A New View of Evolution That Can’t Be Represented by a Tree

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In 1837, Charles Darwin sketched a spindly tree of life in one of his notebooks. Its stick-figure trunk sprouted into four sets of branches. The drawing illustrated his radical idea that, over time, organisms change to give rise to new species.

“I think,” Darwin scrawled, suggestively, above his humble tree.

Biologists have worked since then to fill in the details of that tree. While all beings are related, Darwin intimated, it should be possible to classify all living things into distinct lineages of more closely related species — branches — based on their shared evolutionary histories.

Darwin and others used physical similarities and differences between organisms to add ever more details to his basic tree. Then, after the discovery of DNA’s structure in 1953, scientists began tracing the evolutionary history of life through its shared genetic code.

But that project has now reached a crisis point, David Quammen writes in his new book, “The Tangled Tree.” Genetics is revealing that the branches on Darwin’s tree of life are not so separate from each other as was once thought: Genes sometimes skip from species to unrelated species, effectively fusing different branches together. The big question now is whether Darwin’s tree represents a fundamentally flawed conception of evolutionary history or is merely in need of revision.

Quammen’s sprawling history of evolutionary genetics ranges widely in its answer to that question. He synthesizes a large quantity of disparate material, circling repeatedly back to one scientist in particular: Carl Woese, whose work both fleshed out Darwin’s tree and laid the foundations for its uprooting.

Woese, a biophysicist and microbiologist, was a pioneer in using genetic material to trace the history of life. Soon after setting up his first lab at the University of Illinois at Urbana-Champaign in 1964, Woese began working on the central biological question at the time: how cells translate genetic information into proteins.

An elite group of 20 scientists — the RNA Tie Club, as they were known — had formed to discuss this problem. They met twice a year; members all wore identical embroidered neckties. Not Woese, Quammen writes: “He was a loner by disposition. He took a separate path. Not in the club. No RNA tie.”

Woese developed a new method to compare a type of genetic material called rRNA across bacterial species. In 1977, he revealed that he had successfully used this method to trace the path of bacterial evolution, finding an entirely new domain in the process — a whole branch of the tree of life that others had missed altogether.

At the time, scientists grouped all life into two main categories: the bacteria and the non-bacteria, or eukaryotes. Woese exploded that view. His research showed that there is a third group of organisms, the archaea, which are genetically distinct from other life-forms.

Previously, scientists had lumped the archaea in with the bacteria. Woese proved that archaea and bacteria had sufficiently divergent evolutionary histories to be considered different from one another.

Carl Woese in his laboratory at the University of Illinois at Urbana in 1996.

Woese’s discovery was controversial at the time, though it is no longer. And his work laid the foundations for a new field of science called molecular phylogeny that has delivered astounding insights about evolutionary history.

Quammen details how scientists have now revealed genetic evidence that the branches of the tree of life are not so isolated from one another as Darwin thought. Organisms from different branches can transfer genes to each other — and often do.

Bacteria, plants and animals can swap genes across species lines, and this activity seems to have shaped evolution in profound ways. Scientists call this swapping “horizontal gene transfer,” to distinguish it from the “vertical gene transfer” that occurs between parents and offspring. Horizontal gene transfer explains why bacteria acquire resistance to antibiotics so quickly, for instance: They can transfer antibiotic resistance genes back and forth among species relatively easily.

But horizontal gene transfer also poses a major challenge to the Darwinian concept of evolution, in which species evolve over time into separate lineages. Darwin thought that evolutionary change happened very slowly, as incremental genetic changes were passed down, over hundreds of thousands of generations, from parents to children. And while this slow change does happen, gene-swapping via horizontal gene transfer happens much faster, driving major changes relatively quickly.

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