedly the dynamics to extinction is much richer. We observed three different types of dyna…
Competitive birth-death processes often exhibit an oscillatory behavior. We investigate a particular case where the oscillation cycles are marginally stable on the mean-field level. An iconic example of such a system is the Lotka-Volterra model of predator-prey competition. Fluctuation effects due to discreteness of the populations destroy the mean-field stability and eventually drive the system toward extinction of one or both species. We show that the corresponding extinction time scales as a certain power-law of the population sizes. This behavior should be contrasted with the extinction of…
Population extinction is a rare event which requires overcoming an effective barrier. We show that the extinction rate can be fragile: a small change in the system parameters leads to an exponentially strong change of the rate, with the barrier height depending on the parameters nonanalytically. General conditions of the fragility are established. The fragility is found in one of the best-known models of epidemiology, the SIS model. The analytical expressions are compared with simulations.
Theoretical ecologists have long sought to understand how the persistence of populations depends on biotic and abiotic factors. Classical work showed that demographic stochasticity causes the mean time to extinction to increase exponentially with population size, whereas variation in environmental conditions can lead to a power law scaling. Recent work has focused especially on the influence of the autocorrelation structure ("color") of environmental noise. In theoretical physics, there is a burst of research activity in analyzing large fluctuations in stochastic population dynamics. This rese…
We study inhomogeneous host-pathogen dynamics to model the global amphibian population extinction in a lake basin system. The lake basin system is modeled as quenched disorder. In this model we show that once the pathogen arrives at the lake basin it spreads from one lake to another, eventually spreading to the entire lake basin system in a wave like pattern. The extinction time has been found to depend on the steady state host population and pathogen growth rate. Linear estimate of the extinction time is computed. The steady state host population shows a threshold behavior in the interaction …
We present an explicit unified stochastic model of fluctuations in population size due to random birth, death, density-dependent competition and environmental fluctuations. Stochastic dynamics provide insight into small populations, including processes such as extinction, that cannot be correctly treated by deterministic methods. We present exact analytical and simulation-based results for extinction times of our stochastic model and compare the different effects of environmental stochasticity and intrinsic demographic stochasticity. We use both the discrete master equation approach and an exa…
Extinction appears ubiquitously in many fields, including chemical reactions, population biology, evolution, and epidemiology. Even though extinction as a random process is a rare event, its occurrence is observed in large finite populations. Extinction occurs when fluctuations due to random transitions act as an effective force which drives one or more components or species to vanish. Although there are many random paths to an extinct state, there is an optimal path that maximizes the probability to extinction. In this article, we show that the optimal path is associated with the dynamical sy…
We introduce a new model for plant metapopulations with a seed bank component, living in a fragmented environment in which local extinction events are frequent. This model is an intermediate between population dynamics models with a seed bank component, based on the classical Wright-Fisher model, and Stochastic Patch Occupancy Models (SPOMs) used in metapopulation ecology. Its main feature is the use of "ghost" individuals, which can reproduce but with a very strong selective disadvantage against "real" individuals, to artificially ensure a constant population size. We show the existence of an…
Understanding the mechanisms governing population extinctions is of key importance to many problems in ecology and evolution. Stochastic factors are known to play a central role in extinction, but the interactions between a population's demographic stochasticity and environmental noise remain poorly understood. Here, we model environmental forcing as a stochastic fluctuation between two states, one with a higher death rate than the other. We find that in general there exists a rate of fluctuations that minimizes the mean time to extinction, a phenomenon previously dubbed "resonant activation."…
The question of whether a population will persist or go extinct is of key interest throughout ecology and biology. Various mathematical techniques allow us to generate knowledge regarding individual behaviour, which can be analysed to obtain predictions about the ultimate survival or extinction of the population. A common model employed to describe population dynamics is the lattice-based random walk model with crowding (exclusion). This model can incorporate behaviour such as birth, death and movement, while including natural phenomena such as finite size effects. Performing sufficiently many…
Species extinction is a core process that affects the diversity of life on Earth. Competition between species in a population is considered by ecological niche-based theories as a key factor leading to different severity of species extinctions. There are population dynamics models that describe a simple and easily understandable mechanism for resource competition. However, these models can not efficiently characterize and quantify new emergent extinctions in a large population appearing due to environmental forcing. To address this issue we develop a stochastic physics-inspired approach to ana…
Motivated by modeling the dynamics of a population living in a flowing medium where the environmental factors are random in space, we have studied an asymmetric variant of the one-dimensional contact process, where the quenched random reproduction rates are systematically greater in one direction than in the opposite one. The spatial disorder turns out to be a relevant perturbation but, according to results of Monte Carlo simulations, the behavior of the model at the extinction transition is different from the (infinite randomness) critical behavior of the disordered, symmetric contact process…
In this work we suggest and consider an original, simple mathematical model of a "quasi-rapid" extinction population dynamics. It describes a decrease and final extinction of the population of one prey species by a "quasi-rapid" interaction with one predator species with increasing population. This "quasi-rapid" interaction means ecologically that prey species behaves practically quite passively (since there is no time for any reaction, i.e. defense), like an appropriate environment, in respect to "quasi-rapid" activity of the predator species that can have different "quasi-rapid" hunting abil…
Time-dependent distribution of the global extinction of megafauna is compared with the growth of human population. There is no correlation between the two processes. Furthermore, the size of human population and its growth rate were far too small to have any significant impact on the environment and on the life of megafauna.
