Branches of the tree of life exchange genetic material, enabling entirely new ways of living
Hundreds of millions of years ago, long before the first forests rose and fell, a quiet revolution was unfolding in the microbial world: distantly related lineages were trading genes across the boundaries of species, independently discovering the same way of feeding on the dead. A multinational team of researchers has now traced this history through the genomes of four eukaryotic groups — fungi, Pseudofungi, Labyrinthulea, and Teretosporea — finding that horizontal gene transfer, once considered a bacterial phenomenon, helped each lineage evolve osmotrophy, the absorption-based decomposition that keeps Earth's nutrient cycles turning. The discovery redraws our understanding of how evolutionary innovation spreads, suggesting that the tree of life is less a tidy branching structure than a web of lateral exchanges, where a borrowed gene can open the door to an entirely new way of living.
- Earth's decomposition machinery — the fungal networks and their kin that recycle every fallen tree and dead organism — turns out to have a stranger origin story than anyone expected.
- Four eukaryotic lineages on opposite sides of the family tree somehow arrived at the same metabolic toolkit for osmotrophy, a convergence too precise to be mere coincidence.
- Analyzing hundreds of gene trees, researchers identified 166 likely instances of horizontal gene transfer between these groups, directly challenging the assumption that only bacteria swap genes across species lines.
- The exchanges appear to have occurred between 720 million and one billion years ago, suggesting that borrowed genes — not just inherited ones — helped complex life stake out entirely new ecological roles.
- Critical questions now press forward: scientists do not yet know whether viruses, the environment, or some other mechanism ferried the DNA, nor what each transferred gene actually does inside its new host.
- The field has moved past asking whether eukaryotes engage in horizontal gene transfer — the evidence is now clear — and must now excavate the mechanisms that make such deep genetic borrowing possible.
Fungi and their distant relatives perform one of life's most essential services: they dismantle the dead, releasing carbon, nitrogen, and phosphorus back into the world so other organisms can use them again. Without these decomposers, the planet would be overwhelmed by its own remains. Most of them feed through osmotrophy — absorbing dissolved nutrients directly from their surroundings rather than consuming prey whole. How this strategy arose, and why it arose repeatedly across unrelated lineages, has long been an open question.
A multinational research team set out to answer it by reading backward through genetic history. They focused on four eukaryotic groups that all practice osmotrophy: the familiar fungi, and three lesser-known relatives — Pseudofungi, Labyrinthulea, and Teretosporea. Despite sitting on opposite ends of the eukaryotic family tree, all four share strikingly similar traits: filamentous body structures, tough cell walls, and a common set of genes governing nutrient uptake, ion regulation, and molecular synthesis.
The explanation, the team found, was horizontal gene transfer — the lateral movement of genes between species, crossing boundaries that normally keep genetic material within a lineage. Long assumed to be a quirk of the bacterial world, this mechanism now appears to have shaped eukaryotic evolution as well. Combing through hundreds of gene trees, the researchers identified 166 probable transfer events, most frequently between fungi and Pseudofungi, and between Labyrinthulea and Teretosporea. The findings were published in Nature Ecology and Evolution.
The timing places these exchanges between 720 million and one billion years ago, when complex life was still establishing itself on a changing planet. The gene swapping, it seems, was not incidental — it was the engine that allowed osmotrophy to take hold across multiple lineages, enabling a shared metabolic identity to emerge from separate evolutionary paths.
Yet the discovery opens as many doors as it closes. Researchers do not yet know how the transfers occurred — whether through environmental uptake, viral intermediaries, or some other mechanism — nor what each shared gene actually does within its new host. The central mystery has simply shifted: horizontal gene transfer in eukaryotes is no longer in doubt, but the machinery behind it remains to be uncovered.
Fungi and their distant relatives have a job that keeps the planet alive: they break down dead things. When a tree falls, when leaves pile up on the forest floor, when organisms die, these decomposers move in and disassemble the biomass, releasing carbon, nitrogen, and phosphorus back into the soil and water where other life can use them again. Without this work, Earth would be buried under its own remains. Most of these decomposers—fungi chief among them—feed through osmotrophy, a method of absorbing dissolved nutrients directly from their surroundings rather than engulfing prey whole. But scientists have long puzzled over how this feeding strategy came to exist. How did osmotrophy arise? And why did it arise multiple times, in completely different branches of the evolutionary tree?
