Since the human genome was first sequenced in 2003, the world’s scientific community has been racing to decipher this “book” written in an alphabet of four letters. The applications of these discoveries range from disease detection and the design of personalised treatments to increasing our understanding of human evolution.

However, much of the genetic information generated over these decades lacks ethnic diversity. This under-representation limits the benefits of medical genomic research for many populations and leaves much of our evolutionary history in the dark.

For the first time, an international study under the joint leadership of Spain’s Institute of Evolutionary Biology (IBE), a joint centre of the Spanish National Research Council (CSIC) and the Pompeu Fabra University (UPF), and the University of São Paulo, has deciphered the genome of the population of Brazil. Published in the journal Science, the research includes the African, Native American, and European ancestries making up this population, which has the world’s highest level of recent genetic admixture.

The largest genetic database of the Brazilian population to date

The study has produced 2,723 high-coverage complete genomes of the Brazilian population as part of the project “DNA do Brasil”. They include urban, rural, and riverside communities in Brazil’s five geographical regions, and their main ancestries. The investigation has revealed over 8 million previously unknown genetic variants. Among these, up to 36,637 variants have been identified which are potentially harmful to health.

This new database reveals key information about the country’s history and evolution, and the genetic determinants of its population’s health. “Brazil has the greatest African diversity on the American continent, with a high level of admixture, and studying this can shed light on the health of the Brazilian population,” according to Tábita Hünemeier, the IBE’s lead researcher, who directed the study.
 

Recent genetic admixture marked the DNA of the Brazilian population

The team identified potentially pathogenic genetic variants in 450 genes linked to heart diseases and obesity in the Brazilian population. They also found genetic variants in 815 genes relating to infectious diseases such as malaria, hepatitis, flu, tuberculosis, salmonellosis, and leishmaniasis.

“Exploring these genetic variants can help us understand why some people are more likely to get certain diseases, and how to improve Brazil’s public health,” adds Marcos Araújo Castro e Silva, a postdoctoral researcher at the IBE and the University of São Paulo, and the first author of the study.

The study also identified genetic variants which increase fertility, which alongside genes relating to immune response and metabolism, would have been favoured by natural selection during Brazil’s 500 years of genetic admixture.

“The genome’s natural selection processes usually take place over thousands of years, but in the Brazilian population we can observe a much shorter recent process. This is due to the great genetic diversity of the country after colonisation began, and the selective pressure of pathogens on recent arrivals,” says David Comas, lead researcher at the IBE and professor of Biology in the Medicine and Life Sciences Department (MELIS) of the UPF, who worked on the study.

The ancestries of the Brazilian population reveal the country’s demographic history

Brazil’s unique genetics reflect its history since the 15th century, when approximately 5 million European colonists emigrated to the territory. Their arrival led to the loss of over 90% of the native population, and the forced displacement of 5 million Africans to the country. Now this convulsive demographic history can be “read” in their genomes.

The investigation found more African ancestry in the north of Brazil, and more European in the south. Most of the study sample presents around 60% European, 27% African and 13% indigenous ancestry.

“Although the proportion of native ancestry is higher than had been found in earlier preliminary studies, it is still small, given the large numbers of native American and African populations who lived side by side in the past,” says Comas.

The team concluded that this was due to a historically asymmetrical mating pattern among native American and African men and women. The research found that most Y-chromosome lineages in the study (inherited from men) were of European origin (71%), while most mitochondrial lineages (inherited from women) were African (42%) or native American (35%).

In more recent generations, however, the study detected a pattern of “selective mating”, revealing that the Brazilian population tended to produce offspring within the same ethnic group.

This genetic dataset illustrates the complex social and ethnic network which has developed in Brazil in the last 500 years.

 "Most of the European colonists were men, and considering the history of violence during colonisation, this can explain the occurrence of systematic asymmetrical mating during Brazil’s earliest centuries (16th to 18th centuries). After this period, we see a preference for marriages within people’s own ethnic groups,” Hünemeier notes.

Genetics reveal Brazil’s history and shed light on the health of its population

The new genetic database has revealed for the first time a large number of genetic variants with implications for the health of Brazilian people. In particular, the team has associated more pathogenic variants than expected with native American and African ancestries. However, they conclude that this might be due to the genetics of these populations being under-represented in worldwide genetic databases.

The investigation also attributes some pathogenic variants to the founder effect, a process in which a population originates in a small group of “founding” individuals, who transmit their pathogenic variants to their descendants. This phenomenon is seen in some American indigenous populations, but it could also be the cause of the prevalence of rare diseases with European ancestry, such as Machado-Joseph disease. While rare in Europe, this disease is common in Brazil, probably originating in immigrants from northern Europe and the Portuguese islands, who arrived in the country in small groups in different periods.

The study especially emphasises that the indigenous American populations of Brazil are among the least-studied groups in the world. “However, our discoveries show that it is possible to recover part of their genetic diversity by examining the genomes of the modern-day admixed population,” Hünemeier notes.

The new genomic database opens the door to studying the population of Brazil, a cultural melting-pot with a complex history written in its genes. “Mapping the genetics of Brazil not only can help us improve the health of its population in future research; it also casts light on our evolution and the history of humanity,” concludes Hünemeier.

This research forms part of the Brazil Health Ministry project “DNA do Brasil” and received funding from the Marie Skłodowska Curie EUTOPIA-Science and Innovation Postdoctoral Fellowship COFUND (awarded to Castro e Silva). Marie Curie.

Reference article:

Nunes K, Silva MACe, Ribeiro MR, et al. Admixture's Impact on Brazilian Population Evolution and Health. (2025) Science. DOI: 10.1126/science.adl3564