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Selected Publication:

Type of publication: Journal Article
Type of document: Full Paper

Year: 2020

Authors: Vogl, C; Mikula, LC; Burden, CJ

Title: Maximum likelihood estimators for scaled mutation rates in an equilibrium mutation-drift model.

Source: Theor Popul Biol. 2020; 134:106-118

Authors Vetmeduni Vienna:

Vogl Claus

Vetmed Research Units
Institute of Animal Breeding and Genetics, Unit of Molecular Genetics

Project(s): Population Genetics

The stationary sampling distribution of a neutral decoupled Moran or Wright-Fisher diffusion with neutral mutations is known to first order for a general rate matrix with small but otherwise unconstrained mutation rates. Using this distribution as a starting point we derive results for maximum likelihood estimates of scaled mutation rates from site frequency data under three model assumptions: a twelve-parameter general rate matrix, a nine-parameter reversible rate matrix, and a six-parameter strand-symmetric rate matrix. The site frequency spectrum is assumed to be sampled from a fixed size population in equilibrium, and to consist of allele frequency data at a large number of unlinked sites evolving with a common mutation rate matrix without selective bias. We correct an error in a previous treatment of the same problem (Burden and Tang, 2017) affecting the estimators for the general and strand-symmetric rate matrices. The method is applied to a biological dataset consisting of a site frequency spectrum extracted from short autosomal introns in a sample of Drosophila melanogaster individuals.Copyright © 2020 Elsevier Inc. All rights reserved.

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