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.
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…
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-classic…
We introduce a new model for plant metapopulations with a seed bank component, living in a fragmented environment in which local extinction events are frequent. This model is an intermediate between population dynamics models with a seed bank component, based on the classical Wright-Fisher model, and Stochastic Patch Occupancy Models (SPOMs) used in metapopulation ecology. Its main feature is the use of "ghost" individuals, which can reproduce but with a very strong selective disadvantage against "real" individuals, to artificially ensure a constant population size. We show the existence of an…
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…
We present a new model for seed banks, where direct ancestors of individuals may have lived in the near as well as the very far past. The classical Wright-Fisher model, as well as a seed bank model with bounded age distribution considered by Kaj, Krone and Lascoux (2001) are special cases of our model. We discern three parameter regimes of the seed bank age distribution, which lead to substantially different behaviour in terms of genetic variability, in particular with respect to fixation of types and time to the most recent common ancestor. We prove that for age distributions with finite mean…
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…
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…
We investigate the compact interface property in a recently introduced variant of the stochastic heat equation that incorporates dormancy, or equivalently seed banks. There individuals can enter a dormant state during which they are no longer subject to spatial dispersal and genetic drift. This models a state of low metabolic activity as found in microbial species. Mathematically, one obtains a memory effect since mass accumulated by the active population will be retained for all times in the seed bank. This raises the question whether the introduction of a seed bank into the system leads to a…
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 Lasc…
We consider a system of interacting Fisher-Wright diffusions with seed-bank. Individuals live in colonies and are subject to resampling and migration as long as they are active. Each colony has a structured seed-bank into which individuals can retreat to become dormant, suspending their resampling and migration until they become active again. As geographic space labelling the colonies we consider a countable Abelian group $\mathbb{G}$ endowed with the discrete topology. The key example of interest is the Euclidean lattice $\mathbb{G}=\mathbb{Z}^d$. Our goal is to classify the long-time behavio…
We consider a multi-colony version of the Wright-Fisher model with seed-bank that was recently introduced by Blath et al. Individuals live in colonies and change type via resampling and mutation. Each colony contains a seed-bank that acts as a genetic reservoir. Individuals can enter the seed-bank and become dormant or can exit the seed-bank and become active. In each colony at each generation a fixed fraction of individuals swap state, drawn randomly from the active and the dormant population. While dormant, individuals suspend their resampling. While active, individuals resample from their o…
We consider a system of interacting diffusions labeled by a geographic space that is given by the hierarchical group $Ω_N$ of order $N\in\mathbb{N}$. Individuals live in colonies and are subject to resampling and migration as long as they are active. Each colony has a seed-bank into which individuals can retreat to become dormant, suspending their resampling and migration until they become active again. The migration kernel has a hierarchical structure: individuals hop between colonies at a rate that depends on the hierarchical distance between the colonies. The seed-bank has a layered structu…
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…
We consider a system of interacting Fisher-Wright diffusions with seed-bank. Individuals carry type one of two types, live in colonies, and are subject to resampling and migration as long as they are active. Each colony has a structured seed-bank into which individuals can retreat to become dormant, suspending their resampling and migration until they become active again. As geographic space labelling the colonies we consider a countable Abelian group endowed with the discrete topology. In earlier work we showed that the system has a one-parameter family of equilibria controlled by the relativ…
We consider a system of interacting Moran models with seed-banks. Individuals live in colonies and are subject to resampling and migration as long as they are $active$. Each colony has a seed-bank into which individuals can retreat to become $dormant$, suspending their resampling and migration until they become active again. The colonies are labelled by $\mathbb{Z}^d$, $d \geq 1$, playing the role of a $geographic\, space$. The sizes of the active and the dormant population are $finite$ and depend on the $location$ of the colony. Migration is driven by a random walk transition kernel. Our goal…
We consider a spatial version of the classical Moran model with seed-banks where the constituent populations have finite sizes. Individuals live in colonies labelled by $\mathbb{Z}^d$, $d\geq 1$, playing the role of a geographic space, carry one of the two $types$: $\heartsuit$ or $\spadesuit$, and change type via $resampling$ as long as they are $active$. Each colony contains a seed-bank into which individuals can enter to become $dormant$, suspending their resampling until they exit the seed-bank and become active again. Individuals resample not only from their own colony, but also from othe…
We consider the spatially inhomogeneous Moran model with seed-banks introduced in den Hollander and Nandan (2021). Populations comprising $active$ and $dormant$ individuals are structured in colonies labelled by $\mathbb{Z}^d,~d\geq 1$. The population sizes are drawn from an ergodic, translation-invariant, uniformly elliptic field that form a random environment. Individuals carry one of two types: $\heartsuit$, $\spadesuit$. Dormant individual resides in what is called a seed-bank. Active individuals exchange type from seed-bank of their own colony and resample type by choosing parent from the…
A uniform attachment tree is a random tree that is generated dynamically. Starting from a fixed "seed" tree, vertices are added sequentially by attaching each vertex to an existing vertex chosen uniformly at random. Upon observing a large (unlabeled) tree, one wishes to find the initial seed. We investigate to what extent seed trees can be recovered, at least partially. We consider three types of seeds: a path, a star, and a random uniform attachment tree. We propose and analyze seed-finding algorithms for all three types of seed trees.
