How DNA forensics is transforming studies of ancient manuscripts

In May 2006, Tim Stinson traveled to England to explore the libraries of London, Oxford, and Cambridge. At that time, he was editing a 14th-century poem for his PhD at the University of Virginia in Charlottesville. After months of studying grainy microfilm copies, he was eager to handle an original piece. During a visit to Oxford’s Bodleian Libraries — a place so enchanting that it was featured in the Harry Potter films — he finally got to see one of the manuscripts he had journeyed to examine. However, he became so captivated by the physical book that the text inside seemed secondary.

The manuscript was around 600 years old, bound in worn brown leather, and consisted of 266 yellowed parchment leaves. It displayed signs of extensive use, with faint stains on the pages and worn edges from frequent handling.

“It had its own biography, its own deep history. It seemed like an archaeological site between covers,” Stinson recalls, now a medievalist at North Carolina State University in Raleigh. “The parchment even had a vaguely animal smell, albeit a pleasant one.”

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Stinson pondered whether DNA might be preserved in the animal skins used to create the pages of the book and if this DNA could provide new methods to date and interpret manuscripts beyond traditional markers like handwriting and dialect. His brother, a biologist, noted this was theoretically possible but cautioned that the technological challenges were significant. The required technologies, such as next-generation sequencing methods and computational tools for data interpretation, were still in development. Even if feasible techniques were available, conservators were unlikely to permit destructive sampling of invaluable cultural artifacts.

Almost two decades later, this curiosity has helped establish a new field. The advancement of non-destructive sampling techniques, along with progress in genomics and proteomics, has enabled the extraction of biological information from ancient parchments without causing visible damage. This emerging field, known as biocodicology, merges molecular biology with codicology, the study of books as physical objects.

The findings are revolutionizing scholars’ understanding of human history. By analyzing parchment, researchers are uncovering evidence of trade networks, animal husbandry, medical and ritual practices, climate change, epidemics, and floods.

In doing so, they have discovered that ancient parchments preserve more than just words.

A biological archive

During medieval times, parchment was the dominant writing material in Europe, used for everything from legal documents to sacred texts. It was made by soaking animal skins in lime, stretching them on frames, and scraping them thin as they dried. Even after centuries, parchment retains subtle traces of this process, such as follicle patterns on the hair side, smoother textures on the flesh side, and variations that experienced scholars can almost intuitively read. Its durability has long made medieval manuscripts cherished historical objects.

In a 2009 article, Stinson argued that parchment manuscripts represent a year-by-year record of animal life and human–animal interactions spanning a millennium. He questioned why zooarchaeologists were focused on excavating bones when a vast, precisely dated faunal archive had been sitting on library shelves for centuries.

This idea caught the attention of Matthew Collins, a biomolecular archaeologist jointly based at the University of Copenhagen and the University of Cambridge, UK. Collins pioneered a technique known as zooarchaeology by mass spectrometry (ZooMS) to identify the animal species of old bones. ZooMS works by analyzing fragments of type I collagen, the predominant structural protein in skin, teeth, and bone. Species-specific variations in collagen produce distinctive molecular ‘fingerprints’ when measured in a mass spectrometer.

Collins recalls an excavation project in Scotland where his team analyzed over 1,000 bone fragments. After three years, they could only confidently identify 29 individual animals. “That was a really disappointing project,” he says. When he realized parchment was made from a similar collagen-rich material — and that manuscripts usually announce when and where they were made — Collins was eager to explore its scientific potential.

Without a trace

Sarah Fiddyment was completing a PhD in cardiovascular proteomics at the University of Zaragoza in Spain when a chance lecture about applying scientific techniques to cultural heritage inspired her to pursue a postdoc with Collins. Collins tasked her with developing a method to identify the animal species in parchment. Fiddyment planned to obtain samples by shaving a thin strip from the manuscript’s edge. However, upon arriving at the Borthwick Institute for Archives in York, UK, the conservators refused to let her bring a knife near their documents. “I was effectively faced with a two-year project that was not going to happen.”

The impasse reflected a long-standing divide between the sciences and the humanities — what British novelist and physicist C. P. Snow called the two cultures problem. Scientists are used to drilling into fossil cores or snipping feathers, whereas scholars typically consider even the smallest injury to a medieval page unacceptable. Any method of sampling the biological material in parchment would have to clear an unusually high bar: its effects would need to be invisible, even under a microscope.

