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Ancient Indigenous Caribbean Genome Shows Close Relation to Modern Populations

NEW YORK (GenomeWeb) – Researchers have sequenced the genome of a 1,000-year-old Taino woman who lived in the Bahamas, garnering insight into the peopling of the Caribbean.

Ancestors of the Taino, also known as Lucayans, are thought to have reached the Caribbean from South America about 2,500 years ago, and by the arrival of Europeans to the region, the Taino were the dominant group living in the Greater Antilles, northern Lesser Antilles, and the Bahamas.

Researchers led by the University of Copenhagen's Eske Willerslev sequenced DNA isolated from an ancient tooth uncovered in a cave in the Bahamas. They noted that poor preservation of ancient DNA in the region has constrained past analyses. But, analyzing the data, they found that the Taino were most closely related to present-day Arawakan speakers from northern South America, as they reported in the Proceedings of the National Academy of Sciences this week. Willerslev and his colleagues further found that present-day Caribbean individuals harbor genome sequences similar to those of the ancient woman, indicating they are descendants of the Taino.

"It has always been clear that people in the Caribbean have Native American ancestry, but because the region has such a complex history of migration, it was difficult to prove whether this was specifically indigenous to the Caribbean, until now," Willerslev said in a statement.

Willerslev and his colleagues analyzed a tooth unearthed at Preacher's Cave on the island of Eleuthera in the Bahamas. Radiocarbon dating and strontium isotope analysis indicated that the person to whom the tooth belonged lived about 1,000 years ago and grew up locally.

They sequenced the genome of that individual to 12.4-fold depth using Illumina HiSeq 2500. Based on the number of reads they then mapped to the X and Y chromosomes, they determined the sample came from a woman. They also sequenced the sample's mitochondrial genome and placed it at the root of the Native American haplogroup B2, which is found throughout the Americas.

The researchers compared the ancient Taino genome to 50 other, previously published Native American genomes. Using a number of approaches — including f3-statistics, D-statistics, and principal components analysis — they found that the ancient Taino woman was most closely related to the Palikur and other present-day Arawakan speakers from the Amazon and Orinoco basins. Analysis with the algorithms Admixture and ChromoPainter likewise underscored their similarities and shared haplotypes.

To delve into Taino demographic history, Willerslev and his colleagues examined runs of homozygosity present in the genome they generated as well as in the 12,500-year-old Clovis genome and 53 modern Native American and Siberian genomes. All the Native American genomes, including the Taino genome, harbored evidence of at least one ancestral population bottleneck, which the researchers noted was consistent with the current idea that the Americas were peopled by a small population that was isolated on the Bering land bridge.

The Taino genome included the lowest number of long runs of homozygosity, the researchers noted. This, they said, suggests that the Taino had a relatively large effective population size, which they estimated to be about 1,600 individuals. Because the island of Eleuthera is only about 200 square miles in size, the researchers said that the large effective population size was likely supported by regional movements and networks.

To gauge the level of Taino ancestry among modern Caribbean populations, the researchers focused on the Native American ancestry component of 104 Puerto Ricans from the 1000 Genomes Project.

Using the Admixture tool, Willerslev and his colleagues noted similarities between modern-day Puerto Ricans, Arawakan speakers, and the ancient Taino individual. When they folded in data from additional Native American groups into their analysis, they noted that the Native American ancestry of Puerto Ricans shares more genetic drift with the Taino than with others. Further modeling suggested that the ancestors of the Taino and the ancestors of Puerto Ricans only recently diverged.

A previous study using parent-child trio data from the 1000 Genomes Project likewise uncovered sections of Taino ancestry among modern-day Puerto Ricans.

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