title: Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process.
abstract: The molecular clock of neutral mutations, which represents linear mutation fixation over generations, is theoretically explained by genetic drift in fitness-steady evolution or hitchhiking in adaptive evolution. The present study is the first experimental demonstration for the molecular clock of neutral mutations in a fitness-increasing evolutionary process. The dynamics of genome mutation fixation in the thermal adaptive evolution of Escherichia coli were evaluated in a prolonged evolution experiment in duplicated lineages. The cells from the continuously fitness-increasing evolutionary process were subjected to genome sequencing and analyzed at both the population and single-colony levels. Although the dynamics of genome mutation fixation were complicated by the combination of the stochastic appearance of adaptive mutations and clonal interference, the mutation fixation in the population was simply linear over generations. Each genome in the population accumulated 1.6 synonymous and 3.1 non-synonymous neutral mutations, on average, by the spontaneous mutation accumulation rate, while only a single genome in the population occasionally acquired an adaptive mutation. The neutral mutations that preexisted on the single genome hitchhiked on the domination of the adaptive mutation. The successive fixation processes of the 128 mutations demonstrated that hitchhiking and not genetic drift were responsible for the coincidence of the spontaneous mutation accumulation rate in the genome with the fixation rate of neutral mutations in the population. The molecular clock of neutral mutations to the fitness-increasing evolution suggests that the numerous neutral mutations observed in molecular phylogenetic trees may not always have been fixed in fitness-steady evolution but in adaptive evolution.
authors.affiliation: Faculty of Science, Toho University, Funabashi, Chiba, Japan.
authors.forename: Toshihiko
authors.initials: T
authors.lastname: Kishimoto
authors.affiliation: Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
authors.forename: Bei-Wen
authors.initials: BW
authors.lastname: Ying
authors.affiliation: Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan.
authors.forename: Saburo
authors.initials: S
authors.lastname: Tsuru
authors.affiliation: The Organization for the Promotion of Leading Graduate Schools, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan.
authors.forename: Leo
authors.initials: L
authors.lastname: Iijima
authors.affiliation: QBiC, RIKEN, Suita, Osaka, Japan.
authors.forename: Shingo
authors.initials: S
authors.lastname: Suzuki
authors.affiliation: Faculty of Science, Toho University, Funabashi, Chiba, Japan.
authors.forename: Tomomi
authors.initials: T
authors.lastname: Hashimoto
authors.affiliation: Faculty of Science, Toho University, Funabashi, Chiba, Japan.
authors.forename: Ayana
authors.initials: A
authors.lastname: Oyake
authors.affiliation: Faculty of Science, Toho University, Funabashi, Chiba, Japan.
authors.forename: Hisaka
authors.initials: H
authors.lastname: Kobayashi
authors.affiliation: Faculty of Science, Toho University, Funabashi, Chiba, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Someya
authors.affiliation: Faculty of Science, Toho University, Funabashi, Chiba, Japan.
authors.forename: Dai
authors.initials: D
authors.lastname: Narisawa
authors.affiliation: Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan; Graduate School of Frontier Sciences, Osaka University, Yamadaoka, Suita, Osaka, Japan; Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Agency (JST), Suita, Osaka, Japan.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Yomo
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D019020:Directed Molecular Evolution; D004926:Escherichia coli / Q000235:genetics; D040961:Genetic Drift; D056084:Genetic Fitness; D009154:Mutation / Q000235:genetics; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013696:Temperature