Our use of relaxed-molecular clocks is the main cause for discrepancies between our estimates and previously published divergence dates. Using a strict clock Zanotto et al. found four to five times younger divergences than those presently reported (Table 5 ) [38] . Due to the rejection of the strict clock model, we argue that our approach provides a better estimate of divergence times given the data at hand, although some notes of caution should be raised. Our molecular dating could be hampered by sequencing errors, especially since sequence variation is low. In addition, the low substitution rates, could lead to inaccurate rate estimations [57] . Indeed, our estimates for individual genes approaches the limit of 1610 25 substitutions/site/year below which the temporal signal for heterochronous sampled virus begins to break down [58] and tend not to converge on the true rate when analyzed with BEAST. On that account, the least reliable time estimates are produced by the shortest alignment, which casts doubts on the tRE lower bound that was derived from 204 nt long sequences from the recombinant region. Therefore, although our dating estimates are more accurate than those relying on a poorly fitted molecular clock, more full-length genomes with a wide temporal sampling are required for a definitive assessment of divergence events in the Tick-borne encephalitis virus.