People who sign up for genetic testing from companies like 23andMe can find out how much of their DNA comes from Neanderthals. For those whose ancestry lies outside Africa, that number usually falls somewhere between 1 percent and 2 percent.

Scientists are still a long way from understanding what inheriting a Neanderthal gene means to people. Some Neanderthal genes may be helpful — improving our defenses against infections, for example — but other bits may leave carriers slightly more prone to certain diseases.

On Thursday, a team of scientists revealed that two pieces of Neanderthal DNA may have another effect: They may change the shape of our brains.

The study, published in the journal Current Biology, wasn’t designed to determine how Neanderthal genes influence thought — if they do so at all. Instead, the value of the research lies in its unprecedented glimpse into the genetic changes influencing the evolution of the human brain.

“This study is surely a milestone,” said Emiliano Bruner, a paleoanthropologist researcher at Spain’s National Research Center on Human Evolution, who was not involved in the research.

Neanderthals and modern humans are evolutionary cousins whose ancestors diverged about 530,000 years ago, possibly somewhere in Africa. Neanderthals left Africa long before modern humans, and their bones were found across Europe, the Near East, and even Siberia.

Before they disappeared about 40,000 years ago, Neanderthals left behind signs of sophistication: spears used to hunt big game, for instance, and jewelry made of shells and eagle talons.

Yet scientists still wonder just how much like us these cousins were. Did they speak a full-blown language? Did they think in symbols?

One thing is clear: They were not short on brains. By measuring the volume inside Neanderthal skulls, researchers have found that their brains were as big as ours, on average, perhaps bigger.

But their brains did not mimic ours. “We have roundish brains,” said Philipp Gunz, a paleoanthropologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. “All other human species have elongated brain cases.”

Dr. Gunz and his colleagues study CT scans of fossil skulls to track brain evolution. As it turns out, the oldest skulls of modern humans, dating back 300,000 years, held elongated brains — more like those of Neanderthals than our own.

Skulls from about 120,000 years ago show that brains had gotten somewhat rounder by then, but were still outside the range observed in people today.

But there’s a gap in the fossil record after that period; the next oldest skulls that Dr. Gunz and his colleagues have studied are just 36,000 years old. These have the distinctive roundedness of living humans.

Modern human skulls got rounder because certain regions of the brain changed size. At the back of the brain, for example, a part called the cerebellum dramatically expanded.

A Neanderthal skull, left, and a modern human skull. Video by Philip GunzCredit

Dr. Gunz and his colleagues wondered what sort of genetic changes drove this shift. It occurred to them that an answer might be found in a natural experiment that took place about 60,000 years ago: the interbreeding of modern humans and Neanderthals.

As they left Africa, modern humans encountered and mated with Neanderthals, producing healthy children who inherited a set of chromosomes from each parent. Neanderthal DNA has persisted through the generations in people of non-African descent.

Did Neanderthal genes affect the shape of modern human brains? The effect of any one gene would be exquisitely subtle, and so Dr. Gunz and his colleagues needed to compare a lot of brains to find it.

Fortunately, a number of scientific teams had already begun building databases of brain scans and DNA from volunteers.

Dr. Gunz’s team studied 4,468 people in the Netherlands and Germany. They searched the DNA of the volunteers for over 50,000 common genetic markers inherited from ancient Neanderthals.

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Then the researchers compared the shapes of people’s brains to see whether any Neanderthal gene variants were associated. Two genetic markers jumped out: People who carry them have unusual patterns of gene activity in their brains.

One marker is linked to a gene called PHLPP1. It’s unusually active in the cerebellum of people who carry the Neanderthal version. This gene controls the production of an insulating sleeve that wraps around neurons. Known as myelin, it is crucial for long-range communication in the brain.

The other marked is linked to a gene called UBR4, which in carriers is less active in a region deep in the brain called the putamen. UBR4 helps neurons divide in the brains of children.

These findings suggest that PHLPP1 and UBR4 evolved to work differently in modern human brains. The modern human version of PHLPP1 may have produced extra myelin in the cerebellum. And our version of UBR4 may have made neurons grow faster in the putamen.

Why these changes? Simon Fisher, a co-author of the new study at the Max Planck Institute for Psycholinguistics in the Netherlands, speculated that modern humans evolved more sophisticated powers of language. They may have also become better at making tools.

“Things like tool use and speech articulation are hugely dependent on motor circuitry,” said Dr. Fisher.

Both require the brain to send fast, precise commands to muscles. And it may be no coincidence that the cerebellum and putamen are crucial parts of our motor circuitry — the very regions that helped change the overall shape of the modern human brain.

What does this research mean for people who carry the Neanderthal versions of these brain-shaping genes? There are limits to what genetics can tell us, said John Anthony Capra, an evolutionary biologist at Vanderbilt University who was not involved in the study.

It’s very hard to predict people’s behavior from their genes, he noted — let alone try to account for a few Neanderthal genes. To learn what they are doing in the brain will require that scientists discern very faint signals amid the noise of the human genome.

“That’s a long way off, if ever possible,” Dr. Capra said.

Recent reporting on Neanderthal research
Deep in Human DNA, a Gift From the Neanderthals

A Blended Family: Her Mother Was Neanderthal, Her Father Something Else Entirely

Neanderthals, the World’s First Misunderstood Artists