Understanding how complex eukaryotic cells emerged from prokaryotic ancestors represents a major challenge in biology. A main point of contention in refining eukaryogenesis scenarios revolves around the exact relationship between Archaea and eukaryotes. In new research, scientists from the University of Texas at Austin and elsewhere generated 63 new Asgard archaea genomes from samples obtained from 11 locations around the world. By analyzing the enlarged genomic sampling of Asgard archaea using state-of-the-art analyses, they firmly place eukaryotes as a clade nested within the Asgard archaea, similar to how birds are one of several groups within a larger group called dinosaurs, sharing a common ancestor. By revealing key features regarding the identity, nature and physiology of the last Asgard archaea and eukaryotes common ancestor, their results represent important, thus far missing pieces of the eukaryogenesis puzzle.
Asgard archaeon. Scale bar – 500 nm. Image credit: Imachi et al., doi: 10.1038/s41586-019-1916-6.
“No fossils of eukaryotes have been found from farther back than about 2 billion years ago, suggesting that before that, only various types of microbes existed,” said co-senior author Dr. Brett Baker, a researcher in the Department of Integrative Biology at the University of Texas at Austin.
“So, what events led microbes to evolve into eukaryotes? That’s a big question. Having this common ancestor is a big step in understanding that.”
In their study, Dr. Baker and colleagues identified the closest microbial relative to all complex life forms on the tree of life as a newly described order called the Hodarchaeales.
Hodarchaeales, found in marine sediments, are one of several subgroups within the larger group of Asgard archaea.
The Asgard archaea evolved more than 2 billion years ago, and their descendants are still living.
Some have been discovered in deep sea sediments and hot springs around the world, but so far only two strains have been successfully grown in the lab.
To identify them, the researchers collect their genetic material from the environment and then piece together their genomes.
Based on genetic similarities with other organisms that can be grown in the lab and studied, they can infer metabolism and other features of Asgard archaea.
“Imagine a time machine, not to explore the realms of dinosaurs or ancient civilizations, but to journey deep into the potential metabolic reactions that could have sparked the dawn of complex life,” said co-author Dr. Valerie De Anda, also from the Department of Integrative Biology at the University of Texas at Austin.
“Instead of fossils or ancient artifacts, we look at the genetic blueprints of modern microbes to reconstruct their past.”
“The origin of the eukaryotic cell is one of the most enigmatic events in the evolution of life on Earth, and includes many important details that remain poorly understood,” said co-senior author Dr. Thijs Ettema, a researcher at Wageningen University.
“In particular, how eukaryotic cells obtained their complex and compartmentalized nature is subject to debate.”
“In this study, we identified a specific Asgard archaeal group — the Hodarchaeales — as the closest relatives of eukaryotes, and provide evidence that the genetic basis of some of the eukaryotic complexity can be traced back to the Asgard archaea.”
“Our study involved many detailed phylogenetic analyses of genomic data to determine which microbial group represented the closest relatives of eukaryotes in the tree of life.”
“Resolving such evolutionary relationships is extremely complicated since their last common ancestor dates back to some 2 billion years ago.”
“Since then, the evolutionary signal needed to resolve their relationship has eroded due to the accumulation of mutations in their genomes.”
The scientists expanded the known Asgard genomic diversity, adding 63 undescribed Asgard genomes as input for their modeling.
Their analysis indicates that the ancestor of all modern Asgards appears to have been living in hot environments, consuming carbon dioxide and chemicals to live.
Meanwhile, Hodarchaeales, which are more closely related to eukaryotes, are metabolically more similar to us, eating carbon and living in cooler environments.
“We found that the Asgard archaeal ancestor of eukaryotes already possessed multiple genes for complex cellular processes that had only been found previously in eukaryotes,” said co-author Dr. Daniel Tamarit, a researcher at Utrecht University.
“On top of that, we found that several of its genes evolved via gene duplication events.”
“This is surprising, since archaea and bacteria, unlike eukaryotes, are known to mostly acquire genes from other microbes in a process referred to as horizontal gene transfer.”
“The observed high gene duplication rates in Asgard archaea suggest that their genomes already evolved in a somewhat similar way as eukaryotes did.”
The study was published in the journal Nature.
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L. Eme et al. Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes. Nature, published online June 14, 2023; doi: 10.1038/s41586-023-06186-2
