We present a law of large numbers and a central limit theorem for the time to absorption of Λ-coalescents with dust started from n blocks, as n→∞. The proofs rely on an approximation of the logarithm of the block-counting process by means of a drifted subordinator.

In this paper we give a new flavour to what Peter Jagers and his co-authors call `the path to extinction'. In a neutral population of constant size N, assume that each individual at time 0 carries a distinct type, or allele. Consider the joint dynamics of these N alleles, for example the dynamics of their respective frequencies and more plainly the nonincreasing process counting the number of alleles remaining by time t. Call this process the extinction process. We show that in the Moran model, the extinction process is distributed as the process counting (in backward time) the number of common ancestors to the whole population, also known as the block counting process of the N-Kingman coalescent. Stimulated by this result, we investigate whether it extends (i) to an identity between the frequencies of blocks in the Kingman coalescent and the frequencies of alleles in the extinction process, both evaluated at jump times, and (ii) to the general case of Λ-Fleming‒Viot processes.

We study the impact of a hard selective sweep on the genealogy of partially linked neutral loci in the vicinity of the positively selected allele. We consider a sexual population of stochastically varying size and, focusing on two neighboring loci, derive an approximate formula for the neutral genealogy of a sample of individuals taken at the end of the sweep. Individuals are characterized by ecological parameters depending on their genetic type, and governing their growth rate and interactions with other individuals (competition). As a consequence, the `fitness' of an individual depends on the population state and is not an intrinsic characteristic of individuals. We provide a deep insight into the dynamics of the mutant and wild-type populations during the different stages of a selective sweep.

Identifiability of evolutionary tree models has been a recent topic of discussion and some models have been shown to be nonidentifiable. A coalescent-based rooted population tree model, originally proposed by Nielsen et al. (1998), has been used by many authors in the last few years and is a simple tool to accurately model the changes in allele frequencies in the tree. However, the identifiability of this model has never been proven. Here we prove this model to be identifiable by showing that the model parameters can be expressed as functions of the probability distributions of subsamples, assuming that there are at least two (haploid) individuals sampled from each population. This a step toward proving the consistency of the maximum likelihood estimator of the population tree based on this model.

We describe the processes obtained by time reversal of a class of stationary jump diffusion processes that model the dynamics of genetic variation in populations subject to repeated bottlenecks. Assuming that only one lineage survives each bottleneck, the forward process is a diffusion on [0,1] that jumps to the boundary before diffusing back into the interior. We show that the behavior of the time-reversed process depends on whether the boundaries are accessible to the diffusive motion of the forward process. If a boundary point is inaccessible to the forward diffusion then time reversal leads to a jump diffusion that jumps immediately into the interior whenever it arrives at that point. If, instead, a boundary point is accessible then the jumps off of that point are governed by a weighted local time of the time-reversed process.

Consider a monoecious diploid population with nonoverlapping generations, whose size varies with time according to an irreducible, aperiodic Markov chain with states x1N,…,xKN, where K ≪ N. It is assumed that all matings except for selfing are possible and equally probable. At time 0 a random sample of n ≪ N genes is taken. Given two successive population sizes xjN and xiN, the numbers of gametes that individual parents contribute to offspring can be shown to be exchangeable random variables distributed as Gij. Under minimal conditions on the first three moments of Gij for all i and j, a suitable effective population size Ne is derived. Then if time is recorded in a backward direction in units of 2Ne generations, it can be shown that coalescent theory holds.

Let Kn denote the number of types of a sample of size n taken from an exchangeable coalescent process (Ξ-coalescent) with mutation. A distributional recursion for the sequence (Kn)n∈ℕ is derived. If the coalescent does not have proper frequencies, i.e. if the characterizing measure Ξ on the infinite simplex Δ does not have mass at 0 and satisfies ∫Δ ∣x∣Ξ(dx)/(x,x)<∞, where ∣x∣:=∑i=1∞xi and (x,x)≔∑i=1∞xi2 for x=(x1,x2,…)∈Δ, then Kn/n converges weakly as n→∞ to a limiting variable K that is characterized by an exponential integral of the subordinator associated with the coalescent process. For so-called simple measures Ξ satisfying ∫ΔΞ(d x)/(x,x)<∞, we characterize the distribution of K via a fixed-point equation.

The goal of this paper is to provide formulae for the expectation and variance of the height and length of the ancestral recombination graph (ARG). While the formula for the expectation of the height is known (see, e.g. Krone and Neuhauser (1997)), the other formulae seem to be new. We obtain in particular (see Theorem 4.1) a very simple formula which expresses the expectation of the length of the ARG as a linear combination of the expectations of both the length of the coalescent tree and the height of the ARG. Finally, we study the speed at which the ARG comes down from infinity.

