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. Methods We analyzed genome-wide SNP data from 176 individuals across eight occupational communities in four districts, alongside 158 global and Indian populations and diverse ancient genomes. Population history, including ancestral migration routes, population structure, demography, admixture, and founder effects, was elucidated using diverse population genetic statistics. Thar groups occupy an intermediate position on the Indian north south cline. Pastoralists and artisans (woodcarvers, Persian gold embosser) clustered with West Eurasian lineages, while potters and performers aligned with southern clines. Uniparental data confirmed heterogeneous Indian lineages. Signals of gene culture was evident the lactase persistence allele was higher in pastoralists but lower in gold embossers despite shared ancestry. Noteworthy, the populations retains a high frequency of the European allele of SLC24A5 associated with lighter skin pigmentation despite the desert environment. Demographic analyses indicate admixture 60 to 80 generations ago and strong founder effects in certain groups, particularly tie and dye artisans approx 500 to 600 years ago. Ancient DNA 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 its craft and pastoral communities, this study reveals how ecology and endogamy intersect with population history to generate a unique genetic landscape. These findings provide essential context for studying genetic risk, adaptation, and human resilience in extreme environments.