Infectious Evolution: Ancient virus hit apes, not our ancestors, in the genes

A vicious virus infected ancestral chimpanzees and gorillas in Africa between 4 million and 3 million years ago. Not only did it kill a great many of these primates, but it also infiltrated the surviving animals’ genomes, altering the course of evolution. That’s the picture emerging from a new analysis of modern-primate DNA.

Around 1.5 million years ago, this virus of the class called retroviruses also infected ancestors of modern baboons and macaques, two African monkeys, reports geneticist Evan E. Eichler of the University of Washington in Seattle and his colleagues. However, no molecular remnants of this ancient infection appear in the DNA of people, whose ancestors also inhabited Africa, or in the genes of apes, such as orangutans, from Asia.

Retroviral infection “was almost a cataclysmic event for ancestral chimps and gorillas,” Eichler says. “It’s a mystery to us why the ancestors of people and orangutans were excluded from it.”

While analyzing data from an ongoing project determining the chimpanzee genome, Eichler’s team noticed sequences that dramatically differed from corresponding regions of human DNA. The team identified the sequences as the remains of a retrovirus.

Using chemical probes, the researchers then found more than 100 copies of the retrovirus throughout the chimp genome. These retroviral sequences disturb the workings of at least six genes, including ones found in the brain and testes.

Gorillas, baboons, and macaques also possessed about 100 retroviral copies. The researchers used available estimates of how quickly the retrovirus mutates to calculate when the infections occurred.

Several scenarios could explain the selective infection of ancient chimps and gorillas. African apes might have evolved a susceptibility to the infection, for example, or ancestors of people and Asian apes might have developed a resistance.

The new results, which the researchers report in the April PLoS Biology, fit with a surprising conclusion floated in a 2002 analysis of chimp DNA. That study found a dearth of mutations in chimp genes known to be crucial for repelling infections. Pascal Gagneux of the University of California, San Diego and his colleagues then proposed that this genomic feature was a reflection of an HIV-like retroviral epidemic among ancestral chimps nearly 3 million years ago that left only a few to pass on rare resistance genes. Today’s chimps are thus the offspring of unusually virus-resistant animals.

“Retroviruses are not just diabolical [killers],” says Gagneux. “Under the right conditions, such viruses contribute to the evolution of their hosts.”

Eichler’s group provides “compelling evidence” of separate, comparably ancient retroviral infections in ancestral chimps and gorillas, remarks Harvard University’s Maryellen Ruvolo. Chimps probably came in contact with the virus when they hunted infected monkeys, Ruvolo suggests. It’s not clear how the infection reached gorillas.

The new evidence that closely related primates can contract different retroviral infections is surprising, says Dixie Mager of the University of British Columbia in Vancouver. “Most people in the field would not have predicted this finding,” she adds.

Scientists have estimated that 8 percent of human DNA consists of retroviral sequences that were deposited during infections of our African-ape ancestors between 35 million and 25 million years ago.