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Penguin DNA may reset the molecular clock

PenguinsEuan Young

Scientists use the “molecular clock”—an estimated rate of DNA mutation—to date key events such as migrations and the divergence of species. But just how accurately the clock keeps time has long been debated. A new study of living and ancient Antarctic penguins, like those on Ross Island at left, suggests that DNA mutates six times faster than predicted. That could mean that some species—such as chimps and humans—could have split off from each other much more recently in time than previously thought. The finding should help improve the dating of relatively recent events, including when people domesticated various crops and animals, and when major human migrations occurred.

To use the molecular clock, scientists estimate the rate of mutation in DNA, estimating that the mutations occur in a steady, clocklike manner. For example, if a gene accumulates changes at a rate of five every 1 million years, 25 mutations in a genetic sequence would mean that the sequences had diverged 5 million years ago. The technique has been used to estimate when humans separated from the other great apes, to estimate the arrival of people in the Americas, and to create evolutionary trees for many species. Molecular clocks are usually calibrated by using the age of a known species from the fossil record. But scientists disagree about the speed or rate at which mutations occur and under what circumstances the rate is influenced by natural selection or other factors.

To see just how accurate molecular dating is, David Lambert, an evolutionary biologist at Griffith University in Queensland, Australia, and colleagues looked at Adélie penguins. These Antarctic birds may be the best species yet for building an accurate clock, the team argues, because scientists can study the genetic sequences of both living and ancient members of the species. The penguins generally return each year to the same nesting ground; thus, each rookery can have layers of bones dating far back in time. Indeed, the birds have nested at some rookeries for 44,000 years. “You can take blood samples from the living penguins and then literally collect the bones of their ancestors” in the ground below, says Lambert, because the penguins usually return to their natal colony to mate. Other studies usually can only compare genes from organisms separated in time by millions of years.

Using modern blood and ancient bone samples, the researchers extracted the entire mitochondrial genome from 12 modern and eight ancient penguins, including two that were dated to 44,000 years ago using radiocarbon methods. They then compared the mitochondrial DNA of the living penguins with the ancient ones to determine the number of mutations that had occurred. Because they had radiocarbon dates for the ages of the ancient penguins, the scientists could accurately measure the bird’s average mutation rate, ultimately calculating that its mitochondrial genome had evolved at a rate two-to-six times faster than previously estimated.

The team’s findings, reported in this month’s issue of Trends in Genetics, support similar results for faster clocks in mitochondrial sequences in cattle. But in this new study, the researchers succeeded in calculating the rate of mutation within almost the entire mitochondrial genome, providing “more conclusive evidence,” for a rapidly ticking clock, says Dee Denver, an evolutionary biologist at Oregon State University in Corvallis and one of the paper’s co-authors. They also focused on a region of the genome that is known to not be influenced by natural selection, they write in the paper. Thus, they say that the resulting clock is not merely a reflection of penguin evolutionary history and can be applied to other species.

“It’s novel and groundbreaking work,” says Mark Hauber, an evolutionary biologist at Hunter College in New York City, who was not affiliated with the study. “It’s a significant discovery,” adds Elizabeth Matisoo-Smith, a biological anthropologist at Otago School of Medical Sciences in Dunedin, New Zealand, who expects it will help resolve several discrepancies between genetic data and the archaeological record, such as the peopling of the Pacific Islands and the Americas. However, the penguins’ rapid clock “should be confirmed on a wide diversity of species” before being adopted as the new standard, says Robert Wayne, an evolutionary geneticist at the University of California, Los Angeles.