It’s not every day that scientists accidentally uncover a gorilla paternity scandal. But when a team of researchers led by Søren Besenbacher in Denmark went looking for genetic data on great ape families, one of their gorilla fathers “turned out to be only half as related to the child as expected,” the researchers write.

With some investigation, they discovered that the real father was in fact the 12-year-old son of the gorilla that was thought to be the dad. “This was as much a surprise to us as it was to the zoo that house[s] the gorilla father and son,” they add.

Besenbacher and his colleagues were unintentionally unearthing the dirty secrets of gorilla families because they were interested in mutation rates—how often new changes in DNA appear. Specifically, they were trying to see whether humans are the outliers among our great ape family, as we have an unusually slow rate of accumulated mutations in our genomes. In a paper published in Nature Ecology and Evolution this week, they report their results: yes, we are indeed unusual. And it’s not clear why.

The molecular clock ticks unevenly

When averaged over a population, new mutations appear at a regular average rate. This slow, gentle pace of genetic mutations provides a “molecular clock” that can be used to trace important splits in the history of a species. In humans, the molecular clock has been used to figure out the timeline of human migrations across the globe and also to figure out when we split off from our cousins—both close, like Neanderthals, and more distant, like chimps.

This works because sperm and egg cells don’t always make perfect copies of genetic material: sometimes there’s a small change to the DNA. If that change is really helpful, natural selection will ensure it spreads rapidly through a population; and if it’s harmful, it may hamper survival, stopping the mutation in its tracks. But if the mutation is neutral, then things just keep ticking over normally. Neutral mutations like these will accumulate in a species over time.

If we know how often mutations like these happen, then we can compare how many of them have accumulated in two different branches of a family tree—like humans and chimpanzees—to work out how long ago those branches parted ways. But that’s a big if; mutation rates are complicated, and a lot goes into generating a good estimate of a mutation rate.

In humans, it’s becoming relatively easy to get families together, compare the genomes of parents to their children, and work out an average mutation rate. We now know that, every year, around one change occurs for every 2.3 billion rungs on the twisted ladder of DNA. But if that rate is used to calculate divergence from chimps, it says we diverged 10 million years ago, which is out of step with the fossil record. So, write the researchers, “either the fossil record should be reconsidered, or the mutation rate in humans today is not representative of all the time since our common ancestor with chimpanzees.”

Enter the studbooks

There has been research suggesting that factors like longer generations and later puberty have slowed down the human mutation rate. But to see if it has slowed down, the best way is to look at the rate in other great apes, which means looking at ape families. Besenbacher and his colleagues approached zoos that have kept detailed (albeit apparently not error-free) records on parentage. By matching genetic samples to zoo studbooks, the researchers were able to study several chimp, gorilla, and orangutan families.

They found that all three species had an average annual mutation rate almost 50-percent higher than the human rate. Apparently, the rate in humans slowed down somewhere back in our lineage. “If we use our new rates,” they write, “we find that the human-chimpanzee [split] time is now at 6.6 million years ago, which correlates well with what we know from fossil evidence.” The result also suggests that humans and Neanderthals may have split from our common ancestor more recently than we thought.

The conclusions from this research line up nicely with other work—both theoretical estimates of different mutation rates in apes and the existing fossil record. But because only 10 great ape families (seven chimp, two gorilla, and one orangutan) were used in the work, it’s still “prudent to be cautious with initial interpretations,” says Melissa Wilson, a computational biologist who wasn’t involved with the work.

The work corroborates other suggestions of a slowdown in the human mutation rate, she says. But we still have very little idea of why this might be the case. Generation time and later puberty can explain part of the difference, the authors note, but not all of it. The sample of humans used to estimate our mutation rates skews heavily first-world and Caucasian, meaning that lifestyle or environmental differences could be playing a role, they suggest. Studies with a broader range of people, as well as more great apes, could help to start resolving things.

Wilson also points out that the mutation rate itself covers a world of complexity. It’s different in males and females, for a start, with males contributing more and more mutations as they get older. And mutation rates on the X and Y chromosomes, and in mitochondrial DNA, could also be different. Understanding that internal complexity, she says, could “give us insight into how evolution has happened.”

Nature Ecology and Evolution, 2018. DOI: 10.1038/s41559-018-0778-x  (About DOIs).

https://arstechnica.com/?p=1446389