Discerning the origins of the negritos, first sundal and people: Deep divergence and archaic admixture

Humanpresence in SoutheastAsiadates back to at least 40,000 years ago,whenthe current islands formeda continental shelf called Sundaland. In the Philippine Islands, Peninsular Malaysia, and Andaman Islands, there exist indigenous groups collectively called Negritos whose ancestry can be traced to the "First Sundaland People." To understand the relationship between these Negrito groups and their demographic histories,we generatedgenome-wide single nucleotide polymorphism data in the PhilippineNegritos and compared themwith existing data from other populations. Phylogenetic tree analyses showthatNegritos are basal to other East and Southeast Asians, and that they diverged fromWest Eurasians at least 38,000 years ago.Wealso found relatively high traces of Denisovan admixture in the Philippine Negritos, but not in theMalaysian and Andamanese groups, suggesting independent introgression and/or parallel losses involving Denisovan introgressed regions. Shared genetic loci between all three Negrito groups could be related to skin pigmentation, height, facialmorphology and malarial resistance. These results show the unique status of Negrito groups as descended from the First Sundaland People.