With these two genomes in hand, the Broad Institute designed a dog SNP chip, similar to those used to scan the human for genetic disease. SNPs, or “snips,” are sites of common variation along the DNA. Affymetrix, a SNP chip maker, manufactured the dog SNP chip for Dr. Wayne’s team, letting him have 1,000 chips free, though thereafter they cost $250 apiece. The dog SNP chip brought to light the close relationship between dogs and wolves in the Middle East and also the genetic relationship between various breeds.

Dr. Wayne was surprised to find that all the herding dogs grouped together, as did all the sight hounds and the scent hounds, making a perfect match between dogs’ various functions and the branches on the genetic tree. “I thought there would be many ways to build a herding dog and that they’d come from all over the tree, but there are not,” Dr. Wayne said.

His team has also used the dog SNP chip to scan for genes that show signatures of selection. One such favored dog gene has a human counterpart that has been implicated in Williams syndrome, where it causes exceptional gregariousness. Another two selected genes are involved in memory. Dogs, unlike wolves, are adept at taking cues from human body language, and the two genes could have something to do with this faculty, Dr. Wayne said.

An earlier survey of dog origins, based on a small genetic element known as mitochondrial DNA, concluded that dogs had been domesticated, probably just once, in East Asia. The author of the survey, Peter Savolainen of the Royal Institute of Technology in Stockholm, said he was not convinced by the new report for several reasons, including that it did not sample dogs in East Asia from south of the Yangtze, the region where the diversity of mitochondrial DNA is highest. Also archaeologists in China have been less interested in distinguishing dog and wolf remains, he said.

Two other experts on dog genetics, Carlos Driscoll and Stephen O’Brien, of the National Cancer Institute, said they believed that Dr. Wayne’s team had made a convincing case. “I think they have nailed the locale of dog domestication to the Middle East,” Dr. O’Brien said in an e-mail message from Siberia, where he is attending a tiger management workshop.

Dog domestication and human settlement occurred at the same time, some 15,000 years ago, raising the possibility that dogs may have had a complex impact on the structure of human society. Dogs could have been the sentries that let hunter gatherers settle without fear of surprise attack. They may also have been the first major item of inherited wealth, preceding cattle, and so could have laid the foundations for the gradations of wealth and social hierarchy that differentiated settled groups from the egalitarianism of their hunter-gatherer predecessors. Notions of inheritance and ownership, Dr. Driscoll said, may have been prompted by the first dogs to permeate human society, laying an unexpected track from wolf to wealth.