A team of researchers from institutions across Japan, the United Kingdom, Spain, and elsewhere decided to look backward into genetic history to find answers. They examined the genomes of four eukaryotic groups that all specialize in osmotrophy: fungi, which everyone knows; and three others with less familiar names—Pseudofungi, Labyrinthulea, and Teretosporea. These four groups sit on opposite sides of the eukaryotic family tree, meaning they diverged from common ancestors hundreds of millions of years ago. Yet they all developed similar traits: filamentous networks, tough cell walls, and crucially, a shared set of genes that handle the metabolic work of osmotrophy—genes for nutrient uptake, ion regulation, and building new molecules.
The puzzle was this: if these groups evolved separately, why do they share the same genetic toolkit? The answer, the researchers found, lay in horizontal gene transfer—the process by which genes jump from one species to another, crossing the boundaries that normally keep genetic material within a lineage. This mechanism was long thought to be a bacterial quirk, something that happened in the microbial world but not among the more complex eukaryotes. The new research, published in Nature Ecology and Evolution, challenges that assumption. By analyzing hundreds of gene trees, the team identified 166 instances where horizontal gene transfer likely occurred between these osmotrophic groups, with the exchanges happening most frequently between fungi and Pseudofungi, and between Labyrinthulea and Teretosporea.
The timing matters. These four groups first specialized in osmotrophy somewhere between 720 million and 1 billion years ago—a period when Earth's continents and oceans were taking on more recognizable shapes, when complex life was still finding its footing. The gene swapping appears to have been the mechanism that allowed this specialization to take root. As Professor Gergely Szöllősi, who leads the research unit at the Okinawa Institute of Science and Technology, explained, the findings suggest that branches of the evolutionary tree do not simply pass genes down to their offspring in a neat, vertical line. Instead, they exchange genetic material laterally, and those exchanges can enable entirely new ways of living to emerge.
But the work also opens new questions. The researchers still do not know exactly how these genetic exchanges happened. Did the genes move directly from the environment into cells? Did viruses act as intermediaries, ferrying DNA between species? And while the team has identified which genes were shared, they have not yet determined what each gene actually does within its new host organism. The mystery has shifted, in other words. Scientists are no longer asking whether horizontal gene transfer occurs in eukaryotes—the evidence is now clear that it does. The question now is how it works, and what mechanisms drive it. That answer will require more digging into the deep history of life, and more careful observation of how genes move and settle in the organisms that receive them.
Citações Notáveis
Branches of the tree of life can, and do, exchange genetic material, and those exchanges can allow entirely new ways of making a living to take hold.— Professor Gergely Szöllősi, Okinawa Institute of Science and Technology
The main question is no longer whether horizontal gene transfer takes place in eukaryotes, but how it occurs.— Eduard Ocaña-Pallarès, lead researcher
A Conversa do Hearth Outra perspectiva sobre a história
So fungi are decomposers, and they feed by absorbing nutrients. That's clear enough. But why does it matter that they share genes with these other groups—Pseudofungi and the others?
Because those other groups are not fungi at all. They're completely different branches of the eukaryotic tree. If they all independently evolved the same feeding strategy, you'd expect them to have evolved different genes to do it. But they didn't. They share the same metabolic toolkit. That suggests something moved those genes between them.
And that something is horizontal gene transfer. But I thought that was a bacterial thing. Bacteria swap genes all the time. Why would eukaryotes do it?
That's exactly what people used to think. Eukaryotes were supposed to be different—more organized, more stable, genes passed down cleanly from parent to offspring. But the evidence now says that's not the whole story. These four groups, sitting on opposite sides of the evolutionary tree, somehow exchanged genetic material. The exchanges happened most between groups that shared similar environments—fungi and Pseudofungi together, Labyrinthulea and Teretosporea together.
So proximity matters. Shared ecology creates opportunity for gene swapping.
That's the hypothesis. But here's what we still don't know: how did the genes actually move? Did they float in from the environment? Did a virus carry them? And once they arrived, did they do the same job in the new host that they did in the old one? We've identified 166 cases where transfer likely happened, but we haven't traced the mechanism.
So this is really just the beginning of understanding how it works.
Exactly. The question has shifted from whether it happens to how it happens. That's progress, but it's also humbling. We're still in the dark about the actual mechanics.