Open access funding provided by Uppsala University. We thank S. Köstlbacher, L. Hederstedt, A. Spang and A. J. Roger for discussions; staff at the Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) at Uppsala University and the Swedish National Infrastructure for Computing (SNIC) at the PDC Center for High-Performance Computing for providing computational resources; staff at the Japan Agency for Marine-Earth Science and Technology (JAMSTEC) for taking sediment samples from the Taketomi shallow submarine hydrothermal system; and the crew of the RV Roger Revelle for assisting with the sampling of the ABE and Mariner vent fields along the Eastern Lau Spreading Center during the RR1507 Expedition. The Ngāti Tahu–Ngāti Whaoa Runanga Trust is acknowledged as mana whenua of Radiata Pool and associated samples, and we thank them for their assistance in access and sampling of the Ngatamariki geothermal features. We thank the Kingdom of Tonga for access to the deep-sea hydrothermal vent sites along the ELSC. Sampling in the Eastern Lau Spreading Center and Guaymas Basin (Gulf of California) was supported by the US-National Science Foundation (NSF-OCE-1235432 to A.-L.R. and NSF-OCE-0647633 to A.P.T.).
In the ongoing debates about eukaryogenesis—the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors— members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2–4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.
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Eme, L., Tamarit, D., Caceres, E. F., Stairs, C. W., De Anda, V., Schön, M. E., ... & Ettema, T. J. (2023). Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes. Nature, 1-8.