The “Asgard archaea” are our own cells’ closest relatives

Thanks to microscopy, early biologists were able to make a binary distinction: there were eukaryotes and bacteria. The former had large, complex cells with internal compartments, while the latter were largely featureless. Which raised an obvious question: how did that apparently giant leap in complexity come about? While DNA sequencing provided some hints as to the relations among different branches on the tree of life, the unique features of eukaryotes and the genes that enabled them appeared to have no real antecedents.

Until recently, that is. Last year, a hydrothermal vent in the Arctic named Loki’s Castle yielded organisms that picked up the name Lokiarchaea. Now, researchers have used Lokiarchaea’s genome to find a large group of related species that they are naming the Asgard superphylum. Genetically, these organisms are the closest relatives of complex cells. The relationship is so close that all organisms with complex cells may simply be one branch of this group.

Domain names

One of the big ideas in biology is what’s called the three domains of life. Genetic data revealed that we couldn’t simply divide all living things into complex eukaryotes and simple bacteria. Instead, two very distinct groups lurked behind the seemingly simple cell architecture we used to call bacteria. While one of these groups retained the name bacteria, the second was called archaea to reflect its distinct lineage from early in life’s history. Bacteria, archaea, and eukaryotes thus made up the three domains of life.

But the relationship of eukaryotes to the other groups was difficult to parse. Many of their key genes seemed to be related to those found in archaea. But an early eukaryote seems to have swallowed a bacteria, converted it to an energy-producing structure, and adopted many of its genes, too. Finally, there were a large collection of genes needed to build and maintain all the complex structures within eukaryotic cells; these didn’t seem to have relatives anywhere else.

As a result, most three-domains diagrams of the tree of life had eukaryotes sharing a brief history with archaea before going their separate ways, having been a distinct lineage since early in life’s history on Earth. And, because scientists love to argue about ideas, debates raged as to whether there was something clearly eukaryotic before it swallowed a bacterium or if eukaryotes only started once they had the present energy-producing system in place.

The authors of the new work on Asgard archaea argue so strongly for the latter option that they think we should get rid of the three domains idea entirely. Instead, in their view, there are just two: bacteria and archaea. All organisms with complex cells, from a Paramecium to us, are just a branch of archaea.

Introducing Asgard

But that’s getting a bit ahead of the story. How did researchers find out there was an Asgard archaea in the first place?

As mentioned above, Lokiarchaeota was recently found to be closely related to eukaryotes. But we only found that by sequencing DNA at random from material obtained at the hydrothermal vent—we don’t know how to culture this organism or anything about what it looks like. But the authors figured there must be more critters out there like it. So they obtained samples from places as diverse as Yellowstone Park and a North Carolina estuary, and they sequenced nearly 650 billion bases of DNA (for comparison, the human genome is about 3 billion bases).

Overlapping fragments of sequence were identified and matched to build longer stretches of DNA sequence. The stretches most closely related to Lokiarchaeota were then identified based on having related genes for protein production. Other stretches were then identified based on a statistical similarity to these (similar base frequencies, etc.). The resulting sequences were then used to build a tree of these related organisms.