arXiv subjects

Adrián González Casanova

Publications and source records attributed to Adrián González Casanova.

35 records · Page 2Linked to original sources

arXiv2023

The relative frequency between two continuous-state branching processes with immigration and their genealogy

When two (possibly different in distribution) continuous-state branching processes with immigration are present, we study the relative frequency of one of them when the total mass is forced to be constant at a dense set of times. This leads to a SDE whose unique strong solution will be the definition of a $Λ$-asymmetric frequency process ($Λ$-AFP). We prove that it is a Feller process and we calculate a large population limit when the total mass tends to infinity. This allows us to study the fluctuations of the process around its deterministic limit. Furthermore, we find conditions for the $Λ$-AFP to have a moment dual. The dual can be interpreted in terms of selection, (coordinated) mutation, pairwise branching (efficiency), coalescence, and a novel component that comes from the asymmetry between the reproduction mechanisms. In the particular case of a pair of equally distributed continuous-state branching processes, the associated $Λ$-AFP will be the dual of a $Λ$-coalescent. The map that sends each continuous-state branching process to its associated $Λ$-coalescent (according to the former procedure) is a homeomorphism between metric spaces.

math.PR↗

arXiv2023

Alpha-stable branching and beta-Frequency processes, beyond the IID assumption

Birkner et al. obtained necessary and sufficient conditions for the frequency between two independent and identically distributed continuous-state branching processes time-changed by a functional of the total mass process to be a Markov process. Foucart et al. extended this result to continuous-state branching processes with immigration. We generalize these results by dropping the independent and identically distributed assumption. Our result clarifies under which conditions a multi-type $Λ$-coalescent can be constructed from a multi-type branching process by a time change using the total mass. Finally, we address a problem formulated by Griffiths, by clarifying the relation between 2-type $α$-stable continuous-state branching processes and 2-type $β$-Fleming--Viot processes with mutation and selection.

math.PR↗

arXiv2022

The Symmetric Coalescent and Wright-Fisher models with bottlenecks

We define a new class of $Ξ$-coalescents characterized by a possibly infinite measure over the non negative integers. We call them symmetric coalescents since they are the unique family of exchangeable coalescents satisfying a symmetry property on their coagulation rates: they are invariant under any transformation that consists in moving one element from one block to another without changing the total number of blocks. We illustrate the diversity of behaviors of this family of processes by introducing and studying a one parameter subclass, the $(β,S)$-coalescents. We also embed this family in a larger class of $Ξ$-coalescents arising as the limit genealogies of Wright-Fisher models with bottlenecks. Some convergence results rely on a new Skorokhod type metric, that induces the Meyer-Zheng topology, which allows to study the scaling limit of non-markovian processes using standard techniques.

math.PR↗

arXiv2022

Haldane's formula in Cannings models: The case of moderately strong selection

For a class of Cannings models we prove Haldane's formula, $π(s_N) \sim \frac{2s_N}{ρ^2}$, for the fixation probability of a single beneficial mutant in the limit of large population size $N$ and in the regime of moderately strong selection, i.e. for $s_N \sim N^{-b}$ and $0< b<1/2$. Here, $s_N$ is the selective advantage of an individual carrying the beneficial type, and $ρ^2$ is the (asymptotic) offspring variance. Our assumptions on the reproduction mechanism allow for a coupling of the beneficial allele's frequency process with slightly supercritical Galton-Watson processes in the early phase of fixation.

math.PR↗

arXiv2021

Particle systems with coordination

We consider a generalization of spatial branching coalescing processes in which the behaviour of individuals is not (necessarily) independent, on the contrary, individuals tend to take simultaneous actions. We show that these processes have moment duals, which happen to be multidimensional diffusions with jumps. Moment duality provides a general framework to study structural properties of the processes in this class. We present some conditions under which the expectation of the process is not affected by coordination and comment on the effect of coordination on the variance. We analyse several examples in more detail, including the nested coalescent, the peripatric coalescent with selection and coordinated migration, and the Parabolic Anderson Model.

math.PR↗

arXiv2020

Haldane's formula in Cannings models: The case of moderately weak selection

We introduce a Cannings model with directional selection via a paintbox construction and establish a strong duality with the line counting process of a new \emph{Cannings ancestral selection graph} in discrete time. This duality also yields a formula for the fixation probability of the beneficial type. Haldane's formula states that for a single selectively advantageous individual in a population of haploid individuals of size $N$ the prob\-ability of fixation is asymptotically (as $N\to \infty$) equal to the selective advantage of haploids $s_N$ divided by half of the offspring variance. For a class of offspring distributions within Kingman attraction we prove this asymptotics for sequences $s_N$ obeying $N^{-1} \ll s_N \ll N^{-1/2} $, which is a regime of "moderately weak selection". It turns out that for $ s_N \ll N^{-2/3} $ the Cannings ancestral selection graph is so close to the ancestral selection graph of a Moran model that a suitable coupling argument allows to play the problem back asymptotically to the fixation probability in the Moran model, which can be computed explicitly.

