13.5: Longer term mutation and evolution studies

We can see the spontaneous mutation model applies throughout the biological world. Wherever we look mutations appear to arise by chance. If they persist within the population (see above), they become alleles. It is worth reiterating that because of non-adaptive processes such as genetic drift, new neutral or beneficial mutations may be lost because they are initially extremely rare within the population, while mildly deleterious mutations can become fixed by chance alone.

To study such evolutionary processes in a laboratory setting is not easy, but a now classic example of such a study was carried out by Richard Lenski (b. 1956) and his associates. They have been growing twelve originally identical populations of the bacteria E. coli for more than 25 years and 60,000 generations.^[471] One, of many, characteristics of E. coli that distinguish it from other bacteria is that it is unable to metabolize citrate in the presence of O₂. In the course of their studies, Blount et al observed the appearance of E. coli variants that could metabolize citrate in the presence of O₂; a beneficial evolutionary adaptation, since it provided those cells with a previously un-utilized energy and carbon source.^[472] By tracking backward, the investigators identified a “pre-disposing” mutation that occurred in this lineage around generation 20,000. The presence of this mutation made it more likely that subsequent mutations would enable cells to grow on citrate, producing a Cit⁺ phenotype. Molecular analyses indicated that the initial Cit⁺ phenotype, which appeared around generation ~31,500, was weak and involved a ~3000 bp genomic duplication that led to increased expression of the citT gene. citT encodes a protein involved in the import of citrate into the cell. Subsequent studies identified mutations in other genes in the Cit⁺ strain that further improved the cells’ ability to metabolize citrate.^[473] One of these mutations led to increased expression of DctA, a gene that encodes a membrane transport protein that increases the cell’s ability to import various nutrients normally released into the media, giving the cell a reproductive advantage when grown on citrate. An interesting aspect of these studies was the backlash from some creationists, who rejected the possibility of the evolution of new traits via mutation and selection.^[474]

A second more recent study on bacterial evolution, involved looking at the evolution of antibiotic resistance. It involved a giant agar plate (a “megaplate”) and an antibiotic gradient (↓). Bacterial cells were placed in the regions free of antibiotic and over time their ability to grow into regions of higher and higher antibiotic concentrations was visualized directly (video link). It is possible to watch the emergence of new variants at the boundary regions as new mutations arise.^[475]

An important point to recall about such bacterial evolution studies is that these organisms are reproducing asexually, as clones. That means that they do not interbreed with other organisms in the population, but it also means that (in the absence of horizontal gene transfer) all mutations necessary for a phenotype need to occur independently in a single clonal population. If such mutations lead to a reproductive advantage they can, barring accidental death, take over the population – a process known as a reproductive sweep. This can lead to the loss of alleles present in other clones within the population. If these lost alleles were useful (that is enhanced reproductive success), they would need to appear again, independently, through random mutation and selection (or be transferred horizontally, something that is not occurring in this system). In sexually reproducing organisms, alleles from different individuals can be mixed to more rapidly produce beneficial phenotypes.

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