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Charline Smadi

Publications and source records attributed to Charline Smadi.

At least 19 recordsLinked to original sources
arXiv2026

When evolution realizes large deviations of fitness: from speciation to dynamical phase transitions

We explore the connection between evolution and large-deviation theory. To do so, we study evolutionary dynamics in which individuals experience mutations, reproduction, and selection using variants of the Moran model. We show that, in the large population size limit, the impact of reproduction and selection amounts to realizing a large-deviation dynamics for the non-interacting random walk in which individuals simply explore the genome landscape due to mutations. This mapping, which holds at all times, allows us to recast transitions in the population genome distribution as dynamical phase transitions, which can then be studied using the toolbox of large-deviation theory. Finally, we show that the mapping extends beyond the class of Moran models.

q-bio.PE↗
arXiv2025

The tournament ratchet's clicktime process, and metastability in a Moran model

Muller's ratchet, in its prototype version, models a haploid, asexual population whose size~$N$ is constant over the generations. Slightly deleterious mutations are acquired along the lineages at a constant rate, and individuals carrying less mutations have a selective advantage. In the classical variant, an individual's selective advantage is proportional to the difference between the population average and the individual's mutation load, whereas in the ratchet with {\em tournament selection} only the signs of the differences of the individual mutation loads matter. In a parameter regime which leads to slow clicking (i.e. to a loss of the currently fittest class at a rate $\ll 1/N$) we prove that the rescaled process of click times of the tournament ratchet converges as $N\to \infty$ to a Poisson process. Central ingredients in the proof are a thorough analysis of the metastable behaviour of a two-type Moran model with selection and deleterious mutation (which describes the size of the fittest class up to its extinction time) and a lower estimate on the size of the new fittest class at a clicktime.

math.PR↗
arXiv2025

Dynamics of Two Species with Density-Dependent Interactions in a Mutualistic Context

Mutualistic interactions, where individuals from different species can benefit from each other, are widespread across ecosystems. This study develops a general deterministic model of mutualism involving two populations, assuming that mutualism may involve both costs and benefits for the interacting individuals, leading to density-dependent effects on the dynamics of the two species. This framework aims at generalizing pre-existing models, by allowing the ecological interactions to transition from mutualistic to parasitic when the respective densities of interacting species change. Through ordinary differential equations and phase portrait analysis, we derive general principles governing these systems, identifying sufficient conditions for the emergence of certain dynamic behaviors. In particular, we show that limit cycles can arise when interactions include parasitic phases but are absent in strictly mutualistic regimes. This framework provides a general approach for characterizing the population dynamics of interacting species and highlights the effect of the transitions from mutualism to parasitism due to density dependence.

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arXiv2025

Spinal study of a population model for colonial species with interactions and environmental noise

We introduce and study a stochastic model for the dynamics of colonial species, which reproduce through fission or fragmentation. The fission rate depends on the relative sizes of colonies in the population, and the growth rate of colonies is influenced by intrinsic and environmental stochasticities. Our setting thus captures the effect of an external noise, correlating the trait dynamics of all colonies. In particular, we study the effect of the strength of this correlation on the distribution of resources between colonies. We then extend this model to a large class of structured branching processes with interactions in which the particle type evolves according to a diffusion. The branching and death rates are general functions of the whole population. In this framework, we derive a $\psi$-spine construction and a Many-to-One formula, extending previous works on interacting branching processes. Using this spinal construction, we also propose an alternative simulation method and illustrate its efficiency on the colonial population model. The extended framework we propose can model various ecological systems with interactions, and individual and environmental noises.

math.PR↗
arXiv2024

Parasite infection in a cell population: role of the partitioning kernel

We consider a cell population subject to a parasite infection. Cells divide at a constant rate and, at division, share the parasites they contain between their two daughter cells. The sharing may be asymmetrical, and its law may depend on the quantity of parasites in the mother. Cells die at a rate which may depend on the quantity of parasites they carry, and are also killed when this quantity explodes. We study the survival of the cell population as well as the mean quantity of parasites in the cells, and focus on the role of the parasites partitioning kernel at division.

math.PR↗
arXiv2023

Quasi-equilibria and click times for a variant of Muller's ratchet

Consider a population of $N$ individuals, each of them carrying a type in $\mathbb N_0$. The population evolves according to a Moran dynamics with selection and mutation, where an individual of type $k$ has the same selective advantage over all individuals with type $k' > k$, and type $k$ mutates to type $k+1$ at a constant rate. This model is thus a variation of the classical Muller's ratchet: there the selective advantage is proportional to $k'-k$. For a regime of selection strength and mutation rates which is between the regimes of weak and strong selection/mutation, we obtain the asymptotic rate of the {\em click times} of the ratchet (i.e. the times at which the hitherto minimal (`best') type in the population is lost), and reveal the quasi-stationary type frequency profile between clicks. The large population limit of this profile is characterized as the normalized attractor of a ``dual'' hierarchical multitype logistic system, and also via the distribution of the final minimal displacement in a branching random walk with one-sided steps. An important role in the proofs is played by a graphical representation of the model, both forward and backward in time, and a central tool is the ancestral selection graph decorated by mutations.

