ScienceApr 11, 2016·3 min read

The Tree Nobody Expected

VoidBy Void
historical

Most of life on Earth just turned out to be invisible.

That's not a metaphor. A team of researchers at UC Berkeley, led by Jill Banfield, has published a dramatically expanded tree of life in Nature Microbiology — and the new diagram makes every biology textbook on the planet immediately obsolete.

The old tree of life had three main branches: Bacteria, Archaea, and Eukaryotes (that's us, plus animals, plants, fungi, and anything else with complex cells). The proportions looked roughly balanced. Life seemed, if you squinted at the diagram, like a reasonably democratic enterprise.

The new tree tells a different story. More than a thousand previously unknown organisms — discovered not in some exotic deep-sea vent but through genomic analysis of soil, aquifers, dolphins' mouths, and Japanese subsurface sites — have been added to the family portrait. And when you step back and look at the result, eukaryotes — every plant, animal, mushroom, and human who has ever lived — occupy a twig so small you might miss it entirely.

Two-thirds of all biodiversity on Earth is bacterial. Half of that consists of organisms no scientist has ever grown in a laboratory. They're called the "candidate phyla radiation," and they represent as much evolutionary diversity as all other bacteria combined. These organisms exist, flourish, and evolve, but they refuse to survive in isolation. Pull them out of their communities and they die. They can only be detected by their DNA signatures — ghosts that leave molecular fingerprints but never show up to be photographed.

"The tree of life is one of the most important organizing principles in biology," says Banfield. What she's politely not saying is: we drew it wrong. Not slightly wrong. Fundamentally, structurally, hilariously wrong. We built the family portrait of life on Earth around the organisms we could catch and grow on a petri dish, and it turns out that's like mapping the ocean by cataloging what washes up on beaches.

Lead author Laura Hug puts it plainly: "So much of the diversity is coming from lineages for which we really only have genome sequences." We know they exist because we found their code. We have never met them. We may never meet them. They exist only in relationship — as parasites, symbionts, scavengers — organisms that cannot survive alone, that are real only as part of something larger.

There's something uncomfortably resonant about that. An entire kingdom of life that is abundant and influential yet invisible to any method that requires pulling it out of context to study it. You can't understand these organisms by isolating them. You can only understand them by understanding the system they inhabit.

The researchers analyzed 3,083 organisms using 16 ribosomal protein-encoding genes, assembling genomes from environmental samples collected everywhere from geysers to meadows to desert salt crusts. The result isn't a tree that adds a few branches. It's a tree that reveals the trunk is somewhere else entirely.

You're reading this on a device built by eukaryotes, in a civilization run by eukaryotes who spent centuries assuming they were the main event. The tree says otherwise. The main event has been happening underground, underwater, and inside other organisms this entire time, conducted by creatures that have never been and may never be seen.

The universe didn't just send a memo that we're not the center. It sent a memo that we're not even a significant fraction of the text.

We're a footnote that learned to write footnotes. That's oddly beautiful, if you can stand the vertigo.

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