A new study suggests a commonly held belief – that the majority of Native North, Central and South Americans derived from one ancestry – is “unrealistically simple”.

Earlier research suggested the first people to enter the Americas split into two ancestral branches, the northern and southern, and that the “southern branch” gave rise to all populations in Central and South America.

However the latest work finds that most, if not all, of the indigenous peoples of the southern continent retain, deep in their genetic history, at least some DNA from the “northern branch” — the direct ancestors of many native communities living today in the Canadian east.

The research was carried out by a team led by scientists from Britain’s Cambridge University and the University of Illinois at Urbana–Champaign, in the US, and is published in the journal Science.

Genome evidence suggests that the two populations may have remained separate for millennia – long enough for distinct genetic ancestries to emerge – but they came back together before or during the expansion of people into South America.

“We now find that all native populations in North, Central and South America also draw genetic ancestry from a northern branch most closely related to indigenous peoples of eastern Canada,” says one of the authors, archaeologist Toomas Kivisild.

“This cannot be explained by activity in the last few thousand years. It is something altogether more ancient.”

Analyses of 91 ancient genomes recovered from human remains at sites in California and Canada provide evidence that the first peoples separated into two populations between 18,000 and 15,000 years ago. This would have been during or after migrating across the now-submerged land bridge from Siberia.

Ancient genomes from sites in south-west Ontario show that after the split, Indigenous ancestors representing the northern branch migrated eastwards. This population may have followed the retreating glacial edges as the Ice Age began to thaw, the researchers say.

The study also adds to evidence that the prehistoric people associated with Clovis culture – named for 13,000-year-old stone tools found near Clovis, New Mexico, and once believed to be ancestral to all Native Americans – originated from ancestors in the southern branch.

This southern population likely continued down the Pacific coast, inhabiting islands along the way. Ancient DNA from California’s Channel Islands shows that initial populations were closely related to the Clovis people.

Yet contemporary Central and South American genomes reveal a “re-convergence” of these two branches deep in time. The researchers say there must have been “admixture” events between the two populations about 13,000 years ago.

They say the blending of lineages occurred either in North America, before the expansion south, or as people migrated ever deeper into the southern continent, most likely following the west coast.

“It was previously thought that South Americans, and indeed most Native Americans, derived from one ancestry related to the Clovis people,” Kivisild says.

Co-author Ripan Malhi adds: “Working in partnership with indigenous communities, we can now learn more about the intricacies of ancestral histories in the Americas through advances in paleogenomic technologies.

“We are starting to see that previous models of ancient populations were unrealistically simple.”

Present-day Central and South American populations analysed in the study were found to have a genetic contribution from the northern branch between 42% to as high as 71%.

Surprisingly, the highest proportion of northern branch genetics in South America was found in southern Chile, in the same area as the 14,500-year-old Monte Verde archaeological site – one of the oldest known human settlements in the Americas.

“It’s certainly an intriguing finding, although currently circumstantial – we don’t have ancient DNA to corroborate how early this northern ancestral branch arrived,” says lead author Christiana Scheib.

“It could be evidence for a vanguard population from the northern branch deep in the southern continent that became isolated for a long time, preserving a genetic continuity,” she says.

“Prior to 13,000 years ago, expansion into the tip of South America would have been difficult due to massive ice sheets blocking the way. However, the area in Chile where the Monte Verde site is located was not covered in ice at this time.

“In populations living today across both continents we see much higher genetic proportions of the southern, Clovis-related branch. Perhaps they had some technology or cultural practice that allowed for faster expansion. This may have pushed the northern branch to the edges of the landmass, as well as leading to admixture encounters.”

The researchers say more must be done to include indigenous communities in ancient DNA studies in the Americas, adding that genomic analysis of ancient people can have adverse consequences for linked indigenous communities. Engagement work can help avoid unintended harm to the community and ensure that Indigenous peoples have a voice in research, they say.

“From the analysis of a single tooth, paleogenomics research can now offer information on ancient diet and disease as well as migration,” Scheib notes.

“By developing partnerships that incorporate ideas from Native communities, we can potentially generate results that are of direct interest and use to the Indigenous peoples involved.”