May 6, 1998 Overwhelming evidence from the largest evolutionary study of gene sequences ever performed shows that the major groups of mammals emerged well before the extinction of the dinosaurs, according to Penn State researchers Sudhir Kumar, postdoctoral fellow, and S. Blair Hedges, associate professor of biology, whose research will be published in the April 30, 1998, issue of the journal Nature.
"The evolution of mammals appears to have occurred gradually by the isolation of breeding groups when the continents broke apart, not suddenly by the rapid filling of ecological niches left vacant when the dinosaurs became extinct," Hedges says. The massive gene study suggests that modern orders of mammals first evolved when the continents were separating during the Cretaceous era about 100 million years ago--much earlier than some previous estimates based on fossil studies, which link the evolutionary event to mass extinctions 65 million years ago.
"This is the first time we ever have been able to estimate when all these lifeforms appeared on Earth," Hedges says. "Fossils can't give us this information, partly because there are huge periods of Earth's history from which not enough fossils have been found to make reliable estimates."
To gauge the pace of evolution, Kumar and Hedges mined a burgeoning collection of gene sequences being accumulated at Genbank, the public genetic databases maintained by the National Institutes of Health. "During the past few years there has been a tremendous explosion in the number of known gene sequences, so we had ten times as much data to work with as we did just two years ago," says Hedges, who published a similar but much smaller study with Kumar and others in 1996.
The scientists sifted through many thousands of vertebrate gene sequences from hundreds of species to find those that develop mutations at a constant rate over time, which Kumar and Hedges used like the ticking of a molecular clock to trace the history of each species back to its origin.
Hedges says that, in contrast to the use of gene sequences, the use of fossils to estimate when two species emerged from their last common ancestor necessarily results in an underestimation. "The body structure of a fossilized animal had to have evolved at some earlier date before its lifetime--in many cases, it was many generations and many millions of years earlier. But genes are different--their clock-like mutations start ticking away as soon as a new species evolves, so the molecular clock takes you back to the actual time of origin."
The researchers found that their molecular clock yielded origin dates similar to those based on fossil dating for many species, but for others the genetic clues lead back to a much earlier time. For example, Hedges says "the fossil record for rodents says that mouse and rat split only 10 million years ago, but we have 343 genes in this study telling us that mouse and rat split from their last common ancestor 41 million years ago--four times as long. The rodent fossil record appears to have some major gaps," Hedges says.
By comparing individual genes in pairs of species, the researchers identified 658 genes from 207 vertebrate species that had accumulated mutations at a fairly constant rate relative to one another during their evolution. The scientists then calibrated this molecular clock to an evolutionary event well established by fossil studies--the divergence of birds and mammals about 310 million years ago. "A clock isn't any good unless it is calibrated to a time that everyone else agrees on," Hedges explains, "and just about everyone agrees on the date when reptilian ancestors of birds and mammals appeared because it is based on well-accepted studies of fossils." Using this date as a secure calibration point--and the mutation rate for each of the constant-rate genes as a timing device--the researchers were able to determine how long ago each vertebrate order originated.
"We mined a lot of data by sorting through all the gene sequences in Genbank to find the ones that fit our criteria," says Kumar. "The only way we could have analyzed all the data so quickly was by taking a 'bioinformatic' approach," he says, explaining that they used computers as well as manual methods to compare thousands of gene sequences and test them for rate constancy using different parameters. "It very easily is the largest evolutionary study of gene sequences ever done for estimating the origin of so many species," Kumar comments.
Very few fossils resembling modern mammals or other vertebrates have been found in rocks formed during the Cretaceous period, says Hedges, partly because paleontologists hardly ever look for mammals in rocks that old. "There has not been enough convincing evidence until now for paleontologists to invest their time and money looking for mammal fossils in a time before the dinosaurs became extinct," Hedges says. In addition, many scientists believe that a large number of species suddenly sprang into existence at the very end of the Cretaceous period.
Hedges says he hopes, as a result of this research, that paleontologists will now begin searching for vertebrates in geological strata where they have never looked before. "We are saying mammals definitely were living on Earth during the Cretaceous period from 70 to 100 million years ago. We don't yet know what they look like, but from the genes of their descendants we now know that they were there."
This research was supported in part by the Nationals Institutes of Health and the National Science Foundation.
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The caption for the illustration is: Molecular clocks show that the major groups of mammals arose long before dinosaurs became extinct.
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