Collins recalls that tense moment in the Borthwick archives as a turning point. “‘No’ is a really powerful word for scientists,” he says, “because it makes you kind of think around corners.” Fiddyment spent a month at the archives observing the conservators. She noticed that they routinely cleaned parchment using blocky white erasers, the kind that grace many a primary-school desk. So, she asked whether she could have the eraser crumbs. “Those little fragments you generate that you blow away, those are the bits I collected, and we found that that worked beautifully.”

The crumbs, later called ‘erdu’ for eraser dust, turned out to be molecular gold. When a polyvinyl chloride eraser is pushed across parchment, static electricity lifts microscopic particles from the surface, including collagen and traces of DNA. Fiddyment analyzed the crumbs she’d collected using a version of the ZooMS protocol she called eZooMS.

Fiddyment tested her approach on 13th-century ‘pocket Bibles’, whose tissue-thin pages were long thought to be made from the skins of animals like squirrels and rabbits. Her analysis showed otherwise. The parchment was made from the usual suspects: calf, goat, or sheep skins. This finding highlighted not that unusual materials were used, but that extraordinary craftsmanship was involved.

However, other studies have raised more questions than answers. Stinson recalls the first book he worked on with Fiddyment and Collins: a glossy 12th-century copy of the Gospel of St Luke. To his trained eye, the manuscript seemed to be made entirely of calfskin. “When the results came back, it blew everyone’s mind,” he says. Testing revealed a deliberate alternation between calfskin and sheepskin. Goatskin was also present, but only immediately after the parable of the prodigal son, which includes the text’s lone mention of a goat kid. “Now, it could be a coincidence, we don’t know,” Stinson says. “But this book is deeply weird.”

Reading residues

While effective, the method is labor-intensive. It involves rubbing the same patch of parchment until enough crumbs accumulate to fill the bottom of a microcentrifuge tube. In the rare-books library at Duke University in Durham, North Carolina, Stinson spent days sampling a single volume. “Honestly,” he says, “it’s like tennis elbow after two days of that.”

In search of less-strenuous alternatives, Stinson teamed up with his colleague Kelly Meiklejohn, a forensic scientist who had developed methods to identify toxic plants and fungi as potential biological weapons during a postdoc at the FBI Laboratory in Quantico, Virginia. These substances were often in powdered form and lacked obvious identifying features.

The team experimented with a range of non-destructive methods on old manuscripts purchased online. Some ideas were quickly ruled out: the dull edge of a butter knife, forensic fiber-lifting tools used at crime scenes, and even gecko tape, which adheres to surfaces using microscopic bumps. Although technically non-destructive, the tape kept sticking to the laboratory tweezers and tubes and contained traces of cow DNA, presumably from the manufacturing process.

Ultimately, the researchers focused on two non-destructive approaches: erasers and soft cytology brushes, the disposable tools used for cervical-screening tests. Comparisons showed that the brushes were easier to use and recovered DNA as effectively as the erasers did.

DNA extracted from parchment is typically fragmented into tiny pieces and present in amounts too low to be detected using standard assays. But “we proceed with every sample,” Meiklejohn says, because her lab uses a forensic-style workflow designed for such genetic material.

Her team converts the DNA into sequencing libraries and uses a technique known as hybridization capture to extract animal sequences of interest. Magnetic RNA ‘baits’, designed to match the mitochondrial genomes of species commonly used in parchment, bind to the target DNA, even when sequences differ by as much as 20% from modern genome references. The enriched material is then sequenced and mapped against a panel of 16 reference genomes, including those of human, dog, pig, and various species of deer.

On a computer screen, the results appear as a dense, laddered stack of brightly colored horizontal bars — short stretches of ancient DNA aligning imperfectly but convincingly with modern references. In repeated tests, results using the brush method matched known species identifications and often exceeded expectations.

However, the approach has its logistical quirks. When Meiklejohn had trouble sourcing the right cytology brushes before a planned research trip to the United Kingdom, she took advantage of the opportune timing of her annual gynecological exam to ask where they were purchased. The clinic offered to provide her with a few bags, but another supplier eventually came through.

Beyond species

In collaboration with Duke, the team applied its cytology-brush technique to documents spanning a wide range of time and space, sampling parchments from the 8th to the 20th century and originating from Europe, North Africa, and the Middle East. The unpublished results draw on 351 samples taken from 91 manuscripts. The researchers identified the source species in 58% of cases. Most samples were from sheep, followed by cattle and goats, with a single curious sample suggesting pigskin. They found that species choice mostly followed regional patterns; for instance, sheep were predominantly used in England and goats in Mediterranean regions.

