Rate matrix estimation from site frequency data

DOI10.1016/J.TPB.2016.10.001zbMATH Open1368.92116arXiv1607.04372OpenAlexW2509340825WikidataQ31141499 ScholiaQ31141499MaRDI QIDQ2014385FDOQ2014385

Yurong Tang, Conrad J. Burden

Publication date: 11 August 2017

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

Abstract: A procedure is described for estimating evolutionary rate matrices from observed site frequency data. The procedure assumes (1) that the data are obtained from a constant size population evolving according to a stationary Wright-Fisher model; (2) that the data consist of a multiple alignment of a moderate number of sequenced genomes drawn randomly from the population; and (3) that within the genome a large number of independent, neutral sites evolving with with a common mutation rate matrix can be identified. No restrictions are imposed on the scaled rate matrix other than that the off-diagonal elements are positive and <<1, and that the rows sum to zero. In particular the rate matrix is not assumed to be reversible. The key to the method is an approximate stationary solution to the forward Kolmogorov equation for the multi-allele neutral Wright-Fisher model in the limit of low mutation rates.

Full work available at URL: https://arxiv.org/abs/1607.04372

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zbMATH Keywords

neutral evolutionmulti-allele Wright-Fisherdecoupled Moranevolutionary rate matrices

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10) Problems related to evolution (92D15)

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Cited In (7)

• Maximum likelihood estimators for scaled mutation rates in an equilibrium mutation-drift model
• The stationary and quasi-stationary properties of neutral multi-type branching process diffusions
• An approximate stationary solution for multi-allele neutral diffusion with low mutation rates
• Developments in coalescent theory from single loci to chromosomes
• Stationary distribution of a 2-island 2-allele wright-Fisher diffusion model with slow mutation and migration rates
• The stationary distribution of a sample from the Wright-Fisher diffusion model with general small mutation rates
• The transition distribution of a sample from a Wright-Fisher diffusion with general small mutation rates

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