Tree of life reshaped

by Timothy Oleson
Thursday, October 8, 2015

Since the 1970s, the classic “tree of life” taught in classrooms has portrayed three domains of life — Archaea, Bacteria and Eukaryota — all descending from an unknown common ancestor. But behind the scenes, this textbook picture has been shifting. Many scientists now think the tree’s deepest root lies within the bacteria; and, even more recently, some have begun suspecting that the Eukaryota — including all animals, plants, fungi, slime molds and other organisms whose cells have nuclei — are actually an offshoot from the Archaea, paring the tree from three to two domains. Now, a new study furthers that claim, and with the help of a novel technique for parsing phylogenetic data in greater detail than ever before, suggests a revised backstory for the Archaea — and, by extension, us.

Phylogenetic tree-of-life studies typically reconstruct “universal” trees, simultaneously comparing similarities and differences in marker genes shared among organisms of all three domains. However, in the new study published in Proceedings of the National Academy of Sciences, scientists first “built a tree containing only archaea and eukaryotes using phylogenetic markers” shared by the two groups, then did the same for archaea and bacteria, says Simonetta Gribaldo, a biologist at the Pasteur Institute in Paris and a co-author of the study.

If you compare all three domains at once, “you’re limited to the genes that they all share, and that really reduces down to a set of 30 or 40 genes that everyone has been analyzing repeatedly for quite a while now,” says Tom Williams, an evolutionary biologist at Newcastle University in England who was not involved in the new study. “But, if you look at genes that are shared between just two of those groups, then there are quite a few more” to compare, he says.

In their analysis, Gribaldo and her colleagues included the genomes of 132 archaea, 211 bacteria and 31 eukaryotes, comparing 72 shared marker genes among the archaea and eukaryotes, and 46 among the archaea and bacteria. The first comparison, while confirming a close relationship between Archaea and Eukaryota, did not clarify the exact nature of that relationship, leaving open several possible scenarios, including that the two groups are “sisters” that split from a single common ancestor. This would mean that neither descended from the other, and that the classic three-domain tree could still be correct.

When the researchers added in the second comparison, however, the picture sharpened, showing relationships among different groups of archaea in more detail, and suggesting that Eukaryota does indeed have a place within Archaea. Gribaldo’s team found that eukaryotes are a sister lineage of a subset of archaea called the TACK superphylum, supporting the conclusion of other recent research, Williams says, including his own.

Moreover, the researchers reported that both the TACK archaea and eukaryotes appear to have descended from another archaeal group named Euryarchaeota. Scientists have long known about Euryarchaeota as an archaeal lineage, but did not recognize it as the root of the entire domain. The new result substantially reshapes our understanding of the archaeal tree, Gribaldo and colleagues wrote, as well as of eukaryotic (and thus our own) origins.

The proposal of Euryarchaeota as the root of Archaea is the most novel contribution here, Williams says. Other roots have been proposed before, but there hasn’t been “a particularly strong hypothesis about where the root of the Archaea was,” he says. This work is “really quite convincing, [considering] the combination of the two-step approach [along with] using more genes, using the best available phylogenetic models, and using the broadest taxonomic sampling that’s now available.”

The reshaped archaeal tree “opens up a whole new perspective on the nature of the last [common] archaeal ancestor, and on the early evolution of this domain of life,” Gribaldo says. For instance, it impacts our understanding of when key cellular processes, like microbial methanogenesis, might have first emerged. “This new root indicates that the first divergence in the Archaea led to two large clusters [of descendants], both including methanogenic lineages,” Gribaldo says, which suggests the first archaeon was a methanogen.

The earliest-known biologically produced methane in the geologic record dates back about 3.5 billion years, “potentially providing a minimal date for the last common ancestor of Archaea,” Williams says. Additionally, the revised tree gives a framework for “trying to understand how the different metabolisms that modern archaea use first evolved, starting from a methanogenic ancestor,” he says. “There are quite a lot of interesting implications to tease out.”

Ultimately, Gribaldo says, the results offer more evidence that, with Eukaryota subsumed within Archaea, there really are only two domains of life. More work is needed before the textbook three-domain tree is abandoned entirely, though. “We will surely need to test [the new tree] with different phylogenomic approaches,” and there are yet many “archaeal lineages that are just waiting to reveal their secrets,” she says. “These are really exciting times for research on the Archaea.”