The origin of the medieval Black Death pandemic (ad 1346–1353) has been a topic of continuous investigation because of the pandemic’s extensive demographic impact and long-lasting consequences^1,2. Until now, the most debated archaeological evidence potentially associated with the pandemic’s initiation derives from cemeteries located near Lake Issyk-Kul of modern-day Kyrgyzstan^{1,3,4,5,6,7,8,9}. These sites are thought to have housed victims of a fourteenth-century epidemic as tombstone inscriptions directly dated to 1338–1339 state ‘pestilence’ as the cause of death for the buried individuals⁹. Here we report ancient DNA data from seven individuals exhumed from two of these cemeteries, Kara-Djigach and Burana. Our synthesis of archaeological, historical and ancient genomic data shows a clear involvement of the plague bacterium Yersinia pestis in this epidemic event. Two reconstructed ancient Y. pestis genomes represent a single strain and are identified as the most recent common ancestor of a major diversification commonly associated with the pandemic’s emergence, here dated to the first half of the fourteenth century. Comparisons with present-day diversity from Y. pestis reservoirs in the extended Tian Shan region support a local emergence of the recovered ancient strain. Through multiple lines of evidence, our data support an early fourteenth-century source of the second plague pandemic in central Eurasia.

中世纪黑死病大流行（公元 1346-1353 年）的起源一直 是持续研究的主题，因为该流行病对人口的广泛影响和长期后果^1,2。到目前为止，可能与大流行的开始有关的最具争议的考古证据来自位于现代吉尔吉斯斯坦^{1、3、4、5、6、7、8、9}伊塞克湖附近的墓地。这些遗址被认为安置了 14 世纪流行病的受害者，因为墓碑铭文直接追溯到 1338-1339 年，表明“瘟疫”是被埋葬者的死亡原因⁹. 在这里，我们报告了从其中两个墓地 Kara-Djigach 和 Burana 挖掘出来的 7 个人的古代 DNA 数据。我们对考古、历史和古代基因组数据的综合表明，鼠疫耶尔森氏菌明显参与了这一流行病事件。两个重建的古代鼠疫耶尔森氏菌基因组代表一个单一菌株，并被确定为通常与流行病的出现相关的主要多样化的最新共同祖先，这里可以追溯到 14 世纪上半叶。鼠疫杆菌与现今多样性的比较扩展的天山地区的水库支持了恢复的古代菌株的局部出现。通过多条证据，我们的数据支持了 14 世纪早期欧亚大陆中部第二次瘟疫大流行的来源。