In a 2004 lawsuit, the Havasupai Tribe sued Arizona State University for misleading members about what their DNA would be used to study. That conflict left many researchers reluctant to get embroiled in similar controversy.

As scientists learned how to extract DNA from ancient human remains, a similar conflict arose.

Many museums store Native American skeletons, often exhumed without consent from burial grounds. Native American communities reclaimed many of these remains and often turned down research requests.

In recent years, however, these strains have started to ease.

Each summer, Ripan Malhi, a geneticist at the University of Illinois and co-author of the new study, and his colleagues run a workshop at the University of Illinois to train Native American students in genetics, focusing on research that can help their communities.

He also has established long-running relationships with Native American communities in Canada and Alaska.

Christiana Scheib, another co-author on the new study, traveled to California to meet with tribal representatives. She explained why she wanted to study Native American remains in California museums.

“Some of them were surprised,” said Dr. Scheib, who now heads the ancient DNA research group at the University of Tartu in Estonia. “They said, ‘You’re the first researcher to talk to us and ask our opinion.’”

In the new study, Dr. Scheib, Dr. Malhi and their colleagues searched for DNA in remains they had gained permission to study. They succeeded in finding genetic material in the teeth and ear bones of 91 individuals.