’Fossil genes’ reveal how life sheds form and function

Reading the fossil record, a paleontologist can peer into evolutionary history and see the surface features that plants and animals and, occasionally, microbes have left behind.

Now, scouring the genome of a Japanese yeast, scientists have found a trackway of fossil genes in the making, providing a rare look at how an organism, in response to the demands of its environment, has changed its inner chemistry and lost the ability to metabolize a key sugar.

The finding is a snapshot of evolution at work showing, at the most fundamental level, how traits and features are discarded by virtually all forms of life when they are no longer needed. “Many people think evolution is always happening in a forward direction,” that new features are just tacked on, says Sean B. Carroll, a professor of molecular biology at the Howard Hughes Medical Institute at the University of Wisconsin-Madison. “The other side of the coin is that we lose things. Losses as well as gains make up the story of evolution.”

Writing Sept. 20, in the Proceedings of the National Academy of Sciences, Carroll and colleagues Chris Todd Hittinger and Antonis Rokas describe the discovery of a set of seven genes caught in the act of fossilization.

In the Japanese yeast, known to scientists as Saccharomyces kudriavzevii, the Wisconsin scientists found the decaying genes that, when intact, are all functionally related and make up a pathway that permits the organism to convert the sugar galactose to energy.

The same pathway, among the most studied in biology, exists not only in yeasts, but also in virtually all other microbes, as well as plants and animals, including humans. Their sole function is devoted to the utilization of galactose, suggesting that the yeast experienced an ecological shift that somehow removed galactose from the organism’s menu, thereby making the galactose-processing genes obsolete.

The relic genes, according to Hittinger, are “full of holes,” where numerous DNA bases – the building blocks of all genes – have been edited out through mutation to terminate the physiological message they were responsible for transmitting along the pathway. “Genes become fossilized if there is no use for them,” says Rokas. “If you relax the pressure on the genes to zero, mutations will begin to accumulate. This steady bombardment of mutations will erase the genes over time.”

However, there is a window of preservation before the genes are wiped completely away, leaving relics as diagnostic as any fossil bone and providing scientists with important clues to biological functions discarded as an organism adapts to its environment.

Indeed, probing the genomes of three other species of yeast that are unable to metabolize galactose, the Wisconsin scientists found the genetic pathway almost completely absent from all three, with only a single remaining gene marking the pathway like a faded signpost. “Evolution repeats itself,” Carroll says. “What we see is that three or four times, these genes have been junked in different species. The process of sweeping these genes away is more complete in these other species.”

Relic genes, sometimes called pseudo-genes, have been found elsewhere, including humans. Fossil olfactory genes tell the story of how humans came to depend more on sight as color vision displaced a sense of smell that, in the distant past, was far superior to what humans enjoy today.

In the Japanese yeast, the seven fossil genes that make up the eroding pathway are “still in the same place (on the genome) they are in neighboring species,” says Carroll. “What we have is a picture of an entire set of genes performing related functions becoming fossilized. “To see this, the change has to be relatively recent. Sometime in the last 5 to 10 million years the pressure (on these genes) started to relax,” Carroll explains.