We consider the genealogy of a sample of individuals taken from a spatially structured population when the variance of the offspring distribution is relatively large. The space is structured into discrete sites of a graph G. If the population size at each site is large, spatial coalescents with multiple mergers, so called spatial Lambda-coalescents, for which ancestral lines migrate in space and coalesce according to some Lambda-coalescent mechanism, are shown to be appropriate approximations to the genealogy of a sample of individuals.
We then consider as the graph G the two dimensional torus with side length 2L+1 and show that as L tends to infinity, and time is rescaled appropriately, the partition structure of spatial Lambda-coalescents of individuals sampled far enough apart converges to the partition structure of a non-spatial Kingman coalescent. From a biological point of view this means that in certain circumstances both the spatial structure as well as larger variances of the underlying offspring distribution are harder to detect from the sample. However, supplemental simulations show that for moderately large L the different structure is still evident.
We consider the number of blocks involved in the last merger of a $Λ$-coalescent started with $n$ blocks. We give conditions under which, as $n \to \infty$, the sequence of these random variables a) is tight, b) converges in distribution to a finite random variable or c) converges to infinity in probability. Our conditions are optimal for $Λ$-coalescents that have a dust component. For general $Λ$, we relate the three cases to the existence, uniqueness and non-existence of quasi-invariant measures for the dynamics of the block-counting process, and in case b) investigate the time-reversal of t…
Multiple-merger coalescents, e.g. $Λ$-$n$-coalescents, have been proposed as models of the genealogy of $n$ sampled individuals for a range of populations whose genealogical structures are not captured well by Kingman's $n$-coalescent. $Λ$-$n$-coalescents can be seen as the limit process of the discrete genealogies of Cannings models with fixed population size, when time is rescaled and population size $N\to\infty$. As established for Kingman's $n$-coalescent, moderate population size fluctuations in the discrete population model should be reflected by a time-change of the limit coalescent. Fo…
We define a Markov process on the partitions of $[n]=\{1,\ldots,n\}$ by drawing a sample in $[n]$ at each time of a Poisson process, by merging blocks that contain one of these points and by leaving all other blocks unchanged. This coalescent process appears in the study of the connected components of random graph processes in which connected subgraphs are added over time with probabilities that depend only on their size. First, we determine the asymptotic distribution of the coalescent time. Then, we define a Bienayme-Galton-Watson (BGW) process such that its total population size dominates t…
This paper extends the notion of the $\la$-coalescent of Pitman (1999) to the spatial setting. The partition elements of the spatial $Λ$-coalescent migrate in a (finite) geographical space and may only coalesce if located at the same site of the space. We characterize the $Λ$-coalescents that come down from infinity, in an analogous way to Schweinsberg (2000). Surprisingly, all spatial coalescents that come down from infinity, also come down from infinity in a uniform way. This enables us to study space-time asymptotics of spatial $Λ$-coalescents on large tori in $d\ge 3$ dimensions. Our resul…
We study topological properties of random metric spaces which arise by Lambda-coalescents. These are stochastic processes, which start with an infinite number of lines and evolve through multiple mergers in an exchangeable setting. We show that the resulting Lambda-coalescent measure tree is compact iff the Lambda-coalescent comes down from infinity, i.e. only consists of finitely many lines at any positive time. If the Lambda-coalescent stays infinite, the resulting metric measure space is not even locally compact. Our results are based on general notions of compact and locally compact (isome…
We investigate the infinitely many demes limit of the genealogy of a sample of individuals from a subdivided population subject to sporadic mass extinction events. By exploiting a separation of timescales property of Wright's island model, we show that as the number of demes tends to infinity the limiting form of the genealogy can be described in terms of the alternation of instantaneous 'scattering' phases dominated by local demographic processes, and extended 'collecting' phases dominated by global processes. When extinction and recolonization events are local, this genealogy is given by Kin…
In mathematical population genetics, it is well known that one can represent the genealogy of a population by a tree, which indicates how the ancestral lines of individuals in the population coalesce as they are traced back in time. As the population evolves over time, the tree that represents the genealogy of the population also changes, leading to a tree-valued stochastic process known as the evolving coalescent. Here we will consider the evolving coalescent for populations whose genealogy can be described by a beta coalescent, which is known to give the genealogy of populations with very la…
We study several fundamental properties of a class of stochastic processes called spatial Lambda-coalescents. In these models, a number of particles perform independent random walks on some underlying graph G. In addition, particles on the same vertex merge randomly according to a given coalescing mechanism. A remarkable property of mean-field coalescent processes is that they may come down from infinity, meaning that, starting with an infinite number of particles, only a finite number remains after any positive amount of time, almost surely. We show here however that, in the spatial setting, …
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 sel…
