Homo sapiens may be the last surviving human species, but we were not always alone. For much of our history, we coexisted with other members of our genus, and our prehistoric ancestors engaged in relationships with Neanderthals and Denisovans.
Millennia have passed since then, yet we still carry the consequences of these interactions. Recent advancements in ancient DNA analysis and genome sequencing are allowing scientists to understand how this early genetic mixing continues to shape our health, appearance, and physiology today.
By reviewing existing data on archaic human introgression (the transfer of genetic material from one species into the gene pool of another) in the modern human genome, the authors of a new study explain that as Homo sapiens migrated from Africa in waves, different human populations found themselves in positions to interbreed with Neanderthals in various regions of Eurasia. Consequently, modern individuals exhibit a complex mosaic of introgressive traits inherited from this now-extinct lineage.
Recent work also revealed that Homo sapiens interbred with three distinct Denisovan populations, resulting in all non-African individuals now receiving about 2% of their genome from Neanderthals, while some groups of indigenous people in Oceania possess an additional 2-5% Denisovan DNA.
Investigating how these archaic genes influence us, the authors explain that Neanderthal DNA may have increased the size of our noses, while Denisovan heritage is linked to the width of our lips. This conclusion is based on previous studies indicating that Denisovans likely had narrower lips than the average modern human.
There is also some evidence suggesting that Neanderthal genes may have altered our circadian rhythm, making us more likely to wake up early in the morning.
However, the majority of surviving genetic sequences derived from our extinct relatives are associated with immune system function. The researchers note that this is not particularly surprising, as both Neanderthals and Denisovans would have been better adapted to cope with the types of pathogens in Eurasia than the arriving Homo sapiens from Africa. Thus, interbreeding with local populations allowed our ancient ancestors to acquire beneficial genes that provided protection against infectious microbes, which were then passed on through natural selection.
“However, variants associated with the immune system inherited from archaic hominins that were beneficial for modern humans in these new environments may also contribute to disease susceptibility in contemporary individuals,” the authors state. For example, while one cluster of Neanderthal genes on chromosome 12 appears to provide protection against severe COVID symptoms, another on chromosome 3 may actually increase our susceptibility to the disease.
Meanwhile, an analysis of modern Japanese genomes reveals a link between Denisovan DNA and health conditions such as type II diabetes and coronary artery disease.
Such discoveries have helped unravel the genetic history of our species, yet many gaps remain. For instance, it is still unclear how gene flow between different human species affects the DNA of modern African populations, with some scientists believing that these groups may carry the genetic signature of an unknown “ghost” hominid.
Nevertheless, the authors assert that “recent work continues to provide new insights into the history of gene flow among modern humans, Neanderthals, and Denisovans and clearly demonstrates that admixture has had important functional, phenotypic, and evolutionary consequences for modern humans.”