Study reveals diverse microbial gene sources in early eukaryotic evolution beyond previously identified partners
A large-scale phylogenomic study published in Nature has found that the last eukaryotic common ancestor (LECA) acquired genes not just from Asgard archaea and alphaproteobacteria, but also significantly from Planctomycetota and Myxococcota bacteria, as well as through giant viruses. The research reconstructed a LECA proteome of roughly 7,700–12,900 gene families and traced their ancestries using curated datasets spanning over 65,000 prokaryotic genomes. The findings challenge the prevailing two-partner model of eukaryogenesis and support a more gradual, multi-partner origin of complex cellular life.
Researchers reconstructed the proteome of the last eukaryotic common ancestor (LECA) using three independent datasets of 100 eukaryotic proteomes each, expanded against a broad database of over 65,000 prokaryotic genomes and 1.3 million viral protein clusters. Phylogenetic analysis of roughly 7,751–12,907 gene families revealed that while Alphaproteobacteria (the mitochondrial ancestor, ~4.0% of the proteome) and Asgard archaea (~3.3%) remain the dominant prokaryotic contributors, Myxococcota (~3.9%) and Planctomycetota (~2.2%) represent two additional major bacterial donors with statistically robust signals. Approximately 4.5% of gene acquisitions appear to have been mediated by Nucleocytoviricota giant viruses, which transferred genes of diverse prokaryotic origin—including from Asgard archaea—into the proto-eukaryotic lineage. Branch-length ratio analyses suggest a temporal ordering in which Asgard archaea interacted earliest, followed by Planctomycetota, then Myxococcota and the alphaproteobacterial mitochondrial ancestor, a sequence that mirrors the vertical stratification of these groups in modern microbial mats. The study concludes that eukaryogenesis was likely a gradual, community-level process involving serial symbiotic or syntrophic interactions in complex microbial environments, rather than a single binary merger event.
Data: Nature (article figures)
Limitations & open questions
The study acknowledges that its ancestral metabolic reconstructions are indirect and rely on co-occurrence patterns in extant genomes rather than true ancestral state reconstruction, meaning inferred donor metabolisms carry substantial uncertainty. The analysis cannot distinguish between endosymbiotic, ectosymbiotic, or parasitic modes of interaction for any of the proposed partners, and the precise ecological setting of eukaryogenesis remains speculative. Additionally, the phylogenetic signals for minor donors such as Chloroflexota and Gammaproteobacteria did not pass consistency thresholds across all datasets, leaving open the question of how many additional minor contributors existed.
What different sources said
- Nature NewsCenter
Gene ancestries reveal diverse microbial associations during eukaryogenesis
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