Fig. 4

G31 variola virus from Lauchheim exhibits intermediate genetic characteristics in relation to other ancient strains. A A maximum-likelihood tree illustrating the phylogenetic position of the VARV strain from Lauchheim (red) among other ancient (blue) and modern (black) strains. Numbers at each node are bootstrap support. The tree was inferred using IQTree, with 10,000 ultrafast bootstrap replicates. The tree includes 56 sequences (49 modern and 7 ancient). P-I and P-II refer to VARV primary clade I (corresponding to VARV major and East, Central and South African VARV sequences) and primary clade II (comprising of VARV alastrim minor and West African sequences), respectively. Country codes can be found in the Additional file 1: Table S6. Dates are provided for ancient strains. B Temporal trend of gene inactivation, with the number of inactivated genes shown on the y-axis and the x-axis indicating time into the past. Phylogenetic relationships between viruses are indicated by gray lines. Light blue circles indicate the number of inactivated genes when uncertain inactivations are not taken into account. The gray dotted line and shaded area indicate a linear regression of number of genes against time into the past, indicating that a hypothetical virus with a full set of genes existed ~4116 years into the past (R: 0.92, R²: 0.85, slope: 0.014, y-intercept: 58.76, stderr: 0.002, P: 0.00002)