Scientists attempting to map out the historical migrations of North and South America by analysing ancient bones have revealed that a 10,000-year-old skeleton unearthed in a cave in Nevada is the ancestor of a Native American tribe.

The iconic skeleton, known as the “Spirit Cave mummy”, was reburied this summer by the Fallon Paiute-Shoshone people in Nevada, bringing closure to a decades-long legal dispute with anthropologists who fought for it to remain on display in a museum.

DNA painstakingly extracted from the ancient skull proved the skeleton was an ancestor of the tribe and discredited a longstanding theory that the individual was from a group of “Paleoamericans” that existed in North America before Native Americans.

The full genetic details of the skeleton, which is the world’s oldest natural mummy, are published as part of a wide-ranging international study of the ancestry of North and South America. The project also found evidence of two previously unknown migrations into South America and revealed surprising traces of Australasian ancestry in indigenous South Americans that hint at a far earlier arrival of modern humans to the Americas – potentially dating back 30,000 years or more.

Prof Eske Willerslev, who led the sequencing of the Spirit Cave Mummy and helped interpret genetic data from dozens of ancient specimens spanning about 10,000 years and locations from Alaska to Patagonia, said the findings highlighted the “power of ancient DNA” to reveal untold stories of the distant past.

Willerslev, who holds positions at the University of Copenhagen and the University of Cambridge, attended the reburial of the mummy this summer, which he said involved crying, singing and prayers. The mummy was placed in a casket and people were invited to place farewell gifts alongside it; Willerslev added a box of snuff tobacco.

“What was most amazing is that it was similar to if you and I were burying a very close relative,” he said. “It’s that emotional even though we are burying a mummy that was living 10,000 years ago.”

He said the event challenged claims by some in the scientific community that indigenous groups often fight for repatriation of remains in order to gain a political voice. “This event showed me it’s way more than that, it’s very deep feelings,” he said. “It’s similar to us not being able to bury our grandmother and her skull put on a shelf somewhere.”

The analysis, which was carried out with the involvement and consent of the tribe, also debunked a controversial theory that the skeleton was Paleoamerican, based on earlier work suggesting that Native Americans have different shaped skulls.

“Looking at the bumps and shapes of a head does not help you understand the true genetic ancestry of a population – we have proved that you can have people who look very different but are closely related,” said Willerslev.

The skeleton, an adult male aged around 40 at the time of his death, was wearing moccasins and wrapped in a rabbit-skin blanket and reed mats. His remains were found in 1940, along with the partial remains of three other individuals.

A statement from the Fallon Paiute-Shoshone tribe, said of the study: “[It] confirms what we have always known from our oral tradition and other evidence – that the man taken from his final resting place in Spirit Cave is our Native American ancestor.”

The discovery came as part of a wider investigation that has revealed previously unknown details of what happened after the first American populations diverged from their Siberian and East Asian ancestors nearly 25,000 years ago. The latest findings show that people spread rapidly, yet unevenly, throughout the Americas, and included three different streams of people dispersing from North to South America some time before 15,000 years ago.

“Nearly all Central and South Americans arose from a star-like radiation of the first lineage into at least three branches,” said Cosimo Posth, a geneticist from the Max Planck Institute for the Science of Human History and co-author of one of three scientific papers published by the international team. “With DNA evidence largely based on present-day people, those multiple gene flow events are undetectable, highlighting the power of ancient DNA data.”

One migratory stream was linked to the Clovis people, who are linked to archaeological sites in North America from about 13,000 years ago. But this early group of migrants to South America appeared to have been almost entirely replaced by a subsequent wave 9,000 years ago.

The study revealed traces of Australasian ancestry in ancient Native Americans in South but not North America. This could be evidence of the existence of an ancient population, with deep ancestral links to people who ended up in Australasia, that arrived in the Americas far earlier than the ancestors of Native Americans.

“It really opens the question of whether there has been a much earlier migration into America,” Willerslev said.

Victor Moreno-Mayar, from the Centre for GeoGenetics at the University of Copenhagen, and first author of the study, said: “That this signal has not been previously documented in North America implies that an earlier group possessing it had disappeared or a later arriving group passed through North America without leaving any genetic trace.”

The findings are published in the journals Science, Science Advances and Cell.