Genome sequences are known for two archaic
hominins—Neanderthals and Denisovans—which
interbred with anatomically modern humans as
they dispersed out of Africa. We identified high-confidence
archaic haplotypes in 161 new genomes
spanning 14 island groups in Island Southeast
Asia and New Guinea and found large stretches of
DNA that are inconsistent with a single introgressing
Denisovan origin. Instead, modern Papuans carry
hundreds of gene variants from two deeply divergent
Denisovan lineages that separated over 350
thousand years ago. Spatial and temporal structure
among these lineages suggest that introgression
from one of these Denisovan groups predominantly
took place east of the Wallace line and continued
until near the end of the Pleistocene. A third Denisovan
lineage occurs in modern East Asians. This
regional mosaic suggests considerable complexity
in archaic contact, with modern humans interbreeding
with multiple Denisovan groups that were
geographically isolated from each other over deep
evolutionary time