DNA study of nearly 200 Indigenous genomes reveals unknown Asian 'ghost' population contributed to American ancestry

Humans migrated to South America in three distinct waves over the course of thousands of years, a new large-scale analysis of Indigenous Americans' DNA reveals. The investigation also found that genes related to fertility, metabolism and the immune response helped people adapt to their unique environment in the "final frontier" of human migration, the researchers said.

In a study published Wednesday (April 22) in the journal Nature, an international team of scientists detailed findings from the Indigenous American Genomic Diversity Project, which analyzed 128 genomes from people living in Argentina, Bolivia, Brazil, Colombia, Ecuador, Mexico, Paraguay and Peru — an investigation that included 45 populations and 28 language families. The researchers' goal was to better understand how and when people arrived on the continent and the factors that shaped these populations' genetics.

"Until now, only two Amazonian Indigenous populations had been genetically characterized, and due to the particularity of their environment and their isolation, they were not very representative," study first author Marcos Araújo Castro e Silva, a researcher at the Spanish National Research Council's Institute of Evolutionary Biology (IBE) and Pompeu Fabra University in Spain, said in a translated statement. The research team worked in collaboration with Indigenous communities to develop the study and integrate the findings into Indigenous history, study co-author Tábita Hünemeier, head of the Human Population Genomics Lab at IBE, said in the statement.

An analysis of the 128 new genomes plus 71 previously published Indigenous genomes revealed two new findings and contributed additional data that confirmed two previous discoveries.

The researchers found that South America was populated in at least three waves, one of which was previously unknown. Their genetic data suggested that the earliest wave of people flowed into South America more than 9,000 years ago, followed by a distinct genetic lineage — shared today by the Quechua in Peru — that spread through Central America and into South America around 9,000 years ago.

But the genomes also revealed "a previously unrecognized third dispersal into South America," the researchers wrote in the study, that "probably occurred at least 1,300 years ago" from Mesoamerican-related groups. Although that timeframe roughly matches up with the collapse of Mesoamerican cities like Teotihuacan, which declined between A.D. 650 and 750, the genetic data does not point to a single event, Hünemeier told Live Science in an email.

"What we see is a more gradual and complex process, probably involving increasing connectivity and gene flow between Mesoamerica, the Caribbean and South America over time," Hünemeier said.

The genetic analysis also revealed traces of an ancient Asian "ghost lineage" that contributed genes to both Indigenous Americans and early Australasians, who lived in the subregion of Oceania including present-day Australia, New Zealand and the Pacific Islands. This genetic signal, which the researchers call Ypykuéra (meaning "ancestor" in the Indigenous Tupi language of Brazil), has been present at low-but-consistent levels in Indigenous people for more than 10,000 years, they noted in the study. Although the genetic signal of Ypykuéra has been found in modern people, no fossil evidence of the group has been discovered yet.

"Overall, both findings reinforce the idea that the peopling of the Americas was more dynamic and complex than previously thought," Hünemeier said, including "contributions from ancestral populations that are not yet represented in the archaeological or fossil record."

The Indigenous American Genomic Diversity Project, which nearly tripled the number of Indigenous genomes that scientists have sequenced, also revealed that the Americas' Indigenous population was less genetically diverse than other continental human groups but that it also had more genetic diversity than previously thought, including genes important for surviving in the novel environments of the Americas, such as the Amazon rainforest and the Andes.

"Current genetic diversity is only a fraction of the original, as [European] colonization decimated Indigenous populations by 90%," Hünemeier said in the statement. The combination of population collapse, fragmentation and isolation ‪—‬ along with epidemics, enslavement and warfare ‪—‬ caused major evolutionary bottlenecks, which reduced Indigenous peoples' genetic diversity. "Even so, we observe genetic continuity of more than 9,000 years in some regions," Hünemeier said.

Some of the genes that persisted in Indigenous populations were those associated with immune function, energy metabolism, fertility, fetal growth and malaria protection, the researchers wrote, revealing that diverse biological processes were shaped by natural selection in Indigenous American populations. Some of these genes were found to be shared with modern Australasian populations, suggesting several ancient Ypykuéra traits were positively selected to help Indigenous Americans thrive in a new environment.

"Genetic information from Indigenous American populations is essential because these groups have been historically underrepresented in genomic research, leaving major gaps in our understanding of human diversity, evolution and health," study co-author Carlos Eduardo Amorim, an anthropologist at Arizona State University, said in a statement. "Our findings provide the most comprehensive view of Indigenous American genomic diversity and evolutionary history to date."

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