Lehigh study: Yeast takes a nonlinear evolutionary pathway

Contrary to common belief, evolution sometimes produces organisms that are less fit than their distant ancestors. 

A research group from Lehigh University in Pennsylvania observed exactly that when analyzing populations of yeast that had undergone 1,000 generations of evolution in the lab. 

Their work with yeast provides experimental evidence that a series of adaptive events can produce an organism that’s less fit than its ancestor. 

The research appears in the Dec. 29, 2020 issue of eLife.

The seemingly contradictory outcome is attributed to changes that occurred within the yeast genome as well as an organism, the "killer" virus, that lives in symbiosis with it.

The study began with yeast cells that contained the killer virus, which gave yeast cells hosting the virus the ability to kill neighboring yeast cells by releasing a toxin. The virus also made the host yeast immune to the toxin.

During the course of evolution, mutations occurred in the killer virus causing the yeast to lose its killing ability and then its immunity. At the same time, the yeast cells evolved to reproduce more quickly. The end result was faster-growing yeast that were killed when they encountered the toxin--such as when faced with its ancestor.

The aim of the study was to show how this could occur.

Current Science Daily interviewed Sean Buskirk, lead author of the study, currently an assistant professor at West Chester University of Pennsylvania. Buskirk explained what question his team set out to answer in this study.

"We set out to explain an unexpected observation: an evolved population of yeast that lost in direct competition with its ancient ancestor," Buskirk said.

The nonlinear evolutionary path the yeast took is called non-transitivity.

"Non-transitivity is a paradox that results if the interaction between two entities is the opposite of what is predicted based on the interaction of each entity with a third entity," Buskirk said. "Instead of linear the resulting hierarchy is circular, such that there is no entity that is supreme." 

A 'frozen fossil' record

Laboratory experiments present a unique opportunity to study evolution, the researchers state, because there is a "frozen fossil" record, where you can compete a current generation against an extinct one to determine which is the most fit. This is not possible outside of the laboratory.

"We found the culprit to be the yeast killer virus that was present in the ancestor and had deteriorated during evolution in the lab," Buskirk said. "The killer virus typically encodes a killer toxin and a corresponding immunity component. 

"However, these components were rendered nonfunctional through mutations that accumulated in the viral genome. These viral mutations were selected for because they provided the virus with a competitive advantage over other viruses."

Multilevel selection

Another mechanism highlighted by the study is multilevel selection. Current Science Daily asked Buskirk to explain this.

"Multilevel selection refers to selection that acts on multiple levels of biological organization," he said. "In our system millions of yeast cells are competing against one another, with adaptations resulting from mutations that occur within the yeast genome. At the same time, each yeast cell contains multiple copies of the killer virus, which are competing against each other within a single yeast cell. Selection is acting on both the yeast genome and the viral genome and impacting evolution at both levels: between cells and within cells."

The researchers found that this multilevel selection occurred in almost half of about 140 yeast populations. 

As for the next steps of the research, Buskirk said: "I would like to determine the molecular mechanism that provides the viral variants with an intracellular advantage. Why do certain point mutations allow the viral variants to outcompete other viruses within a yeast cell?"