Neanderthals did not interbreed with modern humans or contribute DNA to people living today.

For decades, the relationship between Neanderthals and modern humans was argued mainly from bones and archaeology. Ancient DNA promised a more direct answer.

The first successful studies focused on mitochondrial DNA. Mitochondria are structures inside cells that carry a small amount of their own DNA, and that DNA is inherited almost entirely through the maternal line.

Neanderthal mitochondrial DNA fell outside the variation seen in living humans. That result was often taken as evidence that Neanderthals had not contributed to people alive today.

But mitochondrial DNA samples only one narrow line of ancestry. Imagine a Neanderthal woman had children with a modern human population, but after many generations her direct mother-to-daughter line happened to end. Her mitochondrial DNA could disappear even while other parts of her genome remained in descendants.

The larger nuclear genome provided the broader test.

In 2010, researchers published a draft Neanderthal nuclear genome and compared it with genomes from living humans. Many people with ancestry outside sub-Saharan Africa carried DNA segments more closely related to Neanderthals, demonstrating ancient interbreeding.

Individual genomes commonly contain roughly 1–2% Neanderthal-derived DNA, with different fragments preserved in different people. Later migrations also carried some of that ancestry into populations in Africa.

The no-interbreeding view was never universal. What whole-genome data did was reveal gene flow that a single small maternal genetic system could easily miss.