Approximation of the allelic frequency spectrum in general supercritical branching populations

DOI10.1016/J.SPA.2020.10.008MaRDI QIDQ1994903zbMATH OpenOpenAlexFDO

Authors Benoit Henry

Publication date 18 February 2021

Published in Stochastic Processes and their Applications (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1701.07281

zbMATH Keywords

allelic frequency spectrumallelic partitionbranching processescentral limit theoremsLaplace distributionneutral mutationssplitting tree

Mathematics Subject Classification ID

Central limit and other weak theorems (60F05) Processes with independent increments; Lévy processes (60G51) Branching processes (Galton-Watson, birth-and-death, etc.) (60J80) Applications of branching processes (60J85) Markov renewal processes, semi-Markov processes (60K15) Genetics and epigenetics (92D10)

Abstract: We consider a general branching population where the lifetimes of individuals are i.i.d. with arbitrary distribution and where each individual gives birth to new individuals at Poisson times independently from each other. In addition, we suppose that individuals experience mutations at Poissonian rate $heta$ under the infinitely many alleles assumption assuming that types are transmitted from parents to offspring. This mechanism leads to a partition of the population by type, called the allelic partition. The main object of this work is the frequency spectrum $A(k,t)$ which counts the number of families of size $k$ in the population at time $t$. The process $(A(k,t),tinmathbb{R}_{+})$ is an example of non-Markovian branching process belonging to the class of general branching processes counted by random characteristics. In this work, we propose methods of approximation to replace the frequency spectrum by simpler quantities. Our main goal is study the asymptotic error made during these approximations through central limit theorems. In a last section, we perform several numerical analysis using this model, in particular to analyze the behavior of one of these approximations with respect to Sabeti's Extended Haplotype Homozygosity [18].

Review text

The author considers a branching population model with the following dynamics: starting with a single individual (called the ancestor) whose lifetime is distributed according to an arbitrary probability distribution on \((0,\infty]\), this ancestor, during its lifetime, gives birth to new individuals according to a Poisson process with a constant rate. Each birth event gives a single new individual. Then each child of the ancestor lives and gives birth according to the same mechanism independently of the other individuals in the population. In addition, neutral mutations can occur on individuals and each new mutation confers to its holder a brand new type (i.e., never seen in the population): this is the infinitely many alleles assumption. It is also supposed that every individual inherits the type of its parent. This model leads to a partition of the population by types. The frequency spectrum of the population alive at time t is defined as the sequence \(A(k,t)\), \(k\in\{1,2,\ldots\}\), where, for each \(k\), \(A(k,t)\) is the number of families (i.e., sets of individuals carrying the same type) of size \(k\) in the population. In general the law of the frequency spectrum \(A(k,t)\), \(k\in\{1,2,\ldots\}\), is hardly tractable. Motivated by this, the author introduced two approximations of the frequency spectrum and investigated their errors. The first approximation is \[ (A(k,t))_{k\in\{1,2,\ldots\}} \approx (c_k)_{k\in\{1,2,\ldots\}}{\mathrm{e}}^{\alpha t} \mathcal{E}, \] where \(c_k\), \(k\in\{1,2,\ldots\}\), are some explicitly given deterministic constants, \(\alpha>0\) (the largest root of the Laplace exponent of the corresponding splitting tree), and \(\mathcal{E}\) is a conditionally exponentially distributed random variable given non-extinction. Here \(\alpha>0\) corresponds to the supercritical case, when \(\alpha\) is also called the Malthusian parameter. The second approximation is \[ (A(k,t))_{k\in\{1,2,\ldots\}} \approx (c_k)_{k\in\{1,2,\ldots\}} N_t, \] where \(N_t\) is the number of living individuals in the population at time \(t\). The process \((N_t)_{t\geq 0}\) is known as a binary homogeneous Crump-Mode-Jagers process. For both approximations, the author shows that the appropriately scaled error converges to a Laplace distribution, where the convergence is understood as convergence of processes for the product topology of \({\mathbb{R}}^{\{1,2,\ldots\}}\). The limit law depends on a parameter related to mutation, and this parameter is supposed to be not equal to \(\alpha\).

Recommendations

• Moments of the frequency spectrum of a splitting tree with neutral Poissonian mutations
• scientific article; zbMATH DE number 4087487
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Cites work

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Cited in

(1)

• Quasi-equilibrium theory for the distribution of rare alleles in a subdivided population: Justification and implications

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