Evolution Unfolding

When Salvador Luria ran his slot machine experiment, he captured a single round of evolution. A population of E. coli faced a challenge—an attack of viruses—and natural selection favored resistant mutants. But in every generation, natural selection can shape a species. New mutations arise, genes mix to form new combinations as they pass from parent to offspring, and the shifting environment creates new challenges. On this grander scale, evolution can be far harder to observe. Life has had millions of years to change, whereas scientists are on this earth for only a few decades. Darwin had resigned himself to studying evolution from a distance, and a century later most evolutionary biologists were following suit. They would compare genes in different species to learn how they diverged or search for new versions of genes that had arisen in response to new challenges. They would look for the effects of natural selection in the past. But in the 1980s a number of scientists decided to watch evolution in the present. They set out to observe E. coli and other bacteria undergo natural selection in their laboratories.

One of those scientists was Richard Lenski. Lenski started his scientific career hiking the Blue Ridge Mountains in search of beetles. He wanted to learn how beetles help hold together the

Southern Appalachian food web. Lenski focused his work on a handful of species of Carabus ground beetles. He hoped to determine what controlled their population—cold snaps and heat waves perhaps, or maybe the competition for prey. The question was not just academic. The ground beetles might well be protecting the forests by keeping tree-destroying pests in check. Understanding the ecology of ground beetles might make it possible to predict outbreaks of pests and perhaps even prevent them.

Each spring, Lenski climbed the slopes and dug holes. He put plastic cups in them, covering the cups with funnels. Beetles tumbled down the funnels into the cups, and Lenski returned each day to count them. He marked the beetles and set them free. He tracked how much weight they gained each summer. He compared how many Carabus sylvosus he caught with how many Carabus limbatus. He compared how many beetles lived in dense forests with how many inhabited clear-cuts.

Lenski looked for patterns. In science, patterns become stronger the more times an experiment can be repeated. Doctors put thousands of people on an experimental drug. Physicists fire a laser millions of times to discover the ways of the photon. Ecologists also replicate their experiments when they can, but each datum demands far more labor. For his clear-cutting study, Lenski built a grand total of four enclosures, two in the clear-cut and two in the forest, each holding sixteen traps. With so few trials he could catch sight of only fleeting shadows, hazy signs of the forces governing the beetles.

Lenski came down from the mountains. He decided he would have to find another creature he could study to get some answers to the big questions on his mind. He found E. coli. When Lenski looked at a flask of E. coli, he saw a mountain. It was an ecosystem filled with billions of individual organisms. Like his beetles, E. coli searched for food and reproduced. They were preyed upon by viruses rather than by salamanders. E. coli's ecosystem might be simpler than the Blue Ridge Mountains, but simplicity can be a virtue in science. A researcher can precisely control every variable in an experiment to see the effect of each one.

Best of all, E. coli is the sort of creature that can, in theory, evolve very fast. Mutations may occur only rarely, but with millions of microbes in a single flask a few mutations will arise in every generation. And because E. coli can reproduce in as little as twenty minutes, a beneficial mutation may let a mutant overtake a colony in a matter of days.

Lenski set up an experiment that was simple yet powerful. He gave his bacteria a limited supply of glucose and thus created a huge evolutionary pressure. Their ancestors had been fed endless meals of sugar, and they had adapted to that diet. The microbes that could convert the food to offspring fastest took over the population. In Lenski's experiment, genes that sped up breeding were no longer beneficial. His bacteria grew slowly if at all. Any new mutation that allowed the microbes to survive the conditions better, Lenski reasoned, would be strongly favored by natural selection.

As E. coli passed through thousands of generations in his laboratory, evolution's mark began to emerge. When Lenski pitted the ancestral bacteria against their descendants on their new diet, the new microbes reproduced faster. The more time passed, the better adapted the bacteria became. After a decade, the bacteria could grow far faster than their ancestors. The course of their evolution was not smooth: the bacteria might spend several hundred generations without any observable change, only to go through a rapid evolutionary burst. And as E. coli evolved to grow faster, Lenski detected other changes.

