The origin of organisms with complex cells, known as eukaryotes, is one of the most crucial parts of life’s evolutionary story. All animals, plants, and fungi are eukaryotes, and if complex cells had not developed on Earth, there would be no fish, flowers, mushrooms, or humans.

While the oldest confirmed fossils of eukaryotes are about one billion years old, the organisms may have had a long-hidden prehistory, according to a new study of chemicals preserved in ancient rocks. This chemical evidence suggests there were complex cells 1.6 billion years ago and possibly even earlier.

The tell-tale chemicals from these cells are the breakdown products of fatty molecules in their membranes. They had gone unnoticed until now because they are not the exact ones found in modern cells. “They are very primordial,” says Benjamin Nettersheim, a geochemist at the University of Bremen in Germany and an author of the new study.

Nettersheim’s team found traces of these fatty molecules in a range of ancient rocks including Australia’s Barney Creek Formation. The findings suggest primitive eukaryotes were widespread between about 1.6 billion and 800 million years ago, comprising what the scientists have called a “lost world” of early complex life.

“It’s really quite substantial and really does change how we view the evidence for biomarkers and eukaryotic evolution,” says Emily Mitchell at the University of Cambridge in the United Kingdom, who studies the early evolution of animals but was not involved in the study.

The evolution of cells

The oldest cellular organisms are bacteria and archaea. Their cells are small and have few internal structures, while eukaryotic cells are much bigger and contain structures such as a nucleus, which houses the DNA, and the sausage-shaped mitochondria that produces energy. Bacteria and archaea arose at least 3.5 billion years ago, but eukaryotes only evolved later.

Despite its importance, the origin of eukaryotes remains one of the biggest mysteries in biology. It seems to have happened between one and two billion years ago, but narrowing this down has proved tricky.

A useful marker is the Last Eukaryotic Common Ancestor (LECA): the most recent species from which all modern eukaryotes are descended. Genetics research suggests LECA lived at least 1.2 billion years ago. However, this organism was not the first eukaryote.

Fossil eukaryotes that came after LECA have been found from around one billion years ago. The best-studied are a multicellular red alga called Bangiomorpha from Proterocladus from northern China. But these early eukaryotes seem to have been rare. Not until 900 million years ago do palaeontologists see them start to diversify—and large-bodied animals don’t show up until around 570 million years ago.

However, other fossils have been found from 1.6 or even 1.8 billion years ago that look like eukaryotes. One example is Shuiyousphaeridium macroreticulatum, a blob-shaped organism with short tendrils, from rock formations in northern China. These early eukaryotes look more primitive and may have lived before LECA.

Tracking how eukaryotes arose and evolved from such early fossils has proven difficult. So Nettersheim and his colleagues set out to find another line of evidence that would help tie down the eukaryote story.

Fatty traces in the rock

The researchers focused on chemicals called lipids, which include all fats and oils. Specifically, they targeted sterols: a group of lipids that are found in the outer membranes of eukaryotic cells. “Almost all eukaryotes produce sterols,” says Nettersheim. Probably the most famous sterol is cholesterol, which plays a major role in human biology.

Over time, sterols break down into chemicals called steranes. Finding steranes in ancient rocks is good evidence that the place was once home to eukaryotes.

Steranes are plentiful in rocks from the last 800 million years, but they have not been detected in older rocks. On face value, this looks like evidence that there were few eukaryotes before 800 million years ago, which flies in the face of the fossil and genetic evidence.

However, Nettersheim and his colleagues have found another way to look at it. They reasoned that early eukaryotes might not have made the same kind of sterols as modern eukaryotes. Instead, the team focused on sterols that today only function as intermediate steps in the reaction pathways of cells. These, they suggest, were once the main sterols used by early eukaryotes, until later organisms found ways to convert them into different molecules, perhaps with more specialised properties.

“They didn’t yet produce the same lipids that modern eukaryotes would produce, but they produced lipids that are now intermediates,” says Nettersheim.

This approach enables researchers to look at the “evolutionary development or precursors” of sterols, says Paul Strother, a palaeobotanist at Boston College in Massachusetts, who was not involved in the study. “To me that is a big step forward.”

The team determined what molecules these primordial sterols would decay into. Then they searched ancient rocks for those breakdown products.

Unlike signs of modern sterols, the bits of these primordial sterols were readily found in rocks older than 800 million years. These include 1.1-billion-year-old rocks of the Taoudeni Basin in Mauritania and the Keweenawan Rift in Michigan. The team was even able to find them in Australia’s Barney Creek Formation, which is 1.6 billion years old.

According to Nettersheim, the finding resolves a major enigma. Previously the chemical record suggested a late origin of eukaryotes, while the microfossil and genetic evidence indicated an earlier one. Now the chemical record has been extended back in time and the three largely align.

“When very independent lines start matching up, then you know that you’ve probably got a very accurate record,” says Mitchell.

Building complex organisms

The new story goes like this. Eukaryotes first evolve at least 1.6 billion years ago, possibly as early as two billion years ago. They use the primordial sterols in their outer membranes. A crucial step occurs where some eukaryotes evolve to use modern sterols, and by 800 million years ago, those organisms had taken over.

But pushing back the origin of eukaryotes to at least 1.6 billion years ago creates a new question: Why did it take so long for complex animals, plants, and fungi to emerge?

One possibility is that complex multicellular organisms evolved earlier than is generally thought. For example, a 2019 study claimed to have found fossil sponges, one of the earliest animal groups, in rocks from 890 million years ago. This would push back the origin of animals by 350 million years. However, Nettersheim says the fossils are “not really convincing,” because some single-celled eukaryotes can produce similar-looking structures.

Nettersheim’s team suggests instead that the early eukaryotes dominated prehistoric ecosystems, and modern eukaryotes could only flourish and diversify when this earlier population died out. Modern sterols help eukaryotes adjust to stresses like dehydration and cold shock, so it may be that the more developed cells were better suited to survive a period of environmental stress.

A possible cause may be conditions called Snowball Earth: a series of episodes in which Earth’s climate cooled considerably, leading to a huge expansion of ice sheets. “Potentially the entire Earth was frozen or at least very cold,” says Nettersheim. Snowball Earth episodes occurred during the Cryogenian Period, between about 720 and 635 million years ago.

Modern sterols could have helped certain eukaryotes survive while others died—and once the glaciation eased, the surviving eukaryotes diversified into plants and animals. “We think this might have been one of the pre-adaptations that helped the modern eukaryotes attain ecological importance,” says Nettersheim.

“It seems like a reasonable suggestion,” says Mitchell. “Whether or not it’s correct, I don’t know.”

Strother is similarly cautious, pointing out that we have so few early eukaryotes preserved that any new discovery could upend the story. “In my view, these paradigms are somewhat fragile,” he says.

What does seem clear is that the early history of eukaryotes was rich and tangled. While the evolution of modern sterols around 800 million years ago was a major event, plenty of important evolutionary steps occurred beforehand. Just last year, Emmanuelle Javaux at the University of Liège in Belgium described microfossils of eukaryotes found in the Democratic Republic of the Congo from one billion years ago. They contained remnants of chlorophyll—indicating there were photosynthetic algae at this early time.

Similarly, in 2021 Strother and his colleagues described another billion-year-old eukaryote called Bicellum brasieri, found in the Scottish Highlands. This one was multicellular, and what’s more, it had two distinct cell types: a precursor to the tissues and organs of later animals and plants.

“If at one billion we’re having these kinds of morphological complexity, that would kind of indicate maybe stuff was happening earlier than 800 million,” he says.