Supplementary Tables S1-S9 from Paleogenomic insights into the red complex bacteria <i>Tannerella forsythia</i> in Pre-Hispanic and Colonial individuals from Mexico

The ‘red complex’ is an aggregate of three oral bacteria (<i>Tannerella forsythia</i>, <i>Porphyromonas gingivalis</i> and <i>Treponema denticola</i>) responsible for severe clinical manifestation of periodontal disease. Here, we report the first direct evidence of ancient Tannerella forsythia DNA in dentin and dental calculus samples from archaeological skeletal remains that span from Pre-Hispanic to Colonial period in Mexico. We recovered 12 partial ancient <i>T. forsythia</i> genomes and observed a distinct phylogenetic placement of samples, suggesting that the strains present in Pre-Hispanic individuals likely arrived with the first human migrations to the Americas and that new strains were introduced with the arrival of European and African populations in the sixteenth century. We also identified instances of the differential presence of genes between periods in the <i>T. forsythia</i> ancient genomes, with certain genes present in Pre-Hispanic individuals and absent in Colonial individuals, and vice versa. This study highlights the potential for studying ancient <i>T. forsythia</i> genomes to unveil past social interactions through analysis of disease transmission. Our results illustrate the long-standing relationship between this oral pathogen and its human host, while also unveiling key evidence to understand its evolutionary history in Pre-Hispanic and Colonial Mexico.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules'.‘红色复合体’是三种口腔细菌——福赛斯坦纳菌（Tannerella forsythia）、牙龈卟啉单胞菌（Porphyromonas gingivalis）与齿密螺旋体（Treponema denticola）——的集合体，可引发牙周病的严重临床症状。本研究首次在墨西哥前西班牙时期至殖民时期的考古骨骼遗骸的牙本质与牙结石样本中，检测到古老福赛斯坦纳菌DNA，为该细菌的古代遗存提供了首个直接证据。我们成功组装得到12条部分完整的古老福赛斯坦纳菌基因组，并观察到样本具有独特的系统发育分布特征。分析表明，前西班牙时期个体体内的该菌株，大概率随首批人类迁徙抵达美洲时传入；而16世纪欧洲与非洲人口迁入美洲后，新型菌株随之被引入。本研究还在不同时期的古老福赛斯坦纳菌基因组中，发现了基因的时期差异性分布现象：部分基因仅存在于前西班牙时期个体的样本中，殖民时期样本未携带此类基因，反之亦然。本研究凸显了通过分析古老福赛斯坦纳菌基因组，借助疾病传播轨迹解析古代人类社会互动的研究潜力。研究结果不仅阐明了该口腔致病菌与人类宿主之间长期共存的演化关系，同时也为解析前西班牙时期至殖民时期墨西哥境内该菌的演化历史提供了关键证据。本文属于‘古代生物分子视角下的健康与疾病洞察’专题议题的一部分。