Understanding how complex eukaryotic cells arose from prokaryotic ancestors represents a major challenge in biology. The main point of contention in refining scenarios of eukaryogenesis revolves around the exact relationship between Archaea and eukaryotes. In the new research, scientists from the University of Texas at Austin and elsewhere have generated 63 new Asgard archaea genomes from samples obtained from 11 locations around the world. By analyzing the increased genomic sampling of Asgard archaea using modern analyses, they firmly place eukaryotes as a clade nested within Asgard archaea, similar to how birds are one of several groups within larger group called dinosaurs, which share a common ancestor. By revealing key features about the identity, nature and physiology of the last Asgard archaea and eukaryotes common ancestor, their results represent important, until now missing pieces of the eukaryogenesis puzzle.
“No fossils of eukaryotes have been found from further back than about 2 billion years ago, suggesting that before that, only different 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 identify the closest microbial relative to all complex life forms on the tree of life as a newly described order called Hodarchaeales.
The 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 alive.
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, researchers collect their genetic material from the environment and then sequence their genomes.
Based on genetic similarities with other organisms that can be grown in the lab and studied, they can indicate the metabolism and other features of Asgard archaea.
“Imagine a time machine, not to explore the realms of dinosaurs or ancient civilizations, but to travel deep into the potential metabolic reactions that may 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’re looking 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 acquired their complex and compartmentalized nature is subject to debate.”
“In this study, we identify 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 involves a lot of detailed phylogenetic analysis of genomic data to determine which microbial group represents the closest relatives of eukaryotes on the tree of life.”
“Resolving such evolutionary relationships is extremely complicated because their last common ancestor dates back to about 2 billion years ago.”
“Since then, the evolutionary signal needed to resolve their relationship has collapsed 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 Asgard appears to have lived in warm environments, consuming carbon dioxide and chemicals to survive.
Meanwhile, the Hodarchaeales, which are more closely related to eukaryotes, are metabolically more similar to us, consuming carbon and living in cooler environments.
“We found that the Asgard archaeal ancestor of eukaryotes already possessed many genes for complex cellular processes previously found only in eukaryotes,” said co-author Dr. Daniel Tamarit, a researcher at Utrecht University.
“Furthermore, we found that some of its genes had changed through gene duplication events.”
“This is surprising, because archaea and bacteria, unlike eukaryotes, are known to often acquire genes from other microbes in a process referred to as horizontal gene transfer.”
“The observed high rates of gene duplication in Asgard archaea indicate that their genomes have evolved in a relatively similar way as eukaryotes did.”
The study was published in the journal Nature.
L. Do et al. Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes. Nature, published online June 14, 2023; doi: 10.1038/s41586-023-06186-2
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