Consider a population evolving as a critical continuous-time Galton-Watson (GW) tree. Conditional on the population surviving until a large time $T$, sample $k$ individuals uniformly at random (without replacement) from amongst those alive at time $T$. What is the genealogy of this sample of individuals? In cases where the offspring distribution has finite variance, the probabilistic properties of the joint ancestry of these $k$ particles are well understood, as seen in \cite{HJR20, J19}. In the present article, we study the joint ancestry of a sample of $k$ particles under the following regim…
We consider diploid bi-parental analogues of Cannings models: in a population of fixed size $N$ the next generation is composed of $V_{i,j}$ offspring from parents $i$ and $j$, where $V=(V_{i,j})_{1\le i\neq j \le N}$ is a (jointly) exchangeable (symmetric) array. Every individual carries two chromosome copies, each of which is inherited from one of its parents. We obtain general conditions, formulated in terms of the vector of the total number of offspring to each individual, for the convergence of the properly scaled ancestral process for an $n$-sample of genes towards a ($Ξ$-)coalescent. Th…
For a class of $Λ$-Fleming-Viot processes with Brownian spatial motion in $\mathbb{R}^d$ whose associated $Λ$-coalescents come down from infinity, we obtain sharp global and local modulus of continuities for the ancestry processes recovered from the lookdown representations. As applications, we prove both global and local modulus of continuities for the $Λ$-Fleming-Viot support processes. In particular, if the $Λ$-coalescent is the Beta$(2-β,β)$ coalescent for $β\in(1,2]$ with $β=2$ corresponding to Kingman's coalescent, then for $h(t)=\sqrt{t\log (1/t)}$, the global modulus of continuity hold…
Trees corresponding to $Λ$- and $Ξ$-$n$-coalescents can be both quite similar and fundamentally different compared to bifurcating tree models based on Kingman's $n$-coalescent. This has consequences for inference of a well-fitting gene genealogy as well as for assessing biological properties of species having such sample genealogies. Here, mathematical properties concerning clade sizes in the tree as well as changes of the tree when the samples are enlargened are highlighted. To be used as realistic genealogy models for real populations, an extension for changing population sizes is discussed.
We construct an extension of the Lambda-coalescent to a spatial continuum and analyse its behaviour. Like the Lambda-coalescent, the individuals in our model can be separated into (i) a dust component and (ii) large blocks of coalesced individuals. We identify a five phase system, where our phases are defined according to changes in the qualitative behaviour of the dust and large blocks. We completely classify the phase behaviour, including necessary and sufficient conditions for the model to come down from infinity. We believe that two of our phases are new to Lambda-coalescent theory and dir…
We investigate a new model for populations evolving in a spatial continuum. This model can be thought of as a spatial version of the Lambda-Fleming-Viot process. It explicitly incorporates both small scale reproduction events and large scale extinction-recolonisation events. The lineages ancestral to a sample from a population evolving according to this model can be described in terms of a spatial version of the Lambda-coalescent. Using a technique of Evans(1997), we prove existence and uniqueness in law for the model. We then investigate the asymptotic behaviour of the genealogy of a finite n…
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…
We study a model of selection acting on a diploid population (one in which each individual carries two copies of each gene) living in one spatial dimension. We suppose a particular gene appears in two forms (alleles) $A$ and $a$, and that individuals carrying $AA$ have a higher fitness than $aa$ individuals, while $Aa$ individuals have a lower fitness than both $AA$ and $aa$ individuals. The proportion of advantageous $A$ alleles expands through the population approximately according to a travelling wave. We prove that on a suitable timescale, the genealogy of a sample of $A$ alleles taken fro…
It is well known that the dynamics of a subpopulation of individuals of a rare type in a Wright-Fisher diffusion can be approximated by a Feller branching process. Here we establish an analogue of that result for a spatially distributed population whose dynamics are described by a spatial Lambda-Fleming-Viot process (SLFV). The subpopulation of rare individuals is then approximated by a superBrownian motion. This result mirrors Cox et al. (2000), where it is shown that when suitably rescaled, sparse voter models converge to superBrownian motion. We also prove the somewhat more surprising resul…
The $N$-particle branching random walk is a discrete time branching particle system with selection. We have $N$ particles located on the real line at all times. At every time step each particle is replaced by two offspring, and each offspring particle makes a jump of non-negative size from its parent's location, independently from the other jumps, according to a given jump distribution. Then only the $N$ rightmost particles survive; the other particles are removed from the system to keep the population size constant. Inspired by work of J. Bérard and P. Maillard, we examine the long term behav…
This paper extends earlier work by Cox and Durrett, who studied the coalescence times for two lineages in the stepping stone model on the two-dimensional torus. We show that the genealogy of a sample of size n is given by a time change of Kingman's coalescent. With DNA sequence data in mind, we investigate mutation patterns under the infinite sites model, which assumes that each mutation occurs at a new site. Our results suggest that the spatial structure of the human population contributes to the haplotype structure and a slower than expected decay of genetic correlation with distance reveale…
