Data from: Revised time scales of RNA virus evolution based on spatial information

The time scales of pathogen evolution are of major concern in the context of public and veterinary health, epidemiology and evolutionary biology. Dating the emergence of a pathogen often relies on estimates of evolutionary rates derived from nucleotide sequence data. For many viruses, this has yielded estimates of evolutionary origins only a few hundred years in the past. Here we demonstrate through the incorporation of geographic information from virus sampling that evolutionary age estimates of two European hantaviruses are severely underestimated because of pervasive mutational saturation of nucleotide sequences. We detected very strong relationships between spatial distance and genetic divergence for both Puumala and Tula hantavirus – irrespective whether nucleotide or derived amino acid sequences were analyzed. Extrapolations from these relationships dated the emergence of these viruses most conservatively to at least 3,700 and 2,500 years ago, respectively. Our minimum estimates for the age of these hantaviruses are ten to a hundred times older than results from current non-spatial methods and in much better accordance with the biogeography of these viruses and their respective hosts. Spatial information can thus provide valuable insights on the deeper time scales of pathogen evolution and improve our understanding of disease emergence.病原体演化的时间尺度，是公共卫生、兽医卫生、流行病学以及演化生物学领域的核心关切问题。确定病原体的出现时间，通常依赖于由核苷酸序列（nucleotide sequence）数据推导得到的演化速率估算值。针对多数病毒，这类方法得到的演化起源估算结果仅可追溯至数百年前。本研究通过整合病毒采样的地理信息，证实两类欧洲汉坦病毒（Hantavirus）的演化年代估算值因核苷酸序列普遍存在突变饱和（mutational saturation）现象而被严重低估。针对普马拉汉坦病毒与杜拉汉坦病毒，无论采用核苷酸序列还是推导得到的氨基酸序列进行分析，均检测到空间距离与遗传分化（genetic divergence）之间存在极强的相关性。基于上述相关性的外推分析显示，保守估计这两类病毒的出现时间分别至少可追溯至3700年和2500年前。本研究得到的汉坦病毒年代下限估算值，比当前非空间方法得到的结果老10至100倍，且与这类病毒及其各自宿主的生物地理学（biogeography）分布特征更为契合。因此，空间信息可为解析病原体演化的深层时间尺度提供宝贵视角，并增进我们对疾病出现机制的理解。