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 evo…
We study the influence of the seed in random trees grown according to the uniform attachment model, also known as uniform random recursive trees. We show that different seeds lead to different distributions of limiting trees from a total variation point of view. To do this, we construct statistics that measure, in a certain well-defined sense, global "balancedness" properties of such trees. Our paper follows recent results on the same question for the preferential attachment model.
We investigate the size of vertex confidence sets for including part of (or the entirety of) the seed in seeded uniform attachment trees, given knowledge of some of the seed's properties, and with a prescribed probability of failure. We also study the problem of identifying the leaves of a seed in a seeded uniform attachment tree, given knowledge of the positions of all internal nodes of the seed.
We study randomly growing trees governed by the affine preferential attachment rule. Starting with a seed tree $S$, vertices are attached one by one, each linked by an edge to a random vertex of the current tree, chosen with a probability proportional to an affine function of its degree. This yields a one-parameter family of preferential attachment trees $(T_n^S)_{n\geq|S|}$, of which the linear model is a particular case. Depending on the choice of the parameter, the power-laws governing the degrees in $T_n^S$ have different exponents. We study the problem of the asymptotic influence of the s…
We are interested in the asymptotics of random trees built by linear preferential attachment, also known in the literature as Barabási-Albert trees or plane-oriented recursive trees. We first prove a conjecture of Bubeck, Mossel \& Rácz concerning the influence of the seed graph on the asymptotic behavior of such trees. Separately we study the geometric structure of nodes of large degrees in a plane version of Barabási-Albert trees via their associated looptrees. As the number of nodes grows, we show that these looptrees, appropriately rescaled, converge in the Gromov-Hausdorff sense towards a…
We study the influence of the seed graph in the preferential attachment model, focusing on the case of trees. We first show that the seed has no effect from a weak local limit point of view. On the other hand, we conjecture that different seeds lead to different distributions of limiting trees from a total variation point of view. We take a first step in proving this conjecture by showing that seeds with different degree profiles lead to different limiting distributions for the (appropriately normalized) maximum degree, implying that such seeds lead to different (in total variation) limiting t…
We consider a dynamic network cascade process developed by Watts applied to a random networks with a specified amount of clustering, belonging to a class of random networks developed by Newman. We adapt existing tree-based methods to formulate an appropriate two-type branching process to describe the spread of a cascade started with a single active node, and obtain a fixed-point equation to implicitly express the extinction probability of such a cascade. In so doing, we also recover a special case of a formula of Hackett et al. giving conditions for certain extinction of the cascade.
This systemic risk paper introduces inhomogeneous random financial networks (IRFNs). Such models are intended to describe parts, or the entirety, of a highly heterogeneous network of banks and their interconnections, in the global financial system. Both the balance sheets and the stylized crisis behaviour of banks are ingredients of the network model. A systemic crisis is pictured as triggered by a shock to banks' balance sheets, which then leads to the propagation of damaging shocks and the potential for amplification of the crisis, ending with the system in a cascade equilibrium. Under some …
We re-examine a lower-tail upper bound for the random variable $$X=\prod_{i=1}^{\infty}\min\left\{\sum_{k=1}^iE_k,1\right\},$$ where $E_1,E_2,\ldots\stackrel{iid}\sim\text{Exp}(1)$. This bound has found use in root-finding and seed-finding algorithms for randomly growing trees, and was initially proved as a lemma in the context of the uniform attachment tree model. We first show that $X$ has a useful representation as a compound product of uniform random variables that allows us to determine its moments and refine the existing nonasymptotic bound. Next we demonstrate that the lower-tail probab…
We investigate properties of node centrality in random growing tree models. We focus on a measure of centrality that computes the maximum subtree size of the tree rooted at each node, with the most central node being the tree centroid. For random trees grown according to a preferential attachment model, a uniform attachment model, or a diffusion processes over a regular tree, we prove that a single node persists as the tree centroid after a finite number of steps, with probability 1. Furthermore, this persistence property generalizes to the top $K \ge 1$ nodes with respect to the same centrali…
