evolutionary forecasting

Simonfoundation |   Michael Doebeli, a mathematical biologist at the University of British Columbia, wondered how E. coli would evolve if it had two kinds of food instead of just one. In the mid-2000s, he ran an experiment in which he provided glucose — the sole staple of Lenski’s experiment — and another compound E. coli can grow on, known as acetate.

Doebeli chose the two compounds because he knew that E. coli treats them very differently. When given a choice between the two, it will devour all the glucose before switching on the molecular machinery for feeding on acetate. That’s because glucose is a better source of energy. Feeding on acetate, by contrast, E. coli can only grow slowly.

Something remarkable happened in Doebeli’s experiment — and it happened over and over again. The bacteria split into two kinds, each specialized for a different way of feeding. One population became better adapted to growing on glucose. These glucose-specialists fed on the sugar until it ran out and then slowly switched over to feeding on acetate. The other population became acetate-specialists; they evolved to switch over to feeding on acetate even before the glucose supply ran out and could grow fairly quickly on acetate.

When two different kinds of organisms are competing for the same food, it’s common for one to outcompete the other. But in Doebeli’s experiment, the two kinds of bacteria developed a stable coexistence. That’s because both strategies, while good, are not perfect. The glucose-specialists start out growing quickly, but once the glucose runs out, they slow down drastically. The acetate-specialists, on the other hand, don’t get as much benefit from the glucose. But they’re able to grow faster than their rivals once the glucose runs out.

Doebeli’s bacteria echoed the evolution of lizards in the Caribbean. Each time the lizards arrived on an island, they diversified into many of the same forms, each with its own set of adaptations. Doebeli’s bacteria diversified as well — and did so in flask after flask.

To get a deeper understanding of this predictable evolution, Doebeli and his postdoctoral researcher, Matthew Herron, sequenced the genomes of some of the bacteria from these experiments. In three separate populations they discovered that the bacteria had evolved in remarkable parallel. In every case, many of the same genes had mutated.

Although Doebeli’s experiments are more complex than Lenski’s, they’re still simple compared with what E. coli encounters in real life. E. coli is a resident of the gut, where it feeds on dozens of compounds, where it coexists with hundreds of other species, where it must survive changing levels of oxygen and pH, and where it must negotiate an uneasy truce with our immune system. Even if E. coli’s evolution might be predictable in a flask of glucose and acetate, it would be difficult to predict how the bacteria would evolve in the jungle of our digestive system.