The time-calibrated phylogeny represents a maximum clade credibility tree inferred for NRR1. Grey tips correspond to bat viruses, green to pangolin, blue to SARS-CoV and red to SARS-CoV-2. The sizes of the black internal node circles are proportional to the posterior node support. 95% credible interval bars are shown for all internal node ages. The inset represents divergence time estimates based on NRR1, NRR2 and NRA3. The boxplots show divergence time estimates (posterior medians) for SARS-CoV-2 (red) and the 2002–2003 SARS-CoV virus (blue) from their most closely related bat virus. Green boxplots show the TMRCA estimate for the RaTG13/SARS-CoV-2 lineage and its most closely related pangolin lineage (Guangdong 2019). Boxplots show interquartile ranges, white lines are medians and box whiskers show the full range of posterior distribution. Transparent bands of interquartile range width and with the same colours are superimposed to highlight the overlap between estimates. In Extended Data Fig. 4 we compare these divergence time estimates to those obtained using the MERS-CoV-centred rate priors for NRR1, NRR2 and NRA3.