Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process.
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 neu...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2015-07-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC4503671?pdf=render |
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| author | Toshihiko Kishimoto Bei-Wen Ying Saburo Tsuru Leo Iijima Shingo Suzuki Tomomi Hashimoto Ayana Oyake Hisaka Kobayashi Yuki Someya Dai Narisawa Tetsuya Yomo |
| author_facet | Toshihiko Kishimoto Bei-Wen Ying Saburo Tsuru Leo Iijima Shingo Suzuki Tomomi Hashimoto Ayana Oyake Hisaka Kobayashi Yuki Someya Dai Narisawa Tetsuya Yomo |
| author_sort | Toshihiko Kishimoto |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T00:53:08Z |
| format | Article |
| id | doaj.art-5dbc3a7efb564e06943c72bb49cd1095 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-04-13T00:53:08Z |
| publishDate | 2015-07-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-5dbc3a7efb564e06943c72bb49cd10952022-12-22T03:09:48ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042015-07-01117e100539210.1371/journal.pgen.1005392Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process.Toshihiko KishimotoBei-Wen YingSaburo TsuruLeo IijimaShingo SuzukiTomomi HashimotoAyana OyakeHisaka KobayashiYuki SomeyaDai NarisawaTetsuya YomoThe 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.http://europepmc.org/articles/PMC4503671?pdf=render |
| spellingShingle | Toshihiko Kishimoto Bei-Wen Ying Saburo Tsuru Leo Iijima Shingo Suzuki Tomomi Hashimoto Ayana Oyake Hisaka Kobayashi Yuki Someya Dai Narisawa Tetsuya Yomo Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process. PLoS Genetics |
| title | Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process. |
| title_full | Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process. |
| title_fullStr | Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process. |
| title_full_unstemmed | Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process. |
| title_short | Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process. |
| title_sort | molecular clock of neutral mutations in a fitness increasing evolutionary process |
| url | http://europepmc.org/articles/PMC4503671?pdf=render |
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