How Scientists Recover DNA from Ancient Bones: From Bone Dust to Genetic Trees

In 1976, tunnel workers in Toronto unearthed a partial cranium and antler fragments that radiocarbon dating later placed at about 12,000 years old. Those remains belong to an extinct hoofed mammal, Torontoceros hypogaeus. Recent genomic sequencing showed it was related to today’s white-tailed deer — a discovery that depended on careful ancient-DNA methods.

Recovering genetic material from bones that old requires strict contamination control, meticulous sampling and a bit of luck. Modern environments are saturated with stray DNA — skin cells, airborne microbes and viral particles — so laboratories that work with ancient material are designed to keep any modern DNA out of the sample.

Sterile conditions and careful sampling

Researchers work in clean rooms treated with ultraviolet (UV) light to sterilize surfaces. Laboratory staff wear full protective suits and N95 masks. Before any internal sampling, the exterior of a fossil is exposed to UV and then physically removed to reduce contamination.

A small drill is used to bore into the bone and produce a fine powder from the interior. That powder is the primary source for ancient-DNA extraction. “We grab the powder, and you’re hoping, fingers crossed, there are cells in that powder that contain fragments of DNA,” says Aaron Shafer, an associate professor at Trent University who led the Torontoceros sequencing effort.

Isolating DNA from the powder

Bone powder contains minerals, proteins and other organics that must be removed. Chemical reagents dissolve proteins and unwanted material while leaving nucleic acids behind. The solution is then mixed with a silica (silicon) powder and spun in a centrifuge. Because DNA carries negative charges, it binds to the positively charged silica, concentrating the genetic material for purification.

When microbes are the target

Not all ancient-DNA studies focus on the host animal. For example, Nicolas Rascovan of the Pasteur Institute analyzed dental pulp from teeth recovered from soldiers who retreated from Russia with Napoleon in 1812. The vascular tissue inside a tooth can preserve microbial DNA; sequencing that material helped identify pathogens responsible for enteric and relapsing fevers in those soldiers.

Sequencing and converting DNA into data

To read DNA, most labs now use next-generation sequencers (machines from Illumina are common). Before running a sample, tiny engineered DNA molecules called adapters are attached to fragments. These adapters allow the sequencer to recognize, amplify and read the fragments.

The sequencer identifies the order of nucleotides — the base pairs that compose DNA — essentially converting the molecules into digital strings of letters. These digital fragments can be stored, searched, compared and analyzed on computers.

Challenges: damage, contamination and interpretation

Older DNA is often fragmented and chemically altered. Over time, predictable types of damage accumulate; bioinformatic and chemical methods can detect characteristic errors and model or repair missing pieces. “If you were to look at the same region of DNA in a fresh sample and an ancient sample, there are certain base pairs that are deviating in the ancient base,” Shafer explains. “That’s your clue that something’s happened to them that isn’t natural.”

Sequencers do not distinguish target DNA from other sources: extracts can include modern human DNA, soil microbes and organisms introduced during excavation or handling. Researchers compare each fragment against large reference databases to identify which sequences belong to the organism of interest (for example, deer or caribou relatives) and which correspond to pathogens, bacteria or contaminant species.

Why preservation and luck still matter

Preservation conditions are critical. Warm, wet burial environments accelerate degradation and can erase recoverable DNA, while cold, dry or permanently frozen contexts favor preservation. Improvements in lab methods and sequencing sensitivity are expanding the range of specimens that can be analyzed — researchers have reported DNA recovered from exceptionally old fossils when preservation conditions were favorable.

Comparative analysis of the recovered sequences allowed Shafer’s team to place Torontoceros on the evolutionary tree and let Rascovan’s team identify historical pathogens. Their successes reflect both technical advances and favorable preservation: when the DNA is present and well preserved, modern methods can retrieve and interpret it.