Greger Larson at the University of Oxford, an author of the paper, and the leader of an international effort to investigate the evolution and domestication of dogs, said the study emphasizes how inseparable are the fates of humans and their animals.

“The Europeans come through. They knock out the humans. They knock out the dogs,” he said. Given the necessary caveats that a pocket of dogs with substantial ancient American ancestry could turn up somewhere, Dr. Larson said that he was convinced by the evidence so far that, “It’s a complete disappearance.”

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Laurent Frantz, an ancient DNA expert at Queen Mary University of London, who led the research, said that until now, there had not been enough evidence to know “the story of these dogs and what happened to them after the Europeans arrived.” Now, he said, it is clear that the pre-contact dogs were an identifiable group, separate from any other, and that some combination of disease and European persecution of native dogs led to their disappearance.

Elaine Ostrander, a comparative geneticist at the National Institutes of Health, who studies dogs as a model for human cancers, and who has reported traces of ancient American dog DNA in some modern breeds, said the study was “unique, really well done.” But she was not giving up hope for the possibility of uncovering dogs somewhere with a substantial portion of DNA from ancient American dogs.

Fifty researchers collaborated on the study, which included both biological and archaeological evidence. They derived DNA from the remains of 71 ancient dogs from the Americas and Siberia and compared them to genomes of modern dogs.