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, 115 (10), 2341-2346

Origins and Genetic Legacies of the Caribbean Taino

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Origins and Genetic Legacies of the Caribbean Taino

Hannes Schroeder et al. Proc Natl Acad Sci U S A.

Abstract

The Caribbean was one of the last parts of the Americas to be settled by humans, but how and when the islands were first occupied remains a matter of debate. Ancient DNA can help answering these questions, but the work has been hampered by poor DNA preservation. We report the genome sequence of a 1,000-year-old Lucayan Taino individual recovered from the site of Preacher's Cave in the Bahamas. We sequenced her genome to 12.4-fold coverage and show that she is genetically most closely related to present-day Arawakan speakers from northern South America, suggesting that the ancestors of the Lucayans originated there. Further, we find no evidence for recent inbreeding or isolation in the ancient genome, suggesting that the Lucayans had a relatively large effective population size. Finally, we show that the native American components in some present-day Caribbean genomes are closely related to the ancient Taino, demonstrating an element of continuity between precontact populations and present-day Latino populations in the Caribbean.

Keywords: ancestry; ancient DNA; archaeology; migration; paleogenomics.

Conflict of interest statement

Conflict of interest statement: H.S. is on the scientific advisory board of Living DNA Ltd, J.R.H. is co-founder of Encompass Bioscience Inc, and C.D.B. is founder of IdentifyGenomics, LLC, and scientific advisor for Personalis Inc, Ancestry.com Inc, and Invitae Inc. This did not affect the design, execution, or interpretation of the experiments and results presented here.

Figures

Fig. 1.
Fig. 1.
The genetic origins of the Taino. The individual from Preacher’s Cave is most closely related to Arawakan and Cariban speakers from the Amazon and Orinoco basins. (A) Heat map of outgroup f3-statistics testing (Yoruba; Taino, X) where X is one of 50 Native American populations (24). Warmer colors indicate higher levels of allele sharing. (B) We computed D-statistics of the form D (Yoruba, Taino; Palikur, X) to test if any other group is more closely related to the Taino than the Palikur. Thick and thin whiskers represent 1 and 3 SEs, respectively. (C) Neighbor-joining tree based on Fst distances. (D) Expected total length (cM) of shared haplotypes between the Taino and 50 Native American groups based on ChromoPainter analysis (26). To avoid the confounding effects of missing data, we ran ChromoPainter (26) on the unmasked dataset. Horizontal bars mark mean values ± SD. For language classification, see SI Appendix, section 1.
Fig. 2.
Fig. 2.
Taino demography. Total estimated length of genomic ROH for the Taino and the Clovis genome (13) and selected Native American and Siberian genomes (15, 31, 32) in a series of length categories. ROH distributions for modern individuals have been condensed into population-level silhouettes (SI Appendix, section 14).
Fig. 3.
Fig. 3.
The genetic legacy of the Taino. (A) Heat map showing the amount of allele sharing between the Native American component in present-day Puerto Ricans, Native Americans, and the Taino. Warmer colors indicate higher levels of allele sharing. (B) Model of Native American population history that fits the patterns of observed allele frequencies in our dataset (max|Z| = 2.6). The Taino and masked Puerto Ricans form a clade that branches off the South American lineage. Branches are colored by language family (SI Appendix, section 1). Drift values are shown in units proportional to FST × 1,000.

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