David Reich of Harvard, the senior author of a paper published Tuesday in the journal Nature, said the DNA pattern was “surprising and unexpected, and we weren’t really looking for it.”

Pontus Skoglund, a researcher working with Dr. Reich who was investigating data gathered for previous research, found the pattern, or signal, as he described it. He and Dr. Reich and their colleagues used numerous forms of analysis, comparing different groups to see how distant they were genetically, to determine if there was some mistake.

But, Dr. Skoglund said, “we can’t make it go away.”

Dr. Reich reported in 2012, based on some of the same evidence, that a group he called the First Americans came from Siberia 15,000 or more years ago, and were the ancestors of most Native Americans on both continents. There was a second and later migration, he said, that gave rise to a group of Indians including the Chipewyan, Apache and Navajo, who speak similar languages. The Inuit are generally agreed to have made a separate, later migration.

Now, based on new evidence and much deeper analysis, he and Dr. Skoglund and colleagues concluded that the first migration, which began 15,000 or more years ago, consisted not only of the group he identified as the First Americans, but of a second group that he calls Population Y. They could have come before, after or around the same time as the First Americans. But Population Y, he writes, “carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans.”

Population Y comes from Ypykuéra, a word meaning ancestor in a language spoken by the two Amazonian groups, the Surui and Karitiana, that show the strongest genetic connection to Australasians.