Retrovirus struck ancestors of chimps and gorillas millions of years ago, but not ancestral humans

The ancestors of chimpanzees and gorillas were infected with a deadly retrovirus about three to four million years ago, but there is no evidence it infected ancestors of modern-day humans, according to research by genome scientists. The virus struck after humans had split off the evolutionary tree from primates, researchers said. The infection may have played a role in the evolution of such great apes as chimps and gorillas. The research appears in the April issue of the journal Public Library of Science-Biology, which is available online on March 1.

Researchers studying portions of the genome containing ’retroelements,’ also known as junk DNA, found many copies of a gene sequence in the chimp and gorilla genome that didn’t appear anywhere in the human genome. They translated that genome sequence into its corresponding protein, and discovered that it was the remnant of a retrovirus, a type of virus that copies its genetic information into the host’s genome. Evidence suggests that the ’retroelement’ originated from an external retrovirus that actively infected ape species in the past.

“The reason retroviruses are so deadly, at the genetic level, is that they have a tremendous potential to mess up a gene and interfere with its expression,” explained Dr. Evan Eichler, UW associate professor of genome sciences and co-author of the study. “That can have negative effects. It’s a double-whammy: the virus infected and possibly killed off some of the population, but also caused genetic errors in survivors. Those errors would have later eliminated more of the population.”

The virus had invaded the genome in the germline – in sperm or egg cells – allowing the sequence to be passed on to future generations. In those animals in which the virus was taken up next to or inside a gene – in the part of the genome that codes for the most important biological functions – the virus had an even stronger effect.

What researchers don’t understand is why the virus affected the ancestors of chimps, gorillas, and Old World monkeys, but didn’t affect the ancestors of humans or of Asian apes like orangutans and gibbons. The infections took place independently, and did not originate in a common ancestor of humans and apes. The event also took place between three and four million years ago, well after the separation of humans from apes. That split is estimated to have occurred five to seven million years ago. During that period, ancestral humans were likely to be living in the same area of Africa as great apes. African apes may have been susceptibile to the virus, or ancestral humans and Asian apes may have been resistant to it. Another possibility is that some early humans may have carried the virus, but eventually died off.

Researchers also don’t know the impact the virus had on the primate species it did affect. They found many copies of the virus in the genomes of both species, but only a tiny fraction of those copies landed in or near a gene, where it would have the greatest impact. Other studies have shown that most retroviruses typically land near or within genes. This difference may mean the animals that had the virus taken up in or near a gene didn’t survive long. Because of that natural selection, researchers believe that the virus may have had major impacts on the formation of the species we now call chimps and gorillas. The virus struck when each of the primate groups was still an incipient species with widely varying populations.

If the virus had killed off much of the population of both species, it may have created what evolutionary biologists call a population bottleneck. This much smaller group of surviving animals would then sort out most of its genetic variation in relatively fewer generations than would a larger group. This would lead to a higher probability of rare genetic variants becoming fixed in a short time. Before long, a genetically disparate population, possibly with wide variations in morphology, would have emerged, leading to today’s chimps and gorillas.