arXiv subjects

Jochen Blath

Publications and source records attributed to Jochen Blath.

At least 19 recordsLinked to original sources

arXiv2026

The interplay of selection and dormancy in a Moran model can lead to coexistence of types

In this paper we propose a Moran model that describes the population dynamics of two types: While the first type has a selective advantage during reproduction, the second type can avoid replacement during reproduction with some positive probability by switching temporarily into a dormant state. We investigate the interplay of both evolutionary strategies by studying the invasion dynamics of the dormant type into the resident (selectively advantageous) population in the large population limit of the system. It turns out that the dormancy trait can not only invade and subsequently fixate under suitable parameter assumptions despite its selective disadvantage (a phenomenon that has already been observed in a related context in Blath and T\'obi\'as (2020)), but that there is also a novel regime of stable coexistence of both types due to a frequency-dependent balancing effect that did not arise in the previous setup with Lotka--Volterra type symmetric competition. The emergence of a coexistence regime here rests in part on specific properties of the Moran modelling framework, in particular its fixed overall population size that enforces instant re-colonization after death events, as well as on the (positive) mortality and resuscitation rates of the dormant state. We provide heuristic explanations for the observed types of behaviour and the corresponding proofs, which involve comparisons to suitable branching processes, approximations by dynamical systems, and an analysis of asymptotic behaviour of the latter.

q-bio.PE↗

arXiv2025

Emergence of microbial host dormancy during a persistent virus epidemic

We study a minimal stochastic individual-based model for a microbial population challenged by a persistent (lytic) virus epidemic. We focus on the situation in which the resident microbial host population and the virus population are in stable coexistence upon arrival of a single new ``mutant'' host individual. We assume that this mutant is capable of switching to a reversible state of dormancy upon contact with virions as a means of avoiding infection by the virus. At the same time, we assume that this new dormancy trait comes with a cost, namely a reduced individual reproduction rate. We prove that there is a non-trivial range of parameters where the mutants can nevertheless invade the resident population with strictly positive probability (bounded away from 0) in the large population limit. Given the reduced reproductive rate, such an invasion would be impossible in the absence of either the dormancy trait or the virus epidemic. We explicitly characterize the parameter regime where this emergence of a (costly) host dormancy trait is possible, determine the success probability of a single invader and the typical amount of time it takes the successful mutants to reach a macroscopic population size. We conclude this study by an investigation of the fate of the population after the successful emergence of a dormancy trait. Heuristic arguments and simulations suggest that after successful invasion, either both host types and the virus will reach coexistence, or the mutants will drive the resident hosts to extinction while the virus will stay in the system.

math.PR↗

arXiv2023

On/off super-Brownian motion: Characterization, construction and long-term behaviour

We introduce and construct on/off super-Brownian motion (on/off SBM) as a measure-valued scaling limit of critical on/off branching Brownian motions. The distinguishing feature of this process is that its infinitesimal particles can switch individually into and out of a state of dormancy, in which they neither move nor reproduce. Related dormancy traits have received interest in mathematical population biology recently, introducing memory and delay (in the form of a seed bank) into the corresponding processes. It turns out that the properties of on/off SBM differ significantly from those of classical super-Brownian motion. In particular, the process does not die out in finite time with probability one despite criticality of reproduction. However, the size of the active subpopulation does hit 0 in finite time with positive probability, a result which can be shown using methods from polynomial diffusion theory. We expect distinct behaviour in various other qualitative and quantitative respects, for which we provide heuristics, and conclude with a brief discussion of several directions for future research.

math.PR↗

arXiv2022

The impact of dormancy on evolutionary branching

In this paper, we investigate the consequences of dormancy in the `rare mutation' and `large population' regime of stochastic adaptive dynamics. Starting from an individual-based micro-model, we first derive the polymorphic evolution sequence of the population, based on previous work by Baar and Bovier (2018). After passing to a second `small mutations' limit, we arrive at the canonical equation of adaptive dynamics, and state a corresponding criterion for evolutionary branching, extending a previous result of Champagnat and M\'el\'eard (2011). The criterion allows a quantitative and qualitative analysis of the effects of dormancy in the well-known model of Dieckmann and Doebeli (1999) for sympatric speciation. In fact, a quite intuitive picture merges: Dormancy enlarges the parameter range for evolutionary branching, increases the carrying capacity and niche width of the post-branching sub-populations, and, depending on the model parameters, can either increase or decrease the `speed of adaptation' of populations. Finally, dormancy increases diversity by increasing the genetic distance between subpopulations.

