Layers in the sand: The genetic imprint of migration, culture, and Indus craft in the Thar desert

The Thar Desert of northwest India, despite its harsh ecology, has sustained settlement of ancient crafts and pastoral communities. Their persistence provides a unique opportunity to study how migration, ecology, and culture have shaped genetic diversity. We analyzed genome-wide SNP data from 176 individuals across eight occupational communities along with global, Indian populations and diverse ancient genomes. Population history, ancestral migration, population structure, demography, admixture, and founder effects were elucidated using diverse population genetic statistical methods. The Thar groups occupy an intermediate position on the Indian north–south cline. Pastoralists and artisans (woodcarvers and Persian gold embossers) with West Eurasian lineages, while potters and performers align with southern clines. Uniparental data confirmed heterogeneous Indian lineages. Gene-culture was evident from the lactase persistence allele being higher in pastoralists but lower in gold-embossers despite shared ancestry. Noteworthy, the populations retain a high frequency of the SLC24A5 allele, associated with lighter skin pigmentation in Europeans, despite the desert environment. Demographic analyses indicate admixture of 60–80 GBP and strong founder effects in certain groups, particularly tie-and-dye and Persian migrant artisans ∼500–600 years ago. aDNA comparisons confirmed continuity with Indus-periphery and historical South Asian populations. The genetic landscape of the Thar is a palimpsest shaped by successive layers of settlement, migration, and cultural continuity. By establishing the first genomic baseline of Thar’s craft and pastoral communities, this study shows how ecology and endogamy with population history shape distinct genetic landscapes. These findings provide essential context for studying genetic risk, adaptation, and human resilience in extreme environments.