Simple type of evolution not so simple after all

When most people consider the concept of evolution, they may imagine a process by which an organism adapts to a new environment, envisioning, for example, the varied beaks of Darwin’s finches. But the vast majority of evolutionary processes don’t act to change an organism—they try to keep it the same. This type of selection pressure is known as purifying selection.

“It’s the simplest, most boring type of evolution you can imagine,” says Joshua Plotkin, a professor in Penn’s Department of Biology in the School of Arts & Sciences. “Purifying selection is just asking an organism to do what it’s doing and keep doing it well.”

In a study out this week in the Proceedings of the National Academy of Sciences, Plotkin and postdoctoral researchers Premal Shah and David McCandlish take a closer look at this type of evolution and find out that it may not be so boring after all. 

They set out to ask whether evolution under purifying selection is contingent on prior events; in other words, whether the genetic mutations that are considered acceptable by evolution depend on the mutations that were accepted earlier. They also asked whether it was possible to revert accepted mutations after a certain period of time had passed.

“We ask these two complementary questions, one looking forward in time and one looking backward in time,” Plotkin says. “One question, in the simplest terms, is, is evolution predictable? The other is, is evolution reversible?”

The researchers addressed these questions using a computational model centered on the bacterial protein argT. Their model randomly proposed mutations to the protein, simulating how it might evolve over the equivalent of roughly 10 million years. Mutations were rejected if they changed the protein’s stability and accepted if they caused little or no change.

They found that, indeed, evolution is dependent on the past.

“The very same mutations that were accepted by evolution when they were proposed, had they been proposed at a much earlier point in time, they would have been deleterious and would have been rejected,” Plotkin says.

This occurred, the researchers discovered, because earlier mutations sometimes resulted in small changes to the protein’s thermodynamic stability that allowed it to withstand certain future changes. 

The Penn biologists’ model also revealed that mutations were increasingly difficult to revert over time, a feature known as entrenchment.

“What this tells us is that, in a deep sense, evolution is unpredictable and in some sense irreversible, because of interactions between mutations,” says Plotkin.

These unexpected findings suggest that researchers will find it extremely challenging to predict the course of evolution, which would be desirable, for example, in anticipating how a pathogen might evolve over time.

“We desperately would like to make such predictions in some applied settings,” Plotkin says, “but these results really rob us of that ability.”

Plotkin Evolution