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Maite Wilke-Berenguer

Publications and source records attributed to Maite Wilke-Berenguer.

11 recordsLinked to original sources

Multi-type $Ξ$-coalescents from structured population models with bottlenecks

We introduce an individual-based model for structured populations undergoing demographic bottlenecks, i.e. drastic reductions in population size that last many generations and can have arbitrary shapes. We first show that the (non-Markovian) allele-frequency process converges to a Markovian diffusion process with jumps in a suitable relaxation of the Skorokhod J1 topology. Backward in time we find that genealogies of samples of individuals are described by multi-type $Ξ$-coalescents presenting multiple simultaneous mergers with simultaneous migrations. These coalescents are also moment-duals of the limiting jump diffusions. We then show through a numerical study that our model is flexible and can predict various shapes for the site frequency spectrum, consistent with real data, using a small number of interpretable parameters.

math.PR↗

The effective strength of selection in random environment

We analyse a family of two-types Wright-Fisher models with selection in a random environment and skewed offspring distribution. We provide a calculable criterion to quantify the impact of different shapes of selection on the fate of the weakest allele, and thus compare them. The main mathematical tool is duality, which we prove to hold, also in presence of random environment (quenched and in some cases annealed), between the population's allele frequencies and genealogy, both in the case of finite population size and in the scaling limit for large size. Duality also yields new insight on properties of branching-coalescing processes in random environment, such as their long term behaviour.

math.PR↗

Stationary distribution approximations of Two-island Wright-Fisher and seed-bank models using Stein's method

We consider two finite population Markov chain models, the two-island Wright-Fisher model with mutation, and the seed-bank model with mutation. Despite the relatively simple descriptions of the two processes, the the exact form of their stationary distributions is in general intractable. For each of the two models we provide two approximation theorems with explicit upper bounds on the distance between the stationary distributions of the finite population Markov chains, and either the stationary distribution of a two-island diffusion model, or the beta distribution. We show that the order of the bounds, and correspondingly the appropriate choice of approximation, depends upon the relative sizes of mutation and migration. In the case where migration and mutation are of the same order, the suitable approximation is the two-island diffusion model, and if migration dominates mutation, then the weighted average of both islands is well approximated by a beta random variable. Our results are derived from a new development of Stein's method for the stationary distribution of the two-island diffusion model for the weak migration results, and utilising the existing framework for Stein's method for the Dirichlet distribution.

math.PR↗

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.

q-bio.PE↗

$Λ$-coalescents arising in populations with dormancy

Consider a population evolving from year to year through three seasons: spring, summer and winter. Every spring starts with $N$ dormant individuals waking up independently of each other according to a given distribution. Once an individual is awake, it starts reproducing at a constant rate. By the end of spring, all individuals are awake and continue reproducing independently as Yule processes during the whole summer. In the winter, $N$ individuals chosen uniformly at random go to sleep until the next spring, and the other individuals die. We show that because an individual that wakes up unusually early can have a large number of surviving descendants, for some choices of model parameters the genealogy of the population will be described by a $Λ$-coalescent. In particular, the beta coalescent can describe the genealogy when the rate at which individuals wake up increases exponentially over time. We also characterize the set of all $Λ$-coalescents that can arise in this framework.

math.PR↗

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.

math.PR↗

The seed bank coalescent with simultaneous switching

We introduce a new Wright-Fisher type model for seed banks incorporating "simultaneous switching", which is motivated by recent work on microbial dormancy. We show that the simultaneous switching mechanism leads to a new jump-diffusion limit for the scaled frequency processes, extending the classical Wright-Fisher and seed bank diffusion limits. We further establish a new dual coalescent structure with multiple activation and deactivation events of lineages. While this seems reminiscent of multiple merger events in general exchangeable coalescents, it actually leads to an entirely new class of coalescent processes with unique qualitative and quantitative behaviour. To illustrate this, we provide a novel kind of condition for coming down from infinity for these coalescents using recent results of Griffiths.

q-bio.PE↗

Structural properties of the seed bank and the two-island diffusion

We investigate various aspects of the (biallelic) Wright-Fisher diffusion with seed bank in conjunction with and contrast to the two-island model analysed e.g. in Kermany, Zhou and Hickey, 2008, and Nath and Griffiths, 1993, including moments, stationary distribution and reversibility, for which our main tool is duality. Further, we show that the Wright-Fisher diffusion with seed bank can be reformulated as a one-dimensional stochastic delay differential equation, providing an elegant interpretation of the age structure in the seed bank also forward in time in the spirit of Kaj, Krone and Lascoux, 2001. We also provide a complete boundary classification for this two-dimensional SDE using martingale-based reasoning known as McKean's argument.

math.PR↗

Random Delta-Hausdorff-attractors

Global random attractors and random point attractors for random dynamical systems have been studied for several decades. Here we introduce two intermediate concepts: $Δ$-attractors are characterized by attracting all deterministic compact sets of Hausdorff dimension at most $Δ$, where $Δ$ is a non-negative number, while cc-attractors attract all countable compact sets. We provide two examples showing that a given random dynamical system may have various different $Δ$-attractors for different values of $Δ$. It seems that both concepts are new even in the context of deterministic dynamical systems.

math.DS↗

A new coalescent for seed-bank models

We identify a new natural coalescent structure, which we call the seed-bank coalescent, that describes the gene genealogy of populations under the influence of a strong seed-bank effect, where "dormant forms" of individuals (such as seeds or spores) may jump a significant number of generations before joining the "active" population. Mathematically, our seed-bank coalescent appears as scaling limit in a Wright-Fisher model with geometric seed-bank age structure if the average time of seed dormancy scales with the order of the total population size $N$. This extends earlier results of Kaj, Krone and Lascoux [J. Appl. Probab. 38 (2011) 285-300] who show that the genealogy of a Wright-Fisher model in the presence of a "weak" seed-bank effect is given by a suitably time-changed Kingman coalescent. The qualitatively new feature of the seed-bank coalescent is that ancestral lineages are independently blocked at a certain rate from taking part in coalescence events, thus strongly altering the predictions of classical coalescent models. In particular, the seed-bank coalescent "does not come down from infinity," and the time to the most recent common ancestor of a sample of size $n$ grows like $\log\log n$. This is in line with the empirical observation that seed-banks drastically increase genetic variability in a population and indicates how they may serve as a buffer against other evolutionary forces such as genetic drift and selection.

math.PR↗

Asymptotics for Lipschitz percolation above tilted planes

We consider Lipschitz percolation in $d+1$ dimensions above planes tilted by an angle $γ$ along one or several coordinate axes. In particular, we are interested in the asymptotics of the critical probability as $d \to \infty$ as well as $γ\to π/4.$ Our principal results show that the convergence of the critical probability to 1 is polynomial as $d\to \infty$ and $γ\to π/4.$ In addition, we identify the correct order of this polynomial convergence and in $d=1$ we also obtain the correct prefactor.

math.PR↗