We Still Have Neanderthal Genes—This Is What They’re Doing to Our Bodies

Researchers at a lab in Kyoto have shed new light on the ancient genetic legacy of Neanderthals and how it still shows up in modern biology. Led by Dr. Ako Agata and Dr. Tadashi Nomura from the Kyoto Prefectural University of Medicine, the team used advanced CRISPR gene-editing technology (think of it as a high-tech pair of molecular scissors) to see if a specific gene mutation might have helped shape some of the unique physical traits we associate with Neanderthals. The study, which appeared in the journal BioRxiv, offers some really interesting insights into our evolutionary past and its fingerprints on human biology today.

Fresh tech and methods

The researchers turned to the revolutionary CRISPR tool to introduce a mutation called R1537C into the DNA of mice. This mutation is nestled in the GLI3 gene, a key part of the Hedgehog signaling pathway. Interestingly, this variant was found in both Neanderthals and Denisovans (ancient human relatives whose genetic markers can still be detected in some people today). By tweaking this gene, they hoped to figure out if it played a part in molding some of the anatomical features we link with Neanderthals.

The R1537C change sits in the gene’s C-terminal transactivation domain. Even with the mutation in place, the protein stayed stable and the Hedgehog pathway kept on ticking normally. Instead, the mutation switched up how developmental genes—those that influence bone shape—are controlled.

What we looked for and what we found

The main goal here was to see whether the R1537C variant was behind some of the physical traits typical of Neanderthals. In the experiments, mice with this mutation showed clear skeletal changes. They ended up with wider skulls, fewer vertebrae, and odd rib cage structures (all of which echo Neanderthal anatomy). The team also noticed early hardening of the skull’s suture lines and spine curves similar to scoliosis in these modified mice. Interestingly, these effects varied depending on the mice’s genetic backgrounds, specifically between the C57BL6 and CD-1 strains (different breeds of lab mice). This tells us that while the mutation doesn’t directly mess with the protein’s function, it does tweak other genes involved in bone growth and development.

How this shows up in people and what it might mean over time

The R1537C variant isn’t just a relic of our ancient relatives—it’s also present in modern human populations. Data from the 1000 Genomes Project shows its frequency ranges from 3.7% to 7.7% among Europeans and about 0.8% among Africans. Even though this mutation isn’t very common today, its presence across diverse groups is pretty fascinating. The researchers suggest that stuff like genetic drift (that’s when random shifts in gene frequencies occur, especially in smaller populations like Neanderthals) may have allowed these traits to hang around over the years.

Comparing with neanderthals

When the team stacked their mouse data against fossil records, the results lined up nicely. The skeletal changes in mice—like larger skulls and spine curves akin to scoliosis—mirror many features seen in Neanderthal remains. Fossil studies also point to stronger rib twisting in Neanderthal infants, which backs up what the experiments showed. This study is just one piece of a bigger puzzle aimed at understanding how remnants of Neanderthal DNA still show up in us today. Earlier work has also linked ancient DNA to differences in our immune responses, how we perceive pain, and various brain traits.

Ethics and access to the data

This whole study was done under strict ethical guidelines (approved by an ethics committee) and used CRISPR-Cas12a (a specific gene editing tool) to develop animal models for safely unpacking these complicated gene interactions. In the spirit of keeping things open and friendly for more research down the line, all the data is available on the DDBJ database and Mendeley Data repositories.

This amazing deep dive into our past shows how ancient genetic twists still help shape the unique body features we see today (pretty wild, huh?). With tools like CRISPR and global genetic datasets, we’re piecing together an ever-richer picture of our long, intertwined history with extinct relatives like Neanderthals—and there’s plenty more out there for curious minds to explore.