Using an expanded molecular clock approach (a new evolutionary model that rewrites the story of early life on Earth), scientists mapped out a clearer timeline as to how early gene families evolved. They discovered that key eukaryotic features emerged — long before mitochondria, or atmospheric oxygen, became abundant…!! 😊
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Reference: “Dated gene duplications elucidate the evolutionary assembly of eukaryotes” 3 December 2025, Nature. DOI: 10.1038/s41586-025-09808-z
Complex Life Started Nearly a Billion Years Earlier Than Previously Thought
By University of Bristol, 3 Dec 2025
Abstract Origin of Life CellsComplex life may have started its rise in Earth’s oxygen-free oceans nearly a billion years earlier than anyone imagined. (Artist’s rendition)
New research indicates that complex life began forming almost a billion years earlier than previously thought…!!
Using an expanded molecular clock approach, scientists mapped out a clearer timeline as to how early gene families evolved. They discovered that key eukaryotic features emerged long before mitochondria or atmospheric oxygen became abundant. The result is a new evolutionary model that rewrites the story of early life.
Early Emergence of Complex Life
New research has uncovered that complex life began forming much earlier, and across a longer timeframe, than scientists had previously assumed. The findings offer fresh insight into the environmental conditions that shaped early evolution and call into question several longstanding scientific ideas in this field.
Led by the University of Bristol and published in Nature (December 3), the study reports that complex organisms arose well before oxygen became abundant in Earth’s atmosphere. Oxygen had long been thought to be essential for the development of advanced life, but the results indicate that this requirement may not hold for the earliest stages of evolution.
“Earth is approximately 4.54 billion years old, with the first microbial life forms appearing more than 4.5 billion years ago. These organisms consisted of two groups – Bacteria, and the distinct but related Archaea, collectively known as prokaryotes [single-celled organisms (e.g., bacteria, cyanobacteria) that have single strands of DNA and neither distinct nucleus with a membrane, nor other specialized organelles),” said co-author Anja Spang, from the Department of Microbiology & Biogeochemistry at the Royal Netherlands Institute for Sea Research.
Prokaryotes dominated the planet for hundreds of millions of years before more complex eukaryotic cells emerged. This latter group includes algae, fungi, plants, and animals.
Eukaryotes Evolution The team has proposed a new evidence-based scenario for the emergence of complex life they have called ‘CALM’ – Complex Archaeon, Late Mitochondrion. Credit: Dr. Christopher Kay
Revisiting the Origins of Eukaryotes
Davide Pisani, Professor of Phylogenomics in the School of Biological Sciences at the University of Bristol and co-author, explained: “Previous ideas on how and when early prokaryotes transformed into complex eukaryotes have largely been in the realm of speculation. Estimates have spanned a billion years, because no intermediate forms exist and definitive fossil evidence has been lacking.”
To address these uncertainties, the international team expanded upon the existing ‘molecular clocks’ technique, which estimates when species last shared a common ancestor.
“The approach was two-fold: by collecting sequence data from hundreds of species and combining these data with known fossil evidence, we were able to create a time-resolved tree of life. We could then apply this framework to better resolve the timing of historical events within individual gene families,” added co-lead author Professor Tom Williams in the Department of Life Sciences at the University of Bath.
By comparing more than 100 gene families across multiple biological systems and focusing on traits that differentiate eukaryotes from prokaryotes, the researchers began reconstructing the sequence of events that shaped the rise of complex life.
Eukaryotes Evolution Figure By collecting evidence from multiple gene families (more than a hundred in total) in multiple biological systems and focusing on the features that distinguish eukaryotes from prokaryotes, the team was able to begin to piece together the developmental pathway for complex life. Credit: Dr. Christopher Kay
A Much Earlier Start to Cellular Complexity
The team found that the transition toward complexity began nearly 2.9 billion years ago, almost a billion years earlier than some prior estimates. Their results also indicate that the nucleus and other internal cellular structures formed well before mitochondria.
“The process of cumulative complexification took place over a much longer time period than previously thought,” said author Gergely Szöllősi, head of the Model-Based Evolutionary Genomics Unit at the Okinawa Institute of Science and Technology (OIST).
These findings enabled the researchers to rule out several existing hypotheses for eukaryogenesis (the evolution of complex life). Because their results did not fully match any current model, they introduced a new scenario called ‘CALM’: Complex Archaeon, and Late Mitochondrion.
Introducing the CALM Model
Lead author Dr. Christopher Kay, Research Associate in the School of Biological Sciences at the University of Bristol, explained: “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: palaeontology 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.”
“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 author Philip Donoghue, Professor of Palaeobiology in the School of Earth Sciences at the University of Bristol.
“This insight ties evolutionary biology directly to Earth’s geochemical history. The archaeal ancestor of eukaryotes began evolving complex features roughly a billion years before oxygen became abundant, in oceans that were entirely anoxic.”