To read E. coli's palimpsest, scientists have had to figure out which parts of its genome are new and which are old. The answer can be found in the genealogy of germs. A family tree of the living strains of E. coli indicates that they all descend from a common ancestor that lived some 10 million to 30 million years ago. Even farther back, E. coli shares an ancestor with other species. Reach back far enough, and you ultimately encounter the ancestor E. coli shares with all other living things, ourselves included.
Reconstructing the tree of life—one that includes E. coli and humans and everything else that lives on Earth—has been one of modern biology's great quests. In 1837, Charles Darwin drew his first version of the tree of life. On a page in his private notebook he sketched a few joined branches, each with a letter at its tip representing a species. Across the top of the page he wrote, "I think."
The fact that species have common ancestors explains why they share many traits. As different as bats and humans may seem, we are both hairy, warm-blooded, five-fingered mammals. Darwin himself did not try to figure out exactly how all the species alive were related to one another, but within a few years of the publication of The Origin of Species, other naturalists did. The German biologist Ernst Haeckel produced gorgeous illustrations of trees sprouting graceful bark-covered boughs. His trees were accurate in many ways, scientists would later find. But Haeckel marred them with a stupendous anthropocentrism. To Haeckel, the history of life was primarily the history of our own species. His tree looked like a plastic Christmas tree, with branches sticking out awkwardly from a central shaft. He labeled the base of the tree Moneran, the name he used for bacteria and other single-celled organisms. Farther up the tree were branches representing species more and more like ourselves—sponges, lampreys, mice. And atop the tree sat Menschen.
This view of life has been a hard one to shake. It probably had something to do with the decision to split life into prokaryotes and eukaryotes, the supposedly primordial bacteria and the "advanced" species like ourselves that evolved from them. It's a deeply flawed view. The evolution of life was not a simple climb from low to high. E. coli is a species admirably adapted to warm-blooded creatures that did not emerge for billions of years after life began. It is as modern as we are.
It took a long time for a more accurate picture of the tree of life to take hold. One major obstacle was the lack of information scientists could use to determine how E. coli is related to other bacteria, or how bacteria are related to us. To compare ourselves to a bat, we can simply use our eyes to study fur, fingers, and other parts of our shared anatomy. Under a microscope, however, many bacteria look like nondescript balls or rods. Microbiologists sometimes classified species of bacteria based on little more than their ability to eat a certain sugar, or the way they turned purple when they were stained with a dye. It was not until the dawn of molecular biology that scientists finally got the tools required to begin drawing the tree of life. Experiments on E. coli helped them to recognize that all living things share the same genetic code, and the same way of passing on genetic information to their descendants. They share these things because they had a common ancestry.
In the 1970s, Carl Woese, a biologist at the University of Illinois, Urbana-Champaign, discovered a way to use those shared molecules to draw a tree of life. Woese and his colleagues teased apart ribosomes, the factories for making proteins, and studied one piece of RNA, known as 16S rRNA. Woese did his work years before scientists could easily read the sequence of RNA or DNA. So he and his colleagues did the next best thing: they sliced up Escherichia coli's 16S rRNA with the help of a virus enzyme. They then cut up the 16S rRNA of other microbes and gauged how similar their fragments were to those of E. coli. They discovered many regions that were identical, base for base, no matter which species they compared. These regions had not changed over billions of years. The regions that had diverged revealed which species were more closely related than others.
Rough and preliminary as the results were, they upended decades of consensus. The standard classifications of many groups of bacteria turned out to be wrong. Most startling of all, Woese and his colleagues found that a number of bacteria were closer to eukaryotes than to other bacteria. They were not bacteria at all. Woese and his colleagues declared that life formed not two major groups of species but three. They dubbed the third domain of life archaea. "We are for the first time beginning to see the overall phylogenetic structure of the living world," Woese and his colleagues declared.
Over the next thirty years, scientists built on Woese's work, drawing a more detailed picture of the tree of life. They studied ribosomal RNA in more species. They found other genes that also made for good comparisons. They used new statistical methods that gave them more confidence in their results. They found many more species of archaea, confirming it as a genuine branch of life. Archaea may look superficially like bacteria, but they have some distinctive traits, such as unique molecules that make up their cell walls.
To measure the diversity of life, Woese and his colleagues counted up the mutations to ribosomal RNA that had accumulated in each branch of life. The more mutations, the longer the branch. The new tree was a far cry from Haeckel's. The animal kingdom became a small tuft of branches nestled in the eukaryotes. Two bacteria that might look identical under a microscope were often separated by a bigger evolutionary gulf than the one that separates us from starfish or sponges. One look at the tree made it clear that the evolutionary history of any individual species of bacterium—E. coli, for example—is a complicated tale.
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