Darwin In a Test Tube

New work with RNA molecules demonstrates some of the classic principles of evolution.

A group of scientists at The Scripps Research Institute has set up the microscopic equivalent of the Galapagos Islands—an artificial ecosystem inside a test tube where molecules evolve to exploit distinct ecological niches, similar to the finches that Charles Darwin famously described in The Origin of the Species 150 years ago.

Using RNA molecules rather than living species, Sarah Voytek, a recent graduate of the Scripps Research Kellogg School of Science and Technology, developed a robust way to study evolution that allows the forces of natural selection to work over the course of mere days, with a trillion molecules in a test tube replicating every few minutes.

"We can study things very quickly," says Scripps professor Gerald Joyce, who worked with Voytek on the project.

On the voyage of the HMS Beagle, Darwin collected and studied different species of finches on several of the Galapagos Islands. The finches differed in their beak structure—some had thick, strong beaks and others had thin, delicate ones. Darwin observed that the different finches were each adapted for the specific types of seeds that served as their primary food source. The big-beaked birds were indigenous to the places where big seeds grew; in areas where there were also small seeds, there were also small-beaked birds.

Darwin reasoned that when two species are competing for resources within a common environment, they become differentiated so that each species adapts to use different preferred resources.

For several years, Joyce has been experimenting with a particular type of enzymatic RNA molecule that can continuously evolve in the test tube. The basis of this evolution comes from the fact that each time one of the molecules replicates, there is a chance it will mutate—typically about once per round of replication—so the population can acquire new traits over time.

Voytek developed a second, unrelated enzymatic RNA molecule that also can continuously evolve. That allowed her to set the two RNAs in evolutionary motion within the same pot, forcing them to compete for common resources.

In the new study, the key resource or "food" was a supply of molecules necessary for each RNA's replication. The RNAs will replicate only if they attach themselves to the food molecules. With ample food, the RNAs will replicate and mutate. As mutations accumulate over time, new forms emerge—some fitter than others.

The researchers placed the two RNA molecules together in a pot with five different food sources, none of which they had encountered previously. At the beginning of the experiment, each RNA used all five types of food—but none particularly well. After hundreds of generations of evolution, however, the two molecules each became independently adapted to use a different one of the five food sources. Further, each highly preferred its own food source and shunned the other molecule's food source.

In the process, the molecules evolved different evolutionary approaches to survival: One became super efficient at gobbling up its food, doing so at a rate that was about 100 times faster than the other. The second was slower at acquiring food, but produced about three times more progeny per generation.

These are both examples of classic evolutionary strategies for survival, says Joyce, and will allow the researchers to study the mechanisms at play in a few days rather than hundreds of thousands of years. 

The research was published in an advance online edition of the Proceedings of the National Academy of Sciences. It was supported by the National Science Foundation, NASA, and the Skaggs Institute for Research.

—By Jason Bardi/The Scripps Research Institute.