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We developed a method,  ArchaicSeeker 2.0 , to identify introgressed hominin sequences and model multiple-wave admixture. The new method enabled us to discern two waves of introgression from both Denisovan-like and Neanderthal-like hominins in present-day Eurasian populations and an ancient Siberian individual. We estimated that an early Denisovan-like introgression occurred in Eurasia around 118.8–94.0 thousand years ago (kya). In contrast, we detected only one single episode of Denisovan-like admixture in indigenous peoples eastern to the Wallace-Line. Modeling ancient admixtures suggested an early dispersal of modern humans throughout Asia before the Toba volcanic super-eruption 74 kya, predating the initial peopling of Asia as proposed by the traditional Out-of-Africa model. Survived archaic sequences are involved in various phenotypes including immune and body mass (e.g.,  ZNF169 ), cardiovascular and lung function (e.g.,  HHAT ), UV response and carbohydrate metabolism (e.g.,  HYAL1/HYAL2/HYAL3 ), while “archaic deserts” are enriched with genes associated with skin development and keratinization.

Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0