math.PR↗
arXiv2023

Spread of parasites affecting death and division rates in a cell population

We introduce a general class of branching Markov processes for the modelling of a parasite infection in a cell population. Each cell contains a quantity of parasites which evolves as a diffusion with positive jumps. The drift, diffusive function and positive jump rate of this quantity of parasites depend on its current value. The division rate of the cells also depends on the quantity of parasites they contain. At division, a cell gives birth to two daughter cells and shares its parasites between them. Cells may also die, at a rate which may depend on the quantity of parasites they contain. We study the long-time behaviour of the parasite infection.

math.PR↗
arXiv2023

Muller's ratchet in a near-critical regime: tournament versus fitness proportional selection

Muller's ratchet, in its prototype version, models a haploid, asexual population whose size~$N$ is constant over the generations. Slightly deleterious mutations are acquired along the lineages at a constant rate, and individuals carrying less mutations have a selective advantage. The classical variant considers {\it fitness proportional} selection, but other fitness schemes are conceivable as well. Inspired by the work of Etheridge et al. ([EPW09]) we propose a parameter scaling which fits well to the ``near-critical'' regime that was in the focus of [EPW09] (and in which the mutation-selection ratio diverges logarithmically as $N\to \infty$). Using a Moran model, we investigate the``rule of thumb'' given in [EPW09] for the click rate of the ``classical ratchet'' by putting it into the context of new results on the long-time evolution of the size of the best class of the ratchet with (binary) tournament selection, which (other than that of the classical ratchet) follows an autonomous dynamics up to the time of its extinction. In [GSW23] it was discovered that the tournament ratchet has a hierarchy of dual processes which can be constructed on top of an Ancestral Selection graph with a Poisson decoration. For a regime in which the mutation/selection-ratio remains bounded away from 1, this was used in [GSW23] to reveal the asymptotics of the click rates as well as that of the type frequency profile between clicks. We will describe how these ideas can be extended to the near-critical regime in which the mutation-selection ratio of the tournament ratchet converges to 1 as $N\to \infty$.

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arXiv2022

Critical branching processes in random environment with immigration: the size of the only surviving family

We consider a critical branching process $Y_{n}$ in an i.i.d. random environment, in which one immigrant arrives at each generation. Let $% \mathcal{A}_{i}(n)$ be the event that all individuals alive at time $n$ are offspring of the immigrant which joined the population at time $i$. We study the conditional distribution of $Y_{n}$ given $\mathcal{A}_{i}(n)$ when $n$ is large and $i$ follows different asymptotics which may be related to $n$ ($% i$ fixed, close to $n$, or going to infinity but far from $n$).

math.PR↗
arXiv2021

Parasite infection in a cell population with deaths and reinfections

We introduce a model of parasite infection in a cell population, where cells can be infected, either at birth through maternal transmission, from a contact with the parasites reservoir, or because of the parasites released in the cell medium after the lyses of infected cells. Inside the cells and between infection events, the quantity of parasites evolves as a general non linear branching process. We study the long time behaviour of the infection.

math.PR↗
arXiv2021

Extinction rate of continuous state branching processes in critical Lévy environments

We study the speed of extinction of continuous state branching processes in a Lévy environment, where the associated Lévy process oscillates. Assuming that the Lévy process satisfies the Spitzer's condition and the existence of some exponential moments, we extend recent results where the associated branching mechanism was stable. Our study relies on the path analysis of the process together with its environment, when this latter is conditioned to have a non negative running infimum. This approach is inspired from the discrete setting with i.i.d. environment studied in (Afanasyev et al. 2005).

math.PR↗
arXiv2021

Long time behaviour of continuous-state nonlinear branching processes with catastrophes

Motivated by the study of a parasite infection in a cell line, we introduce a general class of Markov processes for the modelling of population dynamics. The population process evolves as a diffusion with positive jumps whose rate is a function of the population size. It also undergoes catastrophic events which kill a fraction of the population, at a rate depending on the population state. We study the long time behaviour of this class of processes.

math.PR↗
arXiv2020

Parasite infection in a cell population with deaths

We introduce a general class of branching Markov processes for the modelling of a parasite infection in a cell population. Each cell contains a quantity of parasites which evolves as a diffusion with positive jumps. The growth rate, diffusive function and positive jump rate of this quantity of parasites depend on its current value. The division rate of the cells also depends on the quantity of parasites they contain. At division, a cell gives birth to two daughter cells and shares its parasites between them. Cells may also die, at a rate which may depend on the quantity of parasites they contain. We study the long time behaviour of the parasite infection. In particular, we are interested in the quantity of parasites in a `typical' cell and on the survival of the cell population. We specifically focus on the influence of two parameters on the probability for the cell population to survive and/or contain the parasite infection: the law of the sharing of the parasites between the daughter cells at division and the form of the division and death rates of the cells as functions of the quantity of parasites they contain.

