Splitting trees with neutral Poissonian mutations I: Small families

We consider a neutral dynamical model of biological diversity, where individuals live and reproduce independently. They have i.i.d. lifetime durations (which are not necessarily exponentially distributed) and give birth (singly) at constant rate b. Such a genealogical tree is usually called a splitting tree [9], and the population counting process (N_t;t≥0) is a homogeneous, binary Crump-Mode-Jagers process.We assume that individuals independently experience mutations at constant rate θ during their lifetimes, under the infinite-alleles assumption: each mutation instantaneously confers a brand new type, called an allele, to its carrier. We are interested in the allele frequency spectrum at time t, i.e., the number A(t) of distinct alleles represented in the population at time t, and more specifically, the numbers A(k,t) of alleles represented by k individuals at time t, k=1,2,…,N_t.We mainly use two classes of tools: coalescent point processes, as defined in [15], and branching processes counted by random characteristics, as defined in [11] and [13]. We provide explicit formulae for the expectation of A(k,t) conditional on population size in a coalescent point process, which apply to the special case of splitting trees. We separately derive the a.s. limits of A(k,t)/N_t and of A(t)/N_t thanks to random characteristics, in the same vein as in [19].Last, we separately compute the expected homozygosity by applying a method introduced in [14], characterizing the dynamics of the tree distribution as the origination time of the tree moves back in time, in the spirit of backward Kolmogorov equations.     

Evolution in predator–prey systems

We study the adaptive dynamics of predator–prey systems modeled by a dynamical system in which the traits of predators and prey are allowed to evolve by small mutations. When only the prey are allowed to evolve, and the size of the mutational change tends to 0, the system does not exhibit long term prey coexistence and the trait of the resident prey type converges to the solution of an ODE. When only the predators are allowed to evolve, coexistence of predators occurs. In this case, depending on the parameters being varied, we see that (i) the number of coexisting predators remains tight and the differences in traits from a reference species converge in distribution to a limit, or (ii) the number of coexisting predators tends to infinity, and we calculate the asymptotic rate at which the traits of the least and most “fit” predators in the population increase. This last result is obtained by comparison with a branching random walk killed to the left of a linear boundary and a finite branching–selection particle system.     

Asymptotic results for coalescent processes without proper frequencies and applications to the two-parameter Poisson–Dirichlet coalescent

The class of coalescent processes with simultaneous multiple collisions (Ξ$\Xi$-coalescents) without proper frequencies is considered. We study the asymptotic behavior of the external branch length, the total branch length and the number of mutations on the genealogical tree as the sample size n$n$ tends to infinity. The limiting random variables arising are characterized via exponential integrals of the subordinator associated with the frequency of singletons of the coalescent. The proofs are based on decompositions into external and internal branches. The asymptotics of the external branches is treated via the method of moments. The internal branches do not contribute to the limiting variables since the number _Cn$C_n$ of collisions for coalescents without proper frequencies is asymptotically negligible compared to n$n$. The results are applied to the two-parameter Poisson–Dirichlet coalescent indicating that this particular class of coalescent processes in many respects behaves approximately as the star-shaped coalescent.     

Williams’ decomposition of the Lévy continuum random tree and simultaneous extinction probability for populations with neutral mutations

We consider an initial Eve-population and a population of neutral mutants, such that the total population dies out in finite time. We describe the evolution of the Eve-population and the total population with continuous state branching processes, and the neutral mutation procedure can be seen as an immigration process with intensity proportional to the size of the population. First we establish a Williams’ decomposition of the genealogy of the total population given by a continuum random tree, according to the ancestral lineage of the last individual alive. This allows us to give a closed formula for the probability of simultaneous extinction of the Eve-population and the total population.     

A diffusive predator-prey model with a protection zone

In this paper we study the effects of a protection zone Ω₀ for the prey on a diffusive predator-prey model with Holling type II response and no-flux boundary condition. We show the existence of a critical patch size described by the principal eigenvalue of the Laplacian operator over Ω₀ with homogeneous Dirichlet boundary conditions. If the protection zone is over the critical patch size, i.e., if is less than the prey growth rate, then the dynamics of the model is fundamentally changed from the usual predator-prey dynamics; in such a case, the prey population persists regardless of the growth rate of its predator, and if the predator is strong, then the two populations stabilize at a unique coexistence state. If the protection zone is below the critical patch size, then the dynamics of the model is qualitatively similar to the case without protection zone, but the chances of survival of the prey species increase with the size of the protection zone, as generally expected. Our mathematical approach is based on bifurcation theory, topological degree theory, the comparison principles for elliptic and parabolic equations, and various elliptic estimates.     

