The world in a tidepool

Along the rocky shores of Hopkins Marine Station in Pacific Grove, California, generations of Stanford researchers have waded the same path through a series of tidepools to look for ocean life. 

During each traverse, they search for shell-dwelling species like mussels clinging to slick rocks, comb glassy pools for nudibranchs, and use plastic trays to count snails that roll around like misbehaved marbles. 

“It’s sort of like looking at an impressionist painting,” said Mark Denny, the John B. and Jean De Nault Professor in Marine Science, Emeritus, based at Hopkins Marine Station, which is a part of the Stanford Doerr School of Sustainability. “Stand back and you see the picture, but nose-down there’s this incredible detail you wouldn’t have seen otherwise.”

The invisible line that the researchers walk to collect samples was established by Stanford graduate student Willis Hewatt in 1931. Where the marine station slopes down to the tidepools, Hewatt installed a brass peg to mark one corner of a one-yard-wide corridor extending 108 yards to the sea. For two years, Hewatt counted and categorized the marine animals living within this narrow band. The visual survey became known as Hewatt’s transect and established a baseline for understanding how the variety and abundance of tidepool species in the area have shifted over the decades.

Life along the transect fluctuates with the tides. Pounding surf and surging currents submerge a granite slab along the coast, then recede to expose its pockmarked surface to air. This twice-daily cycle makes intertidal zones worldwide some of the toughest places to live, forcing species to cope with strong waves, exposure to air, and sudden temperature changes. For scientists, the habitat provides a convenient test bed for ecological theories. 

“Some people think it’s extreme events that drive evolution and ecology along the rocky shore, and others say it’s day-to-day trends,” said Denny, who has studied life in the tidepools at Hopkins Marine Station for the past 43 years. “It’s obviously both. Paying attention to the extremes is increasingly important as climate change intensifies.”

Walking the line

In the 1990s, sixty years after Hewatt established his transect, Stanford undergraduates Rafe Sagarin and Sarah Gilman, along with Chuck Baxter, a marine ecologist and Stanford lecturer, retraced the corridor to take a new inventory of the tidepools. 

Their findings, published in Science in 1995, sounded a major alarm: Marine species appeared to be on the move due to climate change. The team had documented the first instance in North America of a relative increase in abundance of southern species, and a decrease in northern species, that corresponded with higher sea surface temperatures. The findings supported predictions of how a warmer climate would impact ecological communities. Southern species of anemones, whelks, and tubesnails appeared in the transect for the first time, and once-common local sea stars, crabs, and limpets had decreased in abundance. 

The paper drew media attention from around the world. President Bill Clinton and Vice President Al Gore visited Hopkins in 1998 to witness the tidepools where climate change seemed to be leaving a visible mark. For some Stanford researchers, the findings underscored the value of building long-term data sets to monitor changes in ocean life and habitat over time.

Sagarin graduated from Stanford in 1994 and continued the survey intermittently, in most years, until his sudden death in 2015. Stanford faculty have repeated the survey, now known as the Hewatt-Sagarin transect, every year since. 

Hewatt recognized the difficulties of maintaining scientific continuity through the years, noting in his 1934 graduate thesis that due to the relatively recent emergence of invertebrate zoology as a scientific discipline at the time, his endeavor was still “in many respects groping and tentative” and that more precise methods in the future could allow for “permanent and definite results.”

Robin Elahi, a lecturer at Hopkins Marine Station and in the Oceans Department and the sixth person to lead the transect, has made documentation of the current methodology more precise, clarifying details such as how deep to dig into the sand and the duration of sampling for each one-square-yard section, or “quadrat.” He has also considered challenges such as the reclassification of certain marine species and how some species are indistinguishable from one another when they’re young. 

“I’ve been reflecting on the human aspect of replicating research,” said Elahi. “Every observer is different, and each day in the field has a different set of challenges. One might overlook species, misidentify species, or incorrectly estimate the abundance of species. These sources of error have the potential to influence our interpretations of biodiversity change.”

These challenges inherent to long-term monitoring do not undermine a vast body of evidence of climate change impacts on ocean temperatures, ecosystems, oxygen levels, and acidity. Although changes in temperature vary regionally, global average sea surface temperatures have been consistently higher during the past three decades than at any other time since reliable observations began in 1880. 

