Sequencing ancient DNA

The quest to trace the roots of the human race has long rested on the tools of molecular biology. Researchers have long peered into our evolutionary history in the sequences of ancient DNA extracted from skeletal remains unearthed by archaeologists. For example, sequencing the DNA of 40,000-year-old remnants of an early modern human from Tianyuan Cave in China revealed that the finds likely belonged to the forbears of many present-day Asians and Native Americans. Likewise, in an earlier milestone for the field of ancient DNA analysis, a high-resolution DNA sequence of an archaic girl was reported using a 50,000-year-old finger bone found in the Denisova Cave in southern Siberia, suggesting that the Denisovans, bygone relatives of Neanderthals, may have interbred with the ancestors of some modern humans. Other examples of whole genome sequencing of ancient humans, including a Paleo-Eskimo, a Tyrolean Iceman, and an Australian Aborigine, pepper the scientific literature.

The well-preserved mummy of an old man (Upper) is displayed in an exhibition in Denmark’s National Museum. The mummy was removed, as displayed, from an excavation in 1875 at Borum Eshøj, near Aarhus, Denmark. Carpenter and colleagues used hair samples from the mummy to isolate ancient DNA and validate the technique. (Lower) Valdiosera isolates ancient DNA from a different sample in a clean room—a highly sanitized laboratory—in the archaeology department at La Trobe University, Melbourne. Images courtesy of Kristian Kristiansen and Cristina Valdiosera.

But decoding ancient DNA sequences at high resolution is no small task: DNA is thought to weather poorly, and ancient DNA typically bears signs of fraying and fragmentation inflicted by exposure to the elements over great gulfs of time, posing challenges to the recovery of material suitable for sequencing. Moreover, ancient DNA, mere traces of which are found in moldering archaeological samples, is often masked by genetic material from the infinite variety of microbes teeming in many environments. Given these difficulties, sequencing ancient DNA can be a prohibitively expensive undertaking, particularly when its proportion in a find is less than 1%.

Molecular biologists Meredith Carpenter, Cristina Valdiosera, Carlos Bustamante, and others may have found a technique to surmount the seemingly insuperable obstacle: The team recently reported a way to enrich ancient DNA that would allow researchers to reduce the amount and, hence, the cost of sequencing needed to cover most of the genome of interest. Using a modern human genome to create RNA probes, which serve as baits for human DNA in a solution, and magnetic beads tagged with a protein that binds to the probes, the team isolated DNA from ancient teeth, bones, and hair found in Bulgaria, Peru, and Denmark, washing away nonhuman DNA and amplifying the target for sequencing (1). “Prior to capture...,” the researchers wrote, “these libraries yielded an average of 1.2% of reads mapping to the human genome. After capture, this fraction increased substantially, with up to 59% of reads mapped to human and enrichment ranging from 6- to 159-fold.”

“Right now, the field of ancient DNA is pretty limited because of how expensive it is to sequence. Enriching these libraries with whole genome capture could be cost-effective not only for ancient DNA sequencing but also for other applications, such as forensic analysis and microbiome analysis,” says Carpenter.