Phase-type distributions in population genetics

DOI10.1016/J.TPB.2019.02.001MaRDI QIDQ1999481zbMATH OpenOpenAlexWikidataFDO

Authors Asger Hobolth, Arno Siri-Jégousse, Mogens Bladt

Publication date 27 June 2019

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

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

zbMATH Keywords

recombinationsite frequency spectrumcoalescent theorysegregating sitesmultiple mergerphase-type theory

Mathematics Subject Classification ID

Genetics and epigenetics (92D10)

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.

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Cited in

(20)

• The shape of a seed bank tree
• The impact of genetic diversity statistics on model selection between coalescents
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• 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
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