The origin of complex life on Earth has long intrigued scientists, as eukaryotic cells, with their intricate structures like nuclei, mitochondria, and cytoskeletons, stand apart from simpler bacterial and archaeal cells. How did these sophisticated cells evolve from prokaryotic ancestors? A new study offers fresh insights, pinpointing deep-sea microbes known as Asgard archaea as the primary builders of the first eukaryotic cells, contributing most of the core genes and systems that define eukaryotes.
The research, published in the journal Nature, draws from an extensive analysis of millions of protein sequences from archaea, bacteria, and eukaryotes. By constructing phylogenetic trees and testing evolutionary hypotheses, the team traced the ancestry of genes present in the last eukaryotic common ancestor (LECA) — the progenitor of all modern eukaryotes. Their findings reveal that Asgard archaea provided the lion’s share of these genes, shaping everything from information-processing machinery to metabolic pathways and membrane systems.
Eukaryotes emerged around two billion years ago, marking a leap in cellular complexity. Unlike prokaryotes, they feature compartmentalized organelles that enable advanced functions like energy production and protein trafficking. Earlier models suggested a chimeric origin, with archaea contributing to information systems and bacteria dominating metabolism. But the discovery of Asgard archaea in deep-sea sediments a decade ago shifted the narrative, as these microbes encode proteins resembling eukaryotic cytoskeletons and membrane remodelers.
In this study, researchers curated vast databases of prokaryotic and eukaryotic genomes, identifying over 13,000 clusters of homologous proteins. They focused on core genes widespread across eukaryotes, ensuring inferences reflected ancient origins rather than recent transfers. The analysis showed Asgard archaea as the dominant source, accounting for about half the likelihood weight in well-supported clusters.
“The results show dominant contributions of Asgard archaea to the origin of most of the conserved eukaryotic functional systems and pathways,” the study states.
Beyond information processing, like replication, transcription, and translation, Asgard influences extended to protein sorting, glycosylation, and even parts of lipid biosynthesis. For instance, enzymes for N-linked glycan synthesis and GPI anchors, which tether proteins to membranes, are strongly traced to Asgard. Even the mevalonate pathway, key for eukaryotic isoprenoid production, showed Asgard roots, hinting at a link to archaeal membrane precursors.
In contrast, contributions from alphaproteobacteria, the ancestors of mitochondria, were focused and limited, mainly involving oxidative phosphorylation and iron-sulfur cluster assembly. These align with the endosymbiotic event where an alphaproteobacterium was engulfed, becoming the mitochondrion. Inputs from other bacteria, like cyanobacteria or actinobacteria, appeared scattered across functions without clear patterns, suggesting sporadic gene acquisitions rather than major symbiotic events.
“A limited contribution from Alphaproteobacteria was identified, relating primarily to energy transformation systems and Fe–S cluster biogenesis, whereas ancestry from other bacterial phyla was scattered across the eukaryotic functional landscape, without clear, consistent trends,” the researchers explain.
This mosaic supports a model where the Asgard lineage evolved many eukaryotic hallmarks before capturing the mitochondrial ancestor. The host cell, already complex with cytoskeleton and endomembranes, then integrated bacterial genes piecemeal. Such a scenario resolves some enigmas, like the bacterial-type membranes in eukaryotes, possibly through early gene transfers enabling a membrane transition.
“These findings imply a model of eukaryogenesis in which key features of eukaryotic cell organization evolved in the Asgard lineage leading to the LECA, followed by the capture of the alphaproteobacterial endosymbiont and augmented by numerous but sporadic horizontal acquisitions of genes from other bacteria both before and after endosymbiosis,” the study concludes.
Citations
V. Tobiasson, E. V. Koonin et al. Dominant contribution of Asgard archaea to eukaryogenesis. Nature. Published online January 14, 2026. DOI: 10.1038/s41586-025-09960-6
