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Study Provides Genetic Look at Historical Interactions Impacting Caribbean Populations

NEW YORK (GenomeWeb News) – Caribbean populations carry combinations of ancestral sequences that can be used to retrace pre- and post-colonial historical events, a new study reveals, while providing insights into genetic diversity in Latino individuals.

Reporting in PLOS Genetics last night, an international team led by researchers at Stanford University and the University of Miami outlined findings from an array-based study involving hundreds of American individuals with ancestry from six Caribbean populations as well as almost 80 Venezuelan individuals descended from three native South American tribes.

Using a refined ancestry analysis method, the researchers assessed ancestry tracts in the admixed genomes, tracing them back to interacting populations from specific areas on several continents. Beyond clues to pre-colonial relationships between native populations in the Americas, for instance, they saw post-colonial European ancestry patterns and signs of subsequent Western African and Central African ancestry reflecting different stages of the slave trade through the region.

The relative representation of such ancestral sequences differed within and between populations, the study authors noted — variation that may ultimately help in teasing apart disease risk patterns and drug response profiles in individuals from Latino or Hispanic populations.

"We're not yet at the point where we are able to say which populations are most likely to have specific diseases," first author Andrés Moreno-Estrada, a genetics researcher at Stanford, said in a statement, "but now we can begin to figure out the important components."

The researchers used Affymetrix arrays to genotype 251 individuals living in South Florida. Of those, 80 had ancestry from Cuba, 27 from Puerto Rico, six from Haiti, 34 from the Dominican Republic, 19 from Honduras, and 85 from Colombia.

They also assessed samples from 79 Venezuelan individuals hailing from native South American populations known as the Yukpa, Bari, or Warao.

Using a new computational approach called ancestry-specific PCA — together with available variant data for thousands of Europeans, Africans, Americans, Native Americans, and Latinos — the team began unraveling ancestry patterns in the Caribbean genomes that offered insights into the region's history.

Ancestry tracts in the admixed genomes suggested that indigenous individuals, mainly from inland South America, likely moved into the Caribbean during a pre-colonial period around 2,500 years ago, consistent with documented language patterns in the region.

And because similar signals are found in inland Amazonian tribes, as well as populations in Central America and the Yucatan peninsula, the team concluded that there may have been widespread mixing between Caribbean populations period prior to European colonization.

In the years after Columbus and his crew arrived in the region, meanwhile, Caribbean populations increasingly carried sequences reminiscent of those found in Europe's Iberian region.

The timing with which European sequences entered populations in mainland and island regions of the Caribbean appears to vary, researchers noted. They also saw differences between the European sequences in Caribbean genomes and those present in the Iberian source population, perhaps due in part to the small number of Europeans arriving in the area originally.

The analysis also pointed to two waves of African ancestry — one occurring in around 1550 and another in the late 18th century — that appear to reflect waves of slave trade across the Atlantic from West Africa and Central Africa, respectively.

"The transatlantic slave trade involved the brutal and forced migration of over 12 million people," Stanford University's Carlos Bustamante, the study's co-senior author, said in a statement. "They were the ancestors to and kin of many people who now live in the Americas, Africa, and throughout the world today."

"Realistically, we are just scratching the surface and seeing that we can find genetics signals that corroborate historical research," he noted, adding that the group is "cautiously optimistic that as technology improves we can delve deeper and help reclaim more of this critically important history."

Finally, results from the study revealed that proportions of European, African, and Native American ancestry varied across and within populations. For example, the Haitian individuals had the highest proportion of ancestry from West Africa, whereas West African ancestry varied from a low of 2 percent all the way up to 78 percent in the Cuban genomes tested.

"[T]he extensive population stratification within sub-continental components implies that medically relevant genetic variants may be geographically restricted," the study authors concluded, "reinforcing the need for sequencing target populations in order to discover local variants that may only be relevant in Latino-specific association studies for disease."