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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.

TREE VERSUS WEB

In the 1980s, some experts on the tree of life became worried. It was slowly becoming clear that horizontal gene transfer was not just a peculiarity of E. coli’s laboratory sex or the modern era of antibiotics. Genes had moved from species to species long before humans had begun to tinker with life. If genes moved too often, some scientists feared, they might make it impossible to reconstruct the tree’s branches.

To reconstruct the tree of life, scientists compare DNA from different species and come up with the most likely pattern of branches that could have produced the differences.