“The Hewatt-Sagarin transect is a prime example of the role that marine stations play as sentinels of change, by providing insight into long-term change through the repetition of studies at particular sites over decades,” said Fiorenza Micheli, the David and Lucile Packard Professor in Marine Science, who led the transect surveys between 2016 and 2020. “By maintaining the transect, we can also detect changes that we can then investigate more thoroughly, with additional approaches.” 

A new generation of scientists

Throughout the years, Elahi and other survey leads like Micheli and Jim Watanabe, lecturer emeritus at Hopkins Marine Station, have enlisted students to expand sampling along the transect. 

“One of the most valuable things marine labs can offer students is studies like this one that immerse them literally and figuratively in natural history,” said Watanabe, a kelp expert who participated in the survey for three years before his retirement in 2018. “You can get students fired up about marine biology while also extending a data time series that, for all its imperfections, is still better than nothing.”

Related: A photo tour of Hopkins Marine Station

For some students, the Hewatt-Sagarin transect has inspired new scientific questions. Meghan Shea, a postdoctoral scholar in the Department of Civil and Environmental Engineering and a 2025 graduate of the Stanford Doerr School of Sustainability’s Emmett Interdisciplinary Program in Environment and Resources (E-IPER), focused her PhD dissertation on approaches to monitoring coastal biodiversity. 

Shea, who also earned an undergraduate degree from Stanford’s Department of Civil and Environmental Engineering, was inspired by Sagarin and Gilman’s undergraduate work. “The transect’s cultural and social persona exists beyond its physicality and ecology, which is part of the reason I was drawn to work here,” she said.

Shea collected bags of seawater from along the transect as part of her dissertation. Each bag contains microscopic bits of tissue shed by organisms as they move through the habitat. Known as environmental DNA, this genetic material can be filtered from the water and sequenced into what researchers call a unique DNA barcode. These barcodes are then compared to a reference library of sequences, indicating which species are present.

Environmental DNA technology has its constraints. For example, researchers can’t determine whether the genetic barcodes retrieved from seawater represent individuals living in the immediate vicinity, existing broadly across the habitat, or just passing through. Often, they retrieve a barcode that doesn’t have a matching reference sequence at all. Scientists have sequenced only a small fraction of an estimated 10 million total on the planet.

When Shea began her PhD program in 2019, co-advised by civil and environmental engineering professor Alexandria Boehm, only a handful of studies had explored the use of environmental DNA in the intertidal zone. Four years later, the California legislature announced a $9 million investment to build out a DNA barcode library of the state’s intertidal biodiversity. The investment highlights a growing recognition among scientists that tidepools are a model system for understanding the ecological forces that shape biodiversity, and how species might fare when climate change tips the balance.

Expanding knowledge

On a foggy day in the spring of 2024, Shea and Elahi led a group of colleagues clad in rubber boots to survey the transect. Elahi led visual surveys, identifying and counting species in quadrats, while Shea collected seawater samples alongside him. Later, she filtered the samples to retrieve DNA fragments, moving quickly in the shade to slow potential DNA degradation. 

The team retrieved complementary data from visual surveys and seawater samples, including drone imagery. For example, when considering mussels, drone imagery revealed the extent of mussel beds, visual surveys indicated the abundance of physically distinct mussel species, and environmental DNA samples yielded a series of genetic barcodes to compare with visual counts.

“Exploring how environmental DNA sampling might extend what’s possible to uncover through conventional visual monitoring is exciting,” said Shea. “But the act of going out and observing the tidepools really deeply is never going to be replicated by a molecular tool.”

The researchers found some differences in the array of species detected through each method. But they were more surprised by instances of overlap, where eDNA analyses and visual surveys identified the same set of species.

Related: Underwater Stanford scientists investigate the kelp forests

Nearly a year after Elahi and Shea co-led the survey and environmental DNA sampling, two of Elahi’s students decided to observe the transect from underwater. 

“I told them they may very well be the first people to snorkel and collect data at high tide along the Hewatt transect,” said Elahi, noting the students’ excitement. “We really don’t know what’s happening along the transect when it is submerged.”

The two students had chosen a calm morning to swim. Their snorkels gently bobbed with the waves as they made steady progress from the sea toward the brass peg onshore. Like dozens of Stanford researchers before them, they would likely observe something new down the line.

“Whatever we learn is a contribution, and sometimes we find something that has a big impact,” said Watanabe. “As long as we keep trying, we learn a few new things by keeping our eyes open. That’s where the reward should be.”