Museomics highlights the importance of scientific museum collections

(Press-News.org) In 1831, Charles Darwin embarked on a five-year voyage to South America aboard the HMS Beagle, which was conducting hydrographic surveys. During the expedition, Darwin explored remote regions of the continent, collecting plants, animals, and fossils and recording detailed observations. These materials were fundamental to the development of his ideas on evolution by natural selection, which are a pillar of modern scientific development. Today, the collection Darwin gathered on his most famous voyage is in the care of the Natural History Museum in London, where it has been organized and preserved for two centuries.

Natural history museums have played a fundamental role in preserving scientific memory. However, many of these museums’ scientific collections have remained underutilized in recent decades. The emergence of sequencing techniques that require recent tissues and intact DNA has made historical collections irrelevant. But this scenario is changing, driven primarily by museomics.

“Museomics can be defined as the application of molecular biology, genomics, and bioinformatics techniques to the study of specimens preserved in museum collections, involving the extraction, sequencing, and analysis of degraded DNA from historical samples [hDNA] from museums, enabling investigations into evolution, biodiversity, population genetics, phylogeny, taxonomy, and conservation,” said Taran Grant, who is a full professor at the Department of Zoology at the Institute of Biosciences and an associate curator of amphibians at the Museum of Zoology, both at the University of São Paulo (USP).

Grant is one of the speakers at the France-Brazil Museology Seminar, which began on June 12th at the Museum of Man in Paris. The seminar was organized by the National Museum of Natural History (MNHN) of France in partnership with FAPESP and the University of São Paulo (USP). It is part of the program for FAPESP Week France 2025.

Grant spoke about how museomics is revolutionizing the way scientific collections are used and valued. By enabling the extraction and analysis of DNA from historical specimens, it opens up possibilities for research in areas such as evolution, extinction, adaptation, environmental change, and biodiversity conservation. “With museomics, we can access genetic information from materials collected over a hundred years ago,” Grant said.

The scientist says he started extracting and sequencing DNA from old museum samples in the 1990s, but he faced major technological limitations in his work. At the time, the 0 method was used, which required long, well-preserved DNA fragments. This was difficult because the genetic material in museum specimens is often highly fragmented and degraded.

“DNA degradation is linked to the age of the sample and the conditions of the museum. In the alcohol used to preserve specimens, the problem is the water content. DNA’s worst enemy is water, which corrupts genetic material. In museums located in warmer regions with high temperatures and no air conditioning, evaporation is greater, so the alcohol must be changed more frequently,” Grant explained to Agência FAPESP.

Technological advances, particularly with the Illumina platform and other next-generation sequencing technologies, have made it possible to work with fragmented or degraded DNA, favoring the use of museum material. However, a new challenge has emerged: the amount of endogenous DNA – that is, authentic DNA from the organism – in tissue samples is extremely small. This makes the samples highly susceptible to contamination from environmental DNA or from handling. Therefore, controlled environments, such as clean room laboratories with sterile conditions, are required for the extraction and analysis of this material to prevent contamination and loss of original genetic information.

With support from FAPESP, Grant and his colleagues set up a clean room at the Department of Zoology at USP. “As far as I know, it’s the only facility of its kind in Latin America dedicated to taxonomy studies. Without FAPESP’s support, this advancement in our research wouldn’t have been possible. This equipment allows us to develop museomics and bring natural history museums back to the epicenter of biodiversity studies,” he said.

DNA collections

“For two centuries, museums were the place where biodiversity research was conducted. Now, museomics allows us to study entire collections that previously had no genetic value. It is estimated that at least 3 billion specimens are preserved in museums worldwide, and now we can access the DNA of many of them,” said Grant.

The results are already starting to show up. For example, the current issue of the Bulletin of the American Museum of Natural History features a 78-page article by Grant, Mariana Lyra, Miguel Trefaut Rodrigues, Vanessa Kruth Verdade, and researchers from Germany and the United Kingdom.

In the article, the authors describe how they used museomics to answer a decades-old question about the classification of amphibians in the Atlantic Rainforest. By sequencing portions of genomes extracted from tiny amounts of ancient DNA preserved in museum specimens, the scientists reclassified rocket frogs into 12 species, three of which are extinct, and proposed a new genus. Previously, it was believed that they were a single species.

“We knew from acoustic and molecular data that there were more species, but we couldn’t compare them with specimens described in the past because there was no way to extract DNA from them. Now this is possible,” said Grant.

The field of taxonomy, which was previously paralyzed by a lack of reliable genetic data from preserved specimens, is moving forward again. With it, the ability to formulate effective conservation policies is advancing as well.

“Without knowing how many and which species exist, there’s no way to protect what’s at risk. Historical material is extremely important for resolving taxonomy, and without taxonomy, there’s no conservation. Because the paradigm for conservation is species, not populations or individuals. If we don’t know how many and which species exist, we can’t formulate conservation policies and strategies,” the USP professor pointed out.

“With advances in technology, we’ve gained a much more accurate picture of diversity over time, which informs not only conservation actions but also biodiversity-related policies.”

According to Grant, the work published in the Bulletin of the American Museum of Natural History began in 2018. It involved collaborating with collections in Brazil and abroad, particularly with the University of Potsdam in Germany.

“The first step was to gain experience with pioneering laboratories. My main collaborator in hDNA is Mariana Lyra, who helped set up our clean room laboratory. Today she works at New York University in Abu Dhabi, but maintains strong ties with Brazil. Her work in Potsdam was fundamental in ensuring the quality and credibility of our work,” he said.

Grant said that, in addition to scientific advancement, museomics represents a symbolic and practical revaluation of natural history museums. “For a long time, museums were seen as exhibition spaces or warehouses. But the true value of museums lies in their collections, which are invisible to the public but now have a new scientific role.”

Not only does museology rekindle the role of natural history museums, it also poses new challenges in terms of preservation, infrastructure, and funding. “We need to think of specimens as sources of DNA, not just as specimens for morphological study. Conserving genetic material must be a priority from the beginning,” he said.

“This requires adequate infrastructure, such as climate control, to prevent the degradation of genetic material. We also need to start extracting and preserving tissue samples from the specimens already in our collections. A ten-year-old specimen will be 110 years old in a century. If we preserve the samples properly, we can halt the process of DNA degradation. And museomics is just getting started,” said Grant.

FAPESP’s participation in VivaTech is part of the FAPESP Week France program. For more information, visit: fapesp.br/week/2025/france.

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