Computer simulations carried out by Alroy (2001) are examined. Contrary to the claim of their Author, there is no convincing evidence that the extinction of megafauna was caused by humans. Intentionally or unintentionally, attempt was made to force the human-induced extinction of megafauna by assuming an absurdly fast growth of the hypothetical human population in North America. The assumed growth rate was around two-orders of magnitude larger than normally expected. It is well known that the past growth of human population was slow, but in these simulations, the growth of the hypothetical hum…
Most infectious diseases including more than half of known human pathogens are not restricted to just one host, yet much of the mathematical modeling of infections has been limited to a single species. We investigate consequences of a single epidemic propagating in multiple species and compare and contrast it with the endemic steady state of the disease. We use the two-species Susceptible-Infected-Recovered (SIR) model to calculate the severity of post-epidemic collapses in populations of two host species as a function of their initial population sizes, the times individuals remain infectious,…
Recently, a first step was made by the authors towards a systematic investigation of the effect of reaction-step-size noise - uncertainty in the step size of the reaction - on the dynamics of stochastic populations. This was done by investigating the effect of bursty influx on the switching dynamics of stochastic populations. Here we extend this formalism to account for bursty reproduction processes, and improve the accuracy of the formalism to include subleading-order corrections. Bursty reproduction appears in various contexts, where notable examples include bursty viral production from infe…
In large but finite populations, weak demographic stochasticity due to random birth and death events can lead to population extinction. The process is analogous to the escaping problem of trapped particles under random forces. Methods widely used in studying such physical systems, for instance, Wentzel-Kramers-Brillouin (WKB) and Fokker-Planck methods, can be applied to solve similar biological problems. In this article, we comparatively analyse applications of WKB and Fokker-Planck methods to some typical stochastic population dynamical models, including the logistic growth, endemic SIR, pred…
The question of whether biological populations survive or are eventually driven to extinction has long been examined using mathematical models. In this work we study population survival or extinction using a stochastic, discrete lattice-based random walk model where individuals undergo movement, birth and death events. The discrete model is defined on a two-dimensional hexagonal lattice with periodic boundary conditions. A key feature of the discrete model is that crowding effects are introduced by specifying two different crowding functions that govern how local agent density influences movem…
We analyse a stochastic SIS epidemic amongst a finite population partitioned into households. Since the population is finite, the epidemic will eventually go extinct, i.e., have no more infectives in the population. We study the effects of population size and within household transmission upon the time to extinction. This is done through two approximations. The first approximation is suitable for all levels of within household transmission and is based upon an Ornstein-Uhlenbeck process approximation for the diseases fluctuations about an endemic level relying on a large population. The second…
We study bifurcations in a spatially extended nonlinear system representing population dynamics with the help of analytic calculations based on the time-independent Schrödinger equation for a quantum particle subjected to a uniform gravitational field. Despite the linear character of the Schrödinger equation, the result we obtain helps in the understanding of the onset of abrupt transitions leading to extinction of biological populations. The result is expressed in terms of Airy functions and sheds light on the behavior of bacteria in a Petri dish as well as of large animals such as rodents mo…
In this study, spatial stochastic and logistic model (SSLM) describing dynamics of a population of a certain species was analysed. The behaviour of the extinction threshold as a function of model parameters was studied. More specifically, we studied how the critical values for the model parameters that separate the cases of extinction and persistence depend on the spatial scales of the competition and dispersal kernels. We compared the simulations and analytical results to examine if and how the mathematical approximations break down at the vicinity of the extinction threshold, and found a fun…
