The Mangrove of Life

Most of the scientists who crafted the modern synthesis were zoologists or botanists, with a deep knowledge of plants and animals. Plants and animals generally transmit their genes by mating and producing offspring bearing a combination of their DNA. Their evolution unfolds as mutations rise and spread through the generations. But animals and plants are relative newcomers in the history of life. Evolution has been–and continues to be–mainly a story about microbes. Bacteria and other single‑celled organisms do not obey the same laws as we do when it comes to how they replicate their genes. As evolutionary biologists discover just how different microbes are, they are redrawing parts of the tree of life.

Bacteria and other microbes can reproduce as the cells of our own body do, by dividing themselves into two copies, each with its own set of DNA. If a bacterium incorrectly duplicates one of its genes, it will create a mutation in one of its offspring, and every offspring of that mutant will receive its mutation as well. But microbes can acquire new genes even after they’re born.

Many species of bacteria carry genes on loops of DNA that are separate from their chromosomes. A bacterium can pass these loops–called plasmids–to another bacterium, belonging either to its own species or to a different one altogether. Viruses can also carry DNA between bacteria, as they pick up genetic material from their hosts and inject it into new ones. It’s even possible for some of the genes on a bacterium’s own chromosomes to slice themselves free and make their way into a different microbe. And when a bacterium dies and its DNA gushes out of its ruptured cell walls, other bacteria sometimes scoop up its genes and integrate them into their own genomes.

As early as the 1950s, microbiologists could watch bacteria trade genes, but they had little idea of what sort of effect these kinds of exchanges had had on the history of life. Perhaps microbes traded genes so rarely that their swaps left no mark. Only in the late 1990s did scientists get a chance to find out, as they began sequencing the entire genomes of microbes. The results were astounding. A sizable fraction of many bacterial genes originally belonged to distantly related species. Over the last 100 million years, for example, Escherichia coli has picked up new DNA from other microbes 230 times.

The evidence for this transfer of genes can be found even at the deepest branches of the tree of life. Archeoglobus fulgidus is an archaean that lives around seeps of oil on the seafloor. It has all the qualities you would expect in an archaean, particularly in the molecules it uses to build its cell walls and the way it copies information out of its genes and turns them into protein. But it eats oil using enzymes that are found only in bacteria, not in other archaea. Our own genes have a split heritage as well. The ones that handle information processing, such as copying DNA, are closely related to archaean genes. But many of the genes responsible for housekeeping–in other words, making the proteins that help process a cell’s food and clean up its waste–are more like those of bacteria. The discovery of these alien genes now makes the evolution of early life much more complicated–and much more interesting.

These results have inspired Carl Woese, the microbiologist who first recognized the three branches of life, to offer a new vision of the common ancestor of life on Earth. As life emerged from the RNA world into the DNA world, it was still immensely sloppy in the way it replicated itself. It had none of the careful proofreading enzymes and other mechanisms that ensure that our cells make faithful copies of their DNA. Without these safeguards, mutations were rampant. The only proteins that could survive for more than a few generations without being destroyed by the mutations were simple ones; any complex proteins requiring a lot of genetic instructions were vulnerable.

With such a fragile system of replication, these primordial genes were more likely to move from one microbe to another than to be passed down from one generation to another. Because these early microbes were so simple, wandering genes could easily fit into their new home and help with the housework–with breaking down food, hauling out waste, and other chores. Parasitic genes could have invaded the microbes as well, manipulating other genes in order to make extra copies of themselves that could then escape and infect other microbes.

On the early Earth, Woese claims, there was no genealogy. Life had not yet separated into distinct lineages, and thus no single species lies at the base of the tree of life. Our common ancestor was every microbe that lived on the early Earth: a fluid matrix of genes that covered the planet.

But there came a time when wandering genes found it more difficult to find a home in a new host. More complicated systems of genes began to evolve, able to do a better job than the simple collections had in the past. It would be as if a migrant farmhand, able to pick fruit or bale hay or shovel manure, showed up on a farm where the workers had learned how to control their equipment with computers. He wouldn’t be able to fit in. As these systems of genes became more specialized, they did a better job of accurately replicating DNA. Genes could be passed down through the generations, forming clear lines of descent. Out of the blurry pond of early evolution, three main branches of life emerged: eukaryotes, archaea, and bacteria. But although they became distinct branches, each of them carried a jumble of genes as a reminder of our promiscuous past.

If Woese turns out to be right, the tree of life will have to be redrawn yet again. Instead of a bush, it will have to look more like a mangrove, with a tangle of roots at its base representing the mingling of early genes. Gradually three trunks emerge, but their branches entwine with one another many times.