Chimp and human lineages may have split twice as long ago as thought

Human and chimpanzee ancestors may have split into different species millions of years earlier than scientists thought, a new study of chimpanzee mutation rates suggests.

In each generation, chimps’ average mutation rate is one DNA chemical unit changed out of every 83 million, researchers report in the June 13 Science. That mutation rate is nearly identical to the rate previously calculated for humans using similar methods (SN Online: 6/13/11). If the human and chimp mutation rates remained constant throughout evolutionary history, the species would have shared their most recent common ancestor about 13 million years ago.

That estimate is far longer ago than the 6 million to 8 million years surmised based on the fossil record. “It’s a number that people will be shocked, surprised and upset by,” says geneticist Gil McVean of the University of Oxford who led the study.

Most of the mutations come from male chimps, which contribute seven to eight times as many errors as female chimps do, the researchers found. The discrepancy arises because females are born with all of their eggs, while males continually produce sperm from puberty on, providing more chances over time for DNA replication machinery to make mistakes. For each year older a male chimp is when he reproduces, his kids stand to inherit three more mutations, the researchers report.

In humans, men pass on three to four times as many mutations as women do. For each year of age, men pass on two additional mutations. Mutations can make a big difference because some lead to genetic diseases.

“There’s a saying that you don’t want an old father,” McVean says. “But what you really don’t want is a father that is an old chimpanzee.”

Although humans and chimps last shared a common genetic ancestor 13 million years ago, McVean says that the figure does not necessarily mean that the human and chimp lineages separated then. It may have taken a million years — or more — for the ancestral populations to accumulate enough changes to actually split into separate species. 

The work provides the first reliable measure of mutation rates in a nonhuman primate, says Aylwyn Scally, an evolutionary geneticist at the University of Cambridge. But it also presents a conundrum. “We have to resolve this discrepancy where the genetic date looks so much older than the fossil record suggests,” he says.

One possibility: Mutation rates could have been faster in the distant past, says Minyoung Wyman, an evolutionary biologist at Columbia University. If human and chimp ancestors’ generations were shorter in the past, the mutation rate would have been faster, and the most recent common ancestor of humans and chimps may have lived more recently than McVean’s group calculates, she says. 

To measure the chimpanzee mutation rate, McVean and his colleagues sequenced the genomes of a three-generation family of nine captive Western chimpanzees, Pan troglodytes verus. By comparing the DNA of parents and offspring, the researchers identified mutations that arose during the production of eggs or sperm. The team found that each baby chimp inherited around 35 new mutations, 30 of which came from the father.

In the wild, the average parental age of male chimps is 24.3 years old. But the captive chimps in the study mated as teenagers. The researchers calculated that wild chimps would bequeath about 69 new mutations to each offspring.

At least one scientist questions whether DNA sequencing really gives an accurate measurement of mutation rates. “It’s very, very, very difficult to figure out what are real mutations and what are errors” in sequencing, says Laurence Moran, a biochemist at the University of Toronto. McVean’s team may have been overly concerned with misidentifying sequencing errors as real mutations and could have underestimated the number of real mutations. The result would be an artificially low mutation rate, inflating the split time between human and chimp ancestors.

But anthropologist John Hawks of the University of Wisconsin–Madison doesn’t share that concern. If the researchers had been too conservative in identifying mutations, they probably would not have seen consistent differences between males and females,Hawks says. “I doubt we are missing a large fraction of real mutations in the estimates.”

Even with drawbacks, the sequencing method is better than other methods for calculating mutation rates, says McVean.“Direct methods really are the most reliable source of information we have about how the genome changes,” he says.