First Lithic Age Caribbean genomes document pre-Ceramic genetic continuity and affinities to Central America and northern South America.

The population history of the Caribbean's first inhabitants has been challenging to reconstruct because few human remains are known from the region's earliest occupation which began around 6,000 years ago in Hispaniola, Cuba, and Puerto Rico. We generated genome-wide data from 19 individuals from Hispaniola's Samaná Peninsula and focused on four who lived during the earliest pre-Ceramic "Lithic Age". Extending the Caribbean genetic record by more than a millennium to ~4,400 calBP, we show that pre-Ceramic Age populations across Hispaniola and Cuba derive from a single ancestry source and document long-term genetic continuity across islands, with some local genetic structure within Hispaniola. Pre-Ceramic Age Caribbean ancestry shares most drift with populations from Central America and northern South America, although no sampled mainland group provides an adequate proxy. We infer very small effective community sizes, consistent with locally structured mating pools and little evidence of close-kin mating. These findings extend our understanding of Caribbean population history into its earliest phase.