New findings suggest that complex life began forming much earlier, and over a far longer period, than researchers previously understood. The study provides fresh insight into the environmental conditions that supported early evolution and challenges several widely accepted ideas about when advanced cellular features first appeared.
Led by the University of Bristol and published in Nature on December 3, the work shows that complex organisms started developing long before oxygen levels in the atmosphere rose to significant levels. Until now, many scientists believed that plentiful oxygen was essential for the emergence of complex life.
“The Earth is approximately 4.5 billion years old, with the first microbial life forms appearing over 4 billion years ago. These organisms consisted of two groups — bacteria and the distinct but related archaea, collectively known as prokaryotes,” said co-author Anja Spang from the Department of Microbiology & Biogeochemistry at the Royal Netherlands Institute for Sea Research.
For hundreds of millions of years, prokaryotes were the only living organisms on the planet. More complex eukaryotic cells eventually evolved, giving rise to algae, fungi, plants and animals.
Rethinking the Origins of Eukaryotes
Davide Pisani, Professor of Phylogenomics in the School of Biological Sciences at the University of Bristol and co-author, noted: “Previous ideas on how and when early prokaryotes transformed into complex eukaryotes has largely been in the realm of speculation. Estimates have spanned a billion years, as no intermediate forms exist and definitive fossil evidence has been lacking.”
To shed light on this long-debated transition, the team expanded the existing ‘molecular clocks’ method, a tool used to estimate when different species last shared an ancestor.
“The approach was two-fold: 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. We could then apply this framework to better resolve the timing of historical events within individual gene families,” explained co-lead author Professor Tom Williams in the Department of Life Sciences at the University of Bath.
A Much Earlier Start to Cellular Complexity
The researchers examined more than one hundred gene families across multiple biological systems and focused on the traits that separate eukaryotes from prokaryotes. This allowed them to reconstruct a clearer picture of how complex cellular features developed.
Their results indicate that the shift toward complexity began nearly 2.9 billion years ago — almost a billion years earlier than some previous estimates. The evidence suggests that structures such as the nucleus emerged 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 allowed the researchers to dismiss some existing models for eukaryogenesis (the evolution of complex life). Since the results did not fully match any current explanation, the team proposed a new scenario called ‘CALM’ — Complex Archaeon, Late Mitochondrion.
Introducing the CALM Model
Lead author Dr. Christopher Kay, Research Associate in the School of Biological Sciences at the University of Bristol, said: “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.”
“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,” added 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.”
