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Ancient DNA Analysis Sheds New Light on Origin of Caribbean Populations

NEW YORK – The Caribbean was first settled by people related to Central and northern South Americans, a new analysis of ancient DNA has found.

Humans first settled the Caribbean about 6,000 years ago and a previous study of ancient DNA has suggested there were multiple waves of migration into the region from North and South America. 

But the new study, which analyzed genomic data from more than 170 ancient individuals from the Caribbean, instead only found evidence of ancestry stemming from Central and South America during the Archaic Age. At the same time, the researchers also found that those Archaic Age lineages were then largely replaced by a ceramic-using population related to northeast South Americans, as they reported Wednesday in Nature.

In an email, co-senior author Alfredo Coppa from Sapienza University of Rome, noted that his group had suspected that the Archaic Age population was replaced in the Ceramic Age based on an analysis of dental morphology, and that this ancient DNA data is "a very solid confirmation" of that theory.

He and his colleagues generated genome-wide data for 174 ancient individuals from The Bahamas, Haiti, the Dominican Republic, Puerto Rico, Curaçao, and Venezuela who lived between 3,100 and 400 years ago. The Archaic Age, marked by the use of stone tools, lasted until the Ceramic Age, which began between 2,300 and 2,500 years ago.

In principal component and admixture analyses, the Ceramic- and Archaic-associated individuals formed their own clusters, while ancient Venezuelans clustered with modern-day Chibchan-speakers.

Based on allele-sharing, the researchers identified three major clades — the Greater Antilles Archaic, the Caribbean Ceramic, and the Venezuelan Ceramic — and a number of subclades. For instance, within the Caribbean Ceramic clade, there was a southeast coast Dominican Republic Ceramic group, a Bahamas-Cuba Ceramic group, as well as further population substructure.

The Greater Antilles Archaic clade shared the most genetic drift with Indigenous groups from Central and northern South America, particularly speakers of the Arawakan, Cariba, Chibchan, Chocoan, Guajiboan, Mataco-Guaicuru, and Tupian language families.

The researchers could not, however, replicate a previous finding that some Archaic Age Caribbean individuals harbored ancestry similar to that of North American populations. Instead, their findings pointed to a single source for Archaic-related Caribbean ancestry. "We find no support for ancestry contributed by a population related to North American individuals," Coppa wrote in an email.

These Archaic Age Caribbean populations, though, were largely replaced in the Ceramic Age. The Ceramic-associated people of the Greater Antilles and The Bahamas only had between 0.5 percent and 2.0 percent Archaic-related ancestry. Instead, a new, genetically homogenous population with ancestry related to Arawak language family-speakers spread from the Lesser Antilles to the Greater Antilles about 1,700 years ago. This ancestry remains in the region today, the researchers added, as present-day Puerto Ricans and Cubans have about 14 percent Ceramic-related ancestry.

At the same time, the researchers' findings provide insight into ancient social structure and demographics of the region. They suggested that the Caribbean populations were interconnected, as they uncovered shared haplotypes across islands as well as male relatives who lived more than 45 miles apart on Hispaniola.

Coppa and his team plan to next examine the population dynamics of the Leeward Antilles, as well as search for additional samples to identify the Central and South American populations that may have contributed to the Archaic Age populations' ancestry.