To shed light on the peopling of South Asia and the origins of the morphological adaptations found there, we analyzed whole-genome sequences from 10 Andamanese individuals and compared them with sequences for 60 individuals from mainland Indian populations with different ethnic histories and with publicly available data from other populations. We show that all Asian and Pacific populations share a single origin and expansion out of Africa, contradicting an earlier proposal of two independent waves of migration1, 2, 3, 4. We also show that populations from South and Southeast Asia harbor a small proportion of ancestry from an unknown extinct hominin, and this ancestry is absent from Europeans and East Asians. The footprints of adaptive selection in the genomes of the Andamanese show that the characteristic distinctive phenotypes of this population (including very short stature) do not reflect an ancient African origin but instead result from strong natural selection on genes related to human body size.

"Both Andamanese (JAR and ONG) populations have a significant amount of Neanderthal introgression (Supplementary Figure 12). The amount is slightly higher than in Europeans, and comparable with other Indian populations. Papuan (PAP) has the highest amount of Neanderthal introgression"

"although AND have shared ancestry with other OOA populations, they (along with other Indian populations, Papuan [PAP], and Aboriginal Australians [AUS]) have ~2-3% fewer African alleles compared to Europeans and East Asians"

"This phenomenon can only be explained by a non-modern human population (hominin) introgression in Andamanese (including Indian) which is still unknown (it is neither Neanderthal nor Denisova)"

"We have similar results with most of other Indian populations."