Trouble in the Fourth Domain?

By Carl Zimmer | July 14, 2011 12:16 pm

In March I wrote about two studies that raised the tantalizing possibility that the tree of life, which till now has appeared to have three main branches, turns out to have a fourth.

Some of the evidence for the fourth branch (or “domain,” as taxonomists would call it) came from a newly discovered and very strange group of viruses. They’re known as giant viruses, because they’re about a hundred times bigger than typical viruses and can have over a thousand genes. If there was indeed a fourth domain , it meant that giant viruses were part of one of the oldest lineages on Earth. By studying them we might learn about the earliest stages in life’s evolution.

Since then, there have been a couple developments that merit a follow-up. In April, Didier Raoult of Mediterranean University in Marseille and his colleagues published a new study on another species of giant virus. Their previous studies on the fourth domain involved giant viruses that were first discovered in the water in air conditioners, infecting amoebae called Acanthamoeba. But now scientists are finding giant viruses all over the world, in lots of different single-celled hosts. One of the newest of these discoveries is a giant virus that infects an ocean-dwelling amoeba called Cafeteria roenbergensis. which lives inside amoebae in the ocean.

Raoult and his colleagues took a close look at the Cafeteria virus’s genes. A number of its genes don’t exist inside other known giant viruses. The ancestors of Cafeteria may have picked up them from hosts, or from unknown viruses. (This shuttling of genes from species to species is called horizontal gene transfer.)

But Raoult and his colleagues found some genes shared by the Cafeteria virus and by other giant viruses. They compared some of these shared genes to versions found in other forms of life, like bacteria and eukaryotes (we are eukaryotes, as are plants, fungi, and amoebae). Raoult and his colleagues found that the most compelling evolutionary tree joining these genes together had a four-branch structure. They concluded that the Cafeteria virus “unabiguously” points to the existence of a fourth domain.

But in June a new study came out that raises some serious doubts about the fourth domain.

The new study is the work of Tom Williams, Martin Embley, and Eva Heinz of the University of Newcastle. They felt that Raoult and his colleagues might have been tricked by the slippery nature of evolution. One of the big challenges in drawing evolutionary trees based on DNA is that similarities can be deceiving. Just because two species have stretches of DNA that look alike doesn’t necessarily mean that they inherited that DNA from a recent ancestor. The DNA may have independently evolved into a similar state in each lineage.

This is no big secret. Everybody in the business of reconstructing evolutionary history from DNA knows they have to contend with this kind of mirage, called homoplasy. Scientists can reduce homoplasy’s confusion by steering clear of genes that are prone to homoplasy. They can look at particular kinds of elements of DNA that are particularly unlikely to suffer from homoplasy. They can also take into account experiments on living organisms that show how likely different kinds of mutations are. Knowing those probabilities can help scientists figure out how likely an evolutionary tree is to be accurate.

Embley and his colleagues performed some new tests on the DNA that was used in the fourth-domain studies. They concluded that Raoult and his colleagues had used an evolutionary model that did a bad job of avoiding homoplasy. Embley and his colleagues then carried out an analysis of their own, using other models that took into account some details of biology that Raoult and his colleagues didn’t think were important. There are twenty amino acids that proteins can be built from, for example. But that doesn’t mean that during evolution a pariticular amino acid can switch to any of the other nineteen. Some switches are simply impossible. So Embley and his colleagues built these constraints into their model.

When Embley and his colleagues redrew the tree of life, the support for a fourth domain “effectively disappeared,” they write. They could not reject the possibility that the supposedly ancient genes in giant viruses are not ancient at all. Instead, the viruses picked the genes up more recently from their amoebae hosts. Once inside the viruses, these genes quickly evolved so that they ended up looking different from their original forms.

I got in touch with Jonathan Eisen of the University of California at Davis to get his comment on the new paper. Eisen, as I wrote in March, was an author on a study on microbial genes scooped up from the ocean; he and his co-authors suggested that the genes might be pointing to a fourth domain, although they were a lot more tentative in their conclusions than Raoult and his colleagues. Eisen thinks Embley’s probably right. “Paper looks pretty sound,” he wrote in an email to me.

For now, Eisen’s undecided on where giant viruses fit into the tree of life. They could have branched off early, he says, “but I think it is equally plausible that even the big viruses have stolen their cellular-organism-like genes from hosts of some kind.”

One way to cut down on the uncertainty would be to fill in more branches on the tree of life. It’s easy to forget that for all the millions of species scientists have discovered, there are millions–maybe tens of millions–more that are waiting to be found. Right now, scientists are forced reconstruct the tree of life by comparing species that are separated by hundreds of millions or billions of years of evolution. The more species scientists add to the tree of life, the closer those comparisons will become. And there’s no telling what sort of strange branches the tree will turn out to have.

“There very well may be some weird stuff out there,” Eisen said.

PS: I also contacted Raoult to comment on Embley’s paper and have yet to hear back. I’ll add his responses when I do.

[Update: revised post to clarify that the host is named Cafeteria. ]

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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.

About Carl Zimmer

Carl Zimmer writes about science regularly for The New York Times and magazines such as DISCOVER, which also hosts his blog, The LoomHe is the author of 12 books, the most recent of which is Science Ink: Tattoos of the Science Obsessed.

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