Trends in Genetics
ReviewExperimental Studies of Evolutionary Dynamics in Microbes
Section snippets
Surprising Complexity in Simple Experiments
For many decades, evolutionary adaptation in microbial populations was thought to proceed by ‘periodic selection’, where individual beneficial mutations arise sequentially and either go extinct or fix in independent selective sweeps [1]. In this picture, evolution is relatively simple: mutations arise randomly and then fix or go extinct at a rate that is commensurate with their individual selective effect. Our ability to predict how a population should evolve is then limited only by our
Studying Evolution without Phenotype
Many studies of adaptation in both natural and laboratory populations are focused primarily on understanding phenotypes; the goal is to characterize adaptive changes and to identify the evolutionary processes by which they arose as well as their genetic and molecular basis. Experimental studies of evolutionary dynamics focus instead on understanding evolution as a stochastic algorithm. That is, given a particular set of biological details (i.e., the set of mutations that can arise and their
Technological Advances in Observing Evolutionary Dynamics
There are three key challenges in observing evolutionary dynamics. First, the underlying events are mutations, and we ultimately want to track the frequencies of all of the genotypes they produce. These are typically difficult to observe directly. Second, evolutionary dynamics are fundamentally stochastic, so we typically wish to quantify the probabilities of different events. This often requires extensive replication. Finally, new mutations arise in single individuals. Their dynamics, while
Which Complications Are Important?
Theoretical studies of very simple models have provided a great deal of insight that underlies much intuition in evolutionary dynamics and population genetics. For example, many studies have analyzed how a population climbs a single fitness peak in the strong-selection-weak-mutation (SSWM) approximation where only one mutation is ever present in the population at a time. Similarly, models of neutral mutation accumulation and the balance between deleterious mutations and selection are often used
Concluding Remarks and Future Perspectives
It could be argued that studies of evolutionary dynamics in artificial and highly simplified laboratory conditions (which often lack spatial structure, temporal variability, interactions with other species, and other complexities) are unrepresentative of evolution in natural systems. However, we view this simplicity instead as a major strength of experimental evolution, which is a powerful tool precisely because complications can be introduced in a controlled, replicable way (see Outstanding
Acknowledgments
M.M.D. acknowledges support from the Simons Foundation (grant 376196), the National Science Foundation (DEB-1655960), and the National Institutes of Health (R01-GM104239).
Glossary
- Clonal interference
- competition between multiple different (and typically beneficial) mutations that are segregating simultaneously within the population.
- DNA barcode
- a DNA sequence that ‘barcodes’ a strain. This often refers to a naturally occurring sequenced used for species identification in ecological applications. In laboratory evolution, barcodes are sometimes instead random sequences (often ∼10–30 bp) that are integrated by the experimenter into a specific genomic location.
- Epistasis
- the
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Microbial experimental evolution in a massively multiplexed and high-throughput era
2022, Current Opinion in Genetics and DevelopmentCitation Excerpt :This era sharpened questions about how biological systems are continuously tuned during adaptation — evolution did not appear to be limited by lack of beneficial mutations. Improvements in genome engineering techniques paved the way to more complex experimental designs, which could now be coupled with problems that were previously only amenable to theoretical treatments [23,24]. For instance, McDonald et al. evolved populations with and without recombination [25,26], confirming theoretical predictions that sex promotes adaptation by both decoupling beneficial mutations from hitchhiking mutations and by alleviating the strength of clonal interference.
High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing
2021, Cell SystemsCitation Excerpt :Evolution experiments conducted in laboratory environments reproduce key aspects of microbial evolution that are observed in chronic infections and bioreactors (Barrick and Lenski, 2013; Gresham and Dunham, 2014). Certain aspects of genomic and phenotypic evolution in these controlled systems predictably occur across multiple replicate populations (Barrick, 2020; Cvijović et al., 2018; Furusawa et al., 2018; McDonald, 2019; Rainey et al., 2017), making them a useful testbed for adaptome mapping methods. In theory, tracking the frequencies of mutations during the earliest stages of clonal evolution from a single cell in these populations should allow one to map that cell’s adaptome.
Genetic Diversity and Evolution of Viral Populations
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