Our dense sampling of Asian populations enables the examination of Denisovan admixture in greater detail than has been previously possible, providing information about population splits or in-flows that occurred at or after the time of admixture (Supplementary Information 10). Our estimates of Denisovan ancestry were highest in Melanesians and the Aeta, intermediate in the Ati and groups from the Indonesian island of Flores, and low (but still significantly greater than 0) in most south, east and southeast Asian populations. We found high levels of Denisovan ancestry in Philippine Negrito groups but not in Malay or Andaman Negritos; these results are qualitatively similar to what was found in a previous study that was based on single-nucleotide polymorphism (SNP) arrays23. The high levels of Denisovan ancestry in Melanesians and the Aeta are consistent with an admixture event into a population that is ancestral to both23; however, two lines of evidence suggest that the ancestors of the Aeta experienced a second Denisovan admixture event. First, multiple analyses found that the Aeta are genetically more similar to populations without appreciable Denisovan ancestry (for example,
