The relationship between modern humans and the archaic populations they encountered during these dispersals has been a major focus of ancient genomics. The initial Neanderthal genome sequencing in 2010 established that non-African modern humans carry approximately 1 to 2 percent Neanderthal DNA—a proportion that is consistent across most non-African populations and reflects admixture that occurred as modern humans dispersed out of Africa and encountered Neanderthal populations in the Middle East or western Asia. Subsequent work refined the timing of this admixture and suggested that the primary Neanderthal-modern human interbreeding event occurred approximately 50,000 to 60,000 years ago, consistent with the genetic signals in living populations.
The Denisovan admixture story is more complex. East Asian populations carry a small amount of Denisovan ancestry, similar in magnitude to the Neanderthal ancestry in non-African populations. But populations in South and Southeast Asia and Oceania—Indigenous Australians, Papua New Guineans, some Philippine groups—carry Denisovan ancestry at levels of 3 to 6 percent, suggesting a more recent or more intense admixture event. The difference in proportion between East Asian and Oceanic populations implies that modern humans encountered Denisovans more than once, in different places, under different circumstances.
One proposed model involves modern humans moving eastward across Asia and encountering Denisovans in multiple waves. The ancestors of East Asian populations interbred with Denisovans once, in Central or East Asia. The ancestors of Oceanic populations interbred with Denisovans again, further south—possibly in Southeast Asia—producing the higher Denisovan ancestry proportion that characterizes those populations today.