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Of course, this is an oversimplification in species with sexual reproduction, multiple beneficial mutations may be brought together by recombination such that the fixation of beneficial genes need not occur sequentially.
In large populations of asexually reproducing organisms, for example, E. coli, multiple beneficial mutations may co-occur.
In addition, recombination may not be an essential process, since if the mutation rate is sufficiently high and the population size large, genomes carrying multiple beneficial mutations should appear even in asexual populations [28], [29].
A second difference between the in vivo approach used for cassette mutagenesis and the in vitro strategy taken here is that the in vivo assay focuses on only two or three residues at a time, making it difficult to identify the cumulative effect of multiple beneficial mutations.
Thus, a subpopulation with a higher mutation rate could benefit from more multiple beneficial mutations, as Figure 3 shown.
Individuals that carry multiple beneficial mutations probably have higher fitness than those with one original beneficial mutation.
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Here, we develop a comprehensive model of adaptive evolution in linked genomes, which integrates interference interactions between multiple beneficial and deleterious mutations into a unified framework.
The role of recombination in bringing together either multiple beneficial or multiple deleterious mutations (in the language of population genetics, the dissolution of negative linkage disequilibrium) lies at the core of modern models of recombination and selection.
These results might suggest that, in the evolutionary dynamics of these populations, there were multiple clones with different beneficial mutations coexisting and competing in the environment, i.e., clonal interference [ 28].
It is established that in asexual populations, two problems affect the adaptation: clonal interference and multiple mutations; clonal interference causes beneficial mutations in different genetic backgrounds compete with one another, while multiple mutations in the same background could assist each other's spread toward fixation [ 40- 44].
The beneficial mutations identified span multiple pathways, and we identified pairs of mutations that individually provide only minor decreases in antibiotic susceptibility but that combine to provide higher tolerance.
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