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Genomic Analysis Elucidates Settlement of Brazilian Coast by Indigenous Peoples

NEW YORK – By analyzing the genomes of modern Native Americans, researchers have begun to piece together how the Brazilian coast was first settled.

During the 15th century, about 900,000 Native Americans, most of whom spoke Tupí, lived along the Brazilian coast. But following the arrival of the Portuguese in the region in the 16th century, the native coastal population declined quickly and became extinct by the end of the 18th century, except for two small admixed communities that self-report as Tupí, the Tupiniquim and the Tupinambá.

Researchers led by the University of São Paulo's Tábita Hünemeier sought to unravel the history of the Tupí by examining the genomes of the Tupiniquim and other Native American populations. Through this, the researchers found that the genetic lineage of the Tupí continues in the Tupiniquim and could be used to reconstruct their history.

As they reported Monday in the Proceedings of the National Academy of Sciences, Hünemeier and her colleagues found evidence of a migration from the Amazon to the Northeast Coast in the pre-Columbian era that became the Tupí coastal population.

"This study elucidates the population dynamics and diversification of the Brazilian natives at a genomic level, which was made possible by recovering data from the Brazilian coastal population through the genomes of mestizo individuals," Hünemeier and her colleagues wrote in their paper.

They generated SNP data from 102 Native Americans from Brazil, including 47 Tupiniquim, 48 Guaraní Mbyá, two Wajãpi, three Parakanã, and two Gavião. They supplemented this cohort with data from publicly available datasets such as the Human Genome Diversity Project and the 1000 Genomes Project as well as from 48 Native Americans, the ancient Anzick-1 sample from Montana, and 15 ancient DNA samples from Brazil.

Through an admixture analysis, the researchers found that individuals from the Tupiniquim community had a greater portion of European and African admixture than the nearby Guaraní Mbyá community. Still, they noted the Tupiniquim had a greater portion of native ancestry than the general Brazilian population. In particular, they estimated that European admixture into the Tupiniquim community first occurred about 11 generations ago, coinciding with the Brazilian Gold Cycle, and African admixture first occurred about eight generations ago, a time of increased colonization and intense slave trade. Another admixture pulse occurred about five generations ago, about when slavery was abolished in Brazil and when there was an increase in migration from Italy.

Principal components and other analyses clustered the Tupiniquim with other Native American populations, though they also found no signs of admixture between Tupiniquim with other Native American populations, suggesting that the Tupiniquim are living descendents of the extinct Tupí branch.

Using the Tupiniquim as a proxy for the Tupí, the researchers sought to trace the Tupí expansion that occurred about 2,000 years ago and led to an explosion in population and language, an event the researchers likened to the Bantu expansion that occurred in Africa. But how this expansion occurred has been unclear. 

With a combination of phylogenetic tree analysis and modeling, the researchers homed in on one scenario in particular: Tupí-speakers moved eastward toward the coast from the mouth of the Amazon and then followed along Brazil's northeast coast, while the Guaraní people spread in a separate migration from the Amazon to the Paraná basin. This, they said, lends credence to the idea that the expansion was driven by Amazonian agriculturists who were searching for cultivable lands.