Rebuilding the genome of a hidden ethnicity

Participants in the 1000 Genomes project reconstruct the genetic variation of a Native American tribe from their descendants.

The Taínos were the first Native Americans to meet European explorers in the Caribbean — and they soon fell victim to the diseases and violence brought by the outsiders. Today, the genomes of most if not all descendents of Taínos now contain few of the unique markers that characterized their ancestors.

But the genetic footprints of these ancestors are scattered throughout the genomes of modern Puerto Ricans, according to geneticist Carlos Bustamante at the Stanford University School of Medicine in Stanford, California. On average, the genomes of Puerto Ricans contain 10–15% Native American DNA, which is largely Taíno, says Bustamante.

At a presentation at the 12th International Congress of Human Genetics in Montreal, Canada, Bustamante described preliminary results from a study that aims to reconstruct the genetic features of the Taíno people. The cryptic information was found in the genomes of 70 modern Puerto Ricans, some of the latest additions to the ongoing 1000 Genomes project, an international consortium whose goal is to find the variations in DNA sequence among the genomes of all human populations.

Window on the past

The genomes of modern Puerto Ricans are a mosaic of African, European and Native American sequences. A set of single-nucleotide locations that are known to vary across these different ancestral groups helped Bustamente and his collaborators to identify whether a given region of the genome was African, European or Native American in origin, and thus begin to stitch together chromosomal segments corresponding to the Taíno heritage. The various Taíno sequences in the 70 different genomes will help to build a more complete picture of the ancestral Native American genomes.

The project has also shed light on the history of interactions between Native Americans, Africans and Europeans in the Caribbean. To infer when the various populations interbred, the team first estimated the lengths of each segment of African, European and Native American DNA in the modern genomes. They found the Taíno segments to be relatively short, suggesting a single 'pulse' of admixture — the result of interbreeding between populations — a few hundred years ago.

The small size of the ancestral segments fits with our understanding of the history of Puerto Rico, says Marc Via, a molecular anthropologist at the University of Barcelona, Spain, who was not involved in the study. "The admixture took place suddenly, so most of the population mixed with the African slaves and European settlers in the very early colonization of Puerto Rico." With every generation, the segments of Taíno genome would become smaller and smaller, he says.

Unlike the rapid mixing of Taíno with African and European genomes, the slave trade created a more complex pattern of African sequences. "The African and European segments have a fair amount of variation in size, which tells us that they are the result of several waves of migration," says Bustamante. Early insights from the study suggest that shorter, and therefore older, African segments come from populations near the coast of Senegal, whereas longer, more recent, segments come from inland African populations. This suggests that slave-traders first captured slaves on the coast but later had to go inland.

Tracking the slave trade

This information is key to understanding the history of the slave trade and African American history, says Bustamante. "Most Africans Americans in the United States have ancestry that largely traces to the African slaves that came through the Caribbean," he says. "We would love to be able to give folks back historical information that can be derived from DNA sequence data about where people came from."

The study, which includes collaborators at the University of Puerto Rico in Mayagüez, will also help address deficiencies in medical genetics data sets, which largely contain sequences of European origin1. "This now opens up the opportunity to undertake large-scale medical genetic studies in Puerto Ricans and in other populations of Afro-Caribbean and Hispanic-Latino descent."
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References:

Young, Susan. 2011. "Rebuilding the genome of a hidden ethnicity". Nature. Posted: October , 2011. Available online: http://www.nature.com/news/2011/111014/full/news.2011.592.html