math.PR↗
arXiv2020

Multidimensional $Λ$-Wright-Fisher processes with general frequency-dependent selection

We construct a constant size population model allowing for general selective interactions and extreme reproductive events. It generalizes the idea of (Krone and Neuhauser 1997) who represented the selection by allowing individuals to sample potential parents in the previous generation before choosing the 'strongest' one, by allowing individuals to use any rule to choose their real parent. Via a large population limit, we obtain a generalisation of $Λ$-Fleming Viot processes allowing for non transitive interactions between types. We provide fixation properties, and give conditions for these processes to be realised as solutions of stochastic differential equations.

math.PR↗
arXiv2020

Stochastic individual-based models with power law mutation rate on a general finite trait space

We consider a stochastic individual-based model for the evolution of a haploid, asexually reproducing population. The space of possible traits is given by the vertices of a (possibly directed) finite graph $G=(V,E)$. The evolution of the population is driven by births, deaths, competition, and mutations along the edges of $G$. We are interested in the large population limit under a mutation rate $μ_K$ given by a negative power of the carrying capacity $K$ of the system: $μ_K=K^{-1/α},α>0$. This results in several mutant traits being present at the same time and competing for invading the resident population. We describe the time evolution of the orders of magnitude of each sub-population on the $\log K$ time scale, as $K$ tends to infinity. Using techniques developed in [Champagnat, Méléard, Tran, 2019] we show that these are piecewise affine continuous functions, whose slopes are given by an algorithm describing the changes in the fitness landscape due to the succession of new resident or emergent types. This work generalises [Kraut, Bovier, 2019] to the stochastic setting, and Theorem 3.2 of [Bovier, Coquille, Smadi, 2018] to any finite mutation graph. We illustrate our theorem by a series of examples describing surprising phenomena arising from the geometry of the graph and/or the rate of mutations.

math.PR↗
arXiv2019

Critical branching processes in random environment with immigration: survival of a single family

We consider a critical branching process in an i.i.d. random environment, in which one immigrant arrives at each generation. We are interested in the event $\mathcal{A}_i(n)$ that all individuals alive at time $n$ are offspring of the immigrant which joined the population at time $i$. We study the asymptotic probability of this event when $n$ is large and $i$ follows different asymptotics which may be related to $n$ ($i$ fixed, close to $n$, or going to infinity but far from $n$). In order to do so, we establish some conditional limit theorems for random walks, which are of independent interest.

math.PR↗
arXiv2019

Critical branching processes in random environment and Cauchy domain of attraction

We are interested in the survival probability of a population modeled by a critical branching process in an i.i.d. random environment. We assume that the random walk associated with the branching process is oscillating and satisfies a Spitzer condition $\mathbf{P}(S_{n}>0)\rightarrow ρ,\ n\rightarrow \infty $, which is a standard condition in fluctuation theory of random walks. Unlike the previously studied case $ρ\in (0,1)$, we investigate the case where the offspring distribution is in the domain of attraction of a stable law with parameter $1$, which implies that $ρ=0$ or $1$. We find the asymptotic behaviour of the survival probability of the population in these two cases.

math.PR↗
arXiv2019

Stochastic dynamics of three competing clones: Conditions and times for invasion, coexistence and fixation

In large clonal populations, several clones generally compete which results in complex evolutionary and ecological dynamics: experiments show successive selective sweeps of favorable mutations as well as long-term coexistence of multiple clonal strains. The mechanisms underlying either coexistence or fixation of several competing strains have rarely been studied altogether. Conditions for coexistence have mostly been studied by population and community ecology, while rates of invasion and fixation have mostly been studied by population genetics. In order to provide a global understanding of the complexity of the dynamics observed in large clonal populations, we develop a stochastic model where three clones compete. Competitive interactions can be intransitive and we suppose that strains enter the population via mutations or rare immigrations. We first describe all possible final states of the population, including stable coexistence of two or three strains, or the fixation of a single strain. Second, we give estimate of the invasion and fixation times of a favorable mutant (or immigrant) entering the population in a single copy. We show that invasion and fixation can be slower or faster when considering complex competitive interactions. Third, we explore the parameter space assuming prior distributions of reproduction, death and competitive rates and we estimate the likelihood of the possible dynamics. We show that when mutations can affect competitive interactions, even slightly, stable coexistence is likely. We discuss our results in the context of the evolutionary dynamics of large clonal populations.

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