How interbreeding between early human species changed our DNA

The story of how early humans interbred with other human species begins with the migration of Homo sapiens out of Africa.

Around 60,000 years ago, small groups of modern humans who left the African continent slowly spread into Europe, Asia and other parts of the world.

As they entered regions already lived in by other hominin species, they met groups such as Neanderthals in Europe and western Asia, Denisovans in parts of eastern and southern Asia, and possibly other archaic human groups in Africa and the islands of Southeast Asia.

Rather than removing these groups at once, Homo sapiens mated with them and passed on traits that are still found in people today.

Neanderthals eventually disappeared from most regions around 40,000 years ago, although isolated populations may have survived in areas such as Gibraltar for several thousand years longer, while Denisovans may have lasted longer in isolated areas. 

According to genetic studies, Neanderthals and Denisovans contributed detectable DNA to modern human genomes.

In 2010, researchers from the Max Planck Institute published the first draft of the Neanderthal genome, which came from bones found in Vindija Cave in Croatia.

That study revealed that people of non-African ancestry inherited between 1 and 2 percent of their DNA from Neanderthals.

In regions such as the Middle East, Homo sapiens met and interbred with Neanderthals soon after arriving from Africa, most likely between 50,000 and 60,000 years ago.

The absence of Neanderthal DNA in most Sub-Saharan African groups indicates that these interbreeding events occurred after the ancestors of non-African populations had already left Africa.

Although, later back-migration into Africa may have reintroduced small amounts of archaic DNA, according to some genetic models. 

In a similar way, Denisovans entered the human story when a finger bone and a molar were unearthed in the Denisova Cave in southern Siberia.

In those remains, scientists discovered a genome that was different from Neanderthals and modern humans.

Genetic evidence showed that modern populations from Papua New Guinea, Australia, and parts of East and Southeast Asia carry up to 5 percent Denisovan DNA.

In some regions, those percentages differ depending on the ancestral group, which suggests that there were several interbreeding events involving different Denisovan groups.

In East Asia, people share Denisovan DNA sequences that do not appear in Oceanian groups, which points to separate episodes of mixing over an extended period of time.

Interestingly, some Aboriginal Australian and Melanesian populations retain between 4 and 5 percent Denisovan ancestry, with upper estimates occasionally reaching 6 percent. 

In real terms, this interbreeding have changed how modern humans developed.

Some inherited genes helped people adapt to new climates and environments. For example, Denisovan genetic material gave ancient Tibetans the ability to tolerate low oxygen levels at high altitudes through a variant of the EPAS1 gene.

Meanwhile, Neanderthal DNA included gene types that helped early humans fight new diseases, regulate body temperature, and process fat and sugar differently in colder conditions.

At the same time, some of those same genes increased tendency to develop autoimmune diseases, mood disorders, and other health issues in today’s populations.

As a result, the benefits and drawbacks of archaic DNA remain visible in present-day humans. 

From another region, the preserved jawbone of one individual from Romania gave more information about how recently this mixing happened.

This individual lived around 40,000 years ago and had a Neanderthal ancestor just four to six generations earlier.

These findings show that interbreeding happened more often and in more places than early scientists had expected.

Some of this archaic ancestry may reflect input from now-extinct populations such as those related to Homo heidelbergensis, or possibly from even more different hominin groups. 

In several other cases, scientists detected genetic traces that came from archaic humans who left no known fossils.

These “ghost populations” appear in DNA data but remain unidentified in the archaeological record, with no definitively recognised fossil remains linked to them so far.

Their presence shows that many groups of archaic humans once shared the planet with Homo sapiens, and that interbreeding with some of them left permanent markers in the genomes of modern people.

One notable example emerged in 2018 when scientists sequenced the genome of a girl from Denisova Cave whose mother was Neanderthal and father Denisovan. 

At several archaeological sites, researchers have uncovered layers of artefacts that suggest close contact between Homo sapiens and Neanderthals.

In caves throughout Europe and western Asia, tools, ornaments, and ritualistic objects that were made with similar methods have been found in close succession.

At the Grotte du Renne site in France, Châtelperronian artefacts dating to around 45,000 years ago include pierced animal teeth and pigments possibly made by Neanderthals that might have been influenced by modern human culture, although some scholars debate whether these tools can be definitively attributed to Neanderthals or resulted from mixed layers of occupation.

Some items display evidence of shared craftsmanship or borrowed techniques, which may have spread through contact or cohabitation.

While such artefacts do not unquestionably prove biological interbreeding, they add weight to the idea that cultural exchange accompanied physical interaction. 

As new techniques for analysing ancient DNA become more advanced, the evidence for widespread interbreeding continues to grow.

From the bones and teeth of long-dead individuals, scientists have reconstructed entire genomes and uncovered patterns of movement across regions and different landscapes over time.

Their research also charted reproductive patterns through successive generations and traced how genetic traits passed forward.

In future research, more discoveries may emerge that identify additional species, locate previously unknown regions of contact, or reveal new episodes of hybridisation between human groups.

Taken together, the evidence shows that, rather than replacing all other hominins immediately, early modern humans absorbed parts of their gene pools and carried those traits forward.

These interactions have resulted in our biology in a way that has affected our ability to adapt, and created a human family that still carries traces of other species long vanished from the earth.