math.PR↗

arXiv2020

The shape of a seed bank tree

We derive the asymptotic behavior of the total, active and inactive branch lengths of the seed bank coalescent, when the size of the initial sample grows to infinity. Those random variables have important applications for populations evolving under some seed bank effects, such as plants and bacteria, and for some cases of structured populations like metapopulations. The proof relies on the study of the tree at a stopping time corresponding to the first time that a deactivated lineage reactivates. We also give conditional sampling formulas for the random partition and we study the system at the time of the first deactivation of a lineage. All these results provide a good picture of the different regimes and behaviors of the block-counting process of the seed bank coalescent.

math.PR↗

arXiv2020

$Λ$-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↗

arXiv2020

Branching processes with interactions: the subcritical cooperative regime

In this paper, we introduce a family of processes with values on the nonnegative integers that describes the dynamics of populations where individuals are allowed to have different types of interactions. The types of interactions that we consider include pairwise interaction, such as competition, annihilation and cooperation; and interaction among several individuals that can be considered as catastrophes. We call such families of processes \textit{branching processes with interactions}. Our aim is to study their long term behaviour under a specific regime of the pairwise interaction parameters that we introduce as {\it subcritical cooperative regime}. Under such regime, we prove that a process in this class comes down from infinity and has a moment dual which turns out to be a jump-diffusion that can be thought as the evolution of the frequency of a trait or phenotype and whose parameters have a classical interpretation in terms of population genetics. The moment dual is an important tool for characterizing the stationary distribution of branching processes with interactions whenever such distribution exists but it is an interesting object on its own right.

math.PR↗

arXiv2019

Modelling and simulating Lenski's long-term evolution experiment

We revisit the model by Wiser, Ribeck, and Lenski (Science \textbf{342} (2013), 1364--1367), which describes how the mean fitness increases over time due to beneficial mutations in Lenski's long-term evolution experiment. We develop the model further both conceptually and mathematically. Conceptually, we describe the experiment with the help of a Cannings model with mutation and selection, where the latter includes diminishing returns epistasis. The analysis sheds light on the growth dynamics within every single day and reveals a runtime effect, that is, the shortening of the daily growth period with increasing fitness; and it allows to clarify the contribution of epistasis to the mean fitness curve. Mathematically, we explain rigorous results in terms of a law of large numbers (in the limit of infinite population size and for a certain asymptotic parameter regime), and present approximations based on heuristics and supported by simulations for finite populations.

q-bio.PE↗

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.

math.PR↗

arXiv2018

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↗

arXiv2018

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↗

arXiv2017

Duality and Fixation in $Ξ$-Wright-Fisher processes with frequency-dependent selection

A two-types, discrete-time population model with finite, constant size is constructed, allowing for a general form of frequency-dependent selection and skewed offspring distribution. Selection is defined based on the idea that individuals first choose a (random) number of $\textit{potential}$ parents from the previous generation and then, from the selected pool, they inherit the type of the fittest parent. The probability distribution function of the number of potential parents per individual thus parametrises entirely the selection mechanism. Using sampling- and moment-duality, weak convergence is then proved both for the allele frequency process of the selectively weak type and for the population's ancestral process. The scaling limits are, respectively, a two-types $Ξ$-Fleming-Viot jump-diffusion process with frequency-dependent selection, and a branching-coalescing process with general branching and simultaneous multiple collisions. Duality also leads to a characterisation of the probability of extinction of the selectively weak allele, in terms of the ancestral process' ergodic properties.

math.PR↗

arXiv2016

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↗

arXiv2016

An individual-based model for the Lenski experiment, and the deceleration of the relative fitness

The Lenski experiment investigates the long-term evolution of bacterial populations. Its design allows the direct comparison of the reproductive fitness of an evolved strain with its founder ancestor. It was observed by Wiser et al. (2013) that the relative fitness over time increases sublinearly, a behaviour which is commonly attributed to effects like clonal interference or epistasis. In this paper we present an individual-based probabilistic model that captures essential features of the design of the Lenski experiment. We assume that each beneficial mutation increases the individual reproduction rate by a fixed amount, which corresponds to the absence of epistasis in the continuous-time (intraday) part of the model, but leads to an epistatic effect in the discrete-time (interday) part of the model. Using an approximation by near-critical Galton-Watson processes, we prove that under some assumptions on the model parameters which exclude clonal interference, the relative fitness process converges, after suitable rescaling, in the large population limit to a power law function.

math.PR↗

arXiv2014

Genealogy of a Wright Fisher model with strong seed bank component

We investigate the behaviour of the genealogy of a Wright-Fisher population model under the influence of a strong seed-bank effect. More precisely, we consider a simple seed-bank age distribution with two atoms, leading to either classical or long genealogical jumps (the latter modeling the effect of seed-dormancy). We assume that the length of these long jumps scales like a power $N^β$ of the original population size $N$, thus giving rise to a `strong' seed-bank effect. For a certain range of $β$, we prove that the ancestral process of a sample of $n$ individuals converges under a non-classical time-scaling to Kingman's $n-$coalescent. Further, for a wider range of parameters, we analyze the time to the most recent common ancestor of two individuals analytically and by simulation.

math.PR↗