The question of human origins has intrigued scientists ever since Darwin first proposed the theory of evolution. Historically, most of the debate has focused on two competing hypotheses: the out of Africa (OOA) theory (Figure 1a) and the multi-regional theory (Figure 1b). The OOA hypothesis posits that anatomically modern humans first evolved in Africa 200,000 to 150,000 years ago and then migrated out of Africa 100,000 to 60,000 years ago, displacing other archaic hominins, and giving rise to all current human populations. The multi-regional theory suggests that archaic hominins spread out of Africa much earlier, and that humans then evolved from this Eurasia-wide population, with some degree of interbreeding, and thus gene flow, among individuals from different populations being responsible for the degree of genetic differentiation between populations we currently observe. Mitochondrial (mt) DNA data first reported in 1987 and subsequent analyses of autosomal DNA seemed to support the OOA hypothesis.

Figure 1 Human origins. Each panel shows a hypothesis for the evolutionary history of humans. The colored bars show the phylogenetic relationships between species, with each color representing a species and blue representing the ancestral hominin species. Arrows represent gene flow, or admixture, with question marks to indicate possible admixture from as yet undiscovered hominins. (a) The Out of Africa (OOA) hypothesis; (b) the multiregional hypothesis; (c) a modification of the OOA hypothesis to include the archaic admixture inferred from recent work. Full size image

However, even before the publication of the Neanderthal genome, analyses of modern human DNA from different geographic sources by Jeffrey Wall and others had suggested that, contrary to the earlier consensus, anatomically modern humans evolved in Africa recently, but admixed with endemic archaic hominids - Neanderthals, Denisovans, or even Homo erectus - as they spread throughout the world (Figure 1c), and that ancestral admixture may be much more common than previously thought.

Wall et al. based their analysis on the pattern of haplotype lengths. After controlling for other confounding factors, such as demographic history and recombination rate variation, they concluded that the observed lengths of these regions could only be accounted for by archaic admixture on the order of 5%. The evidence of admixture from Neanderthal and Denisovan nuclear DNA lends credence to these claims.