A mixed expansion model of East Asian agriculture into northern Pakistan: demic via southern route but cultural from the northern

While East Asian agriculture notably impacted northern Pakistan's prehistory, its diffusion model into this region remains unclear. Here we generated 115 high-coverage whole-genome sequencing (WGS) data from three northern Pakistani populations (Burusho (Hunza), Shina, and Hazarewal), and integrated 2,029 modern and 4,358 ancient genomes from Eurasia. Our results revealed genetic input from East Asia into northern Pakistan, which, albeit with small proportions, contributed to shaping the genetic landscape of both ancient and modern populations in this region. We identified two distinct waves of East Asian ancestry into northern Pakistan—one introduced by rice farmers from the Yangtze River Basin ∼4,800 years ago and a second, ∼1,600 years ago, likely introduced by Tibetan Plateau population historical expansions —both via the southern foothills of the Tibetan Plateau. In contrast, our analyses provided no clear evidence of the tested ancestries associated with the northern Inner Asian Mountain Corridor. We thus propose a mixed model of East Asian agricultural dispersal into northern Pakistan, involving demic diffusion along the southern route, with cultural diffusion as a plausible explanation for the northern route.