A bivariate non-homogeneous birth and death model for predator–prey interactions

We propose a bivariate non-homogeneous birth and death process as a model for predator–prey interactions. Its expectation is periodic, as it is a solution to the classical Lotka–Volterra system. Moreover, the mean age at extinction, as defined in Kendall (1948), is infinite.     

Detection of cellular aging in a Galton–Watson process

We consider the bifurcating Markov chain model introduced by Guyon to detect cellular aging from cell lineage. To take into account the possibility for a cell to die, we use an underlying super-critical binary Galton–Watson process to describe the evolution of the cell lineage. We give in this more general framework a weak law of large number, an invariance principle and thus fluctuation results for the average over all individuals in a given generation, or up to a given generation. We also prove that the fluctuations over each generation are independent. Then we present the natural modifications of the tests given by Guyon in cellular aging detection within the particular case of the auto-regressive model.     

Qualitative analysis of a predator-prey model with Holling type II functional response incorporating a prey refuge

We study a predator-prey model with Holling type II functional response incorporating a prey refuge under homogeneous Neumann boundary condition. We show the existence and non-existence of non-constant positive steady-state solutions depending on the constant m∈(0,1], which provides a condition for protecting (1−m)u of prey u from predation. Moreover, we investigate the asymptotic behavior of spacially inhomogeneous solutions and the local existence of periodic solutions.     

The Markov structure of population growth

Some problems concerning the development of general models of population growth are examined, with particular reference to Markovian modelling. The tenet of the paper is that such models can be more realistically attempted by focusing on temporal rather than spatial modifications. Specifically, the time concept considered is linked to the dependent structure inherent in the partial order of descent from mother to child. The author attempts to develop "a general theory of populations of individuals under what might be called free reproduction. Hence, the only dependence assumed between individuals is that from mothers to children." He suggests that the results "can be translated into assertions about evolution in real, physical time and also about the final, stable or balanced, composition of populations, over ages, types, family structure, and many other aspects of populations."     

Asymptotic profiles of the positive steady state for an SIS epidemic reaction-diffusion model. Part I

To capture the impact of spatial heterogeneity of environment and movement of individuals on the persistence and extinction of a disease, Allen et al. in [L.J.S. Allen, B.M. Bolker, Y. Lou, A.L. Nevai, Asymptotic profiles of the steady states for an SIS epidemic reaction-diffusion model, Discrete Contin. Dyn. Syst. Ser. A 21 (1) (2008) 1-20] proposed a spatial SIS (susceptible-infected-susceptible) reaction-diffusion model, and studied the existence, uniqueness and particularly the asymptotic behavior of the endemic equilibrium as the diffusion rate of the susceptible individuals goes to zero in the case where a so-called low-risk subhabitat is created. In this work, we shall provide further understanding of the impacts of large and small diffusion rates of the susceptible and infected population on the persistence and extinction of the disease, which leads us to determine the asymptotic behaviors of the endemic equilibrium when the diffusion rate of either the susceptible or infected population approaches to infinity or zero in the remaining cases. Consequently, our results reveal that, in order to eliminate the infected population at least in low-risk area, it is necessary that one will have to create a low-risk subhabitat and reduce at least one of the diffusion rates to zero. In this case, our results also show that different strategies of controlling the diffusion rates of individuals may lead to very different spatial distributions of the population; moreover, once the spatial environment is modified to include a low-risk subhabitat, the optimal strategy of eradicating the epidemic disease is to restrict the diffusion rate of the susceptible individuals rather than that of the infected ones.     

Topics on phylogenetic algebraic geometry

This expository work deals with the main aspects of Phylogenetic Algebraic Geometry. In particular, we will focus our attention on the technique of flattening of a n$n$-dimensional tensor. Our interest in flattening is due to the fact that this is strictly related to the study of secant varieties of Segre varieties.     

