Illustration of a human and Neanderthal skull side by side.
Illustration of a human and Neanderthal skull side by side.

Mutation Linked to Difference Between Human and Neanderthal Brains

A single amino acid substitution in a protein causes increased neuron production in the frontal lobes of humans compared to Neanderthals—a tiny difference that could have given our species a cognitive edge, researchers say.

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Dan Robitzski

Dan is a Staff Writer and Editor at The Scientist. He writes and edits for the news desk and oversees the “The Literature” and “Modus Operandi” sections of the monthly TS Digest and quarterly print magazine. He has a background in neuroscience and earned his master's in science journalism at New York University.

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Sep 9, 2022


Even though modern humans are highly similar to our ancient Neanderthal cousins, there are some key differences between us—most notably, more neuron-packed frontal lobes. Now, researchers have identified a possible genetic trigger that led to increased neuron production in that brain region, which is associated with higher-level cognition as well as impulse control and emotional regulation: a mutation that ultimately alters metabolism in cells that become neurons.

The research, published yesterday (September 8) in Science, finds that the modern human and the archaic Neanderthal versions of the gene that codes for the protein transketolase-like 1 (TKTL1) differ by just one base pair. That point mutation in TKTL1 means that the Neanderthal version of the protein has a lysine where the modern human version has an arginine. After conducting experiments with fetal human neocortex tissue, mouse and ferret models, and engineered human brain organoids, the researchers behind the study conclude that the mutated gene’s behavior may explain humanity’s neuron-rich brains and could point to humans having a higher intellect than Neanderthals.

See “Human-Specific Genes Implicated in Brain Size

The study is unique and particularly well-executed, says Carol Marchetto, a neural evolution researcher at the University of California, San Diego, who didn’t work on the study. “What is quite amazing is that it’s only one amino acid substitution that can make a lot of change. . . . I find it really fascinating when this happens. We’re not even talking about knocking out or knocking down the gene.”

What the experiments collectively show is that the solitary lysine-to-arginine substitution in TKTL1 leads to an increase in the production of basal radial glia—neural progenitor cells that, during embryonic development, divide asymmetrically to produce more of themselves as well as most of the neurons in the frontal lobes. Having more of these glia in turn resulted in more neurons developing in the area. While there aren’t any Neanderthals around to recruit for cognitive tests, experts tell The Scientist that the increased neuron count in modern human brains could indicate that our subspecies developed greater cognitive abilities, though the relative intelligence of humans and Neanderthals is subject to substantial debate.

How do you study the Neanderthal brain?

Study coauthor Anneline Pinson, a neuroscientist at the Max Planck Institute of Molecular Cell Biology and Genetics in Germany, explains that they relied on existing genomic data for Neanderthals. Wieland Huttner, in whose lab Pinson works, explains that they focused on TKTL1 because it’s known to be expressed in neural progenitor cells, which the lab has a history of studying.

“Because we cannot have Neanderthal brains, the way to look at it was to study the difference between amino acid composition between [the two],” Huttner says.

Microscopy image of a brain cell called a basal radial glia, stained pink
Microscopy picture of a dividing basal radial glial cell, a progenitor cell type that generates neurons during brain development

For instance, the lab previously found that humans and Neanderthals have a point mutation in another gene, called ARHGAP11B, which increases both neocortex size and brain folding when introduced into nonhuman primates, potentially explaining why hominins have larger brains than other apes. In the current study, Pinson designed several experiments to probe both the overall function of TKTL1 as well as the effects of the lysine-to-arginine substitution.

Starting with embryonic mice, the team induced the overexpression of both forms of TKTL1, analyzing the results four days later. “This is where we first saw the abundance of basal radial glia—but not in the Neanderthal version,” Pinson says. The team then ran the same test on ferrets, the brains of which more closely resemble a primate’s because they have folds and “have more basal radial glia to start with,” she adds. Once again, the human version of the gene yielded a greater increase in the progenitor cells, which in turn resulted in enhanced neurogenesis when compared with ferrets given the Neanderthal version and controls.

See “Neanderthal DNA in Modern Human Genomes Is Not Silent

The team then experimented on human tissue, conducting an ex vivo knockout experiment on fetal human neocortical tissue, using CRISPR-Cas9 to disrupt TKTL1 expression before culturing the tissue for three days. The gene-edited tissue had a reduced abundance of the progenitor cells, further clarifying the human gene’s role in neurogenesis. Finally, the team engineered human brain organoids to express either the human or Neanderthal version of the gene, making sure there were no other differences between the two.

“It’s a beautiful approach to look at, in a very targeted fashion, a single gene and a single change,” says University of Cambridge neuroscientist Madeline Lancaster, who didn’t work on the study.

See “Gene-Edited Organoids Explore Neanderthal Brain Function

As with the animal models, organoids expressing the human gene produced more basal radial glia and more neurons, strengthening the case for a causal relationship between the mutation and increased neurogenesis in humans. The data, however, show that some of the measured effects were subtle, which Lancaster says “matches with what we might expect,” adding that “Neanderthals were actually very smart. . . . The fact that we interbred with them means they must have some level of intelligence that was actually similar [to humans].”

But a subtle effect is an effect nonetheless, says Lancaster. “I was particularly impressed with the amount of work that went into this and the thoroughness of it. This kind of work warrants that care and diligence. I think that the combination of so many different model systems really strengthens the argument.”

The multitude of experiments “is definitely convincing to me that this single amino acid mutation is definitely changing the cell function,” says Marchetto. “I think it is an interesting hypothesis to consider that . . . could have been involved in changes to brain size.”

How does one gene remold the brain?

The new study indicates that TKTL1 is involved somehow in the metabolism of brain cells, specifically when it comes to the process of neural proliferation. However, the exact metabolic pathways by which it acts remain unclear. “We don’t know exactly what’s downstream or upstream,” Pinson says.

Lancaster offers that further organoid research could help reveal those mechanisms in the future, as doing so would allow researchers to also tinker with other genes or other factors that differ between humans and Neanderthals, perhaps revealing how the behavior of one influences another.

See “‘Minibrains’ May Soon Include Neanderthal DNA

Marchetto says it would be interesting to engineer tissue or an organoid with all of the known changes between the human and Neanderthal genome, which would result in the nearest possible approximation of an archaic neuron. She adds that single-cell analyses probing the mitochondrial activity or bioelectric output of a human versus an archaic neuron might reveal some of those mechanistic details as well.

“That would be interesting to see, studying the combinatorial effect of those mutations,” Marchetto says. But, not wanting to detract from the new findings, she adds that “I think it’s very relevant to study single genes. . . . They did a great job with that. It’s an important finding in the field, definitely.”