Deep origin of eukaryotes outside Heimdallarchaeia within Asgardarchaeota

Jiawei Zhang, Xiaoyuan Feng, Meng Li, Yang Liu, Min Liu, Li-Jun Hou () and Hong-Po Dong ()
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Jiawei Zhang: Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education, East China Normal University
Xiaoyuan Feng: Synthetic Biology Research Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Key Laboratory of Marine Microbiome Engineering of Guangdong Higher Education Institutes, Institute for Advanced Study, Shenzhen University
Meng Li: Synthetic Biology Research Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Key Laboratory of Marine Microbiome Engineering of Guangdong Higher Education Institutes, Institute for Advanced Study, Shenzhen University
Yang Liu: Synthetic Biology Research Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Key Laboratory of Marine Microbiome Engineering of Guangdong Higher Education Institutes, Institute for Advanced Study, Shenzhen University
Min Liu: Ministry of Education, East China Normal University
Li-Jun Hou: Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education, East China Normal University
Hong-Po Dong: Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station, Ministry of Education, East China Normal University

Nature, 2025, vol. 642, issue 8069, 990-998

Abstract: Abstract Research on the morphology, physiology and genomics of Asgard archaea has provided valuable insights into the evolutionary history of eukaryotes1–3. A previous study suggested that eukaryotes are nested within Heimdallarchaeia4, but their exact phylogenetic placement within Asgard archaea remains controversial4,5. This debate complicates understanding of the metabolic features and timescales of early eukaryotic ancestors. Here we generated 223 metagenome-assembled nearly complete genomes of Asgard archaea that have not previously been documented. We identify 16 new lineages at the genus level or higher, which substantially expands the known phylogenetic diversity of Asgard archaea. Through sophisticated phylogenomic analysis of this expanded genomic dataset involving several marker sets we infer that eukaryotes evolved before the diversification of all sampled Heimdallarchaeia, rather than branching with Hodarchaeales within the Heimdallarchaeia. This difference in the placement of eukaryotes is probably caused by the previously underappreciated chimeric nature of Njordarchaeales genomes, which we find are composed of sequences of both Asgard and TACK archaea (Asgard’s sister phylum). Using ancestral reconstruction and molecular dating, we infer that the last Asgard archaea and eukaryote common ancestor emerged before the Great Oxidation Event and was probably an anaerobic H2-dependent acetogen. Our findings support the hydrogen hypothesis of eukaryogenesis, which posits that eukaryotes arose from the fusion of a H2-consuming archaeal host and a H2-producing protomitochondrion.

Date: 2025
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DOI: 10.1038/s41586-025-08955-7

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