Lenski's students continue to nurture his dynasty of E. coli from one generation to the next, and other scientists have used similar methods to run experiments of their own. Some have watched E. coli adapt to life at the feverish temperature of 107 degrees Fahrenheit. Others have unleashed viruses on the bacteria and observed them become resistant, only to have the viruses evolve ways to overcome their resistance, starting the cycle all over again. While Lenski's experiment remains the longest running by far, much shorter experiments have been able to yield striking results. Bernhard Palsson and his colleagues, for example, fed five populations of E. coli glycerol, a carbon compound used in soaps and face creams. Ordinary E. coli does a lousy job of feeding on glycerol, but Palsson drove the evolution of glycerol gourmets. After only forty-four days (660 generations of E. coli), the bacteria could grow twice as fast as the founders of the population.

Whether it battles viruses, adapts to a diet of glycerol, or copes with heat, E. coli unmistakably evolves. Its swift pace of evolution in these experiments may reflect rapid evolution in the wild. After all, each time the microbe finds itself in a new environment, its evolutionary pressures suddenly shift. Genes that allow E. coli to thrive in a gut may mutate into forms better suited to life in the soil.

These experiments have allowed scientists to put natural selection under a microscope, teasing apart the individual mutations that benefit E. coli. Each time the microbe divides, it has a roughly 1-in-100,000 chance of mutating in a way that lets its descendants grow faster. The boost is often small, but it can allow a mutant's descendants to outbreed their cousins. And those mutants in turn have a small chance of picking up a second mutation that makes them even faster growers. In Palsson's 660-generation experiment, he and his colleagues confirmed two or three mutations in each population. Lenski estimated that over the course of 40,000 generations his lines have picked up as many as 100 beneficial mutations.

Beneficial mutations can take several forms. Some involve the change of a single base in a gene, something equivalent to changing LIFT to LIFE. These mutations can change the structure of a protein and thus change the way it works. It may slice a molecule more effectively than before, or start responding to a new signal. Other mutations accidentally create an extra copy of a stretch of DNA. In Palsson's experiment these duplicated segments ranged from 9 bases long to 1.3 million. Accidental duplications can create new copies of old genes. Natural selection may favor them because they produce extra proteins, which E. coli can use to grow and reproduce. But over time one of the copies may acquire new mutations, allowing it to take on a new function. Mutations can also snip out chunks of DNA, and microbes that lose genetic material are sometimes favored by natural selection. It's possible that proteins that were originally useful become a burden to E. coli.

Experiments such as these show that mutations arise randomly. And the effects of the mutations depend on how the mutations allow an organism to thrive in its own peculiar set of conditions. But does that mean evolution plays out purely by chance? The late paleontologist Stephen Jay Gould dreamed of an experiment to answer the question, which he called replaying life's tape. "You press the rewind button and, making sure you thoroughly erase everything that actually happened, go back to any time and place in the past...," he wrote in his 1989 book Wonderful Life. "Then let the tape run again and see if the repetition looks at all like the original."

Short of time travel, Gould thought the best way a scientist could answer that question was by examining the fossil record, documenting the emergence and extinction of species. But experiments on E. coli can also address the question, at least on a scale of years. What makes experiments such as Lenski's particularly powerful is that evolution unfolds many times over, not just once. From an identical ancestor, Lenski produced twelve lines, each of which went through its own natural selection. Lenski and his colleagues may not be able to rewind the tape of E. coli's evolution, but they can create twelve identical copies of the same tape and watch what happens when they all play at the same time.

It turns out that the tapes are not identical, nor are they entirely different. In Lenski's experiments all twelve lines grew faster than their ancestors, but some lines grew far faster than others. They all grew larger, but some became round while others remained rod-shaped. When scientists have taken a close look at the genomes of evolved bacteria, they have found many differences in their DNA. One reason evolution can take different paths is that mutations are not simple. A mutation may be beneficial in one microbe but downright harmful in another. That's because a mutated gene's effects depend in part on how it cooperates with other genes. In some cases the genes may work together well, but in other cases they may clash.

Despite those differences, natural selection can override many of the quirky details of history. While Lenski's lines may not be identical, they have tended to evolve in the same direction. They have also converged on a molecular level. Lenski and his colleagues have found several cases in which the same gene has mutated in all their lines. Even genes that have not evolved a new sequence have changed in a similar way. Some genes now make more proteins, and some make fewer. Lenski and his colleagues took a close look at how the expression of genes changed in two lines of E. coli. They found fifty-nine genes, and in all fifty-nine cases, the genes had changed in the same direction in both lines. The evolutionary song remains the same.

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