In the field of modern crime investigation, a new technological approach is gradually emerging, which is ancient DNA (aDNA) technology. Professor Esk Willerslev from the University of Copenhagen, an expert in prehistoric humans and extinct large animals, appeared as a witness in a murder trial in the summer of 2024. This case involves 17-year-old Danish girl Emily Meng, who went missing and was killed in 2016. Her pants have become key physical evidence, but traditional forensic methods are difficult to obtain effective DNA clues due to prolonged exposure to the natural environment. At this time, aDNA technology is highly anticipated. This technology can extract information from DNA fragments as short as 35 base pairs, providing new directions for case investigation through analysis of single nucleotide polymorphisms (SNPs). The case in Denmark and similar cases in the United States demonstrate that although the application of aDNA technology in criminal investigations faces many challenges, it has achieved certain results. Its potential in the field of forensic medicine cannot be underestimated, and it is expected to usher in a new era of forensic identification.
ESKE WILLERSLEV was an unusual witness for a murder trial. An expert in ancient DNA (aDNA) at the University of Copenhagen, his day job involved studying the lives of prehistoric peoples and extinct megafauna. And yet over the summer of 2024 he was asked to persuade a jury that he had something to offer in another field altogether: crime-scene investigation.
The crime in question was the murder of Emilie Meng, a 17-year-old Danish girl who went missing in July 2016 and whose strangled body was found in a lake on Christmas Eve that same year. The police had hoped that Meng’s trousers, found metres from her body, would yield valuable DNA clues for them to follow up. But after being exposed to the elements for six months, any traces of useful material left on the clothes would be seriously damaged. Desperate for answers, the police turned to Dr Willerslev.
The Meng case is one of the first in the world to make use of techniques honed in the sequencing and analysis of time-ravaged scraps of genetic material. It may not be the last. In Denmark standard forensic methods fail to retrieve useful genetic information from 20% to 30% of the items in police custody that may or may not contain DNA. In other, less forensically developed, countries, the figure is likely to be higher, potentially contributing to unsolved cases or even wrongful convictions. The forensics community is rightly conservative when it comes to using new technology that could help, says Dr Willerslev. “But on the other hand, I also think it’s important that you take up these new inventions and start testing [them].” For aDNA techniques, that moment appears to have arrived.
All DNA is made up of four distinct molecules known as bases, strung together in combinations to form long polymer chains. Pairs of chains are linked together by bonds that form between their bases, giving DNA its famous double-helix structure. At certain specific sites along the chains short strings of bases will repeat, often many times in a row, in what are called short tandem repeats (STRs).
Different people will have a different number of STRs at each site, which allows DNA samples to be matched to their owner simply by measuring the number of repeats. If two samples are identical across several sites (a full STR profile usually consists of between 16 and 25 sites), the chances they come from two different people is vanishingly small. The technique is quick and cheap, and massive STR databases of criminals already exist. But it has one big limitation: scientists need stretches of DNA no shorter than 100-400 base-pairs long to be sure of capturing any single STR in full. That is not always possible, as DNA carries on breaking down over time or when exposed to the elements. In such cases, police are left with little to go on.
Researchers working with aDNA cannot afford to be so easily discouraged. In ancient human and animal remains, DNA fragments can easily be as short as 35 base pairs. To extract information from these fragments, researchers must identify or “sequence” every single base they can lay their hands on. This involves carefully dissolving the DNA into a solution and separating it from other gunk in the sample, which may include DNA of hitchhiking microbes. After some more preparation, the DNA is then fed to a next generation sequencing machine that can read millions of fragments in parallel.
Puzzle-solving
Because almost all human DNA is conserved between individuals, software can use a reference genome to put each little fragment in its correct place. The result is long strings of DNA where each pair of bases is identified. Sites where individual pairs of bases differ between individuals are known as single nucleotide polymorphisms (SNPs). Scientists often find tens of thousands of such sites.
Dr Willerslev had been able to obtain SNPs from Meng’s trousers. Then came the task of trying to identify whom they could have come from. In 2023 a man called Philip Patrick Westh was arrested in connection with a kidnapping case in the same area; because of similarities between the cases, the police believed that he had killed Meng too (Mr Westh denies most of the accusations related to the kidnapping case and pleaded not guilty to the charge of killing Meng). To assess the probability that the genetic material from Meng’s trousers had come from Mr Westh, Dr Willerslev made use of a DNA database of ordinary, healthy Danes. If the SNPs found on the trousers were identical to those in Mr Westh’s DNA, went the logic, and enough of them were sufficiently rare variants, the probability that they did indeed come from Mr Westh went up. Dr Willerslev testified that this particular pattern of SNP variants would be at least one million times more likely to turn up if the sample included DNA from Mr Westh, or a close relative, than if it did not.
Modern forensic labs do some SNP analysis already. For instance, says Bo Thisted Simonsen from the Danish state forensic genetics lab at the University of Copenhagen, SNP data is sometimes used to obtain information about a perpetrator’s height, ethnicity and eye colour. In certain cases, police can also upload a suspected perpetrator’s SNP profile to a commercial ancestry database to look for matches. As many home kits allow people to test themselves for certain SNPs, police can often turn up people related to the perpetrator. The American authorities did just this to catch the Golden State Killer in 2018, using DNA collected from an old rape kit.
But identifying a suspect from SNPs is another matter. Degraded samples can be extremely complex to analyse, says Dr Simonsen, in particular if material from several people has been mixed together. There are no standardised forensic protocols for separating out those signals, nor for how to confidently calculate the probability that the DNA belongs to a suspect. That matters because the stakes are somewhat higher in a criminal case than in the study of mammoths and dodos. But, says Dr Simonsen, “We expect that nut to be cracked.” He hopes to learn from Dr Willerslev’s team and develop new forensic tools. The work has already started: in September, researchers from Aalborg University and the University of Copenhagen, with whom he collaborates, published a paper describing an approach for doing identification calculations based on SNPs.
He is not the only one to see potential. An American company called Astrea Forensics has recently spun out from the palaeogenomics group at the University of California in Santa Cruz, to offer aDNA expertise to law enforcement. Their speciality is the nuclear DNA found within hair, which has long been considered too fragmented and scarce to be of any use.
Next-generation forensics
One of the cases that spurred the scientists to start the company involved the rape and murder of a nine-year-old girl called Daralyn Johnson in 1982. Hair found on her underwear was initially linked to a man named Charles Fain. Seventeen years after receiving a death sentence, Mr Fain was exonerated: mitochondrial DNA—which is easier to obtain than nuclear DNA but can only rule people out—found in the hair proved that it did not belong to him. But it was not until the hair’s fragmented nuclear DNA underwent next-generation sequencing for SNPs that a new suspect was found. On June 26th a man called David Dalrymple, who was already serving a sentence of 20 years to life for kidnapping and sex crimes, was found guilty of Johnson’s murder. He has appealed against the verdict and maintains his innocence.
Among prosecutors and scientists looking at aDNA-style analysis, “This is the next big phase of forensic DNA testing,” says Theodore Lagerwall of Canyon County in Idaho, who prosecuted the Johnson case. Kelly Harkins Kincaid, the co-founder of Astrea Forensics, calls the case “historic”; to her knowledge, it is the first time that these methods have identified a suspect in America. Two days after Mr Dalrymple’s conviction, Mr Westh was found guilty of the murder of Emilie Meng; he immediately appealed. The case does not rest entirely on aDNA analysis; conventional forensic techniques also found Meng’s DNA on a roll of tape at his house. The courts have yet to reach a conclusion.
