Ancient American tuberculosis: origin(s), spread, and replacement

人类和其他动物之间的病原体交换由来已久，最近的例子包括艾滋病毒、非典型肺炎、流感病毒和鼠疫耶尔森氏菌（引起鼠疫）。如今，特别是在发展中国家，人类及其驯养动物继续侵占野生动物栖息地，随着暴露程度的增加，跨物种传播（或“溢出”）的机会也在扩大。该项目将深入了解病原体适应新宿主的过程，以及人类迁徙和相互作用对过去病原体传播的影响。特别是，该项目将利用古代DNA和骨骼分析来研究人类迁徙事件和结核分枝杆菌菌株毒力的可能变化如何在人类进化史上促进结核病（TB）的传播，并提出关于结核病如何从动物传播到人类以及从旧大陆传播到美洲的具体假设。更好地了解分枝杆菌（例如引起结核病和麻风病的分枝杆菌）的进化史可以为其他有兴趣开发临床治疗方法的研究人员提供见解。由于人类结核病（及其后代）对其他物种产生了深远的影响，因此它也是一个保护问题。在该项目期间，本科生和研究生都将接受分子技术和数据分析方面的培训。生成的数据将存放在 GenBank 等公共数据库中，数据分析结果将以学术文章以及公众可访问的格式发表。该项目将识别、记录和采样 285 具具有结核病骨骼病变特征的遗骸，这些遗骸可追溯到欧洲人接触美洲之前和之后。新开发的方法将用于从这些样本中提取 DNA，并对古老病原体基因组进行定位和测序。我们组建了一支由古代 DNA、生物考古学、生物信息学和群体遗传学专家组成的团队来解决两个具体目标。第一个是研究美洲致病性分枝杆菌，特别是结核分枝杆菌复合群 (MTBC) 随时间变化的地理格局。具体来说，我们将测试秘鲁和南美洲的史前结核病是否是由鳍足分枝杆菌单次跳跃到人类的结果，北美的史前结核病是否是由与古代南美洲发现的鳍足分枝杆菌菌株关系最密切的 MTBC 菌株引起的，以及在接触前墨西哥的非典型骨骼病理标本中发现的菌株是否是麻风分枝杆菌（一种新发现的分枝杆菌菌株，可引起非典型麻风病）。第二个目标是辨别分枝杆菌随着时间的推移适应人类的特征。为此，我们将测试以下假设：1) 在南美洲“跳入”人类体内的人畜共患病 M. pinnipedii 菌株显示出选择迹象，表明对这一新宿主的适应；2) 美洲当地的分枝杆菌菌株在相对较短的时间内在接触时被毒性更强的菌株所取代（例如：在新世界接触/贸易增加后）。从古代样本中获得的基因组数据以及来自现代菌株的比较数据将用于构建这些病原体的系统发育，评估整个美洲（以及随着时间的推移）的多样性模式，并测试选择信号。随着时间的推移，人类中 MTBC 和其他分枝杆菌的适应模式很有趣，因为它有助于了解这些生物体的成功及其未来可能的发展轨迹。

The exchange of pathogens between humans and other animals has been longstanding, and recent examples include HIV, SARS, flu viruses, and Yersinia pestis (which causes the plague). Today, especially in the developing world, humans and their domesticated animals continue to encroach upon wild animal habitats, with opportunities for cross-species transmission (or "spillover") expanding as exposure increases. This project will provide insight into the process by which pathogens adapt to new hosts and the impact of human migration and interaction on the spread of pathogens in the past. In particular, the project will use ancient DNA and skeletal analyses to investigate how human migration events and possible changes in virulence of M. tuberculosis strains have facilitated the spread of tuberculosis (TB) during human evolutionary history, with specific hypotheses about how tuberculosis may have been transmitted from animals to humans, and from the Old World to the Americas. A better understanding of the evolutionary history of mycobacteria such as those causing TB and leprosy can provide insights for other researchers interested in developing clinical treatments. Because human TB (and its descendants) has had a profound impact on other species, it is thus also a conservation concern. During this project, both undergraduate and graduate students will be trained in molecular techniques and data analysis. The data generated will be deposited in public databases such as GenBank, and the results of data analyses will be published in scholarly articles as well as in formats accessible to the general public.This project will identify, document, and sample 285 remains with skeletal lesions characteristic of TB that date to before and after European contact in the Americas. Newly developed methods will then be used to extract DNA from these samples, as well as to target and sequence the ancient pathogen genomes. We have assembled a team of experts in ancient DNA, bioarchaeology, bioinformatics, and population genetics to address two specific aims. The first is to examine the geographic patterning of pathogenic mycobacteria, particularly M. tuberculosis complex (MTBC), in the Americas through time. Specifically, we will test whether prehistoric TB in Peru and South America were the result of a single jump of M. pinnipedii into humans, if prehistoric TB in North America was caused by MTBC strains that are most closely related to M. pinnipedii strains found in ancient South Americans, and whether strains found in specimens with atypical skeletal pathologies from pre-contact Mexico are M. lepromatosis (a newly discovered strain of mycobacteria that causes atypical leprosy). The second aim is to discern signatures of adaptation to humans by mycobacteria through time. For this aim, we will test the hypotheses that 1) the zoonotic M. pinnipedii strain(s) that "jumped" into humans in South America shows signs of selection that indicate adaptation to this new host and 2) local mycobacterial strains in the Americas were replaced by more virulent strains at contact over a relatively short time period (ex: following contact/increased trade in the New World). The genome data obtained from the ancient samples along with comparative data from modern strains will be used to construct phylogenies of these pathogens, to assess patterns of diversity across the Americas (and through time), and to test for signals of selection. The pattern of adaptation of the MTBC and other mycobacteria in humans over time is of interest since it helps understand the success of these organisms and their possible future trajectories.