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arXiv2022

The Contact Process with Switching

In this paper, we introduce a type switching mechanism for the Contact Process on the lattice $\mathbb{Z}^d$. That is, we allow the individual particles/sites to switch between two (or more) types independently of one another, and the different types may exhibit specific infection and recovery dynamics. Such type switches can eg.\ be motivated from biology, where 'phenotypic switching' is common among micro-organisms. Our framework includes as special cases systems with switches between 'active' and 'dormant' states (the Contact Process with dormancy, CPD), and the Contact Process in a randomly evolving environment (CPREE) introduced by Broman (2007). The 'standard' multi-type Contact Process (without type-switching) can also be recovered as a limiting case. After constructing the process from a graphical representation, we establish several basic properties that are mostly analogous to the classical Contact Process. We then provide couplings between several variants of the system, which in particular yield the existence of a phase transition. Further, we investigate the effect of the switching parameters on the critical value of the system by providing rigorous bounds obtained from the coupling arguments as well as numerical and heuristic results. Finally, we investigate scaling limits for the process as the switching parameters tend to 0 (slow switching regime) resp.\ $\infty$ (fast switching regime). We conclude with a brief discussion of further model variants and questions for future research.

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arXiv2021

Microbial virus epidemics in the presence of contact-mediated host dormancy

We investigate a stochastic individual-based model for the population dynamics of host-virus systems where the microbial hosts may transition into a dormant state upon contact with virions, thus evading infection. Such a contact-mediated defence mechanism was described in Bautista et al (2015) for an archaeal host, while Jackson and Fineran (2019) and Meeske et al (2019) describe a related, CRISPR-Cas induced, dormancy defense of bacterial hosts to curb phage epidemics. We first analyse the effect of the dormancy-related model parameters on the probability and time of invasion of a newly arriving virus into a resident host population. Given successful invasion in the stochastic system, we then show that the emergence (with high probability) of a persistent virus infection ('epidemic') in a large host population can be determined by the existence of a coexistence equilibrium for the dynamical system arising as the deterministic many-particle limit of our model. This is an extension of a dynamical system considered by Beretta and Kuang (1998) that is known to exhibit a Hopf bifurcation, giving rise to a 'paradox of enrichment'. In our system, we verify that the additional dormancy component can, at least for certain parameter ranges, prevent the associated loss of stability. Finally, we show that the presence of contact-mediated dormancy enables the host population to attain higher equilibrium sizes - while still being able to avoid a persistent epidemic - than host populations without this trait.

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arXiv2021

How the interplay of dormancy and selection affects the wave of advance of an advantageous gene

In this paper we investigate the spread of advantageous genes in two variants of the F-KPP model with dormancy. The first variant, in which dormant individuals do not move in space and instead form "localized seed banks", has recently been introduced in Blath, Hammer and Nie (2020). However, there, only a relatively crude upper bound for the critical speed of potential travelling wave solutions has been provided. The second model variant is new and describes a situation in which the dormant forms of individuals are subject to motion, while the "active" individuals remain spatially static instead. This can be motivated e.g. by spore dispersal of fungi, where the "dormant" spores are distributed by wind, water or insects, while the "active" fungi are locally fixed. For both models, we establish the existence of monotone travelling wave solutions, determine the corresponding critical wave speed in terms of the model parameters, and characterize aspects of the asymptotic shape of the waves depending on the decay properties of the initial condition. Interestingly, the slow-down effect of dormancy on the speed of propagation of beneficial alleles is often more serious in model variant II (the "spore model") than in variant I (the "seed bank model"), and this can be understood mathematically via probabilistic representations of solutions in terms of (two variants of) "on/off branching Brownian motions". Our proofs make rather heavy use of probabilistic tools in the tradition of Watanabe (1967), McKean (1975), Bramson (1978), Neveu (1987), Lalley and Sellke (1987), Champneys et al (1995) and others. However, the two-compartment nature of the model and the special forms of dormancy also pose obstacles to the classical formalism, giving rise to a variety of open research questions that we briefly discuss at the end of the paper.

