Maximum likelihood estimators for scaled mutation rates in an equilibrium mutation–drift model

Claus Vogl, Lynette C. Mikula and Conrad J. Burden

Theoretical Population Biology, 2020, vol. 134, issue C, 106-118

Abstract: 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.

Keywords: Mutation–drift model; Decoupled Moran diffusion; Wright–Fisher diffusion; Scaled mutation parameters; Strand-symmetry (search for similar items in EconPapers)
Date: 2020
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Citations: View citations in EconPapers (1)

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Persistent link: https://EconPapers.repec.org/RePEc:eee:thpobi:v:134:y:2020:i:c:p:106-118

DOI: 10.1016/j.tpb.2020.06.001

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