Merging branches —

The tree of life may have only two major branches once again

New analyses strongly suggest that all complex cells are a subset of archaea.

Image of a muddy geyser.
Enlarge / Archaea are often found in extreme environments like this mud volcano in Yellowstone.

Eukaryotes are the category of organisms that include us. We have our DNA partitioned into a nucleus instead of just hanging out loose with other cellular components.

Eukaryotes are thought to have first evolved when a host cell swallowed up a prokaryote, or bacteria. This bacteria paid for its new safe home by providing energy to the cell that engulfed it, eventually persisting in the form of the mitochondria. But the identity of the original host cell is still in dispute. Conventional wisdom held that it was a sort of proto-eukaryote, but what it looked like and how it initially subsumed a bacterial cell was never worked out.

Then, in the 1970s, archaea were discovered. These organisms are single-celled and lack nuclei, like prokaryotes, but their cell membranes and the way they make proteins from DNA are similar to eukaryotes. They are dissimilar enough to both prokaryotes and eukaryotes that they became their own third domain on the tree of life. And they became contenders for the role of eukaryotic ancestor—maybe the cell that initially swallowed a bacterium was an archaea.

Researchers were able to home in on a likely candidate for this proto-eukaryote with the advent of metagenomics, the ability to sequence the DNA of species that cannot be grown in the lab. In 2015, they found a species of archaea that had all the requisite qualifications at a site called Loki’s Castle, a hydrothermal vent under the Arctic. Researchers duly named this organism Lokiarchaea. (Mythology thus informed not only the nomenclature of geologic features on the ocean floor, but of microbes as well.)

The identification of Lokiarchaea led scientists to related species that they inevitably called Thor-, Odin-, and Heimdallarchaeota. The whole group is obviously known as the Asgard superphylum. 

But the three-domain tree of life taxonomy—like all other taxonomies—depends on the species used to build the tree, the genetic sequences chosen from those species, and the methods used to compare those sequences to each other. New thinking in the field is that the three domain model was made using a highly limited dataset—36 genes from 104 taxa—and is too simplistic. A two-domain model, in which eukaryotes are a branch of archaea, fits the data much better.

The 3-D camp counters that the genetic similarities between archaea and eukaryotes, upon which much of the 2-D argument relies, are due to contamination of archaea by eukaryotes and that only fast-evolving archaea were included in the analysis, thus skewing the results. 

So now a group of evolutionary biologists has undertaken a larger analysis, including over 3,000 gene families from 125 species analyzed using three different methods. Unlike the former study, this one incorporated many uncultivated microbes.

Regardless of which genomic data is used and the method by which it’s sliced and diced, the team concluded that a two-domain tree seems to fit it better. Eukaryotes seem to have arisen from the Asgard archaea branch, which has genes that were considered uniquely eukaryotic, not because they were contaminated by eukaryotic samples, but because they are the ancestral versions of the ones eukaryotes now have. 

Nature Ecology and Evolution, 2019. DOI: 10.1038/s41559-019-1040-x (About DOIs).

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Channel Ars Technica