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Consortium Describes Ancestry Patterns in Brazilian Populations

NEW YORK (GenomeWeb) – A team that included members of the Brazilian EPIGEN Project Consortium is using genetic and genomic profiles to chart historical events and ancestry patterns in Brazil.

As they reported in the early, online edition of the Proceedings of the National Academy of Sciences, the researchers used genotyping to tease apart relative proportions of African, European, and Native American ancestry in nearly 6,500 Brazilians from populations in northeastern, southeastern, and southern sites in the country. They also sequenced a few dozen individuals from the same populations.

With these data the study's authors untangled ancestry and admixture events, identifying patterns linked to historical events and migrations in Brazil. "Our population-based and fine-scale analyses revealed novel aspects of the genetic structure of Brazilians," they noted.

Much of Brazil's population had African ancestry in the late 1800s, the team noted, following the influx of almost four million African slaves over centuries. Individuals in the country also carry sequences from ancestral Amerindian populations and from Europeans migrants.

As part of the EPIGEN Brazil Initiative, the study's authors set out to tease apart admixture events between these ancestral groups, starting with data on 6,504 Brazilians genotyped at almost 2.2 million SNPs using HumanOmni2.5-8v1 or HumanOmni5-4v1 chips at an Illumina facility.

Following quality control steps, they were left with data on 6,487 individuals, including 1,309 individuals from Salvador in the northeast; 1,442 individuals from the southeastern city of Bambuí; and 3,736 individuals from Pelotas in Brazil's south.

The team also used the Illumina HiSeq 2000 to do whole-genome sequencing on 10 individuals from each of the populations, selected at random.

Together, the team's results suggest that over much of the country's history, individuals have preferentially mated with other individuals from the same ethnic background, though admixture appears to have been more common in the largest of the three cities, Salvador.

The proportion of African ancestry varied dramatically between populations, peaking at more than 50 percent, on average, in the population from Brazil's Northeast.

While Brazilians in the Salvador area tended to carry sequences similar to those in West African populations such as the Yoruba and Mandenka, individuals in Bambuí and Pelotas had sequences akin to those in the Luhya and other Bantu-speaking central and east African populations, the researchers reported.

The south and southeastern populations had lower proportions of African sequences, comprising almost 16 percent of ancestry in individuals from Pelotas and less than 15 percent ancestry in Bambuí individuals. There, European ancestry was high, making up between 76 and 78 percent of individuals' ancestry, on average.

This European ancestry included relatively recent admixture events and could be traced back to a wide range of locales — from northern Europe, central Europe, and even the Middle East, the team noted.

On the other hand, European ancestry component in individuals from Salvador tended to coincide with sequences from the Iberian Peninsula.

The researchers saw relatively low levels of Native American ancestry in each population, ranging from just over 6 percent in the north to 8 percent in the south, though they expect to see more diverse and pronounced Amerindian ancestry in future studies of populations in other parts of Brazil, including sites near the Amazon.

They also noted that "fine-scale studies on large urban centers … such as Rio de Janeiro or Sao Paulo, that have been the destination of migrants from all over the country during the last decades, may show an even more diversified origin of Brazilians, including Japanese ancestry components, for instance, that we did not identify in our study."