The study of ancient DNA is helping to solve modern crimes

Such techniques have helped secure two convictions this year
今年，此类技术帮助两人被定罪

2024年10月24日 05:34 上午

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.

艾斯凯·威勒斯莱夫 (ESKE WILLERSLEV) 是一起谋杀案审判中的一位不寻常的证人。作为哥本哈根大学古代 DNA (aDNA) 专家，他的日常工作包括研究史前人类和灭绝的巨型动物的生活。然而 2024 年夏天，他被要求说服陪审团相信他可以在另一个领域做出贡献：犯罪现场调查。

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.

这起案件涉及17岁的丹麦女孩艾米丽·孟（Emilie Meng）的谋杀案，她于2016年7月失踪，同年的平安夜，她被勒死的尸体在湖中被发现。警方曾希望在离尸体几米远的地方发现的孟的裤子能提供有价值的DNA线索，供他们跟进。但在暴露在恶劣环境中6个月后，衣服上残留的任何有用物质痕迹都会被严重破坏。警方迫切需要答案，于是求助于威勒斯列夫博士。

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.

孟的案例是世界上第一个利用在对经过时间破坏的遗传物质碎片进行测序和分析中磨练出来的技术的案例之一。这可能不是最后一次。在丹麦，标准法医方法无法从警方扣押的 20% 至 30% 的可能含有或不含 DNA 的物品中检索到有用的遗传信息。在其他法医学欠发达的国家，这一数字可能更高，可能导致案件悬而未决，甚至误判。威勒斯列夫博士表示，在使用可能有所帮助的新技术方面，法医界确实是保守的。“但另一方面，我也认为采用这些新发明并开始测试[它们]也很重要。”对于aDNA 技术来说，这个时刻似乎已经到来。

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).

所有 DNA 均由四种不同的分子（称为碱基）组成，它们组合在一起形成长的聚合物链。成对的链通过碱基之间形成的键连接在一起，使 DNA 具有著名的双螺旋结构。在沿着链的某些特定位点，短碱基串会重复，通常连续多次，即所谓的短串联重复（STR）。

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.

不同的人在每个位点会有不同数量的 STR，这样只需测量重复次数即可将 DNA 样本与其所有者进行匹配。如果两个样本在多个位点上是相同的（完整的 STR 配置文件通常由 16 到 25 个位点组成），那么它们来自两个不同人的可能性就微乎其微。该技术快速且廉价，并且大量犯罪分子 STR 数据库已经存在。但它有一个很大的限制：科学家需要长度不短于 100-400 个碱基对的 DNA 片段，才能确保完整捕获任何单个 STR。但这并不总是可能的，因为随着时间的推移或暴露在自然环境中，DNA 会不断分解。在这种情况下，警方无计可施。

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.

研究 aDNA 的研究人员不能轻易灰心丧气。在古代人类和动物遗骸中，DNA 片段很容易短至 35 个碱基对。为了从这些片段中提取信息，研究人员必须识别或“测序”他们能找到的每一个碱基。这需要小心地将 DNA 溶解到溶液中，并将其与样本中的其他粘性物质分离，其中可能包括搭便车微生物的 DNA。经过更多准备后，DNA 被送入下一代测序机，该机可以并行读取数百万个片段。

Puzzle-solving

解谜

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.

由于几乎所有人类 DNA 在个体之间都是保守的，因此软件可以使用参考基因组将每个小片段放在正确的位置。结果是长长的 DNA 串，其中每对碱基都被识别。个体间个别碱基对不同的位点称为单核苷酸多态性 (SNP)。科学家经常发现数以万计的此类地点。

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.

