Through complex statistical and computational manipulations, the scientists constructed phylogenetic "trees," linking animals that were genetically most closely related. Those calculations allowed them to conclude that while rats and mice are close cousins, as any city dweller can attest, guinea pigs are off on a distant branch and deserve their own order. And with the guinea pig, in theory, would go 17 other types of South American rodents thought to be its close relatives.

Other recent studies have also cast doubt on the presumed kinship between rabbits and rodents, while still others have questioned the relationships between porcupines and other rodents of the Americas. All told, a bit of disorder has shaken the great rodent burrow.

Opponents of the notion of multiple lineages for rodents criticize the strictly molecular approach on many fronts. Dr. Patrick Luckett of the University of Puerto Rico, an expert in rodent anatomy and embryology, said it was ludicrous to reach so many sweeping conclusions about rodent taxonomy based on a sampling of three rodent species, guinea pigs, rats and mice.

"There are 2,021 living species and probably that many extinct ones," Dr. Luckett said. "There are 29 families in the rodent order. The authors of the Nature paper have looked at three species taken from only two rodent families. They say they have a 'comprehensive' data set. Well, 3 out of 2,000 is not comprehensive to me. It's scanty."

Dr. Luckett, Dr. Honeycutt and others pointed out that the integrity of the rodent order was buttressed by vast amounts of data from morphology -- the study of body structure and form -- and paleontology. They said rodents were distinguished by their entire head region. They have specialized incisors with enamel only on the front of the teeth, allowing them to be self-sharpening and ever-growing. The jaw musculature permits them to gnaw with their incisors at the same time that they are chewing with their molars. The fetal membranes found in rodents are unique among mammals, as is the pattern of embryonic development.

"I could show a guinea pig to my 10-year-old daughter," Dr. Honeycutt said, "and she could tell me it's a rodent."

But Dr. Graur insists that molecular results are stronger and more objective than anything to be gleaned by studying anatomy or paleontology.