Key takeaways
Fish specimens collected during a 1907–1910 U.S. expedition to the Philippines were stored in high-proof sugarcane alcohol instead of formalin, unintentionally preserving their DNA.
By comparing DNA from these historical samples with modern fish, researchers discovered that some tropical species have lost significant genetic diversity while others have evolved rapidly in response to pollution, overfishing, and warming seas.
The project not only bridges old and new science, but also counters colonial legacies by partnering with Filipino institutions to build local capacity in genomics and inform more sustainable fisheries management.
At this year’s annual meeting of the Ecological Society of America in Baltimore, almost two dozen students and researchers from the University of California, Santa Cruz, gave presentations on their work. Given the strength of ecology and evolutionary biology research at UC Santa Cruz, that kind of presence wasn’t unusual.
But one of the talks stood out for its buzzworthy title: “Of rum and fishes: genomic change at ecological timescales in the ocean.”
The presenter was UC Santa Cruz’s Malin Pinsky, a world-renowned marine ecologist who studies how climate change is reshaping ocean ecosystems. Hence, the scope of his research spans from the coastal kelp forests nearby to the poles of our planet. But the work he described at the conference on August 12 began somewhere entirely unlikely: in century-old jars containing high-proof sugarcane alcohol—basically rum.
The jars, about 79,000 of them, were from a U.S. scientific expedition to the Philippines in the early 1900s and are now maintained at the Smithsonian National Museum of Natural History. They were stored there because the jars contained something else: tens of thousands of preserved fish specimens from the Asian archipelago.
At the time, museum collectors did not use the chemical formalin that is now standard for preserving biological specimens. Instead, the collectors in the Philippines—recently a U.S. colony—turned to what was available locally: sugarcane alcohol. But, while formalin preserves shape and color well, it chemically alters DNA and makes it inaccessible.
Alcohol, on the other hand, is an excellent long-term preservative for genetic material. This quirk of history presented Pinsky and his colleagues with an unexpected treasure: one of the largest fish DNA collections in the world, still intact after more than a century. Kent Carpenter, a biology professor at Old Dominion University, was the colleague who first realized that the specimens were suspended in what is essentially rum and initiated a National Science Foundation project in 2017 together with Pinsky and Chris Bird, associate professor at Texas A&M University–Corpus Christi.
Malin Pinsky
“Most marine biology research has been done at higher latitudes in places like the United States—that’s where I’ve done a lot of my research as well,” Pinsky said. “So we don’t know if the tropics are similar or different. But we’re now learning that the tropics actually are very different. Marine fishes in the Philippines appear to actually have lost quite a bit of genetic diversity and also appear to be evolving rapidly.”
Old vs. new science
Pinsky also sees a story of old science, the expedition, meeting the modern technologies of whole-genome sequencing and bioinformatics that are deftly being applied by Bird. The original expedition, conducted from 1907 to 1910, indiscriminately collected as many specimens as possible. The “Philippine Expedition” was the longest and most extensive assignment of the Albatross, a U.S. Fish Commission steamer that “was the first vessel built especially for marine research by any government,” according to a NOAA Fisheries historical account.
During its 40 years of service, the Albatross surveyed the Newfoundland Banks, the Bering Sea, visited various archipelagos in the Pacific, as well as served in two wars, the account states. The Philippine Expedition came about because the United States had acquired the Philippines following the Spanish-American War of 1898 and the bloody Philippine-American War of 1899-1902.
The USS Albatross (Source: National Oceanic and Atmospheric Administration Photo Library)
The stated purpose of the expedition was to survey and assess the aquatic resources of the Philippine Islands. The research Pinsky, Bird, and Carpenter are now doing involves cutting-edge technology first developed for mapping the human genome, being used to unlock the hidden history of these colonial-era specimens and reveal genetic changes in tropical fish over the last century.
The team’s main goal is to reconstruct how Philippine ocean ecosystems have changed over that time. Historical ecological baselines for tropical marine environments are largely unknown, according to Pinsky, with most monitoring records going back only 40 to 50 years. By analyzing the fish DNA from the expedition and comparing it with modern samples, researchers hope to answer key questions like which species have persisted, declined, or disappeared entirely—and how human activity has influenced the genetic diversity of coastal marine life.
To compare historical and modern populations, the team is selectively re-sampling species from the same regions targeted in 1908 and 1909. They are measuring physical changes over time in body shape, coloration, and growth rates.
In some cases, they are even testing whether fishing pressure has led to faster, more streamlined swimmers. These morphological data, combined with genetic analyses, could reveal whether environmental and human pressures have altered fish physiology alongside their DNA.
Century of change in the tropics
Over the last hundred years, Philippine coastal ecosystems have undergone sweeping transformations. Sedimentation, pollution, habitat loss, and ocean warming—now nearly one degree Celsius higher than in the early 1900s—have reshaped marine environments. For tropical oceans, where historical data are scarce, this 116-year-old collection offers a rare chance for what the research team calls “genomic time travel,” revealing both the scale and the pace of change.
Pinsky said early findings suggest a complex picture: Some fish species have lost significant genetic diversity, indicating steep population declines, while others appear to have evolved rapidly to survive in degraded environments. These genetic shifts offer clues to the resilience or vulnerability of species that are vital to local fisheries, global seafood markets, and the aquarium trade.
“Marine fish are often seen as very resilient to environmental change. Their populations are very large. Even Atlantic cod, which notoriously has collapsed, still numbers in the millions,” said Pinsky, an associate professor of ecology and evolutionary biology. “For that reason, even when there’s a steep decline, sea fish are generally seen as very resistant to much evolutionary change.”
Countering colonial history through collaboration
While the project addresses fundamental scientific questions about how marine life responds to environmental change, it also has applied goals. The team is partnering with the Philippines’ National Fisheries Research and Development Institute (NFRDI) to integrate genetic insights into fisheries management. By comparing modern fish populations to their early 20th-century ancestors, the researchers can identify long-term trends that day-to-day monitoring would miss, informing more sustainable practices.
Researchers preparing fish samples at the Smithsonian natural history museum’s support center for taking x-rays to measure the shape of the fish skeletons. (Photo by by Mikaela Salvador)
This kind of collaboration counteracts the colonial practices of the original expedition. The project is fostering cross-cultural scientific exchange through training workshops the team is conducting in the Philippines, ranging from intensive week-long sessions for American and Filipino students, to one-day courses for local researchers.
Recent workshops have brought together dozens of students and scientists to envision the next phase of population genetics research in the country. Notable Filipino scientists such as Mudjekeewis Santos at NFRDI, Nadia Palomar-Abesamis at Silliman University, and Rene Abesamis at the University of the Philippines are leading partners in the collaboration.
These sessions cover modern genetic techniques, bioinformatics, and computational biology, complementing existing expertise in the Philippines’ growing genetics community.
Pinsky said the first wave of research papers is now in progress. For his August 12 presentation, he focused on the coral-reef-dwelling cardinal fish and two commercially targeted species of ponyfishes. “We found that cardinal fish populations close to one of the largest cities in the Philippines have lost 4% of their genetic diversity, which is actually a lot when it comes to genetic diversity,” Pinsky explained. “And they’ve evolved to a greater degree than populations in a very remote part of the Philippines, which haven’t lost any genetic diversity.”
With more than two dozen species under investigation, Pinsky said these initial findings suggest that tropical marine fish may be far more sensitive to human impacts than previously assumed—and that a century-old accident of preservation may hold the key to understanding, and perhaps reversing, that trend.