A long-running experiment demonstrates the reality of genetically driven evolution

A long-running experiment demonstrates the reality of genetically driven evolution

 
One of the thought-games that has been played in science is posed by the question: If we rewind the Earth's history, would life develop differently the second time around? Long-term experiments with bacteria suggest that the answer, as posited by the late paleontologist Stephen Jay Gould, would be "yes".
 
Researchers at Michigan State University have been running an experiment for twenty years to address this issue. Inside the lab, a dozen glass flasks containing millions of E. coli bacteria swirl in a temperature-controlled incubator. Each flask contains media with only the minimum requirements for survival - some glucose (a sugar that bacteria use for food) and a few other nutrients. The bacteria replicate, or divide, six or seven times daily, creating a new generation with each round. Each division produces genetic changes and mutations, some of which may help or hurt the bacteria's ability to compete for glucose. The next day, a dilution is done, with 10 percent of the culture within a flask transferred to a new flask; every 500 generations or so, the remaining 90 percent is frozen and stored for later experiments. The dilution acts as a population bottleneck, randomly selecting a subset of the bacteria (and so a subset of accumulated genetic changes) to continue the experiment. No new genes enter the system from migrating microorganisms, and the researchers take no action to affect the course of evolution within the flasks. Only the intrinsic, core processes of evolution (e.g., changes in genes) influence the outcome. Now, 20 years later, the cultures are still growing and have produced more than 45,000 generations of bacteria each.
 
On the surface, the populations in the 12 flasks seem to have traveled similar paths - all have grown larger and become more efficient at using glucose than their ancestors; many of the strains have also accumulated mutations in the same genes. However, no one strain has developed exactly the same genetic changes as another. The researchers noted that after 10,000 generations, it became apparent that the E. coli were not evolving the same. Though the 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 the researchers grew them in direct competition.
 
Other differences have emerged and been noted. As the experiment progressed, several of the flasks began to contain "mutater" 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, at other times, such changes provide an opportunity for better survival. Another interesting change was that within a given flask, some bacteria take slightly different evolutionary paths. One flask now contains two separate strains - one that evolved to make large colonies when grown on petri dishes (as a test to assess changes), 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. Thus, the small-colony and large-colony might be deemed different species.
 
At this point, whether Jay Gould's hypothesis was correct was still arguably in doubt. However, at about 31,500 generations, glucose-eating bacteria in one of the flasks suddenly developed the ability to eat a chemical called citrate, something no other E. coli do. The inability to eat citrate has been a defining characteristic of E. coli, so at least theoretically these bacteria are no longer E. coli. In this case, in contrast to the large-colony and small-colony bacteria described above, one really does see the emergence of a new species.
 
But, as always, the issue is not quite that simple. The researchers went back and tested 40 trillion E. coli bacteria from earlier generations for the ability to eat citrate. Fewer than one in a trillion could. So, while it might make sense to define E. coli as a bacteria that cannot eat citrate, what may have emerged was a very, very latent ability. However, the large-colony and small-colony emergence does suggest that a truly unique differentiation has occurred, and thus may represent speciation. One has to wonder if the concepts of niche and species are really too sloppy to reflect the fine hue of reality.
 
A number of papers have been published over time describing this ongoing experiment. Information on the experiment can be found at http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment, http://myxo.css.msu.edu/ecoli/ [which has links to abstracts of the various papers published], and http://myxo.css.msu.edu/cgi-bin/lenski/prefman.pl?group=aad [a listing of the various papers published].