Tangling the Tree

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I’ve been fascinated by this picture since I first saw it over the weekend. It’s a hint of how we may be visualizing life in years to come.

As Darwin was trying to figure out how new species could evolve from old species, he began to think of evolution as a tree. He scribbled some simple branches in a notebook, and then published a more elaborate one in The Origin of Species. Darwin didn’t actually put any animals or plants on the branches of these trees; he was just thinking about the process itself. Today, though, evolutionary trees are a common sight in scientific journals, whether scientists are reconstructing the origin of a new strain of HIV or are trying to figure out how animals evolved from single-celled ancestors.

But scientists have also realized that drawing trees is harder than it once seemed. Evolution, at its heart, is about changes to DNA. For some organisms, like ourselves, DNA changes almost entirely as the result of mutations when parents bequeath their genes to their offspring. But it is possible for genes from one organism to hop to another. This happens most often in microbes. A bacterium may jam a needle into another bacterium and inject some genes. In other cases, viruses may pick up the genes of one host and bring them to a new host. Once a gene makes this jump, it may then get carried down through normal heredity to the receiver’s descendants, spreading into new species that evolve from it.

Scientists are trying to figure out how important this kind of species hopping has been over the history of life. In a sense, scientists are asking what is the shape of the tree of life? Is it for the most part an ordinary tree as Darwin pictured it, with a few vines representing jumping genes? Or are the vines so dense that they obscure parts of the tree altogether? This debate is not a huge issue when it comes to the evolution of animals (although viruses have shaped our genome). Most of the evidence for these vines comes from bacteria and other microbes, which are very promiscuous with their genes. Most of the diversity of life is microbial, and microbes were the only game in town for the first couple billions years of the history of life. So the stakes of this debate are big.

This picture is a splendid representation of this debate. Scientists at the European Bioinformatics Institute created it by comparing 184 microbes. The scientists first identified genes that the microbes all inherited from a common ancestor that they then passed down in conventional parent-to-offspring fashion. By comparing their different sequences, the scientists were able to draw a conventional tree of the sort Darwin had in mind. Next, they scanned the genomes of these microbes for jumping genes. They drew the jumpers as vines from one branch to the next. They then produced this three-dimensional picture.

As you can see, the branches rise from a common ancestor, but they are enmeshed in vines. What’s particularly fascinating about it is the way in which the vines connect the branches. It is not a random mesh. Instead, a few species are like hubs, with spokes radiating out to the other species. This is the same pattern that turns up in many networks in life, from the genes that interact in a cell to the nodes of the Internet. These hubs can bring a vast number of nodes into close contact. It’s why you can play Six Degrees of Kevin Bacon. In the microbial world, this network allows genes to move quickly through the tree of life, whether those genes provide resistance to antibiotics or allow microbes to cope with some other change in the environment. The Kevin Bacons of the microbial world, at least in the current study, seem to be species that live in habitats where they may come in intimate contact with other species, such as in plant roots. They then act as gene banks from which other species can make withdrawals.

Of course, 184 species of microbes represent a vanishingly small sample of the diversity of life on Earth. It remains to be seen if the Kevin-Bacon structure survives as more branches and vines get added to this picture. But this is an important step forward in how we envision life. Perhaps in the future, this tangled tree will take its place alongside Darwin’s notebook scribbles.