In recent years, scientists have figured out how to grow blobs of hundreds of thousands of living human neurons that look and act like something like a brain.

These so-called brain organoids have been used to study how brains develop into layers, how they spontaneously generate electrical waves, and even how this development might change in weightlessness. Now researchers are using these pea-sized clusters to explore our evolutionary past.

In a study published Thursday, a team of scientists describes how a gene likely carried by Neanderthals and our other old cousins ​​caused remarkable changes in the anatomy and function of brain organoids.

As dramatic as the changes are, scientists say it is too early to know what these changes will mean for the development of the modern human brain. “It’s more of a proof of concept,” said Katerina Semendeferi, co-author of the new study and evolutionary anthropologist at the University of California at San Diego.

To build on these findings, she and her co-author, Alysson Muotri, founded the UC San Diego Archealization Center, a group of researchers focused on studying organoids and making new ones using other ancient genes. “Now we have a beginning and we can begin exploring,” said Dr. Semendeferi.

Dr. Muotri began working with brain organoids more than a decade ago. To understand how Zika causes birth defects, for example, he and his colleagues infected brain organoids with the virus, which prevented the organoids from developing their cortex-like layers.

In other studies, researchers looked at how genetic mutations lead to disorders like autism. They transformed skin samples from volunteers with developmental disorders and transformed the tissue into stem cells. They then grew these stem cells into organoids of the brain. Organoids from people with Rett syndrome, a genetic disorder that leads to intellectual disability and repetitive hand movements, grew few connections between neurons.

Dr. Semendeferi used organoids to better understand the evolution of the human brain. In previous work, she and her colleagues found that in monkeys, neurons that develop in the cerebral cortex stay close together, while in humans, cells can crawl over great distances. “It’s a very different organization,” she said.

However, these comparisons span a wide gap in evolutionary time. Our ancestors split off from chimpanzees about seven million years ago. For millions of years after that, our ancestors were biped monkeys who gradually reached greater heights and brains and evolved into Neanderthals, Denisovans, and other hominins.

It was difficult to follow the evolutionary changes in the brain along the way. Our own line separated from that of the Neanderthals and Denisovans about 600,000 years ago. After this split, as fossils show, our brains eventually became rounder. But what that means for the 80 billion neurons inside is hard to know.

Dr. Muotri and Dr. Semendeferi have teamed up with evolutionary biologists studying fossilized DNA. These researchers were able to reconstruct the entire genome of the Neanderthals by assembling genetic fragments from their bones. Other fossils have produced genomes of the Denisovans, who split off from the Neanderthals 400,000 years ago and lived in Asia for thousands of generations.

Evolutionary biologists identified 61 genes that may have played a crucial role in the evolution of modern humans. Each of these genes has a mutation that is unique to our species and has occurred for some time over the past 600,000 years and has likely had a major impact on the proteins encoded by these genes.

Dr. Muotri and his colleagues wondered what would happen to a brain organoid if they took out one of these mutations and changed a gene back to the way it was in the genome of our distant ancestors. The difference between an ancestral organoid and an ordinary one could provide clues as to how the mutation affected our evolution.

However, it took years for scientists to get the experiment off the ground. They struggled to find a way to precisely alter genes in stem cells before persuading them to turn into organoids.

After finding a successful method, they had to choose a gene. The scientists feared that for their first experiment they might choose a gene that would not harm the organoid. They considered how to increase their chances of success.

“Our analysis led us to say, ‘Let’s get a gene that changes many other genes,” said Dr. Muotri.

One gene on the list looked particularly promising in this regard: NOVA1, which makes a protein that then controls the production of proteins from a number of other genes. The fact that it is mainly only active in the developing brain made it more attractive. And humans have a mutation in NOVA1 that was not found in other vertebrate animals, either living or extinct.

Dr. Muotri’s colleague Cleber Trujillo bred a batch of organoids that carried the ancestral version of the NOVA1 gene. After placing one under a microscope next to an ordinary brain organoid, he invited Dr. Muotri to take a look.

The ancestral NOVA1 organoid had a markedly different appearance with a bumpy popcorn texture instead of a smooth spherical surface. “That’s when things started,” recalled Dr. Muotri. “I said, ‘OK, it does something.'”

The proportion of different types of brain cells was also different in the ancestral organoids. And the neurons in the ancestral organoids began firing spikes in electrical activity a few weeks earlier in their development than modern humans. It also took longer for the electrical peaks to organize in waves.

Other experts were surprised that a single genetic mutation could have such obvious effects on the organoids. They had expected subtle shifts that would be difficult to observe.

“It looks like the authors have found a needle in a haystack that is based on an extremely elegant study design,” said Philipp Gunz, a paleoanthropologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, who was not involved in the research.

Simon Fisher, the director of the Max Planck Institute for Psycholinguistics in the Netherlands, said the results must have come from a mixture of hard work and a little luck. “There must have been some degree of chance,” he said.

Although the researchers don’t know what the changes in the organoids mean for our evolutionary history, Dr. Muotri that there may be connections to the type of thinking made possible by different types of brains. “The real answer is I don’t know,” he said. “But anything we see in the very early stages of neurodevelopment could have an impact later in life.”

In the new research center, Dr. Semendeferi, to carry out careful anatomical studies on organoids of the brain and to compare them with the human brain of the fetus. This comparison will help to understand the changes in the ancestral NOVA1 organoid.

And Dr. Muotri’s team is working on the list of 60 other genes to make more organoids for Dr. Investigate Semendeferi. It’s possible the researchers aren’t as lucky as they were on the first try and don’t see a huge difference in some genes.

“But others could be similar to NOVA1 and point to something new – a new biology that allows us to reconstruct an evolutionary path that helped us become what we are,” said Dr. Muotri.