Genetic analysis of ancient DNA suggests that when Neanderthals and Homo sapiens interbred, the majority of Neanderthal ancestry in modern humans came through male Neanderthals mating with female Homo sapiens, a new study reveals.
Researchers at the University of Pennsylvania reached this conclusion by examining the amount of modern human DNA present on the X chromosomes of Neanderthals. The study, published Thursday in the journal Science, found a significantly lower proportion of Neanderthal DNA on the X chromosome compared to other chromosomes, indicating a pattern of mating preference. “It allows us to say something about the social behaviour of these ancient populations,” said Sarah Tishkoff, professor of genetics and biology and head of the lab that conducted the analysis.
The findings challenge previous assumptions about the nature of interbreeding between the two species, which occurred over tens of thousands of years as Homo sapiens migrated out of Africa and encountered Neanderthal populations in Europe and Asia. While it was previously known that interbreeding occurred, the directionality of those pairings had remained unclear. A separate study published by Reuters on February 26, 2026, also points to this pattern, confirming that Neanderthal men and Homo sapiens women were more likely to interbreed.
The lower presence of Neanderthal DNA on the X chromosome suggests that Neanderthal males may have been less successful at passing on their X chromosomes to subsequent generations. Scientists theorize this could be due to a variety of factors, including potential incompatibilities between the Neanderthal X chromosome and the genetic makeup of female Homo sapiens. The study did not attempt to determine the reasons behind this mating bias, but researchers suggest it could be linked to social preferences or biological factors.
The research builds on the 2010 discovery that early humans and Neanderthals interbred, a finding that revolutionized the understanding of human origins. Geneticists estimate that most people of non-African descent carry between 1% and 4% Neanderthal DNA, a genetic legacy of these ancient encounters. A report in CNN noted that the uneven distribution of Neanderthal ancestry across the genome has long been a puzzle for scientists.
Researchers acknowledge that determining the precise dynamics of these prehistoric relationships is challenging. The study focused on analyzing ancient Neanderthal DNA alongside the genomes of modern-day Africans, who have limited Neanderthal ancestry, to provide a baseline for comparison. The findings offer a new perspective on the complex interactions between Neanderthals and Homo sapiens, suggesting that social dynamics played a significant role in shaping the genetic landscape of modern humans.
The University of Pennsylvania team plans further research to investigate the potential biological mechanisms underlying the observed mating patterns. The study does not address interbreeding with other hominin species, such as Denisovans, with whom both Neanderthals and Homo sapiens also interbred.
