A recent extensive analysis of Indigenous American DNA suggests that human migration into South America occurred across three distinct pulses over millennia. Furthermore, the study uncovered that genes influencing fertility, metabolism, and immune response provided crucial advantages for these populations in adapting to the novel environments at humanity’s “final frontier” of migration, according to the researchers.
The findings, detailed in the journal Nature, stem from an international team that mapped the genomic diversity of Indigenous Americans. This project involved sequencing 128 genomes from individuals spanning 45 distinct populations and 28 language families across Argentina, Bolivia, Brazil, Colombia, Ecuador, Mexico, Paraguay, and Peru. The primary objective was to gain clearer insights into when and how people initially populated the continent, and what specific factors shaped the genetic makeup of these groups.
“Until now, genetic characterization had only been performed on two Indigenous Amazonian populations, and due to their habitat characteristics and isolation, these samples were not sufficiently representative,” noted contributing author Marcos Araújo Castro e Silva from the Institute of Evolutionary Biology (IBE) of the Spanish National Research Council and Pompeu Fabra University in Spain. The research team collaborated closely with Indigenous communities to develop the study and integrate the resulting data into Indigenous histories, explained co-author Tábita Hünemeier, head of the Human Population Genomics Laboratory at IBE.
The examination of these 128 new genomes, augmented by 71 previously published Indigenous genomes, resulted in two novel discoveries, alongside additional data corroborating two prior findings.
Researchers determined that South America was settled in at least three migratory waves, one of which was previously unknown. Their genetic mapping indicates the earliest influx of people arrived in South America more than 9,000 years ago. This was followed by a separate genetic lineage—shared by present-day Quechua people in Peru—that dispersed across Central and South America roughly 9,000 years ago.
However, the genomes also unveiled “a previously unknown third migration into South America,” the researchers reported, which “likely happened at least 1,300 years ago” originating from groups linked to Mesoamerica. While this timeframe roughly coincides with the decline of Mesoamerican urban centers like Teotihuacan (which saw its collapse between 650 and 750 CE), the genetic evidence does not point to a singular event, Hünemeier clarified.
“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 commented.
The genetic testing also uncovered traces of an ancient Asian “ghost lineage” that passed genetic material both to Indigenous Americans and to early Australasians inhabiting the Oceania subregion, encompassing modern-day Australia, New Zealand, and the Pacific islands. This genetic marker, which researchers termed Ypykuéra (meaning “ancestor” in the Tupi language of Brazil), is present at low but consistent levels among Indigenous populations for over 10,000 years, the study observed. Although the Ypykuéra signal is evident in contemporary individuals, definitive fossil evidence for this group remains undiscovered.
“Overall, both findings support the notion that the peopling of the Americas was a more dynamic and intricate process than previously understood,” stated Hünemeier, “involving contributions from ancestral populations that are not yet represented in archaeological or fossil records.”
The Indigenous American Genomic Diversity Project, which nearly tripled the number of sequenced Indigenous American genomes, also established that the Indigenous population of the Americas is genetically less diverse overall compared to other continental human groups. Nonetheless, it exhibits greater genetic variability than previously appreciated, including genes vital for surviving the specific American environments, such as the Amazon rainforest and the Andes mountains.
“The current genetic diversity is only a small remnant of the original, as [European] colonization caused a 90% decline in Indigenous populations,” Hünemeier explained. This substantial population reduction, coupled with fragmentation, isolation, epidemics, enslavement, and warfare, instigated severe evolutionary “bottlenecks” that diminished Indigenous genetic variation. “Nevertheless, in certain locales, we can detect genetic continuity extending beyond 9,000 years.”
The research notes that certain genes preserved within Indigenous populations are linked to immune function, energy metabolism, fertility, prenatal development, and malaria resistance, suggesting that diverse biological processes were shaped by natural selection within these ancient American groups. Some of these shared genes were found in common with modern Australasian populations, indicating that several ancient Ypykuéra traits were positively selected to help Indigenous Americans thrive in their new surroundings.
“The genetic information from Indigenous American populations is critical because these groups have historically been underrepresented in genomic studies, creating significant gaps in our understanding of human variation, evolution, and health,” pointed out contributing author Carlos Eduardo Amorim of Arizona State University. “Our findings offer the most comprehensive view yet of the genomic diversity and evolutionary trajectory of Indigenous Americans.”
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