Ancient Sambaqui Societies Were Genetically Diverse

DNA analysis of ancient remains, obtained across four different parts of Brazil, reveal new insights into the ancient communities that occupied eastern South America thousands of years ago. The study, published in Nature Ecology & Evolution, was led by Dr. André Menezes Strauss, an archaeologist at the University of São Paulo’s Museum of Archeology and Ethnology (MAE-USP). The University of Tübingen’s Senckenberg Center for Human Evolution and Paleoenvironment (Germany) partnered on the project.

Outstanding questions surrounding Sambaqui societies

In pre-colonial South America, populations of Sambaqui societies inhabited large regions across the Atlantic coast from approximately 8,000–1,000 years ago. Sambaqui is a Brazilian term that describes large mounds of fishbones and shells that were built by these ancient communities and often used as cemeteries, homes and markers of territorial boundaries. They are considered an iconic feature of Brazilian archeology, with over 1,000 sambaqui locations recorded in the country’s national register of archeological sites.

According to Strauss and colleagues, Sambaqui societies are “among the most intriguing archaeological phenomena in pre-colonial South America.” However, our understanding of how these populations might have been connected to early Holocene hunter-gatherers – and whether this contributed to the processes that saw the late Holocene ceramists “rule the coast” – is limited.

The Holocene epoch

The “Holocene” refers to the last 11,700 years of our planet’s history.

The earliest evidence of human activity and settlement on the Atlantic coast dates back ~8,700 years ago, with an intensification of sambaqui construction approximately 5,500 years ago. We know that there were both coastal and riverine Sambaqui societies, but there are a number of outstanding questions surrounding their genetic similarities, and their relationship to present-day Indigenous populations, as outlined by Strauss and colleagues in the paper:

  • Were Sambaqui individuals different – genetically – from hunter-gatherers from the inland, such as east-central and northeastern Brazil?
  • Were the riverine Sambaqui groups genetically related to Sambaqui groups on coastal sites?
  • Was there genetic homogeneity across Sambaqui groups from the south and southeast coast of Brazil?
  • Are there genetic connections between Sambaqui groups and other Indigenous populations from Amazonia and northeastern and central Brazil?

Further questions stem from the seemingly mysterious disappearance of the dominant Atlantic coast sambaqui builders: “After the Andean civilizations, the Atlantic coast sambaqui builders were the human phenomenon with the highest demographic density in pre-colonial South America. They were the ‘kings of the coast’ for thousands and thousands of years. They vanished suddenly about 2,000 years ago,” Strauss says. Was the demise of this community associated with an increase in contact with inland populations?

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Eager to address these queries and gain a deeper understanding of the history of Indigenous societies on the eastern coast of South America, Strauss and colleagues produced genome-wide data from 34 ancient individuals, using fossil samples that spanned 10,000 years. The samples were obtained from sambaquis and other aspects of archeological sites including Cabeçuda, Capelinha, Cubatão, Limão, Jabuticabeira II, Palmeiras Xingu, Pedra do Alexandre and Vau Una.

Among the archeological material analyzed by Strauss and team was “Luzio”, São Paulo’s oldest male human skeleton that is estimated to be ~10,400 years old. Luzio was discovered inland from the coast in the Capelinha river midden by Dr. Levy Fitugi, a professor at MAE-USP, and colleagues.

What is a midden?

A midden refers to a concentration of materials that are considered to be evidence of past human activity, such as artefacts used for food processing, hunting and gathering.

“This individual was named ‘Luzio’, as a reference to ‘Luzia’, a final Pleistocene female skeleton found in the Lagoa Santa region in east-central Brazil. Both individuals are at the center of long-lasting debates for exhibiting the so-called paleoamerican cranial morphology that differs from that of present-day indigenous peoples,” the authors write. Luzia, discovered by Fitugi and team in the early 2000s, is the oldest human fossil discovered in South America.

The dissimilarities in cranial morphology led Strauss and team to believe, initially, that Luzio belonged to a different population than present-day Amerindians. However, genome analysis revealed Luzio was, in fact, an Amerindian “like the Tupi, Quechua or Cherokee,” says Strauss. “That doesn’t mean they’re all the same, but from a global perspective, they all derive from a single migratory wave that arrived in the Americas not more than 16,000 years ago. If there was another population here 30,000 years ago, it didn’t leave descendants among these groups.” Luzio is not considered to be a direct ancestor of the huge classical Sambaqui population that appeared later in time, as his remains were discovered in a river midden.


The term Amerindian is used to refer to American Indians, also referred to as Native Americans, Indigenous Americans and Aboriginal Americans. It is a term that was created by the American Anthropological Association.

Coastal and inland populations shared practices but were biologically different

Through analyzing the genetic material obtained from different sites across coastal and inland regions, the researchers identified heterogenous communities that shared cultural practices but were different biologically. “Our analyses show genetic heterogeneity among contemporaneous Sambaqui groups from the southeastern and southern Brazilian coast, contrary to the similarity expressed in the archaeological record,” the authors describe.

“Studies of cranial morphology conducted in the 2000s had already pointed to a subtle difference between these communities, and our genetic analysis confirmed it,” Strauss says. “We discovered that one of the reasons was that these coastal populations weren’t isolated but ‘swapped genes’ with inland communities. Over thousands of years, this process must have contributed to the regional differences between Sambaquis.”

Why did the coastal sambaqui builders vanish? The researchers say that when coastal and inland contact increased – approximately 2,200 years ago – there was a decline in the construction of shell mounds and the introduction of pottery, which led to changes in practices such as cooking. “This information is compatible with a 2014 study that analyzed pottery shards from sambaquis and found that the pots in question were used to cook not domesticated vegetables, but fish. They [the coastal Sambaqui] appropriated technology from the hinterland to process food that was already traditional there,” Strauss explains.

“The complex history of intercultural contact between inland horticulturists and coastal populations becomes genetically evident during the final horizon of sambaqui societies, from around 2,200 yr before present, corroborating evidence of cultural change,” the authors say. They emphasize that their data challenges descriptions of ancient populations in archeological records, and “highlights the need to perform more regional and micro-scale studies to improve our understanding of the genomic history of eastern South America.” 

Reference: Ferraz T, Suarez Villagran X, Nägele K, et al. Genomic history of coastal societies from eastern South America. Nature Ecology & Evolution. 2023. doi:10.1038/s41559-023-02114-9