math.PR↗

arXiv2021

A Stochastic Adaptive Dynamics Model for Bacterial Populations with Mutation, Dormancy and Transfer

This paper introduces a stochastic adaptive dynamics model for the interplay of several crucial traits and mechanisms in bacterial evolution, namely dormancy, horizontal gene transfer (HGT), mutation and competition. In particular, it combines the recent model of Champagnat, M\'el\'eard and Tran (2021) involving HGT with the model for competition-induced dormancy of Blath and T\'obi\'as (2020). Our main result is a convergence theorem which describes the evolution of the different traits in the population on a `doubly logarithmic scale' as piece-wise affine functions. Interestingly, even for a relatively small trait space, the limiting process exhibits a non-monotone dependence of the success of the dormancy trait on the dormancy initiation probability. Further, the model establishes a new `approximate coexistence regime' for multiple traits that has not been observed in previous literature.

math.PR↗

arXiv2020

Population genetic models of dormancy

In the present article, we investigate the effects of dormancy on an abstract population genetic level. We first provide a short review of seed bank models in population genetics, and the role of dormancy for the interplay of evolutionary forces in general, before we discuss two recent paradigmatic models, referring to spontaneous resp. simultaneous switching of individuals between the active and the dormant state. We show that both mechanisms give rise to non-trivial mathematical objects, namely the (continuous) seed bank diffusion and the seed bank diffusion with jumps, as well as their dual processes, the seed bank coalescent and the seed bank coalescent with simultaneous switching.

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arXiv2020

Principles of seed banks: complexity emerging from dormancy

Across the tree of life, populations have evolved the capacity to contend with suboptimal conditions by engaging in dormancy, whereby individuals enter a reversible state of reduced metabolic activity. The resulting seed banks are complex, storing information and imparting memory that gives rise to multi-scale structures and networks spanning collections of cells to entire ecosystems. We outline the fundamental attributes and emergent phenomena associated with dormancy and seed banks, with the vision for a unifying and mathematically based framework that can address problems in the life sciences, ranging from global change to cancer biology.

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arXiv2020

A branching process model for dormancy and seed banks in randomly fluctuating environments

The goal of this article is to contribute towards the conceptual and quantitative understanding of the evolutionary benefits for (microbial) populations to maintain a seed bank (consisting of dormant individuals) when facing fluctuating environmental conditions. To this end, we compare the long term behaviour of `1-type' Bienaym\'e-Galton-Watson branching processes (describing populations consisting of `active' individuals only) with that of a class of `2-type' branching processes, describing populations consisting of `active' and `dormant' individuals. All processes are embedded in an environment changing randomly between `harsh' and `healthy' conditions, affecting the reproductive behaviour of the populations accordingly. For the 2-type branching processes, we consider several different switching regimes between active and dormant states. We also impose overall resource limitations which incorporate the potentially different `production costs' of active and dormant offspring, leading to the notion of `fair comparison' between different populations, and allow for a reproductive trade-off due to the maintenance of the dormancy trait. Our switching regimes include the case where switches from active to dormant states and vice versa happen randomly, irrespective of the state of the environment (`spontaneous switching'), but also the case where switches are triggered by the environment (`responsive switching'), as well as combined strategies. It turns out that there are rather natural scenarios under which either switching strategy can be super-critical, while the others, as well as complete absence of a seed bank, are strictly sub-critical, even under `fair comparison' wrt. available resources. In such a case, we see a clear selective advantage of the super-critical strategy, which is retained even under the presence of a (potentially small) reproductive trade-off. [...]

math.PR↗

arXiv2020

The interplay of dormancy and transfer in bacterial populations: Invasion, fixation and coexistence regimes