Comprehensive models of stochastic, clonally reproducing populations are defined in terms of general branching processes, allowing birth during maternal life, as for higher organisms, or by splitting, as in cell division. The populations are assumed to start small, by mutation or immigration, reproduce supercritically while smaller than the habitat carrying capacity but subcritically above it. Such populations establish themselves with a probability wellknown from branching process theory. Once established, they grow up to a band around the carrying capacity in a time that is logarithmic in th…
Habitat destruction threatens the viability of many populations, but its full consequences can take considerable time to unfold. Much of the discourse surrounding extinction debts--the number of species that persist transiently following habitat loss, despite being headed for extinction--frames ultimate population crashes as the means of settling the debt. However, slow population decline also opens an opportunity to repay the debt by restoring habitat. The timing necessary for such habitat restoration to rescue a population from extinction has not been well studied. Here we determine habitat …
Understanding the spread of diseases through complex networks is of great interest where realistic, heterogeneous contact patterns play a crucial role in the spread. Most works have focused on mean-field behavior -- quantifying how contact patterns affect the emergence and stability of (meta)stable endemic states in networks. On the other hand, much less is known about longer time scale dynamics, such as disease extinction, whereby inherent process stochasticity and contact heterogeneity interact to produce large fluctuations that result in the spontaneous clearance of infection. Here we show …
In the interest of conservation, the importance of having a large habitat available for a species is widely known. Here, we introduce a lattice-based model for a population and look at the importance of fluctuations as well as that of the population density, particularly with respect to Allee effects. We examine the model analytically and by Monte Carlo simulations and find that, while the size of the habitat is important, there exists a critical population density below which extinction is assured. This has large consequences with respect to conservation, especially in the design of habitats …
We investigate stochastic extinction in an epidemic model and the impact of random vaccinations in large populations formulated in terms of an optimal escape path. We find that different random vaccination strategies can have widely different results in decreasing expected time till extinction, for the same total amount of vaccines used. Vaccination strategies are considered in terms of two parameters: average frequency of vaccinations, given by $γ$, and the amplitude of the vaccinations, $ε$, where $ε\ll 1$ refers to the proportion of the population being vaccinated at some particular instant…
Populations of competing biological species exhibit a fascinating interplay between the nonlinear dynamics of evolutionary selection forces and random fluctuations arising from the stochastic nature of the interactions. The processes leading to extinction of species, whose understanding is a key component in the study of evolution and biodiversity, are influenced by both of these factors. In this paper, we investigate a class of stochastic population dynamics models based on generalized Lotka-Volterra systems. In the case of neutral stability of the underlying deterministic model, the impact o…
Interactions in ecological communities are inherently nonlinear and can lead to complex population dynamics including irregular fluctuations induced by chaos. Chaotic population dynamics can exhibit violent oscillations with extremely small or large population abundances that might cause extinction and recurrent outbreaks, respectively. We present a simple method that can guide management efforts to prevent crashes, peaks, or any other undesirable state. At the same time, the irregularity of the dynamics can be preserved when chaos is desirable for the population. The control scheme is easy to…
We study the evolution of cooperation as a birth-death process in spatially extended populations. The benefit from the altruistic behavior of a cooperator is implemented by decreasing the death rate of its direct neighbors. The cost of cooperation is the increase of a cooperator's death rate proportional to the number of its neighbors. When cooperation has higher cost than benefit, cooperators disappear. Then the dynamics reduces to the contact process with defectors as the single particle type. Increasing the benefit-cost ratio above 1, the extinction transition of the contact process splits …
Understanding the conditions ensuring the persistence of a population is an issue of primary importance in population biology. The first theoretical approach to the problem dates back to the 50's with the KiSS (after Kierstead, Slobodkin and Skellam) model, namely a continuous reaction-diffusion equation for a population growing on a patch of finite size $L$ surrounded by a deadly environment with infinite mortality -- i.e. an oasis in a desert. The main outcome of the model is that only patches above a critical size allow for population persistence. Here, we introduce an individual-based anal…
