Rate matrix estimation from site frequency data

DOI10.1016/J.TPB.2016.10.001MaRDI QIDQ2014385zbMATH OpenOpenAlexWikidataFDO

Authors Conrad J. Burden, Yurong Tang

Publication date 11 August 2017

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

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

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)

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.

Recommendations

• Maximum likelihood estimators for scaled mutation rates in an equilibrium mutation-drift model
• An approximate stationary solution for multi-allele neutral diffusion with low mutation rates
• An alternative derivation of the stationary distribution of the multivariate neutral Wright-Fisher model for low mutation rates with a view to mutation rate estimation from site frequency data
• Estimating the scaled mutation rate and mutation bias with site frequency data
• Asymptotic behavior of the scaled mutation rate estimators

Cites work

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Cited in

(8)

• The transition distribution of a sample from a Wright-Fisher diffusion with general small mutation rates
• An approximate stationary solution for multi-allele neutral diffusion with low mutation rates
• 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
• Stationary distribution of a 2-island 2-allele wright-Fisher diffusion model with slow mutation and migration rates
• Developments in coalescent theory from single loci to chromosomes
• Asymptotic behavior of the scaled mutation rate estimators
• The stationary distribution of a sample from the Wright-Fisher diffusion model with general small mutation rates

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