We investigate the interplay between two fundamental mechanisms of microbial population dynamics and evolution called dormancy and horizontal gene transfer. The corresponding traits come in many guises and are ubiquitous in microbial communities, affecting their dynamics in important ways. Recently, they have each moved (separately) into the focus of stochastic individual-based modelling (Billiard et al. 2016, 2018; Champagnat, M\'el\'eard and Tran, 2021; Blath and T\'obi\'as 2020). Here, we examine their combined effects in a unified model. Indeed, we consider the (idealized) scenario of two sub-populations, respectively carrying 'trait 1' and 'trait 2', where trait 1 individuals are able to switch (under competitive pressure) into a dormant state, and trait 2 individuals are able to execute horizontal gene transfer, turning trait 1 individuals into trait 2 ones, at a rate depending on the frequency of individuals. In the large-population limit, we examine the fate of a single trait i individual (a 'mutant') arriving in a trait j resident population living in equilibrium, for $i,j=1,2,i \neq j$. We provide a complete analysis of the invasion dynamics in all cases where the resident population is individually fit and the initial behaviour of the mutant population is non-critical. We identify parameter regimes for the invasion and fixation of the new trait, stable coexistence of the two traits, and 'founder control' (where the initial resident always dominates, irrespective of its trait). The most striking result is that stable coexistence occurs in certain scenarios even if trait 2 (which benefits from transfer at the cost of trait 1) would be unfit when being merely on its own. In the case of founder control, the limiting dynamical system has an unstable coexistence equilibrium. In all cases, we observe the classical (up to 3) phases of invasion dynamics \`a la Champagnat (2006).

math.PR↗

arXiv2020

The stochastic Fisher-KPP Equation with seed bank and on/off-branching-coalescing Brownian motion

We introduce a new class of stochastic partial differential equations (SPDEs) with seed bank modeling the spread of a beneficial allele in a spatial population where individuals may switch between an active and a dormant state. Incorporating dormancy and the resulting seed bank leads to a two-type coupled system of equations with migration between both states. We first discuss existence and uniqueness of seed bank SPDEs and provide an equivalent delay representation that allows a clear interpretation of the age structure in the seed bank component. The delay representation will also be crucial in the proofs. Further, we show that the seed bank SPDEs give rise to an interesting class of "on/off" moment duals. In particular, in the special case of the F-KPP Equation with seed bank, the moment dual is given by an "on/off-branching Brownian motion". This system differs from a classical branching Brownian motion in the sense that independently for all individuals, motion and branching may be "switched off" for an exponential amount of time after which they get "switched on" again. Here, as an application of our duality, we show that the spread of a beneficial allele, which in the classical F-KPP Equation, started from a Heaviside intial condition, evolves as a pulled traveling wave with speed $\sqrt{2}$, is slowed down significantly in the corresponding seed bank F-KPP model. In fact, by computing bounds on the position of the rightmost particle in the dual on/off-branching Brownian motion, we obtain an upper bound for the speed of propagation of the beneficial allele given by $\sqrt{\sqrt{5}-1}\approx 1.111$ under unit switching rates. This shows that seed banks will indeed slow down fitness waves and preserve genetic variability, in line with intuitive reasoning from population genetics and ecology.

math.PR↗

arXiv2020

Invasion and fixation of microbial dormancy traits under competitive pressure

Microbial dormancy is an evolutionary trait that has emerged independently at various positions across the tree of life. It describes the ability of a microorganism to switch to a metabolically inactive state that can withstand unfavorable conditions. However, maintaining such a trait requires additional resources that could otherwise be used to increase e.g. reproductive rates. In this paper, we aim for gaining a basic understanding under which conditions maintaining a seed bank of dormant individuals provides a "fitness advantage" when facing resource limitations and competition for resources among individuals (in an otherwise stable environment). In particular, we wish to understand when an individual with a "dormancy trait" can invade a resident population lacking this trait despite having a lower reproduction rate than the residents. To this end, we follow a stochastic individual-based approach employing birth-and-death processes, where dormancy is triggered by competitive pressure for resources. In the large-population limit, we identify a necessary and sufficient condition under which a complete invasion of mutants has a positive probability. Further, we explicitly determine the limiting probability of invasion and the asymptotic time to fixation of mutants in the case of a successful invasion. In the proofs, we observe the three classical phases of invasion dynamics in the guise of Coron et al. (2017, 2019).

