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Nature. 2017 Nov 2;551(7678):45-50. doi: 10.1038/nature24287. Epub 2017 Oct 18.

The dynamics of molecular evolution over 60,000 generations.

Good BH1,2,3,4,5, McDonald MJ1,2,6, Barrick JE7,8, Lenski RE8,9, Desai MM1,2,3.

Author information

1
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
2
FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
3
Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.
4
Department of Physics, University of California Berkeley, Berkeley, California 94720, USA.
5
Department of Bioengineering, University of California Berkeley, Berkeley, California 94720, USA.
6
Centre for Geometric Biology, School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia.
7
Department of Molecular Biosciences, The University of Texas, Austin, Texas 78712, USA.
8
BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan 48824, USA.
9
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA.

Abstract

The outcomes of evolution are determined by a stochastic dynamical process that governs how mutations arise and spread through a population. However, it is difficult to observe these dynamics directly over long periods and across entire genomes. Here we analyse the dynamics of molecular evolution in twelve experimental populations of Escherichia coli, using whole-genome metagenomic sequencing at five hundred-generation intervals through sixty thousand generations. Although the rate of fitness gain declines over time, molecular evolution is characterized by signatures of rapid adaptation throughout the duration of the experiment, with multiple beneficial variants simultaneously competing for dominance in each population. Interactions between ecological and evolutionary processes play an important role, as long-term quasi-stable coexistence arises spontaneously in most populations, and evolution continues within each clade. We also present evidence that the targets of natural selection change over time, as epistasis and historical contingency alter the strength of selection on different genes. Together, these results show that long-term adaptation to a constant environment can be a more complex and dynamic process than is often assumed.

PMID:
29045390
PMCID:
PMC5788700
DOI:
10.1038/nature24287
[Indexed for MEDLINE]
Free PMC Article

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