East Asian and Native American populations carry the most Neanderthal DNA of any modern human groups, with an average of about 54 megabases of Neanderthal sequence per person. That’s roughly 40% more than Europeans, who average about 49 megabases. The difference is consistent across multiple studies using different detection methods, and it traces back to the complex migration history of early humans leaving Africa.
How the Numbers Compare Across Populations
All non-African populations inherited roughly 1 to 4 percent of their DNA from Neanderthals, a legacy of interbreeding that began when modern humans first migrated into Eurasia around 50,000 to 60,000 years ago. But that inheritance isn’t evenly distributed.
East Asian and Native American populations consistently rank highest, carrying about 54.2 megabases of Neanderthal-derived sequence on average. Europeans follow at around 48.7 megabases. South Asians fall slightly below Europeans, and Oceanian populations (including Melanesians and Aboriginal Australians) sit in a similar range to East Asians for Neanderthal DNA specifically, though the difference between these two groups isn’t statistically significant. Sub-Saharan African populations were long thought to carry no Neanderthal ancestry at all, but more recent work has identified roughly 12.9 megabases per person, introduced through ancient back-migrations of Eurasian peoples into Africa.
One common point of confusion involves Melanesian populations, who carry the highest total amount of archaic DNA of any living group: about 104 megabases per person. But much of that comes from Denisovans, a separate group of archaic humans. When you isolate just the Neanderthal portion, Melanesians carry about 49 megabases, putting them closer to Europeans. Their additional 2 to 4 percent Denisovan ancestry is what makes their total archaic DNA so high.
Why East Asians Carry More Than Europeans
This gap puzzled geneticists for years, since Neanderthals lived primarily in Europe and western Asia, not in East Asia. Several explanations have been proposed, and the answer likely involves more than one factor.
One leading hypothesis involves multiple waves of interbreeding. Analysis of the earliest modern human genomes from different archaeological sites shows that while some populations experienced a single interbreeding event with Neanderthals, others show evidence of additional, more recent admixture. The ancestors of East Asians may have encountered Neanderthal populations at different times or places as they migrated eastward, accumulating slightly more Neanderthal DNA with each contact.
Another factor is what happened to Neanderthal DNA after it entered human genomes. Natural selection has been slowly removing Neanderthal variants that were harmful to human health over tens of thousands of years. The rate of this removal may have differed between populations depending on their size. Smaller populations are less efficient at purging mildly harmful genetic variants, so if ancestral East Asian populations went through tighter population bottlenecks during migration, more Neanderthal DNA could have persisted simply by chance. A 2014 genetics study estimated the Neanderthal admixture rate into East Asians was approximately 40% higher than into Europeans, consistent with either additional interbreeding, differential selection, or both.
What Neanderthal DNA Actually Does
Neanderthal DNA isn’t evenly scattered across the genome. It clusters in regions that affect specific biological functions, and some of these inherited variants still influence health today.
The strongest documented effect involves blood clotting. A Neanderthal-derived variant in a gene that produces a protein on the surface of blood vessels and platelets is associated with hypercoagulable states, meaning blood that clots more readily. This variant, found at about 6.5% frequency in European populations, increases the activity of clotting-related genes in arteries. For early humans moving into colder climates with new injury risks, faster clotting may have been an advantage. Today, it contributes slightly to cardiovascular risk.
Neanderthal variants also play a measurable role in skin biology. They influence keratinocyte development (the cells that form the outer layer of skin) and are associated with actinic keratosis, a precancerous skin condition caused by sun exposure. These skin-related variants likely helped early modern humans adapt to the different UV environments they encountered outside Africa.
Immune function is another area shaped by Neanderthal inheritance. Several introgressed gene variants affect how the immune system recognizes and responds to pathogens. Beyond individual traits, researchers have found that Neanderthal variants collectively explain a statistically significant portion of risk for depression (about 2% of variation), heart attack (about 1.4%), and even susceptibility to certain nutritional deficiencies. A Neanderthal variant in a gene involved in thiamine transport is associated with protein-calorie malnutrition, suggesting it may affect how the body processes certain nutrients.
How Scientists Measure Neanderthal Ancestry
Researchers don’t simply line up a human genome against a Neanderthal genome and count matches. The challenge is distinguishing DNA that was inherited through interbreeding from DNA that looks similar because humans and Neanderthals shared a common ancestor hundreds of thousands of years ago.
The main approaches work by scanning the genome for unusual patterns. One method uses machine learning to identify segments that have telltale features of introgression: stretches of DNA that are too long and too similar to the Neanderthal reference genome to be explained by shared ancestry alone. Another approach uses a statistical measure called S* that detects regions with unusually high genetic diversity in strong linkage (meaning the variants travel together through generations), which is a signature of DNA introduced from a separate population. Both methods then verify candidate segments by comparing them directly against a high-quality Neanderthal reference genome.
These tools have become increasingly precise as more Neanderthal genomes have been sequenced, including high-coverage genomes from multiple Neanderthal individuals. That improved reference data is what allowed researchers to identify the previously undetected Neanderthal ancestry in African populations, revising a decades-old assumption that sub-Saharan Africans carried none.
Native Americans and the East Asian Connection
Native American populations carry Neanderthal DNA levels comparable to East Asian groups, which makes sense given their ancestry. The ancestors of Indigenous peoples in the Americas migrated from northeastern Asia across Beringia (the land bridge connecting Siberia to Alaska) during the last Ice Age. They brought their Neanderthal-derived DNA with them, and because they experienced significant population bottlenecks during and after this migration, those variants were preserved at similar or sometimes even slightly higher frequencies than in the source populations they split from.
This is why genetic studies typically group East Asian and Native American populations together when reporting Neanderthal ancestry levels. The two groups share the same interbreeding legacy, filtered through related but distinct population histories.