Ancient Scottish Fossils Reveal a “Third Way” of Life in Earth’s Earliest Forests

Inside a chunk of ancient Scottish stone, a team of researchers has just upended 165 years of fossil detective work. Prototaxites, the strange 8-metre-tall organism that dominated Earth’s earliest forests, isn’t what anyone thought it was. It’s not a fungus. It’s not an alga. It’s not a plant. It’s something else entirely, something that has no living relative anywhere on Earth.

The story starts with a boomerang-shaped specimen, no bigger than your fist, encased in Rhynie chert from northeastern Scotland. This 407-million-year-old rock has become palaeontologists’ most prized window into the Devonian world, preserving everything from the tiniest bacteria to the creatures that ate them. When Corentin Loron and his colleagues at the University of Edinburgh first examined the specimen—a chunk of Prototaxites taiti barely 5.6 centimetres across—they noticed something peculiar in the rocks around it. Other fossils from the same ecosystem had left chemical fingerprints. Fungi left unmistakable marks. So did plants. But this organism, despite its tube-like body that superficially resembled fungal threads, seemed to exist in a category all its own.

The researchers sliced the specimen into impossibly thin sections and peered through microscopes, building 3D reconstructions of its internal architecture. Inside, they found three distinct types of tubes woven together in a pattern that defied easy classification. Type 1 tubes, pencil-thin and perforated, made up three-quarters of the structure. Larger Type 2 tubes formed a supporting network. But it was Type 3 that made the mystery deepen. These tubes bore annular thickenings, ring-like reinforcements that appear in no known fungus, extinct or living. Not a single one.

“This is where it gets interesting,” says Alexander Hetherington, who coordinated the study. The anatomy alone was enough to trouble the leading hypothesis that Prototaxites was simply an ancient fungus. But anatomy can deceive. Two organisms with radically different origins sometimes converge on similar shapes. To truly know what this thing was, the team needed to look deeper, into its very chemistry.

They ground up a pristine specimen and bombarded it with infrared light, watching how the ancient molecules absorbed specific frequencies. Every organism leaves a signature written in chemical bonds. Fungi carry chitin in their cell walls, a glucose-based polymer that fossilises into a recognisable pattern. Plants leave the mark of lignin. Bacteria write their names in lipids. When the team compared Prototaxites to every other fossil in the Rhynie chert, including fungi, plants, bacteria, arthropods, even single-celled amoebae, it stood apart. Its molecular fingerprint showed aliphatic chains, aromatic compounds, and phenolic structures more reminiscent of lignin, but fundamentally distinct from anything alive today.

The mathematics bore this out. Using machine learning trained on known organisms, researchers built models to classify samples based purely on their spectral signatures. Every time, Prototaxites failed to cluster with fungi, achieving a 91 per cent discrimination accuracy from its supposed closest relatives. When tested against all chitinous organisms together—fungi and arthropods, which share the same cell-wall chemistry—the accuracy climbed to 93 per cent. Prototaxites was chemically alone.

To confirm what they were seeing, the team hunted for perylene, a molecular fossil marker unique to ascomycete fungi. They found it abundantly in the surrounding sediment, in the other fossils trapped there. In Prototaxites itself, there was nothing. Complete absence. It was as if the organism deliberately avoided creating the chemical signatures that every known fungus, without exception, leaves behind.

What emerged from months of analysis is a creature that fits nowhere in our biological taxonomy. It was not a fungus—the anatomical and molecular evidence rules that out categorically. It was not a plant, lacking the isotopic signatures of photosynthesis and the cellular architecture that distinguishes land plants. It wasn’t an alga, not an oomycete, not a bacterium. Loron’s team presents the uncomfortable but inevitable conclusion: Prototaxites belonged to a lineage that has vanished completely from Earth, leaving behind only these fossilised remnants and the questions they pose.

In the Devonian ecosystem preserved at Rhynie, Prototaxites taiti was the largest organism anyone has found. Towering over the primitive plants beginning to colonise the land, it was feeding on decaying matter, breaking down the early forests that were still learning how to grow. For millions of years, such organisms may have dominated Earth’s terrestrial surface. Then something changed. They disappeared, leaving not even a distant modern descendant to tell us how they lived, how they reproduced, or why they vanished.

What draws us now is not closure, but a deepened sense of the strange variety of life that inhabited this planet in its distant past. Before the fungi we know, before the complex plants, before the animals that would eventually inherit the land, there existed something else entirely. Something we can only identify by what it was not, by the absence of the chemical signals that every other organism broadcasts. In solving one mystery, the researchers have merely revealed how much remains unknown about life’s history. And in a world increasingly dominated by familiar biology, that mystery feels rare and precious.

Pre-print (Not peer-reviewed) Study link: https://www.biorxiv.org/content/10.1101/2025.03.14.643340v1.full.pdf