Chapter 11 - Fossil and genetic evidence for Neanderthal introgression

Abstract

Until recently, researchers thought that Homo sapiens emerged in East Africa 200kya (thousand years ago), then moved out to populate the rest of the world around 60kya, assuming that signs of earlier travels, including 80ky–120,000-year-old skulls, and other remains from Israel were from failed migrations. Over the last decade, the story has begun to change as the oldest human fossils ever found outside Africa suggest that H. sapiens evolved around 300kya and spread to the Arabian Peninsula around 180kya. Although it is unclear whether the fossils from the Levant represent a brief incursion or a lasting expansion, these discoveries and others inside Africa have changed the original narrative of one successful migration, and have raised the possibility that humans evolved earlier and perhaps elsewhere in Africa. One of the major questions in human evolution is whether introgression occurred between humans and archaic hominins inside and/or outside of Africa. Evidence for human evolution inside Africa suggests that humans evolved in various regions of Africa and most likely introgressed with other hominids, leading to anatomically modern humans (AMHs). Although the origin and timing of migrations of humans out of Africa is still debated, one thing is clear: humans and Neanderthals shared a common African ancestor. The two groups split from their ancient ancestor and evolved in parallel: humans in Africa and Neanderthals in Eurasia. Early evidence for introgression outside of Africa was suggested by several fossils that appeared as intermediate forms between AMHs and Neanderthals or some other hominid species. After the Neanderthal genome was sequenced, comparisons of Neanderthal and non-African genomes suggested that there was introgression with Neanderthals in non-African humans. However, an alternative explanation for Neanderthal DNA sequences in modern humans is that Neanderthal DNA evidence is linked to ancient population structure. This implies that the subdivision in the ancestral population that gave rise to Neanderthals and AMHs may have resulted in some non-African modern humans being more closely related to Neanderthals than other groups that stayed in Africa. Today, the evidence indicates that when humans left Africa, they mated with Neanderthals. As a result, the presence of Neanderthal DNA in the whole-genome sequences of present-day non-African individuals is the consequence of admixture, likely due to limited interbreeding between modern-day and other archaic humans. Today, people who are not of African descent carry about 1%–4% of Neanderthal DNA, some of which can cause a range of health conditions including depression, nicotine addiction, blood clotting, diabetes, susceptibility to disease, and skin disorders. Other segments of Neanderthal DNA appear to be responsible for resistance to disease, pigmentation, hair color, and increased fertility. Several of these genes inherited from Neanderthals are thought to have had a selective advantage when humans left Africa and were confronted with new environmental challenges, including novel foods, pathogens, and a different climate. Understanding the interactions that occurred between Neanderthals and humans is essential for understanding our genetic past and provides insight into the ancestral forces that structured our genome. While introgression from Neanderthals has been documented in humans outside Africa, until recently the contribution of archaic hominins to the genetics of modern-day Africans was unclear. Today, data has shown that archaic introgression occurred in at least four West African populations and that these populations derive 2%–19% of their genetic ancestry from an archaic population that diverged before the split of Neanderthals and modern humans, representing potential targets of adaptive introgression. Evidence has also indicated Neanderthal ancestry in modern-day Africans due to migrations back to Africa. This relatively small amount of DNA arose predominately from ancestral Europeans, and gene flow into Neanderthals from an early dispersing group of humans out of Africa.