For decades, the theories about the origin of modern humans were summarized in two main competing models: multiregional evolution or recent replacement from Africa [1, 2]. Genetic studies beginning in the 1980s provided explicit support for a recent origin of modern humans in Africa around 200,000 years ago (ya) [3], followed by an expansion out of Africa around 50,000–60,000 ya and subsequent colonization of the rest of the world [4].

There are hundreds of research papers discussing the out-of-Africa migration using archaeological data, present-day human genetic data or even genetic data from the human microbiome. Most of this work refines the recent replacement model, including suggesting a time-frame for the expansion [5] as well as the number of waves and routes taken by humans in their exit from Africa [4]. A few early studies did propose admixture with archaic humans [6, 7], but alternative interpretations of their examples were usually possible [8]. A major revision of the replacement model was introduced as the result of aDNA research published in 2010, in which DNA was retrieved from three Neanderthal bones from the Vindija Cave in Croatia [9] and from a finger bone found in Denisova Cave in southern Siberia [10]. Analyses of DNA from the archaic humans showed strong evidence of a small amount of gene flow to modern humans, giving rise to a ‘leaky replacement’ model. The initial report was met with some criticism, suggesting that ancient population substructure could produce a genetic signal similar to the one interpreted as introgression from Neanderthals [11] (see Box 2 for more details on the D-statistics relevant to this discussion). However, several later studies using different statistics showed that ancient structure alone cannot explain the introgression signal [12, 13].

Neanderthal ancestry in all present-day non-Africans is estimated to be 1.5–2.1 % [14]. The broad geographical distribution, together with the size of the DNA segments contributed by Neanderthals, suggests that the gene flow most likely occurred at an early stage of the out-of-Africa expansion: around 47,000–65,000 ya [12], before the divergence of Eurasian groups from each other. Sequences from the genomes of ancient Eurasians show that they carried longer archaic segments that have been affected by less recombination than those in present-day humans, consistent with the ancient individuals being closer to the time of the admixture event with Neanderthals. For example, a genome sequence from Kostenki 14 who lived in Russia 38,700–36,200 ya had a segment of Neanderthal ancestry of ~3 Mb on chromosome 6 [15], whereas present-day humans carry, on average, introgressed haplotypes of ~57 kb in length [16]. The genome sequence of a 45,000-year-old modern human male named Ust’-Ishim (after the region in Siberia where he was discovered), shows genomic segments of Neanderthal ancestry that are ~1.8–4.2 times longer than those observed in present-day individuals, suggesting that the Neanderthal gene flow occurred 232–430 generations before Ust’-Ishim lived, or approximately 50,000–60,000 ya [17], narrowing the previous range. Moreover, the Neanderthal-derived DNA in all non-Africans is more closely related to a Neanderthal from the Caucasus than it is to either the Neanderthal from Siberia or the Neanderthal from Croatia [14], providing more evidence that archaic admixture occurred in West Asia early during modern humans’ exit from Africa. It remains unclear how frequent mixture between Neanderthals and modern humans was, or how many Neanderthal individuals contributed; however, a higher level of Neanderthal ancestry in East Asians than in Europeans has been proposed to result from a second pulse of Neanderthal gene flow into the ancestors of East Asians [18, 19]. DNA from a 37,000–42,000-year-old modern human from Romania (named Oase) had 6–9 % Neanderthal-derived alleles, including three large segments of Neanderthal ancestry of over 50 centimorgans in size, suggesting that Oase had a Neanderthal ancestor as a fourth-, fifth- or sixth-degree relative [20]. The Oase population appears not to have contributed substantially to later humans in Europe, but the Oase genome provides direct evidence that multiple mixture events between modern humans and Neanderthals have occurred.

Admixture with Denisovans also occurred, possibly in South-East Asia [21], and affected the ancestors of present-day populations in Oceania, introducing 4–6 % Denisovan ancestry (in addition to their Neanderthal ancestry) in today’s New Guineans, Aboriginal Australians and Bougainville Islanders. A low level (~0.2 %) of Denisovan ancestry is also found across Eastern Eurasia and in Native American populations [14], but it is unclear whether this originated via gene flow from the same mixture event or through a second one. Denisovans themselves appear to have received gene flow from other archaic humans. It has been estimated that at least 0.5 % of the Denisovan genome was contributed by Neanderthals and that 0.5–8 % comes from an unknown hominin who split from other hominins between 1.1 and 4 million ya [14]. This complexity in the history of the archaic humans is also evident in the analysis of the oldest hominin sequenced to date: a 400,000-year-old individual from Sima de los Huesos in northern Spain. Their mitochondrial genome revealed evidence of a common ancestor shared with Denisovans rather than with Neanderthals [22], a finding that is surprising both as the Sima de los Huesos individual lived outside the known Denisovan geographical range and as the fossils carry Neanderthal-derived features. Scenarios to explain these results include gene flow between the different archaic species and/or a structure in the common ancestral population leading to Neanderthals, Denisovans and other Homo species. Future findings will likely show that many of the assumptions reported here were simplified and that, even with aDNA, we still have to invoke Occam’s razor to explain the data: that is, until sufficient human fossils have been sequenced.

aDNA evidence has thus supported the replacement model as an explanation for most human variation, but has transformed and enriched this model in ways not anticipated in the earlier debate: first by discovering Denisovans, whose fossil record currently remains unrecognized, and second by revealing the multiplicity of admixture events, which include at least one that cannot be detected in present-day DNA.