Open AccessThe coalescent with replication-independent mutations
Author(s) -
Stephen M. Krone,
Beth M Tuschhoff
Publication year - 2022
Publication title -
peerj
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.927
H-Index - 70
ISSN - 2167-8359
DOI - 10.7717/peerj.12926
Subject(s) - coalescent theory , replication (statistics) , biology , mutation rate , genetics , genetic diversity , genetic drift , estimator , evolutionary biology , gene , genetic variation , statistics , mathematics , phylogenetics , population , demography , virology , sociology
We develop the mathematical structure of the neutral coalescent with both replication-dependent and replication-independent mutations. This allows us to explain and quantify empirical results that explore differences in genetic diversity in bacterial cultures with different growth rates. We also derive an unbiased and consistent estimator for the replication-independent mutation rate that is based on a comparison of total single nucleotide polymorphism counts for two independent well-mixed cultures with different growth rates. In addition to explaining differences in genetic diversity between well-mixed cultures with different (but constant) growth rates, our coalescent also quantifies the effects of fluctuating growth rates—a situation that can be common in natural populations.