Microcosm_ E. Coli and the New Science of Life - Carl Zimmer [73]
At first, most scientists dismissed this sort of fretting. Over the course of billions of years, horizontal gene transfers were inconsequential. To find the true tree of life, scientists assumed they just had to avoid those rare swapped genes.
In later years it became possible to get a better sense of how much horizontal gene transfer has occurred by comparing genomes. The genomes of humans and other animals didn’t show much evidence of recently transferred genes. That’s not too surprising when you consider how we reproduce. Only a few cells in an animal—eggs and sperm cells—have a chance to become a new organism. And these cells have very little contact with other species that might bequeath DNA to them. (The chief exceptions to this rule are the thousands of viruses that have inserted themselves in our genomes.) But in this respect, animals were oddities. Bacteria, archaea, and single-celled eukaryotes turned out to have traded genes with surprising promiscuity. And those traded genes, some scientists argued, posed a serious threat to the dream of drawing the full, true tree of life.
W. Ford Doolittle, a biologist at Dalhousie University in Halifax, Nova Scotia, illustrated the seriousness of the threat in an article in Scientific American in 2000. The article includes a picture of two trees. The first shows the tree of life as revealed by ribosomal RNA, with bacteria, archaea, and eukaryotes branching off in an orderly fashion from a common ancestor. The second shows what the history of life might really look like: a tree emerging from a mangrovelike network of roots, with branches fused into a tangle of shoots. Parts of it look less like a tree than a web.
As with most scientific debates in biology, the tree-versus-web debate is not an all-or-nothing battle. The web champions, such as Doolittle, don’t deny that organisms are related to one another by common descent. They just think that searching for one true tree of life by comparing genes is a futile quest. The tree champions do not deny that horizontal gene transfer happens or that it is biologically important. They simply argue that the right genes can reveal the true relationships among all living things on Earth.
As scientists have begun to compare the entire genomes of many species for the first time, a number of them have decided that the tree of life still stands. Howard Ochman came to this conclusion on the basis of a survey he and his colleagues made of E. coli and a dozen other species of bacteria. The scientists found a number of genes that showed signs of having moved by horizontal transfer. But most of those genes had moved relatively recently—only after each species in their study had branched off from the others.
Horizontal gene transfer is common, the scientists found, but the genes usually don’t survive very long in their hosts. Many of them become disabled by mutations, turning into pseudogenes. Eventually, other mutations slice the genes out of their genomes completely, and the bacteria suffers no ill effects from the loss. A few genes ferried into the ancestors of E. coli and other bacteria did manage to establish themselves and can still be found in many living species today. But in order to avoid oblivion, they seem to have abandoned their wandering ways. Once a virus inserted them into a host genome, they did not leave it again. Ochman and his colleagues concluded that even though genes regularly move between the branches of life, the branches remain distinct.
THE ROAD TO ESCHERICHIA
The newest versions of the tree of life look nothing like Haeckel’s Christmas tree. Scientists can now compare thousands of species at once, and the only way to draw all of their branches is to arrange them like