Phase-type distributions in population genetics

DOI10.1016/J.TPB.2019.02.001zbMATH Open1415.92124arXiv1806.01416OpenAlexW2962798467WikidataQ92044130 ScholiaQ92044130MaRDI QIDQ1999481FDOQ1999481

Authors: Asger Hobolth, Arno Siri-Jégousse, Mogens Bladt 

Publication date: 27 June 2019

Published in: Theoretical Population Biology (Search for Journal in Brave)

Abstract: Probability modelling for DNA sequence evolution is well established and provides a rich framework for understanding genetic variation between samples of individuals from one or more populations. We show that both classical and more recent models for coalescence (with or without recombination) can be described in terms of the so-called phase-type theory, where complicated and tedious calculations are circumvented by the use of matrices. The application of phase-type theory consists of describing the stochastic model as a Markov model by appropriately setting up a state space and calculating the corresponding intensity and reward matrices. Formulae of interest are then expressed in terms of these aforementioned matrices. We illustrate this by a few examples calculating the mean, variance and even higher order moments of the site frequency spectrum in the multiple merger coalescent models, and by analysing the mean and variance for the number of segregating sites for multiple samples in the two-locus ancestral recombination graph. We believe that phase-type theory has great potential as a tool for analysing probability models in population genetics. The compact matrix notation is useful for clarification of current models, in particular their formal manipulation (calculation), but also for further development or extensions.

Full work available at URL: https://arxiv.org/abs/1806.01416

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zbMATH Keywords

recombinationsite frequency spectrumcoalescent theorysegregating sitesmultiple mergerphase-type theory

Mathematics Subject Classification ID

Genetics and epigenetics (92D10)

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Cited In (20)

• Statistical tools for seed bank detection
• The impact of genetic diversity statistics on model selection between coalescents
• A boosting first-hitting-time model for survival analysis in high-dimensional settings
• Rates of convergence in the two-island and isolation-with-migration models
• Seed bank Cannings graphs: how dormancy smoothes random genetic drift
• Sparse moments of univariate step functions and allele frequency spectra
• Phase-type distribution approximations of the waiting time until coordinated mutations get fixed in a population
• Building mean field ODE models using the generalized linear chain trick \& Markov chain theory
• Characterisation of multivariate phase type distributions
• Asymptotics of the frequency spectrum for general Dirichlet \(\Xi\)-coalescents
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• Some results on optimal stopping under phase-type distributed implementation delay
• Identifying Markov chain models from time-to-event data: an algebraic approach
• Site frequency spectrum of the Bolthausen-Sznitman coalescent
• Biological populations as stationary distributions in the space of genotypes
• Graph-based algorithms for phase-type distributions
• Using colored Petri nets to construct coalescent hidden Markov models: automatic translation from demographic specifications to efficient inference methods
• Multivariate phase-type theory for the site frequency spectrum
• Estimating the lambda measure in multiple-merger coalescents
• The shape of a seed bank tree

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