Willerslev 博士已经能够从孟的裤子中获得 SNP。接下来的任务是试图确定它们可能来自谁。2023 年，一名名叫菲利普·帕特里克·韦斯 (Philip Patrick Westh) 的男子因与同一地区的绑架案有关而被捕；由于案件相似，警方认为他也杀死了孟（韦斯先生否认了与绑架案有关的大部分指控，并对杀害孟的指控表示无罪）。为了评估孟晚舟裤子上的遗传物质来自韦斯先生的可能性，威勒斯列夫博士利用了普通健康丹麦人的 DNA 数据库。按照逻辑，如果裤子上发现的单核苷酸多态性与韦斯先生 DNA 中的相同，并且其中有足够多的变异是足够罕见的，那么它们确实来自韦斯先生的可能性就会上升。Willerslev 博士作证说，如果样本中包含 Westh 先生或其近亲的 DNA，则这种 SNP 变体的特殊模式出现的可能性至少比不包含 Westh 先生或其近亲的 DNA 的可能性高出 100 万倍。

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.

现代法医实验室已经进行了一些 SNP 分析。例如，哥本哈根大学丹麦国家法医遗传学实验室的 Bo Thisted Simonsen 表示，SNP 数据有时用于获取有关犯罪者的身高、种族和眼睛颜色的信息。在某些情况下，警方还可以将犯罪嫌疑人的 SNP 资料上传到商业血统数据库以寻找匹配。由于许多家庭工具包允许人们测试自己是否含有某些单核苷酸多态性，警察通常可以找到与犯罪者有关的人。2018 年，美国当局正是利用从旧强奸工具包中收集的 DNA 来抓捕金州杀手。

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.

但从 SNP 中识别嫌疑人则是另一回事。西蒙森博士说，降解样品的分析可能极其复杂，特别是如果来自多个人的材料混合在一起。没有标准化的法医协议来分离这些信号，也没有如何自信地计算 DNA 属于嫌疑人的概率。这很重要，因为刑事案件的风险比猛犸象和渡渡鸟的研究要高一些。但是，西蒙森博士说，“我们希望这个难题能够被解决。”他希望向 Willerslev 博士的团队学习并开发新的法医工具。这项工作已经开始：9月份，他与奥尔堡大学和哥本哈根大学的研究人员合作发表了一篇论文，描述了一种基于SNP进行识别计算的方法。

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.

他并不是唯一一个看到潜力的人。一家名为 Astrea Forensics 的美国公司最近从加州大学圣克鲁斯分校的古基因组学小组中分离出来，为执法部门提供 DNA 专业知识。他们的专长是在头发中发现的核 DNA，长期以来，人们认为这种核 DNA 过于碎片化且稀缺，没有任何用处。

Next-generation forensics

下一代取证

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.

促使科学家们创办这家公司的一个案件涉及 1982 年强奸和谋杀一名名叫达拉琳·约翰逊 (Daralyn Johnson) 的 9 岁女孩。在她内衣上发现的头发最初与一个名叫查尔斯·费恩 (Charles Fain) 的男子有关。被判处死刑十七年后，费恩先生被证明无罪：在头发中发现的线粒体 DNA（比核 DNA 更容易获得，但只能将人排除在外）证明它不属于他。但直到头发的核 DNA 碎片经过新一代 SNP 测序后，才发现了新的嫌疑人。6 月 26 日，一名名叫大卫·达尔林普尔 (David Dalrymple) 的男子因绑架和性犯罪而被判 20 年至无期徒刑，他被判谋杀约翰逊罪名成立。他已对判决提出上诉，并坚称自己无罪。

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. ■
起诉约翰逊案的爱达荷州峡谷县的西奥多·拉格沃尔 (Theodore Lagerwall) 表示，在关注 DNA 式分析的检察官和科学家中，“这是法医 DNA 测试的下一个重要阶段”。Astrea Forensics 的联合创始人凯利·哈金斯·金凯德 (Kelly Harkins Kincaid) 称此案具有“历史性”；据她所知，这是第一次在美国通过这些方法确定嫌疑人。达尔林普尔先生被定罪两天后，韦斯先生被判犯有谋杀艾米莉·孟的罪名。他立即提出上诉。此案并不完全取决于 DNA 分析；传统法医技术还在孟家的一卷胶带上发现了他的DNA。法院尚未得出结论。■