Evolvability of phenotypically and genetically diverse Escherichia coli isolates

Date
2023-08
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Abstract

The potential for adaptive evolution through the production of heritable beneficial variation is commonly referred to as evolvability. Differences in evolvability can determine species’ ability to respond to ecological and climate changes, exploit vacant niche opportunities, or adapt to novel hosts and environments. Previous experimental work is largely limited to closely related laboratory populations, which are not representative of genetically and phenotypically distinct natural populations. Other studies in larger taxa have mostly relied on statistical analyses of demographic data to identify trends in population structure, but lack the support of experimental evidence. The dynamics of adaptation within natural populations, and the impact of selective history or ecological niche breadth on evolvability, are not well reported. To investigate the evolutionary patterns of natural populations naïve to a laboratory setting, I experimentally evolved a diverse collection of Escherichia coli isolates, in replicate, in four single carbon source environments for 1,000 generations. I found that evolvability, represented by increase in fitness, was best predicted by initial fitness of the natural isolate founder, and that ecological breadth and phylogenetic relatedness were not significantly correlated with evolvability. These results suggest that selective history, that shapes both genotype and phenotype, may not be a significant predicter of evolvability. I then sequenced evolved clones to examine the underlying genetic mechanisms of adaptation and assess the mutations available to evolving populations, because access to beneficial variation can dictate evolutionary paths and could be influenced by selective history. I found that mutations were substituted at a lower rate among conserved core genes than they were in accessory genes, and that parallel mutations in the same gene found among multiple evolved clones were more likely driven by selective environment than founder genotype. Finally, I experimentally tested a predicted mechanism through which prior adaptation increased evolvability by substituting new mutations to compensate for conditionally deleterious mutations and unmask the positive effects of pre-existing beneficial alleles. Overall, this work contributes to our growing understanding of evolvability, the underlying genetic mechanisms facilitating it, and how aspects of prior adaptation and selective history can shape the capacity for adaptive success.

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Keywords
Evolvability, Evolution, E. coli
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