Ace Environmental News Desk – Ancient virus genes moved between yeast species, possibly with help from insects, revealing a surprising way evolution works according to study journal

Ancient viruses left behind genes that are still spreading millions of years later

Genes usually move down a family tree, from parents to their offspring. 

In a group of yeasts that live on rotting wood, a bundle of genes left behind by an ancient virus has also moved sideways, from one species into another.

A new genetic study found evidence of at least three of those crossings. 

As far as the researchers know, it’s the first documented case of a whole cluster of genes from an ancient RNA virus moving between species.

Derek Taylor, a biologist at the University at Buffalo, did the work with master’s student Dominic Tringali. 

They suspect that wood-eating insects, which carry these yeasts in their guts and leave them in their droppings, brought different species close enough to swap DNA.

“It’s an evolutionary whodunit, and wood-eating insects had the means and opportunity,” said Taylor, a professor in the university’s Department of Biological Sciences.

All of the evidence came from DNA. The team compared publicly available genomes from 18 yeast species and strains rather than watching a transfer happen in the lab.

A virus left four genes

The genes came from a totivirus, a kind of virus that infects fungi, including yeasts. It mostly passes from one generation of cells to the next when a cell divides.

Totiviruses carry their genes as RNA and have no built-in way to write themselves into a host’s DNA, the way HIV does. 

Even so, a copy of one ended up in an ancestor of these yeasts, which belong to a group called Scheffersomyces.

Exactly how that happened isn’t known. The researchers propose that the yeast cell itself copied the viral RNA into DNA.

Taylor and a colleague first described the cluster in a 2009 paper, working with a yeast called Scheffersomyces stipitis. The cluster holds four genes in a row.

One of them carries both of the virus’s main parts, the instructions for its protein shell and for the enzyme that copies its RNA. 

The other three are extra copies of the shell gene alone, made after the virus’s genes joined the yeast’s DNA.

The team named the cluster STORM. In the yeasts where it was first found, it has held the same spot in the genome for at least 15 million years. It may be much older.

Genes crossed species lines

If genes pass only from parent to offspring, their family tree should match the family tree of the species that carry them. STORM’s tree didn’t.

In two of the crossings, the cluster in one group of yeasts looked most like the cluster in a more distant group. Biologists call this kind of sideways move horizontal gene transfer. 

It’s well known among microbes, and it has been documented in fungi and even plants.

To see how unusual STORM’s pattern was, the team built family trees for 3,527 other genes shared by all 18 yeasts. None of those trees reproduced any of the three STORM patterns in full.

“Now we have compelling evidence that an entire four-gene cluster has crossed species boundaries,” Taylor said.

Crossbreeding between species could in principle produce a similar pattern. 

But it would have taken at least two separate episodes, and the team found no sign that the donor species’ DNA had spread widely through the rest of the genome.

The third crossing replaced only part of the cluster. In one strain of S. stipitis, the first three genes were swapped for versions that most resemble those of a related species, Scheffersomyces segobiensis. 

The fourth gene and the DNA on either side kept their S. stipitis ancestry.

A jumping gene left clues

One crossing left more evidence behind than the others. 

Beside STORM in a yeast called Scheffersomyces insectosa, the team found the broken remains of a jumping gene. 

These stretches of DNA, known as transposons, can move from one place in a genome to another.

The researchers named this family of transposons YEET, short for Yeast Endogenous Element Transposon. 

Its remains near STORM, and a broken yeast gene next to them, both looked like they came from the same donor group as STORM itself.

“Because STORM and a neighboring jumping gene show evidence of the same unusual evolutionary history, we suspect the transposon may have carried STORM between yeast species as extra cargo,” Tringali said.

YEET transposons appear to have crossed between these rotting-wood yeasts on their own, too, in at least five cases. How the other full-cluster crossing happened remains unclear.

Insects bring yeasts together

Scheffersomyces yeasts share living space in rotting logs, in insect droppings, and inside the guts of wood-eating insects. 

One species in the group, described as new in 2025, was isolated from the cocoon wall of a stag beetle.

“In order to exchange genomic material, you have to be in the same place at the same time,” Taylor said.

The authors wrote that these shared homes give different yeasts chances to swap DNA. Contact alone, though, doesn’t show how the DNA actually moved.

STORM evolved unusually fast

RNA viruses change quickly, and genes borrowed from them are generally expected to slow down once they become part of a host’s genome. STORM went the other way.

The team estimated that its proteins changed about seven times faster than those of related viruses that still infect cells. 

Depending on how old the researchers assumed the cluster to be, the estimate ranged from just under six to nearly nine times faster.

“These genes have had an extraordinary evolutionary afterlife,” Tringali said. “Long after the original virus disappeared, its genes continued to evolve, multiply and spread between yeast species.”

The four genes didn’t all change in the same way. The fourth gene changed the most. 

Tests suggested that natural selection weakened on that gene and let changes build up, rather than favoring new versions of it.

Yet that gene held on to a key part of one of the virus’s tricks. Related yeast viruses take the protective chemical cap off the front of the cell’s own RNA messages and use it on their own.

The fourth gene still carries the amino acids that form the virus’s cap-holding pocket.

Selection on the first gene grew stronger instead, compared with the second and third. 

Computer predictions of protein shapes suggested that all four genes still carry instructions for proteins shaped like a virus shell.

Clues to viral defense

The cluster isn’t silent. In genetic data from five yeast species and strains, cells were making RNA copies of all four genes, and the first gene was usually the most active.

In one species, the first and fourth genes were about three times as active in flasks built to mix in more oxygen. 

Those growth tests weren’t designed to probe viral infection, so the genes’ activity could be tied to RNA handling, to the yeasts’ surroundings, or to defense against viruses.

There’s a hint for that last idea. In a 2018 experiment, a shell-like gene from another yeast, Debaryomyces hansenii, cleared a related virus out of baker’s yeast.

Of the two S. segobiensis strains, the one with an intact cluster carried no detectable totivirus. The one without an intact cluster was the only strain in the survey that did.

Viral genes may benefit yeast

“Totiviruses are kind of like a frenemy for yeast. Under some conditions, they help the host deal with physiological stress,” Taylor said. 

“So it might be useful for a yeast to keep a virus’ benefits around without having to worry about controlling the virus.”

What the four STORM proteins actually do inside a yeast cell is still untested. 

The team hopes to grow the yeasts under different kinds of stress and see whether the genes respond.

The results could point to the job the genes now do for their hosts.

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