How eukaryotes evolved from a mosaic of bacterial and archaeal genes

For decades, biologists have described the origin of complex cells—like those in animals, plants, and fungi—as a single dramatic event: a merger between an archaeon and a bacterium. The bacterium became the mitochondrion, the cell’s powerhouse, while the archaeon provided the genetic backbone. Over time, many bacterial genes migrated into the host’s nucleus, creating the hybrid genomes we see today in all eukaryotes. But a new genomic study suggests the story was far more fluid than previously thought.

A single fusion, many gene transfers

The traditional model, known as the endosymbiotic theory, posits that eukaryotic cells arose when an archaeal host engulfed a bacterium roughly 1.5 to 2 billion years ago. The bacterium evolved into mitochondria, and its genes began moving into the host’s nucleus through a process called horizontal gene transfer. Over hundreds of millions of years, these transfers reshaped the host genome, blending bacterial and archaeal DNA into a stable, functioning whole.

Researchers have long known that eukaryotes contain genes from both bacteria and archaea. Some, like those encoding mitochondrial proteins, are clearly bacterial in origin. Others, involved in core cellular processes, align more closely with archaeal sequences. This pattern supported a clean narrative: one fusion, followed by gradual gene migration.

Multiple waves of bacterial DNA infusion

A team of evolutionary biologists has now reconstructed the evolutionary history of nearly 2,000 universal eukaryotic genes—those shared by all living eukaryotes. By comparing these genes across diverse species, they found evidence that bacterial DNA entered the eukaryotic lineage not once, but in several distinct waves. Each wave introduced new functions, from metabolic pathways to structural proteins, diversifying the genetic toolkit available to early complex cells.

Surprisingly, some of these transfers occurred after the initial mitochondrial integration. This challenges the idea of a single, tidy merger. Instead, gene flow between bacteria and early eukaryotes appears to have been continuous and bidirectional. Some bacterial genes were later lost or replaced, while others became permanently embedded in the eukaryotic genome.

The study also highlights the role of bacteria that are now extinct or highly divergent. Many transferred genes do not closely match any living bacterial group, suggesting these donors belonged to lineages no longer present in modern ecosystems. This genetic mosaic reflects a dynamic, interconnected early biosphere where species frequently exchanged DNA.

Rewriting the tree of life

These findings reinforce a broader shift in evolutionary biology: the tree of life is less a neat branching diagram and more a tangled web, especially in its deep history. Horizontal gene transfer was not a rare exception but a major force shaping the genomes of early complex cells. The first eukaryotes were not built from a single fusion event, but from a patchwork of genetic contributions.

This revised view has implications beyond evolutionary theory. It suggests that the boundaries between major biological groups—bacteria, archaea, and eukaryotes—were once far more permeable. It also underscores how horizontal gene transfer continues to influence modern biology, from antibiotic resistance in pathogens to metabolic innovations in environmental microbes.

As genome sequencing becomes more comprehensive, scientists expect to uncover even more layers of genetic exchange in Earth’s ancient past. The first complex cells were not the product of a single merger, but of repeated, opportunistic gene swaps that collectively created the foundation for all complex life.