Population histories of the Indigenous Adivasi and Sinhalese from Sri Lanka using whole genomes

Abstract

Sri Lanka has played a key role in the peopling of South Asia, with archaeological evidence for human presence on the island dating back to ~40,000 years ago. Present-day Indigenous peoples of the island, the Adivasi, are proposed to have descended from early inhabitants of the region, while urban populations like the Sinhalese, the major ethnic group on the island, migrated from India in historical times. Using whole genomes from 19 Adivasi individuals belonging to two clans and from 35 Sinhalese, we find that the Adivasi and Sinhalese share high genetic similarities with each other and with other Sri Lankan and Indian populations, especially those with greater genetic affinity to Ancestral South Indians (ASI). Admixture modeling of the Sri Lankan groups reveals that despite shared ancestral components, the Adivasi retain higher genetic contributions from ancient hunter-gatherers compared with the Sinhalese. Additionally, in contrast to the Sinhalese, the Adivasi have maintained low effective population size and undergone strong founder events, which is consistent with their hunter-gatherer lifestyle, historic relocations, and habitat fragmentation. While the two Adivasi clans are genetically more similar to each other than to any other populations, we observe differing demographic histories, with the Interior Adivasi experiencing a stronger bottleneck than the Coastal Adivasi since their split. This whole-genome-based study addresses gaps in our understanding of the demographic and migratory history of two key Sri Lankan groups and, consequently, of broader South Asia by illuminating complex population structure that has been shaped by both demographic and socio-cultural factors.