Monitoring DNA Contamination in Handled vs. Directly Excavated Ancient Human Skeletal Remains

Bones, teeth and hair are often the only physical evidence of human or animal presence at an archaeological site; they are also the most widely used sources of samples for ancient DNA (aDNA) analysis. Unfortunately, the DNA extracted from ancient samples, already scarce and highly degraded, is widely susceptible to exogenous contaminations that can affect the reliability of aDNA studies. We evaluated the molecular effects of sample handling on five human skeletons freshly excavated from a cemetery dated between the 11 to the 14th century. We collected specimens from several skeletal areas (teeth, ribs, femurs and ulnas) from each individual burial. We then divided the samples into two different sets: one labeled as “virgin samples” (i.e. samples that were taken by archaeologists under contamination-controlled conditions and then immediately sent to the laboratory for genetic analyses), and the second called “lab samples”(i.e. samples that were handled without any particular precautions and subject to normal washing, handling and measuring procedures in the osteological lab). Our results show that genetic profiles from “lab samples” are incomplete or ambiguous in the different skeletal areas while a different outcome is observed in the “virgin samples” set. Generally, all specimens from different skeletal areas in the exception of teeth present incongruent results between “lab” and “virgin” samples. Therefore teeth are less prone to contamination than the other skeletal areas we analyzed and may be considered a material of choice for classical aDNA studies. In addition, we showed that bones can also be a good candidate for human aDNA analysis if they come directly from the excavation site and are accompanied by a clear taphonomic history.

在考古遗址中，骨骼、牙齿与毛发通常是人类或动物存在的唯一实体证据，同时也是古DNA（ancient DNA, aDNA）分析最常用的样本来源。遗憾的是，从古代样本中提取的DNA本就稀缺且高度降解，极易受到外源性污染的影响，进而干扰古DNA研究的可靠性。本研究针对11至14世纪墓葬中出土的五具人类骨骼，评估了样本处理流程对其产生的分子层面效应。研究人员从每位逝者的多个骨骼部位（牙齿、肋骨、股骨及尺骨）采集了样本，并将其分为两组：一组为"洁净样本组"，即由考古人员在污染受控环境下采集后，即刻送检开展遗传分析的样本；另一组为"实验室处理组样本"，即未采取任何特殊防护措施，按照骨学实验室常规清洗、处理及测量流程进行操作的样本。研究结果显示，实验室处理组样本在不同骨骼部位的遗传分型均存在不完整或模糊不清的问题，而洁净样本组则呈现出截然不同的结果。总体而言，除牙齿外，其余所有骨骼部位的样本在实验室处理组与洁净样本组间均呈现出不一致的检测结果。因此，相较于本研究分析的其他骨骼部位，牙齿更不易受到污染，可作为经典古DNA研究的首选样本材料。此外，本研究还证实，若骨骼样本直接取自发掘现场且具备明确的埋藏学背景，则也可作为人类古DNA分析的优质候选材料。