Evolutionary Process More Detailed Than Previously Believed, Study Shows

Working with populations of yeast cells, which were color-coded by fluorescent markers, Katy Kao, assistant professor in the Artie McFerrin Department of Chemical Engineering, and Stanford University colleague Gavin Sherlock were able to evolve the cells while maintaining a visual analysis of the entire process.

Their research, which appears in the December edition of Nature Genetics, shows the evolutionary process to be much more dynamic than initially thought, with multiple beneficial adaptations arising within a population. These adaptations, Kao explained, triggered a competition between these segments, known as “clonal interference.”

It’s the first direct experimental evidence of this phenomenon in eukaryotic cells, or cells with nuclei, and it contrasts the widely accepted classical model of evolution, which doesn’t account for simultaneously developing beneficial adaptations, she said. Instead, that model adopts a linear approach, theorizing that a population acquires such adaptations successively, one after another. Rather than a competition occurring, the model posits a complete replacement of one generation by another better-adapted generation.

That wasn’t the case in Kao’s sample.

Observing the color-coded yeast populations as they evolved to respond to their environment, Kao saw some colors expand while others contracted – a sign that adaptations were occurring. But rather than one segment of the population continuing to shrink until it was completely replaced, some segments were able to compete long enough to acquire further adaptations. When this happened, Kao explained, these populations of cells – once apparently less-fit – began to swell while once-dominant populations started to shrink. This constant reduction and burgeoning of populations signaled the development of multiple beneficial adaptations and a subsequent competition by the cells that acquired them, Kao said.

“Essentially, we were watching evolution in action,” Kao said. “We’re watching evolution in real time. We’re actually seeing a mutation that shows these things have adapted and seeing their population thrive and expand from this adaptation. This is how evolution works.

“In one of our experiments we were able to see five independent population expansions. We had one adaptive mutation that allowed a population to expand, but before it was able to completely take over another un-mutated population of the same cells acquired a different mutation that allowed it to succeed and impede the expansion of the first population.”

In addition to determining if and when a population acquired an adaptation, Kao also identified the specific adaptations that were acquired. She accomplished this using a DNA-based technology that enabled her to determine the specific locations on the genes of the yeast cells that expressed beneficial adaptations.

What she found was that as populations rise and fall, some of these beneficial adaptations factor into the continued evolution of the organism; others don’t.

“Due to the possibility of this competition, beneficial mutations that have been lost during the evolution of an organism will not be identified from just the final generation of that organism,” Kao explained. “Indeed, we found that several of the mutations were nearly lost in the population by the end of the experiment due to this competition.”

In other words, as Mother Nature sorts things out, some adaptations go by the wayside, with the latest generation of an organism sometimes showing no traces of them.

“Think of this as another piece of the evolution puzzle,” Kao said. “We’re gaining a comprehensive understanding of the way a microorganism adapts to its environment as it fights to survive. We’re demonstrating that the evolutionary journey has many more ‘twists and turns’ than we once thought.”

The knowledge of those twists and turns ultimately could prove to be very important, Kao explained, because it helps paint a complete picture of an organism’s evolution. With that picture intact, scientists stand to gain a better understanding of the way certain highly resistant infections develop and progress.

One such infection, Kao noted, occurs within the bodies of people with weakened immune systems. In such cases, a fungus that is normally kept in check increases to dangerous infectious levels, prompting doctors to prescribe antifungal treatments. Sometimes these treatments become ineffective, and Kao says that one of the reasons for that ineffectiveness is that the human body becomes a vessel for evolution, much like what occurred in her laboratory experiment.

“The fungus is being subjected to a selected pressure, in this instance drugs,” Kao said. “As it fights for its survival, mutations occur that help make this fungus resistant to the drug treatments. Most of the clinical studies of these patients isolate just one sample of the mutation at one point in time. But a recent study that isolated these samples from different periods in time suggested that some of the later ones were not derived from earlier ones.”

Understanding how this fungus evolves from its initial stages to its most recent stage could lead to the development of better treatments for it, Kao said.

The knowledge of an organism’s complete “adaptive landscape” also is likely to benefit the rapidly growing field of metabolic engineering, Kao noted.

As scientists attempt to enhance cells so that they perform such beneficial activities as producing energy or disposing of waste, they’ll need to know all of the particular pathways where genes are involved in the expression of a particular trait, Kao said. This is especially important as scientists work to enhance microorganisms so that they possess a higher tolerance to the products they produce, Kao said.

For example, a microorganism might be genetically enhanced to produce butanol as a potential biofuel, she said. The problem however, Kao explained, is these microorganisms generally have a low tolerance to butanol, and at very low concentrations they will start to die from what they are producing.

One way to address this problem is to evolve these microorganisms into forms with a higher tolerance, Kao noted. By examining the entire evolutionary process of such a microorganism, scientists could discover a once-overlooked beneficial adaptation that arose somewhere along the way that would help enhance tolerance. That adaptation might otherwise not be apparent if only the current generation of the microorganism is examined, she said.