Complex life emerged long before oxygen flooded Earth

A sweeping new analysis argues that complex cells began evolving almost a billion years earlier than many timelines suggest, long before oxygen became abundant in Earth’s atmosphere.

Led by the University of Bristol, the work redraws the early evolutionary map by tracing when hallmark features of eukaryotic cells emerged. It also proposes a new, evidence-based scenario for how complexity unfolded.

Birth of complex cells

For much of Earth’s history, life was strictly microbial. “The Earth is approximately 4.5 billion years old, with the first microbial life forms appearing over 4 billion years ago,” said co-author Anja Spang from the Royal Netherlands Institute for Sea Research (NIOZ).

“These organisms consisted of two groups – bacteria and the distinct but related archaea, collectively known as prokaryotes.”

Prokaryotes dominated the planet for hundreds of millions of years before eukaryotes (cells with internal compartments such as a nucleus) appeared and ultimately gave rise to algae, fungi, plants, and animals.

Exactly when, how, and in what order the defining features of eukaryotes emerged has been a long-standing puzzle. Previous ideas on how and when early prokaryotes transformed into complex eukaryotes have largely been speculation.

“Estimates have spanned a billion years, as no intermediate forms exist and definitive fossil evidence has been lacking,” said Davide Pisani, a professor of phylogenomics at Bristol.

Rebuilding life’s ancient timeline

To move beyond speculation, the team expanded and refined “molecular clock” approaches. By collating genetic sequence data across hundreds of species and anchoring them with fossil constraints, they built a more precise tree of life.

Then, they drilled down into the histories of more than a hundred gene families that encode functions uniquely associated with cellular complexity.

“The approach was twofold: by collecting sequence data from hundreds of species and combining this with known fossil evidence, we were able to create a time-resolved tree of life,” said co-lead author Tom Williams from the University of Bath.

“We could then apply this framework to better resolve the timing of historical events within individual gene families.”

The research frames eukaryote origins as gradual, with traits like vesicle transport, cytoskeletal systems, and a nucleus emerging in stages.

By mapping when these functional systems appear to have arisen, the team reconstructed the sequence of innovations that gradually transformed an archaeal ancestor into a complex cell.

Complex life’s early rise

The headline result is a sharp revision of the timescale. The analyses suggest the move toward complexity began around 2.9 billion years ago, far earlier than many previous estimates. They indicate that this transition unfolded gradually over a long span of time.

Strikingly, several major eukaryotic features appeared to have evolved before mitochondria arrived. For years, these energy-producing symbionts were considered the spark for complexity.

The implication is profound: eukaryotic architecture did not hinge on a single, late-coming energy upgrade.

Instead, an archaeal lineage may have been gradually acquiring the toolkit of complexity in an oxygen-poor world, only later incorporating the mitochondrial endosymbiont.

A fresh evolutionary framework

Because the evidence didn’t cleanly fit existing hypotheses, the authors propose a new framework, CALM (Complex Archaeon, Late Mitochondrion).

In this scenario, an archaeal host lineage first developed complex cellular systems, including a nucleus and vesicle trafficking, and only later acquired mitochondria. The timing of mitochondrial arrival aligns with Earth’s geochemical record.

“One of our most significant findings was that the mitochondria arose significantly later than expected. The timing coincides with the first substantial rise in atmospheric oxygen,” said Philip Donoghue, a professor of paleobiology at Bristol.

That correspondence knits biology to planetary change. “This insight ties evolutionary biology directly to Earth’s geochemical history,” said Donoghue.

“The archaeal ancestor of eukaryotes began evolving complex features roughly a billion years before oxygen became abundant, in oceans that were entirely anoxic.”

Rebuilding deep genetic history

A distinctive strength of the work lies in its focus on what the genes actually do. The researchers dated gene families tied to key eukaryotic processes and identified when interacting proteins first appeared in evolutionary history.

By cross-referencing these gene ages with fossils and with the broader phylogenetic scaffold, they could order the acquisition of cellular life systems in absolute time.

Study lead author Christopher Kay highlighted the interdisciplinary effort required to pull this off. “What sets this study apart is looking into detail about what these gene families actually do – and which proteins interact with which – all in absolute time.”

“It has required the combination of a number of disciplines to do this: paleontology to inform the timeline, phylogenetics to create faithful and useful trees, and molecular biology to give these gene families a context. It was a big job.”

Rethinking life’s conditions

The finding that complex traits emerged in a low-oxygen world challenges a widely held assumption that plentiful oxygen was a prerequisite for eukaryotic complexity.

Instead, the data support a staggered, modular combination of complex systems within an archaeal lineage, with mitochondria arriving later.

This view also helps explain the patchwork of prior signals in genomic data. If complexity accreted across many gene families over nearly a billion years, no single marker would define the “moment” of eukaryote origin.

CALM reframes eukaryogenesis as a prolonged evolutionary program rather than a single event.

Implications for life’s origins

The study links gene-family timelines to Earth’s environmental history, creating a bridge between evolutionary biology and geochemistry.

This connection shows how complex cell life took shape in ancient, anoxic oceans and later aligned with rising oxygen levels.

It narrows eukaryote origin timelines and shows mitochondria arrived late while offering a roadmap for future gene-function evolution research.

The research also invites a fresh look at the environments that can nurture complexity.

If intricate cellular systems began to bloom long before oxygen was abundant, life’s evolutionary potential may be less constrained by planetary atmospheres than once assumed. This possibility also opens the door to new ideas about extraterrestrial life.

The study is published in the journal Nature.

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