This article is part of our latest special report on Museums, which focuses on reopening, reinvention and resilience.

When most of us hear the word “evolution” we think of Charles Darwin or the Lucy skeleton. We generally do not think about nonliving things, like rocks.

But in recent years, scientists have begun applying the concept of evolution to a specific nonliving — but ubiquitous — object: minerals. This new perspective allows for a different kind of storytelling about both minerals, which are often found as sparkly, colorful crystals within rock, and the history of the planet.

As the American Museum of Natural History in New York City prepares to reopen its redesigned Allison and Roberto Mignone Halls of Gems and Minerals on June 12, evolution is front and center.

George Harlow, a geologist who has been the curator of gems and minerals at the museum for nearly 45 years, said when scientists talk about the evolution of inanimate things, they are referring to changes that happen over time. “It’s an answer to the question of why, as life on Earth has changed over the last 4.5 billion years, have nonliving minerals changed too.”

Today, there are more than 5,000 species of minerals — over triple the number from when they first developed — and over time they have diversified in chemical composition and color. The story of how that happened, that evolution, is a new one for the museum, Dr. Harlow said. “For the first time in this gallery, we are looking at life’s impact on the mineral kingdom.”

The incorporation of this new science (it entered the scientific mainstream around 2008) is evident throughout the galleries, which have been redesigned for the first time since 1976, by Ralph Appelbaum Associates in collaboration with the museum’s exhibition department, led by Lauri Halderman, vice president for exhibitions at the museum.

The old iteration of the exhibit hall was dark and had a layout reminiscent of Chutes and Ladders: stairs and winding passages filled with interactive exhibits and touchable rocks. But all that has changed. The space is much less of a labyrinth now, Ms. Halderman said. “And less mysterious.”

The redesign feels spacious, brighter and intentional, with higher ceilings and a palette of neutral grays; even the lighting inside the cases has been meticulously planned and executed.

Entering the new space, visitors are greeted by a pair of towering amethyst geodes, one 12 feet high and the other nine. Their massive interiors look a little like the universe itself, with pinpoints of white light scattered among glittering, dark purple crystals.

In each glass case, minerals are displayed with the help of custom handmade mounts — a specialty of the museum — so that each specimen appears to be floating. In fact, the whole gallery is designed to let the minerals and gems take center stage, with little distraction.

“This is very conscious on our part,” Ms. Halderman said. “We want the room to recede when you’re here. Although it’s a beautiful space, it’s not the focus.”

Touch screens in the galleries will remain untouchable monitors for now, although one has been adapted so that visitors can see the information on their phones.

One of the first exhibits is a spiraling timeline. A tiny dot of light at center signifies the Big Bang (although Dr. Harlow noted light did not actually exist then) and moves outward, with lines marking events that made possible the birth of minerals, including the formation of the solar system, the development of the Earth’s crust and the emergence of life.

And then there are the colors. One of the more compelling of those events was “the great oxygenation,” a period when the Earth’s atmosphere and oceans first experienced a rise in oxygen, between 2 billion and 2.5 billion years ago, which resulted in a burst of color in minerals, a characteristic that hadn’t existed before. The exhibit includes some spectacular examples, like an intense blue-green chrysocolla; a pockmarked, deep orange crocoite; and a glittery, blood-red chunk of rhodochrosite.

Storytelling plays a big role in these exhibits, whether about shifting continental plates, the movement of water or the history of a particular mine. “Science standards today emphasize big ideas that connect across disciplines, such as patterns in nature, cause and effect, structure and function,” Ms. Halderman said. “Those help you understand how minerals form, but also how everything forms.”

In the Gem Hall, about 2,000 of the museum’s collection of more than 4,700 gems are displayed in warmly lit cases lining a three-sided room. Gems are minerals, too, ones that have been cut, ground and polished to enhance their appearance.

Old favorites are still here but shown in an entirely new light (quite literally), like the luminous 563-carat Star of India Sapphire and the 632-carat Patricia Emerald. A new addition to the collection, donated by the New York jewelry dealer Siegelson, is the Organdie Necklace, designed by Michelle Ong, with more than 110 carats of diamonds set in platinum and made to resemble a delicately woven lace collar. (The necklace was worn by the singer Rihanna on a recent cover of Essence magazine.)

Here, too, the focus is on storytelling (for now, small monitors will display a scannable QR code that allows visitors to see identification information on their phones). “We made a decision to use our labels to tell visitors global stories,” Ms. Halderman said. Those include stories of the places where gems are found, how they are cut, their colors and unique properties, chemical composition, industrial uses, cultural uses and significance.

A standout in the redesigned Halls is the Minerals and Light room, with displays that aim to show how light illuminates and interacts with gems and minerals, including those hidden deep within rock.

The room feels a bit like a small theater, but in the place of a movie screen is a giant, glass-encased slab of rock — 19 feet long and nine feet high, weighing nearly 10 tons — taken from the Sterling Hill Mine, a once-active zinc mine in New Jersey that is now a mineral and mining museum.

In daylight, this hulking rock is just a drab brown, but when hit with ultraviolet light its appearance is transformed, as layers of minerals light up in fluorescent colors. When the wavelength of light changes so do the colors, from stripes of magenta and pale green to an almost blinding orange and lime green.

Everywhere in this redesigned gallery are reminders of the importance of both scale and time, and reminders that the living and the nonliving — life and rocks — may seem on the surface to be opposites but are actually deeply and profoundly connected.