2019/11/27 by Claus Vogl, Vogl, Claus, Lynette Caitlin Mikula +3 · 1 citation
Biochemistry, Genetics and Molecular Biology · #Evolution and Genetic Dynamics #FOS: Biological sciences #Genetic Mapping and Diversity in Plants and Animals #Genetic diversity and population structure #Populations and Evolution (q-bio.PE)
paper · pdf · doi:10.48550/arxiv.1911.12494
openalex publication_date 2019/11/27 · openalex created_date 2022/07/26 · openalex updated_date 2026/07/28
The stationary sampling distribution of a neutral decoupled Moran or\nWright-Fisher diffusion with neutral mutations is known to first order for a\ngeneral rate matrix with small but otherwise unconstrained mutation rates.\nUsing this distribution as a starting point we derive results for maximum\nlikelihood estimates of scaled mutation rates from site frequency data under\nthree model assumptions: a twelve-parameter general rate matrix, a\nnine-parameter reversible rate matrix, and a six-parameter strand-symmetric\nrate matrix. The site frequency spectrum is assumed to be sampled from a fixed\nsize population in equilibrium, and to consist of allele frequency data at a\nlarge number of unlinked sites evolving with a common mutation rate matrix\nwithout selective bias. We correct an error in a previous treatment of the same\nproblem (Burden and Tang, 2017) affecting the estimators for the general and\nstrand-symmetric rate matrices. The method is applied to a biological dataset\nconsisting of a site frequency spectrum extracted from short autosomal introns\nin a sample of Drosophila melanogaster individuals.\n