One 13th-century Greek New Testament produced a tantalizing near-match to red deer (Cervus elaphus hippelaphus), but the signal fell just short of the threshold required for a definitive identification.

During a visit to Duke, I joined Stinson as he collected additional samples from that mysterious manuscript. In a quiet reading room, Andrew Armacost, the curator of rare-book collections, had arranged several volumes of medieval manuscripts along a long table under clear, even light. The book pages were filled with elegant script in black and red ink — some bound in dark, cracked leather, others reduced to single, orphaned sheets. As we observed, Stinson donned gloves, set a timer, and gently swept a brush in slow circles across a blank spot of parchment for one minute before snapping the brush head off into a tube.

Armacost has had to turn down requests for destructive sampling from otherwise promising projects, unwilling to see even one centimeter cut from the collection. He is excited to see non-destructive methods take hold and curious about what they might reveal. “We’ve always sort of thought of [parchments] as textual resources,” he says, “but maybe they have lots of other stories to tell as well.”

An expanding field

These stories are beginning to emerge. Today, scientists can determine the sex of source animals, classify specific breeds, and detect pathogens. For example, researchers have identified sheep pox in numerous parchment samples. Because the virus evolves slowly — about one mutation every two years — scientists can use phylogenetic analyses to date a given strain within a roughly 50-year window.

Biocodicology also allows scientists to reconstruct how ancient manuscripts were handled and the environments in which they circulated.

Salt, for instance, was crucial to medieval parchment production. Different regions relied on distinct types of salt, and the salt-loving — or halophilic — bacteria left on the skins can serve as geographical signatures⁹. Even insect damage tells a story. ‘Bookworms’ are actually the larvae of various furniture beetles that burrow into medieval book bindings. The exit holes and the DNA the larvae leave behind reveal where the insects — and books — existed. Remarkably, the distribution of these beetles closely tracks the geographical boundaries of the Protestant Reformation. “We call them the Protestant and Catholic beetles,” says Stinson.

Non-destructive methods can also reveal practices that are rarely documented in text. Fiddyment used eZooMS to sample residues from a medieval birth girdle, a religious talisman worn to protect women during pregnancy and labor. From one late-15th-century girdle, she recovered traces of cervico-vaginal fluid as well as evidence of goat’s milk, eggs, honey, and various plant species — ingredients drawn from medieval childbirth recipes. “It was the first sort of direct evidence,” Fiddyment says, “that people were actually wearing it.”

Some scientists are even using biocodicology in climate science. To reconstruct historical rainfall patterns, Collins’s group has developed a solvent-based suction technique to extract lipids from ancient parchment. Oxygen isotopes preserved in the lipids record past rainfall and temperature levels, allowing researchers to detect global climate events such as the 1816 ‘year without a summer’, which followed the 1815 volcanic eruption of Indonesia’s Mount Tambora. Taken at scale, Collins suggests, parchment could rival tree rings as a climate archive.

The future

However, the ability to pursue such expansive questions varies widely. While researchers in the United States have faced abrupt funding losses, Europe has committed more than €20 million (US$23 million) to biocodicology through European Research Council initiatives such as Beasts to Craft and CODICUM. Collins notes that some funding agencies value pushing technologies to their limits, partly because methods developed for ancient manuscripts can have broader applications to modern problems such as food security, medicine, and forensic science.

Stinson lost his grant from the US National Endowment for the Arts, but he managed to take another research trip to the United Kingdom last June using funding from his university. During this visit, he went to the Norfolk Record Office in Norwich, where he collected 100 brush samples from historical manor court rolls. The volume of biological materials available was staggering: the archive holds 1.7 million parchment items, much more than he could hope to sample in a lifetime. “This is just one county,” he says. The UK National Archives in London “have miles and miles” of shelves of parchment. “We’re talking about a massive, massive faunal archive. No one’s ever conceived of it that way.”

At the Norfolk office, Stinson received a badge that allowed him to roam the facility freely, with the stark warning that if an alarm were triggered, he would have only moments to leave before the fire-suppression system would suck all of the oxygen from the room.

He needs no reminder to be careful. These ancient artifacts are precious, not just because of the text inscribed on their pages, but also because of the biological histories they contain, waiting to be read.

This article is reproduced with permission and was first published on April 7, 2026.