Passage IV

NATURAL SCIENCE: This passage is adapted from the article "Molecular Evolution" by Tina Hesman Saey (©2009 by Society for Science & the Public).

Richard Lenski, an evolutionary biologist, is among the scientists hitting the rewind button on evolution. Meter-high letters taped to the window of his lab spell out the lab's motto: EVOLVE.

Inside the lab, a dozen glass flasks containing clear liquid swirl in a temperature-controlled incubator. Although the naked eye can't see them, millions of E. coli bacteria grow in the flasks, doing what the window exhorts.Lenski started the cultures in 1988, intending to follow the course of natural selection for several hundred generations. Now, two decades later, the cultures are still growing and have produced more than 45,000 generations of bacteria each.

These 12 flasks "represent the stripped-down bare essentials of evolution," says Zachary Blount, a gradu­ate student in Lenski's lab. The environment never changes. No new genes enter the system from migrating microorganisms. And the scientists take no. action to affect the course of evolution within the flasks. Only the intrinsic. core processes of evolution influence the outcome, Blount says.

Lenski and his colleagues have watched the game play out, occasionally analyzing DNA to peer over the players' shoulders and find out what cards they hold. On the surface, the populations in the 12 flasks seem to have traveled similar paths-all now grow larger cells and have become more efficient at using glucose than their ancestors. And many of the strains have accumu­lated mutations in the same genes. Notably, though, none of the strains developed exactly the same genetic changes.

Randomness is an important part of the evolution­ary equation, as the experiment illustrates. During the first 2,000 generations, all of the 12 populations rapidly increased in size and fitness. But then these changes began to slow down, hitting the evolutionary equivalent of a dieter's plateau.

After 10,000 generations, it became apparent that not all the flasks were on the same trajectory. Though cells in all the flasks became larger, each population differed in the maximum size the cells reached. The populations also differed in how much fitter they were than their ancestors, when grown in direct competition. Several of the flasks now contain mutator strains, bacteria that have defects in their DNA replication system. Such defects make mistakes more likely to happen every time those bacterial strains copy their DNA to divide. Sometimes a mistake can have lethal conse­quences, damaging a gene crucial for survival. But other times coloring a bit outside the lines creates opportunity for advancement.

Even within a given flask, some bacteria take slightly different paths. One flask now contains two separate strains one that makes large colonies when grown on petri dishes, and one that makes small colonies. The large- and small-colony strains have coexisted for more than 12,000 generations. The large­ colony producers are much better at using glucose so they grow quickly, but they make by-products that the small-colony producers can eat. Both strains have increased in fitness over the generations.

Still, though the details were different, replaying evolution in a dozen flasks produced very similar outcomes in each.

But then something completely unexpected happened. After about 31,500 generations, glucose-eating bacteria in one flask suddenly developed the ability to eat a chemical called citrate, something no other E. coli do.

The switch was clearly a radical change of destination for the bacteria. The inability to eat citrate is a biochemical hallmark of theE. coli species, so by some definitions, the citrate eaters in that flask are no longer E.coli.

But a single change did not a citrate eater make.The researchers found that the bacteria went through a series of steps before evolving the ability to use citrate. One initial mutation happened at least 11,000 genera­tions before the citrate eaters appeared. Lenski doesn’t yet know which specific DNA changes Jed to citrate use, but it's clear that the ability to use citrate is contin­gent upon those earlier changes. And even bacteria that have undergone those initial changes are still not guar­anteed to eat citrate. Blount tested 40 trillion bacteria from earlier generations to see if any could evolve the ability to eat citrate. Fewer than one in a trillion could.

The profound difference between the citrate caters and the other 11 strains, as well as the dependence of the citrate change on earlier mutations, seems to suggest that replaying evolution will result in some surprise endings.