Kingman's model describes the evolution of a one-locus haploid population of infinite size and discrete generations under the competition of selection and mutation. A random generalisation has been made in a previous paper which assumes all mutation probabilities to be i.i.d.. The weak convergence of fitness distributions to a globally stable equilibrium for any initial distribution was proved. A condensation occurs if almost surely a positive proportion of the population travels to and condensates on the largest fitness value due to the dominance of selection over mutation. A criterion of condensation was given which relies on the equilibrium whose explicit expression is however unknown. This paper tackles these problems based on the discovery of a matrix representation of the random model. An explicit expression of the equilibrium is obtained and the key quantity in the condensation criterion can be estimated. Moreover we examine how the design of randomness in Kingman's model affects the fitness level of the equilibrium by comparisons between different models. The discovered facts are conjectured to hold in other more sophisticated models.
Kingman's model of selection and mutation studies the limit type value distribution in an asexual population of discrete generations and infinite size undergoing selection and mutation. This paper generalizes the model to analyse the long-term evolution of Escherichia. coli in Lenski experiment. Weak assumptions for fitness functions are proposed and the mutation mechanism is the same as in Kingman's model. General macroscopic epistasis are designable through fitness functions. Convergence to the unique limit type distribution is obtained.
Kingman's House-of-Cards model is a simple and celebrated model to describe the evolution of population under the competition of selection and mutation. Letting mutation probabilities vary on generations makes the model more realistic and meaningful. This paper considers the condensation phenomenon and limit fitness distribution when Kingman's model is put into a random environment consisting of i.i.d. random mutation probabilities. It turns out that the random model is completely dominated by Kingman's model in terms of condensation and fitness. Another random model where all mutation probabi…
For a one-locus haploid infinite population with discrete generations, the celebrated Kingman's model describes the evolution of fitness distributions under the competition of selection and mutation, with a constant mutation probability. Letting mutation probabilities vary on generations reflects the influence of a random environment. This paper generalises Kingman's model by using a sequence of i.i.d. random mutation probabilities. For any distribution of the sequence, the weak convergence of fitness distributions to the globally stable equilibrium for any initial fitness distribution is prov…
We describe the onset of condensation in the simple model for the balance between selection and mutation given by Kingman in terms of a scaling limit theorem. Loosely speaking, this shows that the wave moving towards genes of maximal fitness has the shape of a gamma distribution. We conjecture that this wave shape is a universal phenomenon that can also be found in a variety of more complex models, well beyond the genetics context, and provide some further evidence for this.
The Ancestral Selection Graph (ASG) is an important genealogical process which extends the well-known Kingman coalescent to incorporate natural selection. We show that the number of lineages of the ASG with and without mutation is asymptotic to $2/t$ as $t\to 0$, in agreement with the limiting behaviour of the Kingman coalescent. We couple these processes on the same probability space using a Poisson random measure construction that allows us to precisely compare their hitting times. These comparisons enable us to characterise the speed of coming down from infinity of the ASG as well as its fl…
In this paper we introduce a multilocus diffusion model of a population of $N$ haploid, asexually reproducing individuals. The model includes parent-dependent mutation and interlocus selection, the latter limited to pairwise relationships but among a large number of simultaneous loci. The diffusion is expressed as a system of stochastic differential equations (SDEs) that are coupled in the drift functions through a Shahshahani gradient-like structure for interlocus selection. The system of SDEs is derived from a sequence of Markov chains by weak convergence. We find the explicit stationary (in…
The results in this paper provide new information on asymptotic properties of classical models: the neutral Kingman coalescent under a general finite-alleles, parent-dependent mutation mechanism, and its generalisation, the ancestral selection graph. Several relevant quantities related to these fundamental models are not explicitly known when mutations are parent dependent. Examples include the probability that a sample taken from a population has a certain type configuration, and the transition probabilities of their block counting jump chains. In this paper, asymptotic results are derived fo…
Let $Λ$ be a finite measure on the unit interval. A $Λ$-Fleming-Viot process is a probability measure valued Markov process which is dual to a coalescent with multiple collisions ($Λ$-coalescent) in analogy to the duality known for the classical Fleming Viot process and Kingman's coalescent, where $Λ$ is the Dirac measure in 0. We explicitly construct a dual process of the coalescent with simultaneous multiple collisions ($Ξ$-coalescent) with mutation, the $Ξ$-Fleming-Viot process with mutation, and provide a representation based on the empirical measure of an exchangeable particle system alon…
Consider a haploid population of fixed finite size with a finite number of allele types and having Cannings exchangeable genealogy with neutral mutation. The stationary distribution of the Markov chain of allele counts in each generation is an important quantity in population genetics but has no tractable description in general. We provide upper bounds on the distributional distance between the Dirichlet distribution and this finite population stationary distribution for the Wright-Fisher genealogy with general mutation structure and the Cannings exchangeable genealogy with parent independent …
When an advantageous mutation occurs in a population, the favorable allele may spread to the entire population in a short time, an event known as a selective sweep. As a result, when we sample $n$ individuals from a population and trace their ancestral lines backwards in time, many lineages may coalesce almost instantaneously at the time of a selective sweep. We show that as the population size goes to infinity, this process converges to a coalescent process called a coalescent with multiple collisions. A better approximation for finite populations can be obtained using a coalescent with simul…
When a beneficial mutation occurs in a population, the new, favored allele may spread to the entire population. This process is known as a selective sweep. Suppose we sample $n$ individuals at the end of a selective sweep. If we focus on a site on the chromosome that is close to the location of the beneficial mutation, then many of the lineages will likely be descended from the individual that had the beneficial mutation, while others will be descended from a different individual because of recombination between the two sites. We introduce two approximations for the effect of a selective sweep…
During an infection, HIV experiences strong selection by immune system T cells. Recent experimental work has shown that MHC escape mutations form an important pathway for HIV to avoid such selection. In this paper, we study a model of MHC escape mutation. The model is a predator-prey model with two prey, composed of two HIV variants, and one predator, the immune system CD8 cells. We assume that one HIV variant is visible to CD8 cells and one is not. The model takes the form of a system of stochastic differential equations. Motivated by well-known results concerning the short life-cycle of HIV …
