The Brain Navigates New Spaces by ‘Flickering’ Between Reality and Old Mental Maps

Have you ever gotten a flash of a different route you could have taken while stuck in traffic? This isn’t just a fleeting thought, but rather a fundamental neurological process, according to findings recently published in Nature Communications.

The hippocampus—the brain’s GPS—creates an internal representation of our surrounding environment, known as a cognitive map. And a true cognitive map, says senior author George Dragoi, MD, PhD, allows for flexible navigation, not just memorized paths.

“If you can operate a detour in any path that you think of, that means your brain has a map," says Dragoi, associate professor of psychiatry and of neuroscience at Yale School of Medicine.

He and his team have now discovered how the hippocampus creates and modifies these maps and how that allows us to better navigate new and unexpected spaces.

The researchers studied rats—which have hippocampal circuitry like our own—while they navigated a maze with four arms. Tiny probes recorded activity in their hippocampus throughout the experiment.

The rats first ran the maze in its normal form, then rested while their brain activity was recorded. Researchers then added a surprise detour by replacing part of the track with a u-shaped path, which the rats had to navigate during later runs. In the final phase, the maze was restored to its original shape, and the rats ran it again.

This setup allowed the team to track how the rats’ brains responded in real time to familiar paths, surprising detours, and rest. By comparing neural activity across these different states, the researchers could see how the new detour experience was consolidated during sleep and how it altered the animals’ mental map of the original maze later.

Before the rats encountered the detour, the research team observed that their brains were already firing in patterns that seemed to "imagine" alternate unfamiliar mental routes while they slept. When the researchers compared these sleep patterns to the neural activity during the actual detour, some of them matched.

“What was surprising was that the rats' brains were already prepared for this novel detour before they ever encountered it,” says Yuchen Zhou, lead author of the study and a postdoctoral fellow in the Dragoi Lab.

This pre-wiring helped the rats learn astonishingly fast, Zhou says. Within just one or two trips around the detour, their brains were already running with what researchers refer to as theta sequences—neuronal sequences embedded in brain rhythms found in the hippocampus that help link sequential locations into experienced trajectories and support learning, memory, and navigation.

When the rats navigated the detour route, their brains didn't just focus on where they were. Instead, their neural activity "flickered," jumping back and forth between their current location and the memory of the original path that no longer existed. This mental juggling act is highly organized by phases of theta brain waves that allow rapid comparison between current and alternate recalled experiences, Dragoi says.

When the rats were placed back on the original track after the detour was removed, their neural representation of that track was different from what it was before the detour experience. The brain didn't simply revert to its old map. It created an updated one that incorporated the memory of the detour.

While the study focused on spatial navigation, Dragoi and his team see deeper implications.

“Sometimes old memories can intrude on new ones. When that gets out of control, as in post-traumatic stress disorder, the brain mixes past and present in a way that interferes with how we experience reality,” Dragoi says. “The same brain networks that normally help us imagine shortcuts or possibilities can, when disrupted, trap us in intrusive memories or hallucinations.”