Neanderthal & Denisovan DNA Is Found in Autosomal DNA, Not in Y-Chromosome or Mitochondrial DNA

Modern humans once shared the Earth with other kinds of humans, our archaic cousins, the Neanderthals and Denisovans. Though extinct, fragments of their DNA live on in many of us, subtly shaping who we are today.

Neanderthals (Homo neanderthalensis) lived across Europe and western Asia for over 350,000 years. Adapted to Ice Age climates, they had robust builds, large brains, and sophisticated tools. Far from the brutish stereotype, they buried their dead, made symbolic art, and may have had language.

In 2010, Svante Pääbo’s team at the Max Planck Institute sequenced the Neanderthal genome from remains in Vindija Cave, Croatia, revealing that Neanderthals interbred with modern humans. As a result, most non-Africans carry about 1-2% Neanderthal DNA.

This inheritance influences modern traits such as skin tone, immune response, and disease susceptibility. Some variants aided adaptation to cold or pathogens, while others increased risks for conditions like depression or nicotine addiction.

Denisovans, unlike Neanderthals, were unknown until DNA from a finger bone found in Siberia’s Denisova Cave in 2010 revealed a new human lineage. Sequencing in 2012 showed Denisovans diverged from Neanderthals around 400,000-500,000 years ago. Though their fossils are scarce, their genes survive—especially in Southeast Asian, Oceanian, and Indigenous Australian populations, where Denisovan ancestry can reach 5-6%.

A 2018 study by Browning showed at least two separate Denisovan interbreeding events, and DNA from a 34,000-year-old individual in Mongolia confirmed Denisovan ancestry in East Asians. Neanderthals and Denisovans also interbred with each other; in 2018, scientists identified a first-generation hybrid, born to a Neanderthal mother and a Denisovan father.

These encounters shaped human survival. Archaic genes helped modern humans adapt to new climates and diseases. For example, a Denisovan-derived gene, EPAS1, enables Tibetans to thrive at high altitudes by enhancing oxygen efficiency.

Yet no Neanderthal or Denisovan Y-chromosome or mitochondrial DNA (mtDNA) survives in modern humans, only autosomal DNA remains.

Several factors explain this:

Genetic Drift: Y-chromosome and mtDNA lineages, inherited clonally, may have disappeared over time through chance loss.

Natural Selection: Archaic Y or mtDNA may have carried harmful mutations, removed by selective sweeps.

Sex-Biased Gene Flow: Interbreeding likely involved mostly archaic males and modern human females, meaning offspring inherited modern mtDNA. Over generations, archaic maternal lines vanished.

Low Interbreeding Rates: Models suggest admixture was rare-perhaps one pair every 70+ generations-reducing the odds of archaic uniparental DNA persisting.

Demographic Bottlenecks: Population crashes may have further erased these rare lineages.

Ancient DNA confirms that Neanderthal and Denisovan mtDNA and Y sequences differ from ours, indicating no direct lineage continuity.

Adding to this complexity, Rogers (2020) found evidence that Denisovans inherited DNA from an even older “super-archaic” group-meaning our genomes carry echoes of species even more ancient.

Together, these findings reveal that:

• Modern humans absorbed Neanderthal and Denisovan DNA that still influences us.

• Autosomal DNA preserves this legacy through recombination.

• Uniparental markers, inherited without recombination, were more easily lost.

The traces of Neanderthals and Denisovans in our genomes are not evolutionary accidents, they’re part of what made us human. Our species emerged not as a pure lineage, but as a mosaic of ancient encounters that left enduring genetic signatures.

The persistence of archaic DNA is a living connection to deep time, a testament to survival, adaptation, and the intertwined story of humanity.