The history of the human family is complex, involving multiple groups of early humans. Neanderthals, an extinct group of archaic humans, inhabited Europe and Western and Central Asia for hundreds of thousands of years, appearing around 400,000 years ago and disappearing roughly 40,000 years ago. Their existence overlapped with the dispersal of early modern humans, Homo sapiens, out of Africa and into Eurasia. Genetic evidence confirms that these two groups interbred, resulting in a permanent genetic exchange. This ancient admixture event, likely occurring between 45,000 and 50,000 years ago in Western Eurasia, explains why the Neanderthal genetic signature persists in the modern human genome today.
The Legacy of Admixture
The genetic contribution from Neanderthals is not uniform across the global human population but follows a distinct geographical pattern. The vast majority of people with ancestry outside of Africa carry a measurable percentage of Neanderthal DNA, typically ranging from 1% to 4% of their total genome.
This presence is a direct consequence of interbreeding that occurred after modern humans migrated out of Africa. Populations whose ancestors remained in sub-Saharan Africa generally have little to no Neanderthal DNA. Studies show that East Asian populations tend to carry a slightly higher mean percentage than European populations. Although any single individual carries only a small percentage, combining the DNA of all modern non-Africans reveals that approximately 20% of the entire Neanderthal genome survives scattered across the human gene pool.
Neanderthal Traits in Modern Humans
The segments of Neanderthal DNA that were retained provided an evolutionary advantage to early modern humans encountering new environments outside of Africa. Many common Neanderthal-derived gene variants relate to skin, hair, and keratin production. These genes likely helped Homo sapiens adapt to the colder climates and different levels of sunlight exposure in Eurasia.
The immune system was also impacted by this genetic exchange. Neanderthal genes contributed to the human leukocyte antigen (HLA) complex, which helps the immune system fight off new pathogens. While beneficial for adapting to local infectious diseases, this archaic DNA also has less favorable effects. Neanderthal variants are associated with sun-induced skin lesions and a higher risk for conditions like hypercoagulation, or increased blood clotting.
Researchers have also linked Neanderthal DNA to various neurological and behavioral traits. Specific genetic segments influence the risk for developing depression, a propensity for nicotine addiction, and variations in sleep patterns. These associations highlight the subtle influence of this archaic DNA on the health and biology of present-day humans.
Purged DNA and Incompatible Genes
Despite the beneficial traits that persisted, a significant portion of the Neanderthal genome was removed from the modern human gene pool. This process, known as negative selection, eliminates genetic variants detrimental to an organism’s fitness. Areas where Neanderthal DNA is virtually absent are referred to as “Neanderthal deserts.”
A striking example of this purging is found on the X chromosome, which shows a five-fold depletion of Neanderthal ancestry compared to the rest of the genome. This pattern suggests that interbreeding produced hybrid offspring with reduced fertility or viability, particularly in males, since genes related to male fertility are enriched in these desert regions. Because Neanderthals had a smaller population size, mildly disadvantageous variants could persist, but once transferred to the much larger modern human population, these variants were efficiently selected against and removed.
How Scientists Reconstructed the Past
Quantifying and understanding the legacy of Neanderthal DNA is a recent scientific achievement, made possible by advancements in ancient DNA analysis. Geneticist Svante Pääbo pioneered the foundational work, developing techniques to extract and sequence highly fragmented and contaminated ancient DNA (aDNA) from fossil remains. Pääbo’s team successfully published a preliminary version of the complete Neanderthal genome in 2010, marking a breakthrough in paleogenomics.
This achievement relied on high-throughput sequencing technology, which allowed scientists to read millions of short DNA fragments simultaneously. After creating this high-quality reference genome, researchers used sophisticated computational methods to compare the Neanderthal sequence with the genomes of thousands of modern humans. By identifying specific genetic variants unique to Neanderthals and tracking their presence, scientists could precisely map the location, measure the percentage, and determine the functional consequences of the ancient genetic material.