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Ancient DNA analyses add new complexity to South America settlement
John Lindo in Carlos Museum

Emory anthropologist John Lindo specializes in mapping little-explored human lineages of the Americas in his ancient DNA lab. “As more whole genomes from South America are sequenced and published, they are likely to reveal more nuances about how South America was first settled,” he says.

Genomic analyses of ancient individuals from South America add surprising twists in the story of early human settlement of the continent. The Royal Society Proceedings B published the results, which show ancestral evidence in the Americas for extinct hominins known as Denisovans. 

The work, providing the most complete genetic evidence to date for ancient Central American and South American migration routes, was led by archeologists at Florida Atlantic University and anthropologists at Emory University.

Identification of Denisovan DNA goes back only to 2010, after Russian scientists uncovered a finger bone dated 50,000 to 30,000 years ago in a cave in the Altai Mountains of Siberia. Additional specimens from the Siberian cave were subsequently tied genetically to Denisovans, an archaic hominin with an affinity to Neanderthals, along with a single specimen from a cave on the Tibetan Plateau in China.

“It’s phenomenal that Denisovan ancestry made it all the way to South America,” says John Lindo, a co-corresponding author of the paper and an anthropologist at Emory who specializes in ancient DNA analysis. “The admixture must have occurred a long time before, perhaps 40,000 years ago.”

The fact that the Denisovan lineage persisted and its genetic signal made it into an ancient individual from Uruguay that is only 1,500 years old suggests that it was a large admixture event between a population of humans and Denisovans, Lindo says.

First author of the paper is Andrew Luiz Campelo dos Santos, an archeologist now at Florida Atlantic University who was formerly at the Federal University of Pernambuco in Recife, Brazil. Dos Santos uncovered the remains of two individuals from northeastern Brazil, who date back 2,000 years and are included in the analyses.

Co-corresponding author is Michael DeGiorgio from Florida Atlantic University, a population geneticist specializing in human, evolutionary and computational genomics.

The Americas were the last continents that humans populated. Evidence suggests that Paleolithic hunter-gatherers entered North America from a land bridge that formed between northeastern Siberia and western Alaska during a period of lower sea level around 26,000 to 19,000 years ago.

The current analyzes compared two newly sequenced ancient whole genomes from northeastern Brazil with present-day genomes and other ancient whole genomes from South America and Panama.

The results showed distinct relationships between Meso America, or parts of the modern-day countries of Mexico and Central America, and both present-day South Americans and ancient individuals from northeastern and southeastern Brazil, Uruguay and Panama. The analyses also detected a strong Australasian signal in the ancient genomes from near the Atlantic coast in Brazil. 

These ancestral connections provide new genetic evidence — in support of existing archeological evidence — for an ancient migration route through Panama and along the Atlantic coast of South America.

Adding to the complexity is the detection of a stronger signal for Denisovan ancestry in the ancient Uruguay and Panama individuals than in those from ancient Brazil. That suggests multiple waves of ancestral migrations along the Atlantic coast, the researchers conclude.

The Lindo ancient DNA lab specializes in mapping little-explored human lineages of the Americas. Previously, little focus has been put on sequencing ancient DNA from South America. One reason is that warmer, more humid climates throughout much of the continent have made it more challenging to collect usable ancient DNA specimens, although advances in sequencing technology are helping to remove some of these limitations.

As of the publication date of this paper, Lindo notes, only 12 ancient whole genomes from South America have been sequenced and published, in contrast to hundreds from Europe. 

Other published ancient genomic sequences from the continent have been limited to mitochondrial DNA (which is typically transmitted exclusively by maternal inheritance) and targeted DNA sequencing (which captures less than one percent of the genome).

“In this paper we’ve analyzed all of the ancient whole genomes available for South America and found some surprises,” Lindo says. “As more whole genomes from South America are sequenced and published, they are likely to reveal more nuances about how South America was first settled.”

Co-authors of the current paper include Amanda Owings (Emory), Henry Socrates Lavalle Sullasi (Federal University of Pernambuco) and Omer Gokcumen (State University of New York at Buffalo).

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