math.PR↗

arXiv2020

The symbiotic branching model: duality and interfaces

The symbiotic branching model describes the dynamics of a spatial two-type population, where locally particles branch at a rate given by the frequency of the other type combined with nearest-neighbour migration. This model generalizes various classic models in population dynamics, such as the stepping stone model and the mutually catalytic branching model. We are particularly interested in understanding the region of coexistence, i.e. the interface between the two types. In this chapter, we give an overview over our results that describe the dynamics of these interfaces at large scales. One of the reasons that this system is tractable is that it exhibits a rich duality theory. So at the same time, we take the opportunity to provide an introduction to the strength of duality methods in the context of spatial population models.

math.PR↗

arXiv2020

Statistical tools for seed bank detection

In this article, we derive statistical tools to analyze and distinguish the patterns of genetic variability produced by classical and recent population genetic models related to seed banks. In particular, we are concerned with models described by the Kingman coalescent (K), models exhibiting so-called weak seed banks described by a time-changed Kingman coalescent (W), models with so-called strong seed bank described by the seed bank coalescent (S) and the classical two-island model by Wright, described by the structured coalescent (TI). As the presence of a (strong) seed bank should stratify a population, we expect it to produce a signal roughly comparable to the presence of population structure. We begin with a brief analysis of Wright's $F_{ST}$, which is a classical but crude measure for population structure, followed by a derivation of the expected site frequency spectrum (SFS) in the infinite sites model based on 'phase-type distribution calculus' as recently discussed by Hobolth et al. (2019). Both the $F_{ST}$ and the SFS can be readily computed under various population models, they discard statistical signal. Hence we also derive exact likelihoods for the full sampling probabilities, which can be achieved via recursions and a Monte Carlo scheme both in the infinite alleles and the infinite sites model. We employ a pseudo-marginal Metropolis-Hastings algorithm of Andrieu and Roberts (2009) to provide a method for simultaneous model selection and parameter inference under the so-called infinitely-many sites model, which is the most relevant in real applications. It turns out that this full likelihood method can reliably distinguish among the model classes (K, W), (S) and (TI) on the basis of simulated data even from moderate sample sizes. It is also possible to infer mutation rates, and in particular determine whether mutation is taking place in the (strong) seed bank.

q-bio.PE↗

arXiv2019

Genealogies and inference for populations with highly skewed offspring distributions

We review recent progress in the understanding of the role of multiple- and simultaneous multiple merger coalescents as models for the genealogy in idealised and real populations with exceptional reproductive behaviour. In particular, we discuss models with `skewed offspring distribution' (or under other non-classical evolutionary forces) which lead in the single locus haploid case to multiple merger coalescents, and in the multi-locus diploid case to simultaneous multiple merger coalescents. Further, we discuss inference methods under the infinitely-many sites model which allow both model selection and estimation of model parameters under these coalescents.

math.PR↗

arXiv2019

Separation of time-scales for the seed bank diffusion and its jump-diffusion limit

We investigate the scaling limit of the seed bank diffusion when reproduction and migration (to and from the seed bank) happen on different time-scales. More precisely, we consider the case when migration is `slow' and reproduction is `standard' (in the original time-scale) and then switch to a new, accelerated time-scale, where migration is `standard' and reproduction is `fast'. This is motivated by models for bacterial dormancy, where periods of quiescence can be orders of magnitude larger than reproductive times, and where it is expected to find non-trivial degenerate genealogies on the evolutionary time-scale. However, the above scaling regime is not only interesting from a biological perspective, but also from a mathematical point of view, since it provides a prototypical example where the expected scaling limit of a continuous diffusion should (and will be) a jump-diffusion. For this situation, standard convergence results often seem to fail in multiple ways. For example, since the set of continuous paths from a closed subset of the càdlàg paths in each of the classical Skorohod topologies $J_1, J_2, M_1$ and $M_2$, none of them can be employed for tightness on path-space. Further, a naïve direct rescaling of the Markov generator corresponding to the continuous diffusion immediately leads to a blow-up of the diffusion coefficient. Still, one can identify a well-defined limit via duality in a surprisingly non-technical way. Indeed, we show that a certain duality relation is in some sense stable under passage to the limit and allows an identification of the limit, avoiding all technicalities related to the blow-up in the classical generator. The result then boils down to a convergence criterion for time-continuous Markov chains in a separation of time-scales regime, which is of independent interest.

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