Table S1. Description of VIPs from Ancient RNA virus epidemics through the lens of recent adaptation in human genomes

Over the course of the last several million years of evolution, humans likely have been plagued by hundreds or perhaps thousands of epidemics. Little is known about such ancient epidemics and a deep evolutionary perspective on current pathogenic threats is lacking. The study of past epidemics has typically been limited in temporal scope to recorded history, and in physical scope to pathogens that left sufficient DNA behind, such as <i>Yersinia pestis</i> during the Great Plague. Host genomes, however, offer an indirect way to detect ancient epidemics beyond the current temporal and physical limits. Arms races with pathogens have shaped the genomes of the hosts by driving a large number of adaptations at many genes, and these signals can be used to detect and further characterize ancient epidemics. Here, we detect the genomic footprints left by ancient viral epidemics that took place in the past approximately 50 000 years in the 26 human populations represented in the 1000 Genomes Project. By using the enrichment in signals of adaptation at approximately 4500 host loci that interact with specific types of viruses, we provide evidence that RNA viruses have driven a particularly large number of adaptive events across diverse human populations. These results suggest that different types of viruses may have exerted different selective pressures during human evolution. Knowledge of these past selective pressures will provide a deeper evolutionary perspective on current pathogenic threats.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.

在过去数百万年的演化历程中，人类大概率曾遭受过数百乃至数千次流行病的侵扰。然而，学界对这类远古流行病的认知仍极为匮乏，且缺乏针对当前致病威胁的深度演化视角。过往流行病研究的时间范围通常局限于有文字记录的历史，物理层面则仅能聚焦于留下足量DNA痕迹的病原体，例如大瘟疫时期的鼠疫耶尔森菌（Yersinia pestis）。不过，宿主基因组为突破现有时间与物理限制、探测远古流行病提供了间接途径。病原体与宿主的军备竞赛通过驱动众多基因产生大量适应性变异，塑造了宿主基因组，这类信号可用于探测并进一步刻画远古流行病的特征。本研究针对千人基因组计划（1000 Genomes Project）涵盖的26个人类群体，探测了约5万年前发生的远古病毒性流行病留下的基因组足迹。通过富集分析约4500个与特定类型病毒相互作用的宿主基因位点的适应性信号，我们发现RNA病毒在不同人类群体中驱动了数量格外庞大的适应性演化事件。研究结果表明，不同类型的病毒在人类演化过程中施加了各异的选择压力。对这些过往选择压力的认知，将为理解当前的致病威胁提供更深入的演化视角。本文属于‘来自古代生物分子的健康与疾病洞察（Insights into health and disease from ancient biomolecules）’主题专栏的一部分。