Kingman's classical theory of the coalescent uncovered the basic pattern of genealogical trees of random samples of individuals in large but time-constant populations. Time is viewed as being discrete and is identified with non-overlapping generations. Reproduction can be very generally taken as exchangeable (meaning that the labelling of individuals in each generation carries no significance). Recent generalisations have dealt with population sizes exhibiting given deterministic or (minor) random fluctuations. We consider population sizes which constitute a stationary Markov chain, explicitly allowing large fluctuations in short times. Convergence of the genealogical tree, as population size tends to infinity, towards the (time-scaled) coalescent is proved under minimal conditions. As a result, we obtain a formula for effective population size, generalising the well-known harmonic mean expression for effective size.

A class of haploid population models with population size N, nonoverlapping generations and exchangeable offspring distribution is considered. Based on an analysis of the discrete ancestral process, we present solutions, algorithms and strong upper bounds for the expected time back to the most recent common ancestor which hold for arbitrary sample size n ∈ {1,…,N}. New insights into the asymptotic behaviour of the expected time back to the most recent common ancestor for large population size are presented relating the results to coalescent theory.

We study the genealogical structure of a population with stochastically fluctuating size. If such fluctuations, after suitable rescaling, can be approximated by a nice continuous-time process, we prove weak convergence in the Skorokhod topology of the scaled ancestral process to a stochastic time change of Kingman's coalescent, the time change being given by an additive functional of the limiting backward size process.

We study the genealogical structure of samples from a population for which any given generation is made up of direct descendants from several previous generations. These occur in nature when there are seed banks or egg banks allowing an individual to leave offspring several generations in the future. We show how this temporal structure in the reproduction mechanism causes a decrease in the coalescence rate. We also investigate the effects of age-dependent neutral mutations. Our main result gives weak convergence of the scaled ancestral process, with the usual diffusion scaling, to a coalescent process which is equivalent to a time-changed version of Kingman's coalescent.

Haploid population models with non-overlapping generations and fixed population size N are considered. It is assumed that the family sizes ν1,…,νN within a generation are exchangeable random variables. Rates of convergence for the finite-dimensional distributions of a properly time-scaled ancestral coalescent process are established and expressed in terms of the transition probabilities of the ancestral process, i.e., in terms of the joint factorial moments of the offspring variables ν1,…,νN.

The Kingman coalescent appears in the limit as the population size N tends to infinity if and only if triple mergers are asymptotically negligible in comparison with binary mergers. In this case, a simple upper bound for the rate of convergence of the finite-dimensional distributions is derived. It depends (up to some constants) only on the three factorial moments E((ν1)2), E((ν1)3) and E((ν1)2(ν2)2), where (x)k := x(x-1)…(x-k+1). Examples are the Wright-Fisher model, where the rate of convergence is of order N-1, and the Moran model, with a convergence rate of order N-2.

Take a sample of individuals in the fixed-size population model with exchangeable family sizes. Follow the ancestral lines for the sampled individuals backwards in time to observe the ancestral process. We describe a class of asymptotic structures for the ancestral process via a convergence criterion. One of the basic conditions of the criterion prevents simultaneous mergers of ancestral lines. Another key condition implies that the marginal distribution of the family size is attracted by an infinitely divisible distribution. If the latter is normal the coalescent allows only for pairwise mergers (Kingman's coalescent). Otherwise multiple mergers happen with positive probability.

Previous study of the time to a common ancestor of all present-day individuals has focused on models in which each individual has just one parent in the previous generation. For example, ‘mitochondrial Eve’ is the most recent common ancestor (MRCA) when ancestry is defined only through maternal lines. In the standard Wright-Fisher model with population size n, the expected number of generations to the MRCA is about 2n, and the standard deviation of this time is also of order n. Here we study a two-parent analog of the Wright-Fisher model that defines ancestry using both parents. In this model, if the population size n is large, the number of generations, 𝒯n, back to a MRCA has a distribution that is concentrated around lgn (where lg denotes base-2 logarithm), in the sense that the ratio 𝒯n(lgn) converges in probability to 1 as n→∞. Also, continuing to trace back further into the past, at about 1.77 lgn generations before the present, all partial ancestry of the current population ends, in the following sense: with high probability for large n, in each generation at least 1.77lgn generations before the present, all individuals who have any descendants among the present-day individuals are actually ancestors of all present-day individuals.

A simple convergence theorem for sequences of Markov chains is presented in order to derive new ‘convergence-to-the-coalescent’ results for diploid neutral population models.

For the so-called diploid Wright-Fisher model with selfing probability s and mutation rate θ, it is shown that the ancestral structure of n sampled genes can be treated in the framework of an n-coalescent with mutation rate ̃θ := θ(1-s/2), if the population size N is large and if the time is measured in units of (2-s)N generations.

‘Convergence-to-the-coalescent’ theorems for two-sex neutral population models are presented. For the two-sex Wright-Fisher model the ancestry of n sampled genes behaves like the usual n-coalescent, if the population size N is large and if the time is measured in units of 4N generations. Generalisations to a larger class of two-sex models are discussed.

A new Markov chain is introduced which can be used to describe the family relationships among n individuals drawn from a particular generation of a large haploid population. The properties of this process can be studied, simultaneously for all n, by coupling techniques. Recent results in neutral mutation theory are seen as consequences of the genealogy described by the chain.