Limit theorems for strongly and intermediately supercritical branching processes in random environment with linear fractional offspring distributions

In the present paper, we characterize the behavior of supercritical branching processes in random environment with linear fractional offspring distributions, conditioned on having small, but positive values at some large generation. As it has been noticed in previous works, there is a phase transition in the behavior of the process. Here, we examine the strongly and intermediately supercritical regimes The main result is a conditional limit theorem for the rescaled associated random walk in the intermediately case.     

On the length of an external branch in the Beta-coalescent

In this paper, we consider Beta(2−α,α)$(2-\alpha ,\alpha )$ (with 1<α<2$1<\alpha <2$) and related Λ$\Lambda$-coalescents. If T⁽ⁿ⁾$T^{\left(n\right)}$ denotes the length of a randomly chosen external branch of the n$n$-coalescent, we prove the convergence of n^α−1T⁽ⁿ⁾$n^{\alpha -1}{T}^{\left(n\right)}$ when n$n$ tends to ∞$\infty$, and give the limit. To this aim, we give asymptotics for the number σ⁽ⁿ⁾${\sigma }^{\left(n\right)}$ of collisions which occur in the n$n$-coalescent until the end of the chosen external branch, and for the block counting process associated with the n$n$-coalescent.     

A chain of evolution algebras

We introduce a notion of chain of evolution algebras. The sequence of matrices of the structural constants for this chain of evolution algebras satisfies an analogue of Chapman-Kolmogorov equation. We give several examples (time homogenous, time non-homogenous, periodic, etc.) of such chains. For a periodic chain of evolution algebras we construct a continuum set of non-isomorphic evolution algebras and show that the corresponding discrete time chain of evolution algebras is dense in the set. We obtain a criteria for an evolution algebra to be baric and give a concept of a property transition. For several chains of evolution algebras we describe the behavior of the baric property depending on the time. For a chain of evolution algebras given by the matrix of a two-state evolution we define a baric property controller function and under some conditions on this controller we prove that the chain is not baric almost surely (with respect to Lebesgue measure). We also construct examples of the almost surely baric chains of evolution algebras. We show that there are chains of evolution algebras such that if it has a unique (resp. infinitely many) absolute nilpotent element at a fixed time, then it has unique (resp. infinitely many) absolute nilpotent element any time; also there are chains of evolution algebras which have not such property. For an example of two dimensional chain of evolution algebras we give the full set of idempotent elements and show that for some values of parameters the number of idempotent elements does not depend on time, but for other values of parameters there is a critical time t_c such that the chain has only two idempotent elements if time t?t_c and it has four idempotent elements if time t<t_c.     

Perturbation of Transition Functions and a Feynman-Kac Formula for the Incorporation of Mortality

Markov transition kernels are perturbed by output kernels with a special emphasis on building mortality into structured population models. A Feynman-Kac formula is derived which illustrates the interplay of mortality with a Markov process associated with the unperturbed kernel. partially supported by NSF grants DMS-0314529 and SES-0345945 partially supported by NSF grants DMS-9706787 and DMS-0314529     

Sharpness versus robustness of the percolation transition in 2d contact processes

We study versions of the contact process with three states, and with infections occurring at a rate depending on the overall infection density. Motivated by a model described in Kéfi et al. (2007) for vegetation patterns in arid landscapes, we focus on percolation under invariant measures of such processes. We prove that the percolation transition is sharp (for one of our models this requires a reasonable assumption). This is shown to contradict a form of ‘robust critical behaviour’ with power law cluster size distribution for a range of parameter values, as suggested in Kéfi et al. (2007).     

Localization for branching random walks in random environment

We consider branching random walks in d$d$-dimensional integer lattice with time–space i.i.d. offspring distributions. This model is known to exhibit a phase transition: If d≥3$d\ge 3$ and the environment is “not too random”, then, the total population grows as fast as its expectation with strictly positive probability. If, on the other hand, d≤2$d\le 2$, or the environment is “random enough”, then the total population grows strictly slower than its expectation almost surely. We show the equivalence between the slow population growth and a natural localization property in terms of “replica overlap”. We also prove a certain stronger localization property, whenever the total population grows strictly slower than its expectation almost surely.