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Researchers Reconstructing Genome of Indigenous Population Using 1000 Genomes Data

This article has been updated to remove the word "extinct" to describe the Taino population. Though the researcher who gave the talk described them as such at the conference, he has since clarified his comments based on feedback from the Taino community.

By Andrea Anderson

MONTREAL (GenomeWeb News) – Using sequence data generated for dozens of Puerto Rican parent-child trios through the 1000 Genomes Project, researchers have started to reconstruct the genomes of individuals from an ancestral indigenous population known as the Taino, who lived in the Bahamas, Greater Antilles, and Lesser Antilles before the Caribbean was colonized by Spanish settlers in the 1500s.

The Taino population dropped off dramatically in the 100 years after they came into contact with Europeans, co-author Jake Byrnes explained during his presentation during an evolutionary genetics session at the International Congress of Human Genetics here this week.

In collaboration with investigators from the 1000 Genomes Project, the University of Puerto Rico, the University of California at San Francisco, and Cornell University, Byrnes and other Stanford University researchers are sifting through low-coverage whole-genome data and higher depth exome sequence data on 70 Puerto Ricans sampled through the 1000 Genomes Project to find and catalog chunks of genomic sequence passed down from Taino ancestors.

This genomic reconstruction is possible because the proportion of Taino ancestry remaining in the Puerto Rican and other Caribbean populations is roughly 10 to 15 percent, Stanford researcher Carlos Bustamante, a leader on the study, said during a media briefing at ICHG yesterday.

The team found genomic patterns that corresponded to the three-way European, African, and Taino ancestry that exists in the Puerto Rican population. They are now working to reconstruct fine-scale maps of the sequenced individuals' genomes to determine which pieces were passed down from Europeans, Native Americans, and Africans.

Down the road, they plan to stitch the Taino segments of the genome together to get a complete picture of Taino sequences across the genome.

By looking at local ancestry tracts, Byrnes explained, it should also be possible to reconstruct site frequency spectra from high-coverage exome sequence data to learn more about genetic diversity of aboriginal peoples in the Caribbean.

The overall sequence patterns in the Puerto Rican genomes point to a rapid decline in the Taino population, Bustamante said, as evidenced by a pulse of Taino ancestry that seems to have percolated down through the Puerto Rican population over time. In contrast, he explained, African and European signals in the genome are consistent with several waves of migration and ancestry from those populations.

The genome data also promises to offer a peek at other historical events, including insights into the slave trade and the source populations in Africa contributing to Caribbean ancestry.

For example, the team's preliminary analyses have uncovered ancestry patterns consistent with two waves of slave trade from Africa to Puerto Rico, one from the Cape Verde area in the mid-1500s to mid-1600s and another from southern Africa that started around 100 to 150 years later.

Additional information on the Taino Genome Project is available through a University of Puerto Rico at Mayaguez genomic diversity lab website.

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